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Sample records for damaged d-ala-d-ala binding

  1. The Carboxyl Terminus of Eremomycin Facilitates Binding to the Non-d-Ala-d-Ala Segment of the Peptidoglycan Pentapeptide Stem.

    PubMed

    Chang, James; Zhou, Hongyu; Preobrazhenskaya, Maria; Tao, Peng; Kim, Sung Joon

    2016-06-21

    Glycopeptide antibiotics inhibit cell wall biosynthesis in Gram-positive bacteria by targeting the peptidoglycan (PG) pentapeptide stem structure (l-Ala-d-iso-Gln-l-Lys-d-Ala-d-Ala). Structures of the glycopeptide complexed with a PG stem mimic have shown that the d-Ala-d-Ala segment is the primary drug binding site; however, biochemical evidence suggests that the glycopeptide-PG interaction involves more than d-Ala-d-Ala binding. Interactions of the glycopeptide with the non-d-Ala-d-Ala segment of the PG stem were investigated using solid-state nuclear magnetic resonance (NMR). LCTA-1421, a double (15)N-enriched eremomycin derivative with a C-terminal [(15)N]amide and [(15)N]Asn amide, was complexed with whole cells of Staphylococcus aureus grown in a defined medium containing l-[3-(13)C]Ala and d-[1-(13)C]Ala in the presence of alanine racemase inhibitor alaphosphin. (13)C{(15)N} and (15)N{(13)C} rotational-echo double-resonance (REDOR) NMR measurements determined the (13)C-(15)N internuclear distances between the [(15)N]Asn amide of LCTA-1421 and the (13)C atoms of the bound d-[1-(13)C]Ala-d-[1-(13)C]Ala to be 5.1 and 4.8 Å, respectively. These measurements also determined the distance from the C-terminal [(15)N]amide of LCTA-1421 to the l-[3-(13)C]Ala of PG to be 3.5 Å. The measured REDOR distance constraints position the C-terminus of the glycopeptide in the proximity of the l-Ala of the PG, suggesting that the C-terminus of the glycopeptide interacts near the l-Ala segment of the PG stem. In vivo REDOR measurements provided structural insight into how C-terminally modified glycopeptide antibiotics operate. PMID:27243469

  2. The β-Lactamase Gene Regulator AmpR Is a Tetramer That Recognizes and Binds the d-Ala-d-Ala Motif of Its Repressor UDP-N-acetylmuramic Acid (MurNAc)-pentapeptide*

    PubMed Central

    Vadlamani, Grishma; Thomas, Misty D.; Patel, Trushar R.; Donald, Lynda J.; Reeve, Thomas M.; Stetefeld, Jörg; Standing, Kenneth G.; Vocadlo, David J.; Mark, Brian L.

    2015-01-01

    Inducible expression of chromosomal AmpC β-lactamase is a major cause of β-lactam antibiotic resistance in the Gram-negative bacteria Pseudomonas aeruginosa and Enterobacteriaceae. AmpC expression is induced by the LysR-type transcriptional regulator (LTTR) AmpR, which activates ampC expression in response to changes in peptidoglycan (PG) metabolite levels that occur during exposure to β-lactams. Under normal conditions, AmpR represses ampC transcription by binding the PG precursor UDP-N-acetylmuramic acid (MurNAc)-pentapeptide. When exposed to β-lactams, however, PG catabolites (1,6-anhydroMurNAc-peptides) accumulate in the cytosol, which have been proposed to competitively displace UDP-MurNAc-pentapeptide from AmpR and convert it into an activator of ampC transcription. Here we describe the molecular interactions between AmpR (from Citrobacter freundii), its DNA operator, and repressor UDP-MurNAc-pentapeptide. Non-denaturing mass spectrometry revealed AmpR to be a homotetramer that is stabilized by DNA containing the T-N11-A LTTR binding motif and revealed that it can bind four repressor molecules in an apparently stepwise manner. A crystal structure of the AmpR effector-binding domain bound to UDP-MurNAc-pentapeptide revealed that the terminal d-Ala-d-Ala motif of the repressor forms the primary contacts with the protein. This observation suggests that 1,6-anhydroMurNAc-pentapeptide may convert AmpR into an activator of ampC transcription more effectively than 1,6-anhydroMurNAc-tripeptide (which lacks the d-Ala-d-Ala motif). Finally, small angle x-ray scattering demonstrates that the AmpR·DNA complex adopts a flat conformation similar to the LTTR protein AphB and undergoes only a slight conformational change when binding UDP-MurNAc-pentapeptide. Modeling the AmpR·DNA tetramer bound to UDP-MurNAc-pentapeptide predicts that the UDP-MurNAc moiety of the repressor participates in modulating AmpR function. PMID:25480792

  3. The β-lactamase gene regulator AmpR is a tetramer that recognizes and binds the D-Ala-D-Ala motif of its repressor UDP-N-acetylmuramic acid (MurNAc)-pentapeptide.

    PubMed

    Vadlamani, Grishma; Thomas, Misty D; Patel, Trushar R; Donald, Lynda J; Reeve, Thomas M; Stetefeld, Jörg; Standing, Kenneth G; Vocadlo, David J; Mark, Brian L

    2015-01-30

    Inducible expression of chromosomal AmpC β-lactamase is a major cause of β-lactam antibiotic resistance in the Gram-negative bacteria Pseudomonas aeruginosa and Enterobacteriaceae. AmpC expression is induced by the LysR-type transcriptional regulator (LTTR) AmpR, which activates ampC expression in response to changes in peptidoglycan (PG) metabolite levels that occur during exposure to β-lactams. Under normal conditions, AmpR represses ampC transcription by binding the PG precursor UDP-N-acetylmuramic acid (MurNAc)-pentapeptide. When exposed to β-lactams, however, PG catabolites (1,6-anhydroMurNAc-peptides) accumulate in the cytosol, which have been proposed to competitively displace UDP-MurNAc-pentapeptide from AmpR and convert it into an activator of ampC transcription. Here we describe the molecular interactions between AmpR (from Citrobacter freundii), its DNA operator, and repressor UDP-MurNAc-pentapeptide. Non-denaturing mass spectrometry revealed AmpR to be a homotetramer that is stabilized by DNA containing the T-N11-A LTTR binding motif and revealed that it can bind four repressor molecules in an apparently stepwise manner. A crystal structure of the AmpR effector-binding domain bound to UDP-MurNAc-pentapeptide revealed that the terminal D-Ala-D-Ala motif of the repressor forms the primary contacts with the protein. This observation suggests that 1,6-anhydroMurNAc-pentapeptide may convert AmpR into an activator of ampC transcription more effectively than 1,6-anhydroMurNAc-tripeptide (which lacks the D-Ala-D-Ala motif). Finally, small angle x-ray scattering demonstrates that the AmpR·DNA complex adopts a flat conformation similar to the LTTR protein AphB and undergoes only a slight conformational change when binding UDP-MurNAc-pentapeptide. Modeling the AmpR·DNA tetramer bound to UDP-MurNAc-pentapeptide predicts that the UDP-MurNAc moiety of the repressor participates in modulating AmpR function. PMID:25480792

  4. Structure of vancomycin and a vancomycin/D-Ala-D-Ala complex in solution

    SciTech Connect

    Molinari, H.; Pastore, A. ); Lian, Luyun ); Hawkes, G.E.; Sales, K. )

    1990-03-06

    Restrained molecular dynamics simulations were used to study the interactions between the glycopeptide antibiotic vancomycin and the dipeptide Ac-D-Ala-D-Ala. Restraints were obtained from a combination of homonuclear and heteronuclear two-dimensional NMR experiments (NOESY, ROESY, {sup 1}H-{sup 15}N inverse correlation). The comparison between the structures obtained for vancomycin alone and for the complex suggests a new hypothesis on the binding mode of this system. The numerical simulations were not straightforward because vancomycin is made of building blocks for which standard force-fields are not available. The representation of unusual chemical environments is also mandatory. The authors believe that the extension of the force-field parameters to their system could be of more general interest. Furthermore, they consider vancomycin and its complex a good example for exploring the more general problem of molecular recognition, a challenge that has been widely approached in the past few years but for which no unique and general methodology has, so far, been recognized.

  5. Total Syntheses and Initial Evaluation of [Ψ[C(=S)NH]Tpg4]vancomycin, [Ψ[C(=NH)NH]Tpg4]vancomycin, [Ψ[CH2NH]Tpg4]vancomycin and their (4-Chlorobiphenyl)methyl Derivatives: Synergistic Binding Pocket and Peripheral Modifications for the Glycopeptide Antibiotics

    PubMed Central

    Okano, Akinori; Nakayama, Atsushi; Wu, Kejia; Lindsey, Erick A.; Schammel, Alex W.; Feng, Yiqing; Collins, Karen C.

    2015-01-01

    Full details of studies are disclosed on the total synthesis of binding pocket analogues of vancomycin, bearing the peripheral L-vancosaminyl-1,2-D-glucosyl disaccharide, that contain changes to a key single atom in the residue 4 amide (residue 4 carbonyl O → S, NH, H2) designed to directly address the underlying molecular basis of resistance to vancomycin. Also disclosed are studies piloting the late stage transformations conducted on the synthetically more accessible C-terminus hydroxymethyl aglycon derivatives and full details of the peripheral chlorobiphenyl functionalization of all the binding pocket modified vancomycin analogues designed for dual D-Ala-D-Ala/D-Ala-D-Lac binding are reported. Their collective assessment indicate that combined binding pocket and chlorobiphenyl peripherally modified analogues exhibit a remarkable spectrum of antimicrobial activity (VSSA, MRSA, VanA and VanB VRE) and impressive potencies against both vancomycin-sensitive and vancomycin-resistant bacteria (MICs = 0.06–0.005 μg/mL and 0.5–0.06 μg/mL for the amidine and methylene analogues, respectively) and likely benefit from two independent and synergistic mechanisms of action, only one of which is dependent on D-Ala-D-Ala/D-Ala-D-Lac binding. Such analogues are likely to display especially durable antibiotic activity not prone to rapidly acquired clinical resistance. PMID:25750995

  6. The Tipper-Strominger Hypothesis and Triggering of Allostery in Penicillin-Binding Protein 2a of Methicillin-Resistant Staphylococcus aureus (MRSA)

    PubMed Central

    Fishovitz, Jennifer; Taghizadeh, Negin; Fisher, Jed F.; Chang, Mayland; Mobashery, Shahriar

    2015-01-01

    The transpeptidases involved in the synthesis of the bacterial cell wall (also known as penicillin-binding proteins, PBPs) have evolved to bind the acyl-d-Ala-d-Ala segment of the stem peptide of the nascent peptidoglycan for the physiologically important crosslinking of the cell wall. The Tipper-Strominger hypothesis stipulates that β-lactam antibiotics mimic the acyl-d-Ala-d-Ala moiety of the stem, and thus are recognized by the PBPs with bactericidal consequences. We document that this mimicry exists also at the allosteric site of PBP2a of methicillin-resistant Staphylococcus aureus (MRSA). Interactions of different classes of β-lactam antibiotics, as mimics of the acyl-d-Ala-d-Ala moiety at the allosteric site, lead to a conformational change, across a distance of 60 Å to the active site. We directly visualize this change using an environmentally sensitive fluorescent probe affixed to the protein loops that frame the active site. This conformational mobility, documented in real time, allows antibiotic access to the active site of PBP2a. Furthermore, we document that this allosteric trigger enables synergy between two different β-lactam antibiotics, wherein occupancy at the allosteric site by one facilitates occupancy by a second at the transpeptidase catalytic site, thus lowering the minimal-inhibitory concentration. This synergy has important implications for the mitigation of facile emergence of resistance to these antibiotics by MRSA. PMID:25964995

  7. The Effect of Environment on the Recognition and Binding of Vancomycin to Native and Resistant Forms of Lipid II

    PubMed Central

    Jia, ZhiGuang; O'Mara, Megan L.; Zuegg, Johannes; Cooper, Matthew A.; Mark, Alan E.

    2011-01-01

    Molecular dynamics simulations and free energy calculations have been used to examine in detail the mechanism by which a receptor molecule (the glycopeptide antibiotic vancomycin) recognizes and binds to a target molecule (lipid II) embedded within a membrane environment. The simulations show that the direct interaction of vancomycin with lipid II, as opposed to initial binding to the membrane, leads most readily to the formation of a stable complex. The recognition of lipid II by vancomycin occurred via the N-terminal amine group of vancomycin and the C-terminal carboxyl group of lipid II. Despite lying at the membrane-water interface, the interaction of vancomycin with lipid II was found to be essentially identical to that of soluble tripeptide analogs of lipid II (Ac-d-Ala-d-Ala; root mean-square deviation 0.11 nm). Free energy calculations also suggest that the relative binding affinity of vancomycin for native, resistant, and synthetic forms of membrane-bound lipid II was unaffected by the membrane environment. The effect of the dimerization of vancomycin on the binding of lipid II, the position of lipid II within a biological membrane, and the effect of the isoamylene tail of lipid II on membrane fluidity have also been examined. PMID:22261057

  8. Determination of Noncovalent Binding Using a Continuous Stirred Tank Reactor as a Flow Injection Device Coupled to Electrospray Ionization Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Santos, Inês C.; Waybright, Veronica B.; Fan, Hui; Ramirez, Sabra; Mesquita, Raquel B. R.; Rangel, António O. S. S.; Fryčák, Petr; Schug, Kevin A.

    2015-07-01

    Described is a new method based on the concept of controlled band dispersion, achieved by hyphenating flow injection analysis with ESI-MS for noncovalent binding determinations. A continuous stirred tank reactor (CSTR) was used as a FIA device for exponential dilution of an equimolar host-guest solution over time. The data obtained was treated for the noncovalent binding determination using an equimolar binding model. Dissociation constants between vancomycin and Ac-Lys(Ac)-Ala-Ala-OH peptide stereoisomers were determined using both the positive and negative ionization modes. The results obtained for Ac- L-Lys(Ac)- D-Ala- D-Ala (a model for a Gram-positive bacterial cell wall) binding were in reasonable agreement with literature values made by other mass spectrometry binding determination techniques. Also, the developed method allowed the determination of dissociation constants for vancomycin with Ac- L-Lys(Ac)- D-Ala- L-Ala, Ac- L-Lys(Ac)- L-Ala- D-Ala, and Ac- L-Lys(Ac)- L-Ala- L-Ala. Although some differences in measured binding affinities were noted using different ionization modes, the results of each determination were generally consistent. Differences are likely attributable to the influence of a pseudo-physiological ammonium acetate buffer solution on the formation of positively- and negatively-charged ionic complexes.

  9. Determination of Noncovalent Binding Using a Continuous Stirred Tank Reactor as a Flow Injection Device Coupled to Electrospray Ionization Mass Spectrometry.

    PubMed

    Santos, Inês C; Waybright, Veronica B; Fan, Hui; Ramirez, Sabra; Mesquita, Raquel B R; Rangel, António O S S; Fryčák, Petr; Schug, Kevin A

    2015-07-01

    Described is a new method based on the concept of controlled band dispersion, achieved by hyphenating flow injection analysis with ESI-MS for noncovalent binding determinations. A continuous stirred tank reactor (CSTR) was used as a FIA device for exponential dilution of an equimolar host-guest solution over time. The data obtained was treated for the noncovalent binding determination using an equimolar binding model. Dissociation constants between vancomycin and Ac-Lys(Ac)-Ala-Ala-OH peptide stereoisomers were determined using both the positive and negative ionization modes. The results obtained for Ac-L-Lys(Ac)-D-Ala-D-Ala (a model for a Gram-positive bacterial cell wall) binding were in reasonable agreement with literature values made by other mass spectrometry binding determination techniques. Also, the developed method allowed the determination of dissociation constants for vancomycin with Ac-L-Lys(Ac)-D-Ala-L-Ala, Ac-L-Lys(Ac)-L-Ala-D-Ala, and Ac-L-Lys(Ac)-L-Ala-L-Ala. Although some differences in measured binding affinities were noted using different ionization modes, the results of each determination were generally consistent. Differences are likely attributable to the influence of a pseudo-physiological ammonium acetate buffer solution on the formation of positively- and negatively-charged ionic complexes. PMID:25832030

  10. Experimental Strategies for Functional Annotation and Metabolism Discovery: Targeted Screening of Solute Binding Proteins and Unbiased Panning of Metabolomes

    PubMed Central

    2015-01-01

    The rate at which genome sequencing data is accruing demands enhanced methods for functional annotation and metabolism discovery. Solute binding proteins (SBPs) facilitate the transport of the first reactant in a metabolic pathway, thereby constraining the regions of chemical space and the chemistries that must be considered for pathway reconstruction. We describe high-throughput protein production and differential scanning fluorimetry platforms, which enabled the screening of 158 SBPs against a 189 component library specifically tailored for this class of proteins. Like all screening efforts, this approach is limited by the practical constraints imposed by construction of the library, i.e., we can study only those metabolites that are known to exist and which can be made in sufficient quantities for experimentation. To move beyond these inherent limitations, we illustrate the promise of crystallographic- and mass spectrometric-based approaches for the unbiased use of entire metabolomes as screening libraries. Together, our approaches identified 40 new SBP ligands, generated experiment-based annotations for 2084 SBPs in 71 isofunctional clusters, and defined numerous metabolic pathways, including novel catabolic pathways for the utilization of ethanolamine as sole nitrogen source and the use of d-Ala-d-Ala as sole carbon source. These efforts begin to define an integrated strategy for realizing the full value of amassing genome sequence data. PMID:25540822

  11. A microplate assay for the coupled transglycosylase-transpeptidase activity of the penicillin binding proteins; a vancomycin-neutralizing tripeptide combination prevents penicillin inhibition of peptidoglycan synthesis.

    PubMed

    Kumar, Vidya P; Basavannacharya, Chandrakala; de Sousa, Sunita M

    2014-07-18

    A microplate, scintillation proximity assay to measure the coupled transglycosylase-transpeptidase activity of the penicillin binding proteins in Escherichia coli membranes was developed. Membranes were incubated with the two peptidoglycan sugar precursors UDP-N-acetyl muramylpentapeptide (UDP-MurNAc(pp)) and UDP-[(3)H]N-acetylglucosamine in the presence of 40 μM vancomycin to allow in situ accumulation of lipid II. In a second step, vancomycin inhibition was relieved by addition of a tripeptide (Lys-D-ala-D-ala) or UDP-MurNAc(pp), resulting in conversion of lipid II to cross-linked peptidoglycan. Inhibitors of the transglycosylase or transpeptidase were added at step 2. Moenomycin, a transglycosylase inhibitor, had an IC50 of 8 nM. Vancomycin and nisin also inhibited the assay. Surprisingly, the transpeptidase inhibitors penicillin and ampicillin showed no inhibition. In a pathway assay of peptidoglycan synthesis, starting from the UDP linked sugar precursors, inhibition by penicillin was reversed by a 'neutral' combination of vancomycin plus tripeptide, suggesting an interaction thus far unreported. PMID:24944023

  12. Structural Variations of the Cell Wall Precursor Lipid II and Their Influence on Binding and Activity of the Lipoglycopeptide Antibiotic Oritavancin

    PubMed Central

    Münch, Daniela; Engels, Ina; Müller, Anna; Reder-Christ, Katrin; Falkenstein-Paul, Hildegard; Bierbaum, Gabriele; Grein, Fabian; Bendas, Gerd; Sahl, Hans-Georg

    2014-01-01

    Oritavancin is a semisynthetic derivative of the glycopeptide antibiotic chloroeremomycin with activity against Gram-positive pathogens, including vancomycin-resistant staphylococci and enterococci. Compared to vancomycin, oritavancin is characterized by the presence of two additional residues, a hydrophobic 4′-chlorobiphenyl methyl moiety and a 4-epi-vancosamine substituent, which is also present in chloroeremomycin. Here, we show that oritavancin and its des-N-methylleucyl variant (des-oritavancin) effectively inhibit lipid I- and lipid II-consuming peptidoglycan biosynthesis reactions in vitro. In contrast to that for vancomycin, the binding affinity of oritavancin to the cell wall precursor lipid II appears to involve, in addition to the d-Ala-d-Ala terminus, other species-specific binding sites of the lipid II molecule, i.e., the crossbridge and d-isoglutamine in position 2 of the lipid II stem peptide, both characteristic for a number of Gram-positive pathogens, including staphylococci and enterococci. Using purified lipid II and modified lipid II variants, we studied the impact of these modifications on the binding of oritavancin and compared it to those of vancomycin, chloroeremomycin, and des-oritavancin. Analysis of the binding parameters revealed that additional intramolecular interactions of oritavancin with the peptidoglycan precursor appear to compensate for the loss of a crucial hydrogen bond in vancomycin-resistant strains, resulting in enhanced binding affinity. Augmenting previous findings, we show that amidation of the lipid II stem peptide predominantly accounts for the increased binding of oritavancin to the modified intermediates ending in d-Ala-d-Lac. Corroborating our conclusions, we further provide biochemical evidence for the phenomenon of the antagonistic effects of mecA and vanA resistance determinants in Staphylococcus aureus, thus partially explaining the low frequency of methicillin-resistant S. aureus (MRSA) acquiring high

  13. Experimental and Theoretical Studies of the Structures and Interactions of Vancomycin Antibiotics with Cell Wall Analogues

    SciTech Connect

    Yang, Zhibo; Vorpagel, Erich R.; Laskin, Julia

    2008-10-01

    Surface-induced dissociation (SID) of the singly protonated complex of vancomycin antibiotic with cell wall peptide analogue (Nα,Nε-diacetyl-L-Lys-D-Ala-D-Ala) was studied using a 6 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FT-ICR MS) specially configured for SID experiments. The binding energy between the vancomycin and the peptide was obtained from the RRKM modeling of the time- and energy resolved fragmentation efficiency curves (TFECs) of the precursor ion and its fragments. Electronic structure calculations of the geometries, proton affinities and binding energies were performed for several model systems including vancomycin (V), vancomycin aglycon (VA), Nα,Nε-diacetyl-L-Lys-D-Ala-D-Ala, and non-covalent complexes of VA with N-acetyl-D-Ala-D-Ala and Nα,Nε-diacetyl-L-Lys-D-Ala-D-Ala at the B3LYP/6-31G(d) level of theory. Comparison between the experimental and computational results suggests that the most probable structure of the complex observed in our experiments corresponds to the neutral peptide bound to the vancomycin protonated at the secondary amino group of the N-methyl-leucine residue. The experimental binding energy of 30.9 ± 1.8 kcal/mol is in good agreement with the binding energy of 29.3 ± 2.5 kcal/mol calculated for the model system representing the preferred structure of the complex.

  14. Synthesis and mode of action of hydrophobic derivatives of the glycopeptide antibiotic eremomycin and des-(N-methyl-D-leucyl)eremomycin against glycopeptide-sensitive and -resistant bacteria.

    PubMed

    Printsevskaya, Svetlana S; Pavlov, Andrey Y; Olsufyeva, Evgenia N; Mirchink, Elena P; Isakova, Elena B; Reznikova, Marina I; Goldman, Robert C; Branstrom, Arthur A; Baizman, Eugene R; Longley, Clifford B; Sztaricskai, Ferenc; Batta, Gyula; Preobrazhenskaya, Maria N

    2002-03-14

    Des-(N-methyl-D-leucyl)eremomycin was obtained by Edman degradation of eremomycin. Derivatives with a hydrophobic substituent at the exterior of the molecule were then synthesized, and their antibacterial activities were compared with similar derivatives of eremomycin. Comparison of derivatives of eremomycin containing the n-decyl or p-(p-chlorophenyl)benzyl substituent in the eremosamine moiety (N') and n-decyl or p-(p-chlorophenyl)benzylamides with similar derivatives of eremomycin possessing the damaged peptide core (a defective binding pocket) showed that compounds of both types are almost equally active against glycopeptide-resistant strains of enterococci (GRE), whereas eremomycin derivatives are more active against staphylococci. Hydrophobic 7d-alkylaminomethylated derivatives of eremomycin (9, 10) demonstrated similar antibacterial properties. Since the basic mode of action of glycopeptide antibiotics involves binding to cell wall intermediates terminating in -D-Ala-D-Ala and this interaction is seriously decreased in the hexapeptide derivatives (lacking the critical N-methyl-D-leucine), we suggest that these hydrophobic derivatives may inhibit peptidoglycan synthesis in the absence of dipeptide binding. NMR binding experiments using Ac-D-Ala-D-Ala show that binding constants of these hexapeptide derivativies are decreased in comparison with the corresponding heptapeptides with intact binding pocket. This is in agreement with the decreased biological activity of the hexapeptide derivatives against vancomycin-sensitive strains in comparison with the activity of parent compounds. Binding to the lactate cell wall analogue Ac-D-Ala-D-Lac with decylamide of eremomycin 8 was not observed, demonstrating that the interaction with this target in GRE does not occur. While hydrophobic glycopeptide derivatives retain the ability to inhibit the synthesis of peptidoglycan in manner of natural glycopeptides, biochemical investigation supports the hypothesis that they

  15. Roles of RNA-Binding Proteins in DNA Damage Response

    PubMed Central

    Kai, Mihoko

    2016-01-01

    Living cells experience DNA damage as a result of replication errors and oxidative metabolism, exposure to environmental agents (e.g., ultraviolet light, ionizing radiation (IR)), and radiation therapies and chemotherapies for cancer treatments. Accumulation of DNA damage can lead to multiple diseases such as neurodegenerative disorders, cancers, immune deficiencies, infertility, and also aging. Cells have evolved elaborate mechanisms to deal with DNA damage. Networks of DNA damage response (DDR) pathways are coordinated to detect and repair DNA damage, regulate cell cycle and transcription, and determine the cell fate. Upstream factors of DNA damage checkpoints and repair, “sensor” proteins, detect DNA damage and send the signals to downstream factors in order to maintain genomic integrity. Unexpectedly, we have discovered that an RNA-processing factor is involved in DNA repair processes. We have identified a gene that contributes to glioblastoma multiforme (GBM)’s treatment resistance and recurrence. This gene, RBM14, is known to function in transcription and RNA splicing. RBM14 is also required for maintaining the stem-like state of GBM spheres, and it controls the DNA-PK-dependent non-homologous end-joining (NHEJ) pathway by interacting with KU80. RBM14 is a RNA-binding protein (RBP) with low complexity domains, called intrinsically disordered proteins (IDPs), and it also physically interacts with PARP1. Furthermore, RBM14 is recruited to DNA double-strand breaks (DSBs) in a poly(ADP-ribose) (PAR)-dependent manner (unpublished data). DNA-dependent PARP1 (poly-(ADP) ribose polymerase 1) makes key contributions in the DNA damage response (DDR) network. RBM14 therefore plays an important role in a PARP-dependent DSB repair process. Most recently, it was shown that the other RBPs with intrinsically disordered domains are recruited to DNA damage sites in a PAR-dependent manner, and that these RBPs form liquid compartments (also known as

  16. Roles of RNA-Binding Proteins in DNA Damage Response.

    PubMed

    Kai, Mihoko

    2016-01-01

    Living cells experience DNA damage as a result of replication errors and oxidative metabolism, exposure to environmental agents (e.g., ultraviolet light, ionizing radiation (IR)), and radiation therapies and chemotherapies for cancer treatments. Accumulation of DNA damage can lead to multiple diseases such as neurodegenerative disorders, cancers, immune deficiencies, infertility, and also aging. Cells have evolved elaborate mechanisms to deal with DNA damage. Networks of DNA damage response (DDR) pathways are coordinated to detect and repair DNA damage, regulate cell cycle and transcription, and determine the cell fate. Upstream factors of DNA damage checkpoints and repair, "sensor" proteins, detect DNA damage and send the signals to downstream factors in order to maintain genomic integrity. Unexpectedly, we have discovered that an RNA-processing factor is involved in DNA repair processes. We have identified a gene that contributes to glioblastoma multiforme (GBM)'s treatment resistance and recurrence. This gene, RBM14, is known to function in transcription and RNA splicing. RBM14 is also required for maintaining the stem-like state of GBM spheres, and it controls the DNA-PK-dependent non-homologous end-joining (NHEJ) pathway by interacting with KU80. RBM14 is a RNA-binding protein (RBP) with low complexity domains, called intrinsically disordered proteins (IDPs), and it also physically interacts with PARP1. Furthermore, RBM14 is recruited to DNA double-strand breaks (DSBs) in a poly(ADP-ribose) (PAR)-dependent manner (unpublished data). DNA-dependent PARP1 (poly-(ADP) ribose polymerase 1) makes key contributions in the DNA damage response (DDR) network. RBM14 therefore plays an important role in a PARP-dependent DSB repair process. Most recently, it was shown that the other RBPs with intrinsically disordered domains are recruited to DNA damage sites in a PAR-dependent manner, and that these RBPs form liquid compartments (also known as "liquid-demixing"). Among the

  17. Using surface plasmon resonance to directly measure slow binding of low-molecular mass inhibitors to a VanX chip.

    PubMed

    Chang, Yi-Pin; Tseng, Min-Jen; Chu, Yen-Ho

    2006-12-01

    VanX, a d,d-dipeptidase, is one of five gene products responsible for vancomycin resistance in pathogenic bacteria and is an attractive drug target in circumventing clinical drug resistance. Our previous combinatorial search of VanX substrates in a dipeptide library of d-X(1)-d-X(2) (19(2)=361) forms has led to the discovery of three new compounds (d-Ala-d-Phe, d-Ala-d-Tyr, and d-Ala-d-Trp) having higher k(cat)/K(M) values than those of its natural substrate, d-Ala-d-Ala. Based on structures of newly identified substrates, two representative transition state analogs of substrates, d-Ala(P,O)d-Phe (6a) and d-Ala(P,O)d-Ala (6b) dipeptide phosphonates, used as VanX inhibitor were rationally designed and chemically synthesized. In the synthesis, eight synthetic steps in total were employed for preparing each VanX inhibitor, and their overall isolated yields were 21 and 11% for 6a and 6b, respectively. Binding interactions of d-Ala(P,O)d-Phe (6a) and d-Ala(P,O)d-Ala (6b) with VanX were confirmed unambiguously and measured quantitatively by surface plasmon resonance. The result reveals that both dipeptide phosphonates are slow-binding inhibitors of VanX (for 6a, k(on)=1.18 x 10(3)M(-1)s(-1), k(off)=2.31 x 10(-3) s(-1), K(D)=1.96 microM, chi(2)=0.0737; for 6b, k(on)=1.09 x 10(3)M(-1)s(-1), k(off)=1.80 x 10(-2)s(-1), K(D)=16.5 microM, chi(2)=0.0599). This suggests that only a fraction of the conformers of the inhibitors in solution adopts a conformation best suited for binding interaction with VanX and that the VanX-inhibitor complex may concomitantly undergo a conformational isomerization from an initial but fast weak-binding adduct to slowly convert to a tight-binding complex with a more stable bound geometry. Moreover, in comparison with 6b, an additional aromatic interaction of 6a with the Phe79 residue in the active site of the enzyme, through an energetically favorable face-to-face offset stacked orientation, may account for its higher affinity than 6b to VanX. PMID

  18. Vitellogenin Recognizes Cell Damage through Membrane Binding and Shields Living Cells from Reactive Oxygen Species*

    PubMed Central

    Havukainen, Heli; Münch, Daniel; Baumann, Anne; Zhong, Shi; Halskau, Øyvind; Krogsgaard, Michelle; Amdam, Gro V.

    2013-01-01

    Large lipid transfer proteins are involved in lipid transportation and diverse other molecular processes. These serum proteins include vitellogenins, which are egg yolk precursors and pathogen pattern recognition receptors, and apolipoprotein B, which is an anti-inflammatory cholesterol carrier. In the honey bee, vitellogenin acts as an antioxidant, and elevated vitellogenin titer is linked to prolonged life span in this animal. Here, we show that vitellogenin has cell and membrane binding activity and that it binds preferentially to dead and damaged cells. Vitellogenin binds directly to phosphatidylcholine liposomes and with higher affinity to liposomes containing phosphatidylserine, a lipid of the inner leaflet of cell membranes that is exposed in damaged cells. Vitellogenin binding to live cells, furthermore, improves cell oxidative stress tolerance. This study can shed more light on why large lipid transfer proteins have a well conserved α-helical domain, because we locate the lipid bilayer-binding ability of vitellogenin largely to this region. We suggest that recognition of cell damage and oxidation shield properties are two mechanisms that allow vitellogenin to extend honey bee life span. PMID:23897804

  19. Effect of oxidative DNA damage in promoter elements on transcription factor binding.

    PubMed Central

    Ghosh, R; Mitchell, D L

    1999-01-01

    Reactive oxygen species produced by endogenous metabolic activity and exposure to a multitude of exogenous agents impact cells in a variety of ways. The DNA base damage 8-oxodeoxyguanosine (8-oxodG) is a prominent indicator of oxidative stress and has been well-characterized as a premutagenic lesion in mammalian cells and putative initiator of the carcinogenic process. Commensurate with the recent interest in epigenetic pathways of cancer causation we investigated how 8-oxodG alters the interaction between cis elements located on gene promoters and sequence-specific DNA binding proteins associated with these promoters. Consensus binding sequences for the transcription factors AP-1, NF-kappaB and Sp1 were modified site-specifically at guanine residues and electrophoretic mobility shift assays were performed to assess DNA-protein interactions. Our results indicate that whereas a single 8-oxodG was sufficient to inhibit transcription factor binding to AP-1 and Sp1 sequences it had no effect on binding to NF-kappaB, regardless of its position. We conclude from these data that minor alterations in base composition at a crucial position within some, but not all, promoter elements have the ability to disrupt transcription factor binding. The lack of inhibition by damaged NF-kappaB sequences suggests that DNA-protein contact sites may not be as determinative for stable p50 binding to this promoter as other, as yet undefined, structural parameters. PMID:10454620

  20. Autophosphorylation and Pin1 binding coordinate DNA damage-induced HIPK2 activation and cell death.

    PubMed

    Bitomsky, Nadja; Conrad, Elisa; Moritz, Christian; Polonio-Vallon, Tilman; Sombroek, Dirk; Schultheiss, Kathrin; Glas, Carolina; Greiner, Vera; Herbel, Christoph; Mantovani, Fiamma; del Sal, Giannino; Peri, Francesca; Hofmann, Thomas G

    2013-11-01

    Excessive genome damage activates the apoptosis response. Protein kinase HIPK2 is a key regulator of DNA damage-induced apoptosis. Here, we deciphered the molecular mechanism of HIPK2 activation and show its relevance for DNA damage-induced apoptosis in cellulo and in vivo. HIPK2 autointeracts and site-specifically autophosphorylates upon DNA damage at Thr880/Ser882. Autophosphorylation regulates HIPK2 activity and mutation of the phosphorylation-acceptor sites deregulates p53 Ser46 phosphorylation and apoptosis in cellulo. Moreover, HIPK2 autophosphorylation is conserved between human and zebrafish and is important for DNA damage-induced apoptosis in vivo. Mechanistically, autophosphorylation creates a binding signal for the phospho-specific isomerase Pin1. Pin1 links HIPK2 activation to its stabilization by inhibiting HIPK2 polyubiquitination and modulating Siah-1-HIPK2 interaction. Concordantly, Pin1 is required for DNA damage-induced HIPK2 stabilization and p53 Ser46 phosphorylation and is essential for induction of apotosis both in cellulo and in zebrafish. Our results identify an evolutionary conserved mechanism regulating DNA damage-induced apoptosis. PMID:24145406

  1. DNA damaging, cell cytotoxicity and serum albumin binding efficacy of the rutin-Cu(ii) complex.

    PubMed

    Roy, Atanu Singha; Tripathy, Debi Ranjan; Samanta, Sintu; Ghosh, Sudip K; Dasgupta, Swagata

    2016-04-26

    Flavonoids are widely used as anti-oxidants, anti-cancer agents and possess metal ion chelation properties. In this report we have investigated the DNA binding (and damaging), cell cytotoxicity and serum albumin (SA) binding efficacy of the rutin-Cu(ii) complex using differential spectroscopic methods. The rutin-Cu(ii) complex was able to intercalate into calf thymus DNA (ct-DNA) at lower concentrations and its DNA damaging properties were also confirmed from the agarose gel based assay, fluorescence and UV-vis studies. The copper complex was found to be effective against the growth of HeLa cells in vivo. The binding constants (Kb) of the rutin-Cu(ii) complex towards HSA and BSA were found to be (0.98 ± 0.03) and (1.05 ± 0.02) × 10(5) M(-1), respectively, at 299 K and observed to increase with the increase in temperature. Site selectivity studies revealed that the rutin-Cu(ii) complex binds near site 1 (subdomain IIA) of SAs. Thermodynamic parameters indicated that the mode of interaction of rutin and its copper complex with SAs are different from each other. Both ΔH° and ΔS° were observed to be positive for the interaction of the rutin-Cu(ii) complex with SAs, indicating the presence of hydrophobic association in binding. The values of ΔH° were estimated to be negative (-42.07 ± 2.92 and -23.29 ± 2.33 kJ mol(-1) for HSA and BSA respectively) in the binding of rutin with SAs. It implies that after chelation with Cu(ii) ion, rutin alters its binding mode which could have varying applications to its other physicochemical activities. PMID:27035097

  2. Negative superhelicity promotes ATP-dependent binding of yeast RAD3 protein to ultraviolet-damaged DNA.

    PubMed

    Sung, P; Watkins, J F; Prakash, L; Prakash, S

    1994-03-18

    The RAD3 gene of Saccharomyces cerevisiae is required for excision repair of UV-damaged DNA and is essential for cell viability. Remarkable homology exists between RAD3 and the human excision repair gene XPD, whose mutational inactivation underlies the cancer-prone disorder in xeroderma pigmentosum group D patients. Our previous work demonstrated that RAD3-encoded protein contains a DNA helicase activity. Here, we show that RAD3 binds preferentially to UV-damaged DNA over nondamaged DNA. Removal of pyrimidine dimers from damaged DNA by enzymatic photoreactivation does not affect binding, suggesting an affinity of RAD3 for pyrimidine (6-4) pyrimidone photoproducts. Damage-specific binding by RAD3 is strongly dependent on ATP and on the degree of negative superhelicity in DNA. The requirement of superhelicity in damage binding may target RAD3 to regions of DNA undergoing transcription, resulting in the preferential repair of these regions. The rad3 Arg-48 mutant protein, which lacks the DNA helicase activity, also binds UV-damaged DNA preferentially, indicating that DNA helicase and damage binding are two distinct and separable functional entities in RAD3. PMID:8132553

  3. DNA damage-inducible SUMOylation of HERC2 promotes RNF8 binding via a novel SUMO-binding Zinc finger.

    PubMed

    Danielsen, Jannie Rendtlew; Povlsen, Lou Klitgaard; Villumsen, Bine Hare; Streicher, Werner; Nilsson, Jakob; Wikström, Mats; Bekker-Jensen, Simon; Mailand, Niels

    2012-04-16

    Nonproteolytic ubiquitylation of chromatin surrounding deoxyribonucleic acid (DNA) double-strand breaks (DSBs) by the RNF8/RNF168/HERC2 ubiquitin ligases facilitates restoration of genome integrity by licensing chromatin to concentrate genome caretaker proteins near the lesions. In parallel, SUMOylation of so-far elusive upstream DSB regulators is also required for execution of this ubiquitin-dependent chromatin response. We show that HERC2 and RNF168 are novel DNA damage-dependent SUMOylation targets in human cells. In response to DSBs, both HERC2 and RNF168 were specifically modified with SUMO1 at DSB sites in a manner dependent on the SUMO E3 ligase PIAS4. SUMOylation of HERC2 was required for its DSB-induced association with RNF8 and for stabilizing the RNF8-Ubc13 complex. We also demonstrate that the ZZ Zinc finger in HERC2 defined a novel SUMO-specific binding module, which together with its concomitant SUMOylation and T4827 phosphorylation promoted binding to RNF8. Our findings provide novel insight into the regulatory complexity of how ubiquitylation and SUMOylation cooperate to orchestrate protein interactions with DSB repair foci. PMID:22508508

  4. Distinct binding of BRCA2 BRC repeats to RAD51 generates differential DNA damage sensitivity

    PubMed Central

    Chatterjee, Gouri; Jimenez-Sainz, Judit; Presti, Thomas; Nguyen, Tiffany; Jensen, Ryan B.

    2016-01-01

    BRCA2 is a multi-faceted protein critical for the proper regulation of homology-directed repair of DNA double-strand breaks. Elucidating the mechanistic features of BRCA2 is crucial for understanding homologous recombination and how patient-derived mutations impact future cancer risk. Eight centrally located BRC repeats in BRCA2 mediate binding and regulation of RAD51 on resected DNA substrates. Herein, we dissect the biochemical and cellular features of the BRC repeats tethered to the DNA binding domain of BRCA2. To understand how the BRC repeats and isolated domains of BRCA2 contribute to RAD51 binding, we analyzed both the biochemical and cellular properties of these proteins. In contrast to the individual BRC repeat units, we find that the BRC5–8 region potentiates RAD51-mediated DNA strand pairing and provides complementation functions exceeding those of BRC repeats 1–4. Furthermore, BRC5–8 can efficiently repair nuclease-induced DNA double-strand breaks and accelerate the assembly of RAD51 repair complexes upon DNA damage. These findings highlight the importance of the BRC5–8 domain in stabilizing the RAD51 filament and promoting homology-directed repair under conditions of cellular DNA damage. PMID:27084934

  5. Characterization of DNA recognition by the human UV-damaged DNA-binding protein.

    PubMed

    Fujiwara, Y; Masutani, C; Mizukoshi, T; Kondo, J; Hanaoka, F; Iwai, S

    1999-07-01

    The UV-damaged DNA-binding (UV-DDB) protein is the major factor that binds DNA containing damage caused by UV radiation in mammalian cells. We have investigated the DNA recognition by this protein in vitro, using synthetic oligonucleotide duplexes and the protein purified from a HeLa cell extract. When a 32P-labeled 30-mer duplex containing the (6-4) photoproduct at a single site was used as a probe, only a single complex was detected in an electrophoretic mobility shift assay. It was demonstrated by Western blotting that both of the subunits (p48 and p127) were present in this complex. Electrophoretic mobility shift assays using various duplexes showed that the UV-DDB protein formed a specific, high affinity complex with the duplex containing an abasic site analog, in addition to the (6-4) photoproduct. By circular permutation analyses, these DNA duplexes were found to be bent at angles of 54 degrees and 57 degrees in the complexes with this protein. From the previously reported NMR studies and the fluorescence resonance energy transfer experiments in the present study, it can be concluded that the UV-DDB protein binds DNA that can be bent easily at the above angle. PMID:10391953

  6. Radiation-induced oxidative damage to the DNA-binding domain of the lactose repressor.

    PubMed

    Gillard, Nathalie; Goffinont, Stephane; Buré, Corinne; Davidkova, Marie; Maurizot, Jean-Claude; Cadene, Martine; Spotheim-Maurizot, Melanie

    2007-05-01

    Understanding the cellular effects of radiation-induced oxidation requires the unravelling of key molecular events, particularly damage to proteins with important cellular functions. The Escherichia coli lactose operon is a classical model of gene regulation systems. Its functional mechanism involves the specific binding of a protein, the repressor, to a specific DNA sequence, the operator. We have shown previously that upon irradiation with gamma-rays in solution, the repressor loses its ability to bind the operator. Water radiolysis generates hydroxyl radicals (OH* radicals) which attack the protein. Damage of the repressor DNA-binding domain, called the headpiece, is most likely to be responsible of this loss of function. Using CD, fluorescence spectroscopy and a combination of proteolytic cleavage with MS, we have examined the state of the irradiated headpiece. CD measurements revealed a dose-dependent conformational change involving metastable intermediate states. Fluorescence measurements showed a gradual degradation of tyrosine residues. MS was used to count the number of oxidations in different regions of the headpiece and to narrow down the parts of the sequence bearing oxidized residues. By calculating the relative probabilities of reaction of each amino acid with OH. radicals, we can predict the most probable oxidation targets. By comparing the experimental results with the predictions we conclude that Tyr7, Tyr12, Tyr17, Met42 and Tyr47 are the most likely hotspots of oxidation. The loss of repressor function is thus correlated with chemical modifications and conformational changes of the headpiece. PMID:17263689

  7. Radiation-induced oxidative damage to the DNA-binding domain of the lactose repressor

    PubMed Central

    Gillard, Nathalie; Goffinont, Stephane; Buré, Corinne; Davidkova, Marie; Maurizot, Jean-Claude; Cadene, Martine; Spotheim-Maurizot, Melanie

    2007-01-01

    Understanding the cellular effects of radiation-induced oxidation requires the unravelling of key molecular events, particularly damage to proteins with important cellular functions. The Escherichia coli lactose operon is a classical model of gene regulation systems. Its functional mechanism involves the specific binding of a protein, the repressor, to a specific DNA sequence, the operator. We have shown previously that upon irradiation with γ-rays in solution, the repressor loses its ability to bind the operator. Water radiolysis generates hydroxyl radicals (OH· radicals) which attack the protein. Damage of the repressor DNA-binding domain, called the headpiece, is most likely to be responsible of this loss of function. Using CD, fluorescence spectroscopy and a combination of proteolytic cleavage with MS, we have examined the state of the irradiated headpiece. CD measurements revealed a dose-dependent conformational change involving metastable intermediate states. Fluorescence measurements showed a gradual degradation of tyrosine residues. MS was used to count the number of oxidations in different regions of the headpiece and to narrow down the parts of the sequence bearing oxidized residues. By calculating the relative probabilities of reaction of each amino acid with OH· radicals, we can predict the most probable oxidation targets. By comparing the experimental results with the predictions we conclude that Tyr7, Tyr12, Tyr17, Met42 and Tyr47 are the most likely hotspots of oxidation. The loss of repressor function is thus correlated with chemical modifications and conformational changes of the headpiece. PMID:17263689

  8. Distinct binding of BRCA2 BRC repeats to RAD51 generates differential DNA damage sensitivity.

    PubMed

    Chatterjee, Gouri; Jimenez-Sainz, Judit; Presti, Thomas; Nguyen, Tiffany; Jensen, Ryan B

    2016-06-20

    BRCA2 is a multi-faceted protein critical for the proper regulation of homology-directed repair of DNA double-strand breaks. Elucidating the mechanistic features of BRCA2 is crucial for understanding homologous recombination and how patient-derived mutations impact future cancer risk. Eight centrally located BRC repeats in BRCA2 mediate binding and regulation of RAD51 on resected DNA substrates. Herein, we dissect the biochemical and cellular features of the BRC repeats tethered to the DNA binding domain of BRCA2. To understand how the BRC repeats and isolated domains of BRCA2 contribute to RAD51 binding, we analyzed both the biochemical and cellular properties of these proteins. In contrast to the individual BRC repeat units, we find that the BRC5-8 region potentiates RAD51-mediated DNA strand pairing and provides complementation functions exceeding those of BRC repeats 1-4. Furthermore, BRC5-8 can efficiently repair nuclease-induced DNA double-strand breaks and accelerate the assembly of RAD51 repair complexes upon DNA damage. These findings highlight the importance of the BRC5-8 domain in stabilizing the RAD51 filament and promoting homology-directed repair under conditions of cellular DNA damage. PMID:27084934

  9. Purification of a novel UV-damaged-DNA binding protein highly specific for (6-4) photoproduct.

    PubMed

    Wakasugi, M; Abe, Y; Yoshida, Y; Matsunaga, T; Nikaido, O

    1996-03-15

    UV damage-specific binding proteins are considered to play important roles in early responses of cells irradiated with UV, including damage recognition in the DNA repair process. We have surveyed nuclear and cytoplasmic proteins which bind selectively to UV-irradiated DNA using an electrophoretic mobility shift assay. We detected four distinct binding activities with different mobilities in fractions separated from HeLa cells by heparin chromatography. Three of them were found in nuclear extracts and one in cytoplasmic extracts. We purified one of the binding factors from nuclear extracts to homogeneity, which was designated NF-10 (the 10th fraction of nuclear extract on heparin chromatography). It migrated as a 40 kDa polypeptide in SDS-PAGE, and bound to UV-irradiated double- stranded DNA but not to unirradiated DNA. The binding pattern of the NF-10 protein to DNA irradiated with UV corresponded to the induction kinetics of (6-4) photoproduct. Removal of (6-4) photoproducts from UV- irradiated DNA by (6-4) photoproduct-specific photolyase diminished the binding of NF-10 protein. These results suggest that the NF-10 protein binds to UV-damaged DNA through (6-4) photoproduct. Immunoblot analysis using a monoclonal antibody revealed that the NF-10 protein was expressed in cell lines from all complementation groups of xeroderma pigmentosum, indicating that the NF-10 protein is a novel UV-damaged-DNA binding protein. PMID:8604344

  10. Structural Analysis of Shu Proteins Reveals a DNA Binding Role Essential for Resisting Damage*

    PubMed Central

    Tao, Yuyong; Li, Xu; Liu, Yiwei; Ruan, Jianbin; Qi, Shali; Niu, Liwen; Teng, Maikun

    2012-01-01

    The yeast Shu complex, consisting of the proteins Shu1, Shu2, Psy3, and Csm2, maintains genomic stability by coupling post-replication repair to homologous recombination. However, a lack of biochemical and structural information on the Shu proteins precludes revealing their precise roles within the pathway. Here, we report on the 1.9-Å crystal structure of the Psy3-Csm2 complex. The crystal structure shows that Psy3 forms a heterodimer with Csm2 mainly through a hydrophobic core. Unexpectedly, Psy3 and Csm2 share a similar architecture that closely resembles the ATPase core domain of Rad51. The L2 loop present in Psy3 and Csm2 is similar to that of Rad51 and confers the DNA binding activity of the Shu complex. As with Rad51, the Shu complex appears to form a nucleoprotein filament by binding nonspecifically to DNA. Structure-based mutagenesis studies have demonstrated that the DNA binding activity of the Shu complex is essential for repair of the methyl methanesulfonate-induced DNA damage. Our findings provide good foundations for the understanding of the Srs2 regulation by the Shu complex. PMID:22465956

  11. Binding of the UvrB dimer to non-damaged and damaged DNA: residues Y92 and Y93 influence the stability of both subunits.

    PubMed

    Moolenaar, Geri F; Schut, Menno; Goosen, Nora

    2005-06-01

    UvrB is the ultimate damage-binding protein in bacterial nucleotide excision repair. Previous AFM experiments have indicated that UvrB binds to a damage as a dimer. In this paper we visualize for the first time a UvrB dimer in a gel retardation assay, with the second subunit (B2) more loosely bound than the subunit (B1) that interacts with the damage. A beta-hairpin motif in UvrB plays an important role in damage specific binding. Alanine substitutions of Y92 or Y93 in the beta-hairpin result in proteins that kill E. coli cells as a consequence of incision in non-damaged DNA. Apparently, both residues are needed to prevent binding of UvrB to non-damaged DNA. The lethality of Y93A results from UvrC-mediated incisions, whereas that of Y92A is due to incisions by Cho. This difference could be ascribed to a difference in stability of the B2 subunit in the mutant UvrB-DNA complexes. We show that for 3' incision UvrC needs to displace this second UvrB subunit from the complex, whereas Cho seems capable to incise the dimer-complex. Footprint analysis of the contacts of UvrB with damaged DNA revealed that the B2 subunit interacts with the flanking DNA at the 3' side of the lesion. The B2 subunit of mutant Y92A appeared to be more firmly associated with the DNA, indicating that even when B1 is bound to a lesion, the B2 subunit probes the adjacent DNA for presence of damage. We propose this to be a reflection of the process that the UvrB dimer uses to find lesions in the DNA. In addition to preventing binding to non-damaged DNA, the Y92 and Y93 residues appear also important for making specific contacts (of B1) with the damaged site. We show that the concerted action of the two tyrosines lead to a conformational change in the DNA surrounding the lesion, which is required for the 3' incision reaction. PMID:15886069

  12. Preferential binding of high mobility group 1 protein to UV-damaged DNA. Role of the COOH-terminal domain.

    PubMed

    Pasheva, E A; Pashev, I G; Favre, A

    1998-09-18

    Binding of chromosomal high mobility group 1 protein (HMG1) to UV-damaged DNA has been studied with oligonucleotides containing a single dipyrimidine site for formation of UV photolesions. Irradiation of an oligonucleotide with unique TT dinucleotide resulted in generation of cyclobutane pyrimidine dimer with no evidence for induction of (6-4) photoproducts, whereas the analysis of irradiated TC-containing oligonucleotide detected (6-4) photoproducts but not cyclobutane pyrimidine dimers. Mobility shift assays have revealed that HMG1 protein binds preferentially to irradiated TT and TC oligonucleotides. Photoreversal of cyclobutane pyrimidine dimers with DNA photolyase and hydrolysis of the (6-4) photoproducts with hot alkali substantially reduced but did not eliminate binding of HMG1. The protein, therefore, appears to bind the two main types of UV damages in DNA, but some other photolesion(s) contributes to the preferential binding of HMG1 to irradiated DNA. By quantifying gel shift assays and considering the efficiencies of lesion formation, we determined dissociation constants of 1.2 +/- 0.5 and 4.0 +/- 1.5 microM for irradiated TT and TC oligonucleotides, respectively, and 70 +/- 20 microM for the control non-irradiated probes. Tryptic removal of the acidic COOH-terminal domain of HMG1 significantly affected binding of the protein to both irradiated and intact oligonucleotides. The potential role of HMG1 in recognition of the UV lesions in DNA is discussed. PMID:9733773

  13. Tomato MBD5, a methyl CpG binding domain protein, physically interacting with UV-damaged DNA binding protein-1, functions in multiple processes.

    PubMed

    Li, Yuxiang; Deng, Heng; Miao, Min; Li, Huirong; Huang, Shengxiong; Wang, Songhu; Liu, Yongsheng

    2016-04-01

    In tomato (Solanum lycopersicum), high pigment mutations (hp-1 and hp-2) were mapped to genes encoding UV-damaged DNA binding protein 1 (DDB1) and de-etiolated-1 (DET1), respectively. Here we characterized a tomato methyl-CpG-binding domain protein SlMBD5 identified by yeast two-hybrid screening using SlDDB1 as a bait. Yeast two-hybrid assay demonstrated that the physical interaction of SlMBD5 with SlDDB1 is mediated by the C-termini of SlMBD5 and the β-propeller-C (BPC) of SlDDB1. Co-immunoprecipitation analyses revealed that SlMBD5 associates with SlDDB1-interacting partners including SlDET1, SlCUL4, SlRBX1a and SlRBX1b in vivo. SlMBD5 was shown to target to nucleus and dimerizes via its MBD motif. Electrophoresis mobility shift analysis suggested that the MBD of SlMBD5 specifically binds to methylated CpG dinucleotides but not to methylated CpHpG or CpHpH dinucleotides. SlMBD5 expressed in protoplast is capable of activating transcription of CG islands, whereas CUL4/DDB1 antagonizes this effect. Overexpressing SlMBD5 resulted in diverse developmental alterations including darker green fruits with increased plastid level and elevated pigmentation, as well as enhanced expression of SlGLK2, a key regulator of plastid biogenesis. Taken together, we hypothesize that the physical interaction of SlMBD5 with the CUL4-DDB1-DET1 complex component may affect its binding activity to methylated DNA and subsequently attenuate its transcription activation of downstream genes. PMID:26551231

  14. Thermodynamics of Damaged DNA Binding and Catalysis by Human AP Endonuclease 1.

    PubMed

    Miroshnikova, A D; Kuznetsova, A A; Kuznetsov, N A; Fedorova, O S

    2016-01-01

    Apurinic/apyrimidinic (AP) endonucleases play an important role in DNA repair and initiation of AP site elimination. One of the most topical problems in the field of DNA repair is to understand the mechanism of the enzymatic process involving the human enzyme APE1 that provides recognition of AP sites and efficient cleavage of the 5'-phosphodiester bond. In this study, a thermodynamic analysis of the interaction between APE1 and a DNA substrate containing a stable AP site analog lacking the C1' hydroxyl group (F site) was performed. Based on stopped-flow kinetic data at different temperatures, the steps of DNA binding, catalysis, and DNA product release were characterized. The changes in the standard Gibbs energy, enthalpy, and entropy of sequential specific steps of the repair process were determined. The thermodynamic analysis of the data suggests that the initial step of the DNA substrate binding includes formation of non-specific contacts between the enzyme binding surface and DNA, as well as insertion of the amino acid residues Arg177 and Met270 into the duplex, which results in the removal of "crystalline" water molecules from DNA grooves. The second binding step involves the F site flipping-out process and formation of specific contacts between the enzyme active site and the everted 5'-phosphate-2'-deoxyribose residue. It was shown that non-specific interactions between the binding surfaces of the enzyme and DNA provide the main contribution into the thermodynamic parameters of the DNA product release step. PMID:27099790

  15. Radiation damage to a DNA-binding protein. Combined circular dichroism and molecular dynamics simulation analysis.

    PubMed

    Mazier, S; Villette, S; Goffinont, S; Renouard, S; Maurizot, J C; Genest, D; Spotheim-Maurizot, M

    2008-11-01

    The E. coli lactose operon, the paradigm of gene expression regulation systems, is the best model for studying the effect of radiation on such systems. The operon function requires the binding of a protein, the repressor, to a specific DNA sequence, the operator. We have previously shown that upon irradiation the repressor loses its operator binding ability. The main radiation-induced lesions of the headpiece have been identified by mass spectrometry. All tyrosine residues are oxidized into 3,4-dihydroxyphenylalanine (DOPA). In the present study we report a detailed characterization of the headpiece radiation-induced modification. An original approach combining circular dichroism measurements and the analysis of molecular dynamics simulation of headpieces bearing DOPA-s instead of tyrosines has been applied. The CD measurements reveal an irreversible modification of the headpiece structure and stability. The molecular dynamics simulation shows a loss of stability shown by an increase in internal dynamics and allows the estimation of the modifications due to tyrosine oxidation for each structural element of the protein. The changes in headpiece structure and stability can explain at least in part the radiation-induced loss of binding ability of the repressor to the operator. This conclusion should hold for all proteins containing radiosensitive amino acids in their DNA-binding site. PMID:18959464

  16. Multivalent binding of p53 to the STAGA complex mediates coactivator recruitment after UV damage.

    PubMed

    Gamper, Armin M; Roeder, Robert G

    2008-04-01

    The recruitment of transcriptional coactivators, including histone modifying enzymes, is an important step in transcription regulation. A typical activator is thought to interact with several cofactors, presumably in a sequential manner. The common use of several cofactors raises the question of how activators achieve both cofactor selectivity and diversity. Human STAGA is a multiprotein complex with the acetyltransferase GCN5L as the catalytic subunit. Here, we first show, through RNA interference-mediated knock-down and chromatin immunoprecipitation assays, that GCN5 plays a role in p53-dependent gene activation. We then employ p53 mutagenesis, in vitro binding, protein-protein cross-linking, and chromatin immunoprecipitation assays to establish a novel role for the second p53 activation subdomain (AD2) in STAGA recruitment and, further, to demonstrate that optimal binding of STAGA to p53 involves interactions of STAGA subunits TAF9, GCN5, and ADA2b, respectively, with AD1, AD2, and carboxy-terminal domains of p53. These results provide concrete evidence for mediation of transcription factor binding to coactivator complexes through multiple interactions. Based on our data, we propose a cooperative and modular binding mode for the recruitment of coactivator complexes to promoters. PMID:18250150

  17. Thermodynamics of Damaged DNA Binding and Catalysis by Human AP Endonuclease 1

    PubMed Central

    Miroshnikova, A. D.; Kuznetsova, A. A.; Kuznetsov, N. A.; Fedorova, O. S.

    2016-01-01

    Apurinic/apyrimidinic (AP) endonucleases play an important role in DNA repair and initiation of AP site elimination. One of the most topical problems in the field of DNA repair is to understand the mechanism of the enzymatic process involving the human enzyme APE1 that provides recognition of AP sites and efficient cleavage of the 5’-phosphodiester bond. In this study, a thermodynamic analysis of the interaction between APE1 and a DNA substrate containing a stable AP site analog lacking the C1’ hydroxyl group (F site) was performed. Based on stopped-flow kinetic data at different temperatures, the steps of DNA binding, catalysis, and DNA product release were characterized. The changes in the standard Gibbs energy, enthalpy, and entropy of sequential specific steps of the repair process were determined. The thermodynamic analysis of the data suggests that the initial step of the DNA substrate binding includes formation of non-specific contacts between the enzyme binding surface and DNA, as well as insertion of the amino acid residues Arg177 and Met270 into the duplex, which results in the removal of “crystalline” water molecules from DNA grooves. The second binding step involves the F site flipping-out process and formation of specific contacts between the enzyme active site and the everted 5’-phosphate-2’-deoxyribose residue. It was shown that non-specific interactions between the binding surfaces of the enzyme and DNA provide the main contribution into the thermodynamic parameters of the DNA product release step. PMID:27099790

  18. Morphological damage induced by Escherichia coli lipopolysaccharide in cultured hepatocytes: localization and binding properties.

    PubMed Central

    Pagani, R.; Portolés, M. T.; Díaz-Laviada, I.; Municio, A. M.

    1988-01-01

    Lipopolysaccharides (LPS) from Gram-negative bacteria are considered to be the responsible agents for the induction of endotoxic shock, affecting the liver as a target organ. In this study, the cell morphology and some biochemical properties of 24 h-culture-hepatocyte monolayers treated with Escherichia coli 0111:B4 lipopolysaccharide, were observed. Cell morphology was observed by scanning electron microscopy and immunofluorescence methods. LPS interaction induced an increase in rounded cells with diminished adhesion capacity. As biochemical parameters, albumin synthesis and 2-deoxyglucose uptake were measured. LPS decreased the hexose uptake in a dose-dependent manner. Binding of (14C)LPS to cultured hepatocytes showed that LPS binds to non-specific constituents of the membrane bilayer. Images Fig. 1 Fig. 2 Fig. 3 Fig. 7 PMID:3052562

  19. The downregulation of the RNA-binding protein Staufen2 in response to DNA damage promotes apoptosis.

    PubMed

    Zhang, Xin; Trépanier, Véronique; Beaujois, Remy; Viranaicken, Wildriss; Drobetsky, Elliot; DesGroseillers, Luc

    2016-05-01

    Staufen2 (Stau2) is an RNA-binding protein involved in cell fate decision by controlling several facets of mRNA processing including localization, splicing, translation and stability. Herein we report that exposure to DNA-damaging agents that generate replicative stress such as camptothecin (CPT), 5-fluoro-uracil (5FU) and ultraviolet radiation (UVC) causes downregulation of Stau2 in HCT116 colorectal cancer cells. In contrast, other agents such as doxorubicin and ionizing radiation had no effect on Stau2 expression. Consistently, Stau2 expression is regulated by the ataxia telangiectasia and Rad3-related (ATR) signaling pathway but not by the DNA-PK or ataxia telangiectasia mutated/checkpoint kinase 2 pathways. Stau2 downregulation is initiated at the level of transcription, independently of apoptosis induction. Promoter analysis identified a short 198 bp region which is necessary and sufficient for both basal and CPT-regulated Stau2 expression. The E2F1 transcription factor regulates Stau2 in untreated cells, an effect that is abolished by CPT treatment due to E2F1 displacement from the promoter. Strikingly, Stau2 downregulation enhances levels of DNA damage and promotes apoptosis in CPT-treated cells. Taken together our results suggest that Stau2 is an anti-apoptotic protein that could be involved in DNA replication and/or maintenance of genome integrity and that its expression is regulated by E2F1 via the ATR signaling pathway. PMID:26843428

  20. FBXL5-mediated degradation of single-stranded DNA-binding protein hSSB1 controls DNA damage response

    PubMed Central

    Chen, Zhi-Wei; Liu, Bin; Tang, Nai-Wang; Xu, Yun-Hua; Ye, Xiang-Yun; Li, Zi-Ming; Niu, Xiao-Min; Shen, Sheng-Ping; Lu, Shun; Xu, Ling

    2014-01-01

    Human single-strand (ss) DNA binding proteins 1 (hSSB1) has been shown to participate in DNA damage response and maintenance of genome stability by regulating the initiation of ATM-dependent signaling. ATM phosphorylates hSSB1 and prevents hSSB1 from ubiquitin-proteasome-mediated degradation. However, the E3 ligase that targets hSSB1 for destruction is still unknown. Here, we report that hSSB1 is the bona fide substrate for an Fbxl5-containing SCF (Skp1-Cul1-F box) E3 ligase. Fbxl5 interacts with and targets hSSB1 for ubiquitination and degradation, which could be prevented by ATM-mediated hSSB1 T117 phosphorylation. Furthermore, cells overexpression of Fbxl5 abrogated the cellular response to DSBs, including activation of ATM and phosphorylation of ATM targets and exhibited increased radiosensitivity, chemosensitivity and defective checkpoint activation after genotoxic stress stimuli. Moreover, the protein levels of hSSB1 and Fbxl5 showed an inverse correlation in lung cancer cells lines and clinical lung cancer samples. Therefore, Fbxl5 may negatively modulate hSSB1 to regulate DNA damage response, implicating Fbxl5 as a novel, promising therapeutic target for lung cancers. PMID:25249620

  1. FBXL5-mediated degradation of single-stranded DNA-binding protein hSSB1 controls DNA damage response.

    PubMed

    Chen, Zhi-Wei; Liu, Bin; Tang, Nai-Wang; Xu, Yun-Hua; Ye, Xiang-Yun; Li, Zi-Ming; Niu, Xiao-Min; Shen, Sheng-Ping; Lu, Shun; Xu, Ling

    2014-10-01

    Human single-strand (ss) DNA binding proteins 1 (hSSB1) has been shown to participate in DNA damage response and maintenance of genome stability by regulating the initiation of ATM-dependent signaling. ATM phosphorylates hSSB1 and prevents hSSB1 from ubiquitin-proteasome-mediated degradation. However, the E3 ligase that targets hSSB1 for destruction is still unknown. Here, we report that hSSB1 is the bona fide substrate for an Fbxl5-containing SCF (Skp1-Cul1-F box) E3 ligase. Fbxl5 interacts with and targets hSSB1 for ubiquitination and degradation, which could be prevented by ATM-mediated hSSB1 T117 phosphorylation. Furthermore, cells overexpression of Fbxl5 abrogated the cellular response to DSBs, including activation of ATM and phosphorylation of ATM targets and exhibited increased radiosensitivity, chemosensitivity and defective checkpoint activation after genotoxic stress stimuli. Moreover, the protein levels of hSSB1 and Fbxl5 showed an inverse correlation in lung cancer cells lines and clinical lung cancer samples. Therefore, Fbxl5 may negatively modulate hSSB1 to regulate DNA damage response, implicating Fbxl5 as a novel, promising therapeutic target for lung cancers. PMID:25249620

  2. The downregulation of the RNA-binding protein Staufen2 in response to DNA damage promotes apoptosis

    PubMed Central

    Zhang, Xin; Trépanier, Véronique; Beaujois, Remy; Viranaicken, Wildriss; Drobetsky, Elliot; DesGroseillers, Luc

    2016-01-01

    Staufen2 (Stau2) is an RNA-binding protein involved in cell fate decision by controlling several facets of mRNA processing including localization, splicing, translation and stability. Herein we report that exposure to DNA-damaging agents that generate replicative stress such as camptothecin (CPT), 5-fluoro-uracil (5FU) and ultraviolet radiation (UVC) causes downregulation of Stau2 in HCT116 colorectal cancer cells. In contrast, other agents such as doxorubicin and ionizing radiation had no effect on Stau2 expression. Consistently, Stau2 expression is regulated by the ataxia telangiectasia and Rad3-related (ATR) signaling pathway but not by the DNA-PK or ataxia telangiectasia mutated/checkpoint kinase 2 pathways. Stau2 downregulation is initiated at the level of transcription, independently of apoptosis induction. Promoter analysis identified a short 198 bp region which is necessary and sufficient for both basal and CPT-regulated Stau2 expression. The E2F1 transcription factor regulates Stau2 in untreated cells, an effect that is abolished by CPT treatment due to E2F1 displacement from the promoter. Strikingly, Stau2 downregulation enhances levels of DNA damage and promotes apoptosis in CPT-treated cells. Taken together our results suggest that Stau2 is an anti-apoptotic protein that could be involved in DNA replication and/or maintenance of genome integrity and that its expression is regulated by E2F1 via the ATR signaling pathway. PMID:26843428

  3. Overexpression of UV-DAMAGED DNA BINDING PROTEIN 1 links plant development and phytonutrient accumulation in high pigment-1 tomato

    PubMed Central

    Azari, Raviv; Reuveni, Moshe; Evenor, Dalia; Nahon, Sahadia; Shlomo, Haviva; Chen, Lea; Levin, Ilan

    2010-01-01

    Fruits of tomato plants carrying the high pigment-1 mutations hp-1 and hp-1w are characterized by an increased number of plastids coupled with enhanced levels of functional metabolites. Unfortunately, hp-1 mutant plants are also typified by light-dependent retardation in seedling and whole-plant growth and development, which limits their cultivation. These mutations were mapped to the gene encoding UV-DAMAGED DNA BINDING PROTEIN 1 (DDB1) and, recently, fruit-specific RNA interference studies have demonstrated an increased number of plastids and enhanced carotenoid accumulation in the transgenic tomato fruits. However, whole-plant overexpression of DDB1, required to substantiate its effects on seedling and plant development and to couple them with fruit phenotypes, has heretofore been unsuccessful. In this study, five transgenic lines constitutively overexpressing normal DDB1 in hp-1 mutant plants were analysed. Eleven-day-old seedlings, representing these lines, displayed up to ∼73- and ∼221-fold overexpression of the gene in hypocotyls and cotyledons, respectively. This overexpression resulted in statistically significant reversion to the non-mutant developmental phenotypes, including more than a full quantitative reversion. This reversion of phenotypes was generally accompanied by correlated responses in chlorophyll accumulation and altered expression of selected light signalling genes: PHYTOCHROME A, CRYPTOCHROME 1, ELONGATED HYPOCOTYL 5, and the gene encoding CHLOROPHYLL A/B-BINDING PROTEIN 4. Cumulatively, these results provide the missing link between DDB1 and its effects on tomato plant development. PMID:20566564

  4. The single-strand DNA binding activity of human PC4 preventsmutagenesis and killing by oxidative DNA damage

    SciTech Connect

    Wang, Jen-Yeu; Sarker, Altaf Hossain; Cooper, Priscilla K.; Volkert, Michael R.

    2004-02-01

    Human positive cofactor 4 (PC4) is a transcriptional coactivator with a highly conserved single-strand DNA (ssDNA) binding domain of unknown function. We identified PC4 as a suppressor of the oxidative mutator phenotype of the Escherichia coli fpg mutY mutant and demonstrate that this suppression requires its ssDNA binding activity. Yeast mutants lacking their PC4 ortholog Sub1 are sensitive to hydrogen peroxide and exhibit spontaneous and peroxide induced hypermutability. PC4 expression suppresses the peroxide sensitivity of the yeast sub l{Delta} mutant, suggesting that the human protein has a similar function. A role for yeast and human proteins in DNA repair is suggested by the demonstration that Sub1 acts in a peroxide-resistance pathway involving Rad2 and by the physical interaction of PC4 with the human Rad2 homolog XPG. We show XPG recruits PC4 to a bubble-containing DNA substrate with resulting displacement of XPG and formation of a PC4-DNA complex. We discuss the possible requirement for PC4 in either global or transcription-coupled repair of oxidative DNA damage to mediate the release of XPG bound to its substrate.

  5. Single-molecule analysis reveals human UV-damaged DNA-binding protein (UV-DDB) dimerizes on DNA via multiple kinetic intermediates

    PubMed Central

    Ghodke, Harshad; Wang, Hong; Hsieh, Ching L.; Woldemeskel, Selamawit; Watkins, Simon C.; Rapić-Otrin, Vesna; Van Houten, Bennett

    2014-01-01

    How human DNA repair proteins survey the genome for UV-induced photoproducts remains a poorly understood aspect of the initial damage recognition step in nucleotide excision repair (NER). To understand this process, we performed single-molecule experiments, which revealed that the human UV-damaged DNA-binding protein (UV-DDB) performs a 3D search mechanism and displays a remarkable heterogeneity in the kinetics of damage recognition. Our results indicate that UV-DDB examines sites on DNA in discrete steps before forming long-lived, nonmotile UV-DDB dimers (DDB1-DDB2)2 at sites of damage. Analysis of the rates of dissociation for the transient binding molecules on both undamaged and damaged DNA show multiple dwell times over three orders of magnitude: 0.3–0.8, 8.1, and 113–126 s. These intermediate states are believed to represent discrete UV-DDB conformers on the trajectory to stable damage detection. DNA damage promoted the formation of highly stable dimers lasting for at least 15 min. The xeroderma pigmentosum group E (XP-E) causing K244E mutant of DDB2 found in patient XP82TO, supported UV-DDB dimerization but was found to slide on DNA and failed to stably engage lesions. These findings provide molecular insight into the loss of damage discrimination observed in this XP-E patient. This study proposes that UV-DDB recognizes lesions via multiple kinetic intermediates, through a conformational proofreading mechanism. PMID:24760829

  6. Protection from Inflammatory Organ Damage in a Murine Model of Hemophagocytic Lymphohistiocytosis Using Treatment with IL-18 Binding Protein

    PubMed Central

    Chiossone, Laura; Audonnet, Sandra; Chetaille, Bruno; Chasson, Lionel; Farnarier, Catherine; Berda-Haddad, Yael; Jordan, Stefan; Koszinowski, Ulrich H.; Dalod, Marc; Mazodier, Karin; Novick, Daniela; Dinarello, Charles A.; Vivier, Eric; Kaplanski, Gilles

    2012-01-01

    Hemophagocytic lymphohistiocytosis (HLH) is a life-threatening condition due to the association of an infectious agent with lymphocyte cytotoxicity defects, either of congenital genetic origin in children or presumably acquired in adults. In HLH patients, an excess of lymphocyte or macrophage cytokines, such as IFN-γ and TNFα is present in serum. In animal models of the disease, IFN-γ and TNF-α have been shown to play a central pathogenic role. In humans, unusually high concentrations of IL-18, an inducer of IFN-γ, and TNF-α have been reported, and are associated with an imbalance between IL-18 and its natural inhibitor IL-18 binding protein (IL-18BP) resulting in an excess of free IL-18. Here we studied whether IL-18BP could reduce disease severity in an animal model of HLH. Mouse cytomegalovirus infection in perforin-1 knock-out mice induced a lethal condition similar to human HLH characterized by cytopenia with marked inflammatory lesions in the liver and spleen as well as the presence of hemophagocytosis in bone marrow. IL-18BP treatment decreased hemophagocytosis and reversed liver as well as spleen damage. IL-18BP treatment also reduced both IFN-γ and TNF-α production by CD8+ T and NK cells, as well as Fas ligand expression on NK cell surface. These data suggest that IL-18BP is beneficial in an animal model of HLH and in combination with anti-infectious therapy may be a promising strategy to treat HLH patients. PMID:22891066

  7. An ataxia-telangiectasia-mutated (ATM) kinase mediated response to DNA damage down-regulates the mRNA-binding potential of THOC5

    PubMed Central

    Ramachandran, Sheetal; Tran, Doan Duy Hai; Klebba-Faerber, Sabine; Kardinal, Christian; Whetton, Anthony D.; Tamura, Teruko

    2011-01-01

    In response to DNA damage, transcription is blocked by inhibition of RNA polymerase II activity. The regulation of a preexisting pool of mRNAs, therefore, plays a key role in DNA repair, cell cycle arrest, or inhibition of differentiation. THOC5 is a member of the THO complex and plays a role in the export of a subset of mRNA, which plays an important role in hematopoiesis and maintaining primitive cells. Since three serine residues in the PEST domain of THOC5 have been shown to be directly phosphorylated by ataxia-telangiectasia-mutated (ATM) kinase, we examined the THOC5-dependent mRNA export under DNA damage. We show here that DNA damage drastically decreased the cytoplasmic pool of a set of THOC5-dependent mRNAs and impaired the THOC5/mRNA complex formation. The mRNP complex formed with nonphosphorylation mutant (S307/312/314A) THOC5, but not with a C-terminal deletion mutant after DNA damage, suggesting that the C-terminal domain of THOC5, but not its phosphorylation in the PEST domain, is necessary for the regulation of the mRNA-binding potency of THOC5. The cytoplasmic THOC5-dependent mRNAs were recovered by treatment with ATM kinase-specific or p53-specific siRNA, as well as by treatment with ATM kinase inhibitor, KU55933, under DNA damage conditions, suggesting that the ATM–kinase–p53 pathway is involved in this response to the DNA damage. Furthermore, the treatment with KU55933 blocked DNA damage-induced THOC5mRNP complex dissociation, indicating that activation of ATM kinase suppresses the ability of THOC5 to bind to its target mRNAs. PMID:21937706

  8. Metabolic activation of tris(2,3-dibromopropyl)phosphate to reactive intermediates. II. Covalent binding, reactive metabolite formation, and differential metabolite-specific DNA damage in vivo.

    PubMed

    Pearson, P G; Omichinski, J G; Holme, J A; McClanahan, R H; Brunborg, G; Søderlund, E J; Dybing, E; Nelson, S D

    1993-02-01

    Analogs of tris(2,3-dibromopropyl)phosphate (Tris-BP) either labeled at specific positions with carbon-14 and phosphorus-32 or dual-labeled with both deuterium and tritium were administered to male Wistar rats at a nephrotoxic dose of 360 mumol/kg. The covalent binding of Tris-BP metabolites to hepatic, renal, and testicular proteins was determined after 9 and 24 hr, and plasma concentrations of bis(2,3-dibromopropyl)-phosphate (Bis-BP) formed metabolically from Tris-BP were measured at intervals throughout the initial 9-hr postdosing period. The covalent binding of 14C-Tris-BP metabolites in the kidney (2495 +/- 404 pmol/mg protein) was greater than that in the liver (476 +/- 123 pmol/mg protein) or testes (94 +/- 11 pmol/mg protein); the extent of renal covalent protein binding of Tris-BP metabolites was decreased by 82 and 84% when deuterium was substituted at carbon-2 and carbon-3, respectively. Substitution of Tris-BP with deuterium at carbon-2 or carbon-3 also decreased the mean area under the curve for Bis-BP plasma concentration by 48 and 57%, respectively. The mechanism of Tris-BP-induced renal and hepatic DNA damage was evaluated in Wistar rats by an automated alkaline elution procedure after the administration of analogs of Tris-BP or Bis-BP labeled at specific positions with deuterium. Renal DNA damage was decreased when Tris-BP was substituted with deuterium at either carbon-2 or carbon-3; the magnitude of the change correlated with both a decrease in the area under the Bis-BP plasma curve and a decrease in renal covalent binding of Tris-BP metabolites for each of the deuterated analogs. In marked contrast, analogs of Bis-BP labeled with deuterium at carbon-2 or carbon-3 did not show a decrease in the severity of renal DNA damage compared to unlabeled Bis-BP. On the basis of these observations a metabolic scheme for hepatic P-450-mediated oxidation at either carbon-2 or carbon-3 of Tris-BP affording Bis-BP by two alternate pathways that are susceptible

  9. Direct Binding to Replication Protein A (RPA)-coated Single-stranded DNA Allows Recruitment of the ATR Activator TopBP1 to Sites of DNA Damage.

    PubMed

    Acevedo, Julyana; Yan, Shan; Michael, W Matthew

    2016-06-17

    A critical event for the ability of cells to tolerate DNA damage and replication stress is activation of the ATR kinase. ATR activation is dependent on the BRCT (BRCA1 C terminus) repeat-containing protein TopBP1. Previous work has shown that recruitment of TopBP1 to sites of DNA damage and stalled replication forks is necessary for downstream events in ATR activation; however, the mechanism for this recruitment was not known. Here, we use protein binding assays and functional studies in Xenopus egg extracts to show that TopBP1 makes a direct interaction, via its BRCT2 domain, with RPA-coated single-stranded DNA. We identify a point mutant that abrogates this interaction and show that this mutant fails to accumulate at sites of DNA damage and that the mutant cannot activate ATR. These data thus supply a mechanism for how the critical ATR activator, TopBP1, senses DNA damage and stalled replication forks to initiate assembly of checkpoint signaling complexes. PMID:27129245

  10. Substrate Inhibition of VanA by d-Alanine Reduces Vancomycin Resistance in a VanX-Dependent Manner.

    PubMed

    van der Aart, Lizah T; Lemmens, Nicole; van Wamel, Willem J; van Wezel, Gilles P

    2016-08-01

    The increasing resistance of clinical pathogens against the glycopeptide antibiotic vancomycin, a last-resort drug against infections with Gram-positive pathogens, is a major problem in the nosocomial environment. Vancomycin inhibits peptidoglycan synthesis by binding to the d-Ala-d-Ala terminal dipeptide moiety of the cell wall precursor lipid II. Plasmid-transferable resistance is conferred by modification of the terminal dipeptide into the vancomycin-insensitive variant d-Ala-d-Lac, which is produced by VanA. Here we show that exogenous d-Ala competes with d-Lac as a substrate for VanA, increasing the ratio of wild-type to mutant dipeptide, an effect that was augmented by several orders of magnitude in the absence of the d-Ala-d-Ala peptidase VanX. Liquid chromatography-mass spectrometry (LC-MS) analysis showed that high concentrations of d-Ala led to the production of a significant amount of wild-type cell wall precursors, while vanX-null mutants produced primarily wild-type precursors. This enhanced the efficacy of vancomycin in the vancomycin-resistant model organism Streptomyces coelicolor, and the susceptibility of vancomycin-resistant clinical isolates of Enterococcus faecium (VRE) increased by up to 100-fold. The enhanced vancomycin sensitivity of S. coelicolor cells correlated directly to increased binding of the antibiotic to the cell wall. Our work offers new perspectives for the treatment of diseases associated with vancomycin-resistant pathogens and for the development of drugs that target vancomycin resistance. PMID:27270282

  11. ENHANCED BINDING OF AUTOLOGOUS RED CELLS TO THE MACROPHAGE PLASMA MEMBRANE AS A SENSITIVE INDICATOR OF POLLUTANT DAMAGE

    EPA Science Inventory

    The alveolar macrophage (AM) represents the primary line of defense in host protection against inhaled infectious organisms. Following exposure to oxidant gases, the ability of the host to resist airborne bacterial infection is severely impaired, and damage to the AM defense syst...

  12. DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin

    PubMed Central

    Nowicka, Urszula; Zhang, Daoning; Walker, Olivier; Krutauz, Daria; Castañeda, Carlos A.; Chaturvedi, Apurva; Chen, Tony Y.; Reis, Noa; Glickman, Michael H.; Fushman, David

    2015-01-01

    SUMMARY Ddi1 belongs to a family of shuttle proteins targeting polyubiquitinated substrates for proteasomal degradation. Unlike the other proteasomal shuttles, Rad23 and Dsk2, Ddi1 remains an enigma: its function is not fully understood and structural properties are poorly characterized. We determined the structure and binding properties of the ubiquitin-like (UBL) and ubiquitin-associated (UBA) domains of Ddi1 from Saccharomyces cerevisiae. We found that, while Ddi1UBA forms a characteristic UBA:ubiquitin complex, Ddi1UBL has entirely uncharacteristic binding preferences. Despite having a ubiquitin-like fold, Ddi1UBL does not interact with typical UBL-receptors but, unexpectedly, binds ubiquitin, forming a unique interface mediated by hydrophobic contacts and by salt-bridges between oppositely-charged residues of Ddi1UBL and ubiquitin. In stark contrast with ubiquitin and other UBLs, the β-sheet surface of Ddi1UBL is negatively charged and, therefore, is recognized in a completely different way. The dual functionality of Ddi1UBL, capable of binding both ubiquitin and proteasome, suggests a novel mechanism for Ddi1 as a proteasomal shuttle. PMID:25703377

  13. BINDING OF CARCINOGENS TO DNA AND COVALENT ADDUCTS DNA DAMAGE - PAH, AROMATIC AMINES, NITRO-AROMATIC COMPOUNDS, AND HALOGENATED COMPOUNDS

    EPA Science Inventory

    DNA adducts are the covalent addition products resulting from binding of reactive chemical species to DNA bases. The cancer initiating role of DNA adducts is well-established, and is clearly reflected in the high cancer incidence observed in individuals with deficiencies in any o...

  14. The Lipopeptide Antibiotic Paenibacterin Binds to the Bacterial Outer Membrane and Exerts Bactericidal Activity through Cytoplasmic Membrane Damage

    PubMed Central

    Huang, En

    2014-01-01

    Paenibacterin is a broad-spectrum lipopeptide antimicrobial agent produced by Paenibacillus thiaminolyticus OSY-SE. The compound consists of a cyclic 13-residue peptide and an N-terminal C15 fatty acyl chain. The mechanism of action of paenibacterin against Escherichia coli and Staphylococcus aureus was investigated in this study. The cationic lipopeptide paenibacterin showed a strong affinity for the negatively charged lipopolysaccharides (LPS) from the outer membrane of Gram-negative bacteria. Addition of LPS (100 μg/ml) completely eliminated the antimicrobial activity of paenibacterin against E. coli. The electrostatic interaction between paenibacterin and LPS may have displaced the divalent cations on the LPS network and thus facilitated the uptake of antibiotic into Gram-negative cells. Paenibacterin also damaged the bacterial cytoplasmic membrane, as evidenced by the depolarization of membrane potential and leakage of intracellular potassium ions from cells of E. coli and S. aureus. Therefore, the bactericidal activity of paenibacterin is attributed to disruption of the outer membrane of Gram-negative bacteria and damage of the cytoplasmic membrane of both Gram-negative and Gram-positive bacteria. Despite the evidence of membrane damage, this study does not rule out additional bactericidal mechanisms potentially exerted by paenibacterin. PMID:24561581

  15. DNA Damage: Quantum Mechanics/Molecular Mechanics Study on the Oxygen Binding and Substrate Hydroxylation Step in AlkB Repair Enzymes

    PubMed Central

    Quesne, Matthew G; Latifi, Reza; Gonzalez-Ovalle, Luis E; Kumar, Devesh; de Visser, Sam P

    2014-01-01

    AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N1-methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)–oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate-determining hydrogen-atom abstraction on competitive σ-and π-pathways on a quintet spin-state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen-bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained. PMID:24339041

  16. Crystal structures of the complexes between vancomycin and cell-wall precursor analogs.

    PubMed

    Nitanai, Yasushi; Kikuchi, Takanori; Kakoi, Kouji; Hanamaki, Shinji; Fujisawa, Ikuhide; Aoki, Katsuyuki

    2009-02-01

    The crystal structures of three vancomycin complexes with two vancomycin-sensitive cell-wall precursor analogs (diacetyl-Lys-D-Ala-D-Ala and acetyl-D-Ala-D-Ala) and a vancomycin-resistant cell-wall precursor analog (diacetyl-Lys-D-Ala-D-lactate) were determined at atomic resolutions of 1.80 A, 1.07 A, and 0.93 A, respectively. These structures not only reconfirm the "back-to-back" dimerization of vancomycin monomers and the ligand-binding scheme proposed by previous experiments but also show important structural features of strategies for the generation of new glycopeptide antibiotics. These structural features involve a water-mediated antibiotic-ligand interaction and supramolecular structures such as "side-by-side" arranged dimer-to-dimer structures, in addition to ligand-mediated and "face-to-face" arranged dimer-to-dimer structures. In the diacetyl-Lys-D-Ala-D-lactate complex, the interatomic O...O distance between the carbonyl oxygen of the fourth residue of the antibiotic backbone and the ester oxygen of the D-lactate moiety of the ligand is clearly longer than the corresponding N-H...O hydrogen-bonding distance observed in the two other complexes due to electrostatic repulsion. In addition, two neighboring hydrogen bonds are concomitantly lengthened. These observations provide, at least in part, a molecular basis for the reduced antibacterial activity of vancomycin toward vancomycin-resistant bacteria with cell-wall precursors terminating in -D-Ala-D-lactate. PMID:18976660

  17. Ambient UV-B exposure reduces the binding of ofloxacin with bacterial DNA gyrase and induces DNA damage mediated apoptosis.

    PubMed

    Singh, Jyoti; Dwivedi, Ashish; Mujtaba, Syed Faiz; Singh, Krishna P; Pal, Manish Kumar; Chopra, Deepti; Goyal, Shruti; Srivastav, Ajeet K; Dubey, Divya; Gupta, Shailendra K; Haldar, Chandana; Ray, Ratan Singh

    2016-04-01

    Ofloxacin (OFLX) is a broad spectrum antibiotic, which generates photo-products under sunlight exposure. Previous studies have failed to explain the attenuated anti-bacterial activity of OFLX. The study was extended to explore the unknown molecular mechanism of photogenotoxicity on human skin cell line (HaCaT) under environmental UV-B irradiation. Photochemically OFLX generates ROS and caused 2'-dGuO photodegradation. We have addressed the binding affinity of OFLX and its photo-products against DNA gyrase. Significant free radical generation such as (1)O2, O2(•-) and (•)OH reduces antioxidants and demonstrated the ROS mediated OFLX phototoxicity. However, the formation of micronuclei and CPDs showed photogenotoxic potential of OFLX. OFLX induced cell cycle arrest in sub-G1 peak. OFLX triggers apoptosis via permeabilization of mitochondrial membrane with the downregulation of anti-apoptotic Bcl-2 and caspase-3 whereas, upregulation of pro-apoptotic Bax and Cyto-C proteins. Our study illustrated that binding affinity of OFLX photo-products with DNA gyrase was mainly responsible for the attenuated antimicrobial activity. It was proved through molecular docking study. Thus, study suggests that sunlight exposure should avoid by drug users especially during peak hours for their safety from photosensitivity. Clinicians may guide patients regarding the safer use of photosensitive drugs during treatment. PMID:26812543

  18. Ran Binding Protein 9 (RanBP9) is a novel mediator of cellular DNA damage response in lung cancer cells

    PubMed Central

    Palmieri, Dario; Scarpa, Mario; Tessari, Anna; Uka, Rexhep; Amari, Foued; Lee, Cindy; Richmond, Timothy; Foray, Claudia; Sheetz, Tyler; Braddom, Ashley; Burd, Christin E.; Parvin, Jeffrey D.; Ludwig, Thomas; Croce, Carlo M.; Coppola, Vincenzo

    2016-01-01

    Ran Binding Protein 9 (RanBP9, also known as RanBPM) is an evolutionary conserved scaffold protein present both in the nucleus and the cytoplasm of cells whose biological functions remain elusive. We show that active ATM phosphorylates RanBP9 on at least two different residues (S181 and S603). In response to IR, RanBP9 rapidly accumulates into the nucleus of lung cancer cells, but this nuclear accumulation is prevented by ATM inhibition. RanBP9 stable silencing in three different lung cancer cell lines significantly affects the DNA Damage Response (DDR), resulting in delayed activation of key components of the cellular response to IR such as ATM itself, Chk2, γH2AX, and p53. Accordingly, abrogation of RanBP9 expression reduces homologous recombination-dependent DNA repair efficiency, causing an abnormal activation of IR-induced senescence and apoptosis. In summary, here we report that RanBP9 is a novel mediator of the cellular DDR, whose accumulation into the nucleus upon IR is dependent on ATM kinase activity. RanBP9 absence hampers the molecular mechanisms leading to efficient repair of damaged DNA, resulting in enhanced sensitivity to genotoxic stress. These findings suggest that targeting RanBP9 might enhance lung cancer cell sensitivity to genotoxic anti-neoplastic treatment. PMID:26943034

  19. THAP5 is a DNA binding transcriptional repressor that is regulated in melanoma cells during DNA damage-induced cell death

    PubMed Central

    Balakrishnan, Meenakshi P.; Cilenti, Lucia; Ambivero, Camilla; Goto, Yamafumi; Takata, Minoru; Turkson, James; Li, Xiaoman Shawn; Zervos, Antonis S.

    2011-01-01

    THAP5 was originally isolated as a specific interactor and substrate of the mitochondrial pro-apoptotic Omi/HtrA2 protease. It is a human zinc finger protein characterized by a restricted pattern of expression and the lack of orthologs in mouse and rat. The biological function of THAP5 is unknown but our previous studies suggest it could regulate G2/M transition in kidney cells and could be involved in human cardiomyocyte cell death associated with coronary artery disease (CAD). In this report, we expanded our studies on the properties and function of THAP5 in human melanoma cells. THAP5 was expressed in primary human melanocytes as well as in all melanoma cell lines that were tested. THAP5 protein level was significantly induced by UV irradiation or cisplatin treatment, conditions known to cause DNA damage. The induction of THAP5 correlated with a significant increase in apoptotic cell death. In addition, we show that THAP5 is a nuclear protein that could recognize and bind a specific DNA motif. THAP5 could also repress the transcription of a reporter gene in a heterologous system. Our work suggests that THAP5 is a DNA binding protein and a transcriptional repressor. Furthermore, THAP5 has a pro-apoptotic function and it was induced in melanoma cells under conditions that promoted cell death. PMID:21110952

  20. THAP5 is a DNA-binding transcriptional repressor that is regulated in melanoma cells during DNA damage-induced cell death

    SciTech Connect

    Balakrishnan, Meenakshi P.; Cilenti, Lucia; Ambivero, Camilla; Goto, Yamafumi; Takata, Minoru; Turkson, James; Li, Xiaoman Shawn; Zervos, Antonis S.

    2011-01-07

    Research highlights: {yields} THAP5 is a DNA-binding protein and a transcriptional repressor. {yields} THAP5 is induced in melanoma cells upon exposure to UV or treatment with cisplatin. {yields} THAP5 induction correlates with the degree of apoptosis in melanoma cell population. {yields} THAP5 is a pro-apoptotic protein involved in melanoma cell death. -- Abstract: THAP5 was originally isolated as a specific interactor and substrate of the mitochondrial pro-apoptotic Omi/HtrA2 protease. It is a human zinc finger protein characterized by a restricted pattern of expression and the lack of orthologs in mouse and rat. The biological function of THAP5 is unknown but our previous studies suggest it could regulate G2/M transition in kidney cells and could be involved in human cardiomyocyte cell death associated with coronary artery disease (CAD). In this report, we expanded our studies on the properties and function of THAP5 in human melanoma cells. THAP5 was expressed in primary human melanocytes as well as in all melanoma cell lines that were tested. THAP5 protein level was significantly induced by UV irradiation or cisplatin treatment, conditions known to cause DNA damage. The induction of THAP5 correlated with a significant increase in apoptotic cell death. In addition, we show that THAP5 is a nuclear protein that could recognize and bind a specific DNA motif. THAP5 could also repress the transcription of a reporter gene in a heterologous system. Our work suggests that THAP5 is a DNA-binding protein and a transcriptional repressor. Furthermore, THAP5 has a pro-apoptotic function and it was induced in melanoma cells under conditions that promoted cell death.

  1. Identification of DNA-Damage DNA-Binding Protein 1 as a Conditional Essential Factor for Cytomegalovirus Replication in Interferon-γ-Stimulated Cells

    PubMed Central

    Trilling, Mirko; Le, Vu Thuy Khanh; Fiedler, Manuela; Zimmermann, Albert; Bleifuß, Elke; Hengel, Hartmut

    2011-01-01

    The mouse cytomegaloviral (MCMV) protein pM27 represents an indispensable factor for viral fitness in vivo selectively, antagonizing signal transducer and activator of transcription 2 (STAT2)-mediated interferon signal transduction. We wished to explore by which molecular mechanism pM27 accomplishes this effect. We demonstrate that pM27 is essential and sufficient to curtail the protein half-life of STAT2 molecules. Pharmacologic inhibition of the proteasome restored STAT2 amounts, leading to poly-ubiquitin-conjugated STAT2 forms. PM27 was found in complexes with an essential host ubiquitin ligase complex adaptor protein, DNA-damage DNA-binding protein (DDB) 1. Truncation mutants of pM27 showed a strict correlation between DDB1 interaction and their ability to degrade STAT2. SiRNA-mediated knock-down of DDB1 restored STAT2 in the presence of pM27 and strongly impaired viral replication in interferon conditioned cells, thus phenocopying the growth attenuation of M27-deficient virus. In a constructive process, pM27 recruits DDB1 to exploit ubiquitin ligase complexes catalyzing the obstruction of the STAT2-dependent antiviral state of cells to permit viral replication. PMID:21698215

  2. A 127 kDa component of a UV-damaged DNA-binding complex, which is defective in some xeroderma pigmentosum group E patients, is homologous to a slime mold protein.

    PubMed Central

    Takao, M; Abramic, M; Moos, M; Otrin, V R; Wootton, J C; McLenigan, M; Levine, A S; Protic, M

    1993-01-01

    A cDNA which encodes a approximately 127 kDa UV-damaged DNA-binding (UV-DDB) protein with high affinity for (6-4)pyrimidine dimers [Abramic', M., Levine, A.S. & Protic', M., J. Biol. Chem. 266: 22493-22500, 1991] has been isolated from a monkey cell cDNA library. The presence of this protein in complexes bound to UV-damaged DNA was confirmed by immunoblotting. The human cognate of the UV-DDB gene was localized to chromosome 11. UV-DDB mRNA was expressed in all human tissues examined, including cells from two patients with xeroderma pigmentosum (group E) that are deficient in UV-DDB activity, which suggests that the binding defect in these cells may reside in a dysfunctional UV-DDB protein. Database searches have revealed significant homology of the UV-DDB protein sequence with partial sequences of yet uncharacterized proteins from Dictyostelium discoideum (44% identity over 529 amino acids) and Oryza sativa (54% identity over 74 residues). According to our results, the UV-DDB polypeptide belongs to a highly conserved, structurally novel family of proteins that may be involved in the early steps of the UV response, e.g., DNA damage recognition. Images PMID:8371985

  3. Naturally occurring germline and tumor-associated mutations within the ATP-binding motifs of PTEN lead to oxidative damage of DNA associated with decreased nuclear p53

    PubMed Central

    He, Xin; Ni, Ying; Wang, Yu; Romigh, Todd; Eng, Charis

    2011-01-01

    Somatic and germline mutations in PTEN (phosphatase and tensin homolog deleted on chromosome 10) are found in sporadic cancers and Cowden syndrome patients, respectively. Recent identification of naturally occurring cancer and germline mutations within the ATP-binding motifs of PTEN (heretofore referred to as PTEN ATP-binding mutations) has revealed that these mutations disrupted the subcellular localization and tumor-suppressor activity of PTEN. However, very little is known about the underlying mechanisms of PTEN ATP-binding mutations in tumorigenesis. Here we show that these mutations impair PTEN's function both qualitatively and quantitatively. On the one hand, PTEN ATP-binding mutants lose their phosphatase activity and the effect of downregulation of cyclin D1. On the other, the mislocalized mutant PTEN results in a significantly decreased nuclear p53 protein level and transcriptional activity, enhanced production of reactive oxygen species, induction of Cu/Zn superoxide dismutase as well as dramatically increased DNA double-strand breaks (DSBs). When compared with wild-type PTEN, the ATP-binding mutant PTEN has reduced half-life in vitro and decreased protein expression levels in vivo. Our data, thus, reveal a novel mechanism of tumorigenesis in patients with germline or somatic mutations affecting PTEN ATP-binding motifs, i.e. qualitative and quantitative impairment of PTEN due to the loss of its phosphatase activity, and nuclear mislocalization, resulting in rapid PTEN protein degradation, suppression of p53-mediated transcriptional activity, loss of protection against oxidative stress as well as accumulation of spontaneous DNA DSBs. PMID:20926450

  4. Gene vanXYC encodes D,D -dipeptidase (VanX) and D,D-carboxypeptidase (VanY) activities in vancomycin-resistant Enterococcus gallinarum BM4174.

    PubMed

    Reynolds, P E; Arias, C A; Courvalin, P

    1999-10-01

    VanX and VanY have strict D,D-dipeptidase and D,D-carboxypeptidase activity, respectively, that eliminates production of peptidoglycan precursors ending in D-alanyl-D-alanine (D-Ala-D-Ala) in glycopeptide-resistant enterococci in which the C-terminal D-Ala residue has been replaced by D-lactate. Enterococcus gallinarum BM4174 synthesizes peptidoglycan precursors ending in D-Ala-D-serine (D-Ala-D-Ser) essential for VanC-type vancomycin resistance. Insertional inactivation of the vanC-1 gene encoding the ligase that catalyses synthesis of D-Ala-D-Ser has a polar effect on both D, D-dipeptidase and D,D-carboxypeptidase activities. The open reading frame downstream from vanC-1 encoded a soluble protein designated VanXYC (Mr 22 318), which had both of these activities. It had 39% identity and 74% similarity to VanY in an overlap of 158 amino acids, and contained consensus sequences for binding zinc, stabilizing the binding of substrate and catalysing hydrolysis that are present in both VanX- and VanY-type enzymes. It had very low dipeptidase activity against D-Ala-D-Ser, unlike VanX, and no activity against UDP-MurNAc-pentapeptide[D-Ser], unlike VanY. The introduction of plasmid pAT708(vanC-1,XYC) or pAT717(vanXYC) into vancomycin-susceptible Enterococcus faecalis JH2-2 conferred low-level vancomycin resistance only when D-Ser was present in the growth medium. The peptidoglycan precursor profiles of E. faecalis JH2-2 and JH2-2(pAT708) and JH2-2(pAT717) indicated that the function of VanXYC was hydrolysis of D-Ala-D-Ala and removal of D-Ala from UDP-MurNAc-pentapeptide[D-Ala]. VanC-1 and VanXYC were essential, but not sufficient, for vancomycin resistance. PMID:10564477

  5. Light scattered by model phantom bacteria reveals molecular interactions at their surface

    NASA Astrophysics Data System (ADS)

    Ghetta, A.; Prosperi, D.; Mantegazza, F.; Panza, L.; Riva, S.; Bellini, T.

    2005-11-01

    Testing molecular interactions is an ubiquitous need in modern biology and molecular medicine. Here, we present a qualitative and quantitative method rooted in the basic properties of the scattering of light, enabling detailed measurement of ligand-receptor interactions occurring on the surface of colloids. The key factor is the use of receptor-coated nanospheres matched in refractive index with water and therefore optically undetectable ("phantom") when not involved in adhesion processes. At the occurrence of ligand binding at the receptor sites, optically unmatched material adsorbs on the nanoparticle surface, giving rise to an increment in their scattering cross section up to a maximum corresponding to saturated binding sites. The analysis of the scattering growth pattern enables extracting the binding affinity. This label-free method has been assessed through the determination of the binding constant of the antibiotic vancomycin with the tripeptide L-Lys-D-Ala-D-Ala and of the vancomycin dimerization constant. We shed light on the role of chelate effect and molecular hindrance in the activity of this glycopeptide. binding affinity | nanoparticles | vancomycin | ligand-receptor recognition

  6. Purification and characterization of VanXY(C), a D,D-dipeptidase/D,D-carboxypeptidase in vancomycin-resistant Enterococcus gallinarum BM4174.

    PubMed

    Podmore, Adrian H B; Reynolds, Peter E

    2002-06-01

    VanXY(C), a bifunctional enzyme from VanC-phenotype Enterococcus gallinarum BM4174 that catalyses D,D-peptidase and D,D-carboxypeptidase activities, was purified as the native protein, as a maltose-binding protein fusion and with an N-terminal tag containing six histidine residues. The kinetic parameters of His(6)-VanXY(C) were measured for a variety of precursors of peptidoglycan synthesis involved in resistance: for D-Ala-D-Ala, the K(m) was 3.6 mm and k(cat), 2.5 s(-1); for UDP-MurNAc-L-Ala-D-Glu-L-Lys-DAla-D-Ala (UDP-MurNAc-pentapeptide[Ala]), K(m) was 18.8 mm and k(cat) 6.2 s(-1); for D-Ala-D-Ser, K(m) was 15.5 mm and k(cat) 0.35 s(-1). His(6)-VanXYC was inactive against the peptidoglycan precursor UDP-MurNAc-L-Ala-D-Glu-L-Lys-D-Ala-D-Ser (UDP-MurNAc-pentapeptide[Ser]). The rate of hydrolysis of the terminal D-Ala of UDP-MurNAc-pentapeptide[Ala] was inhibited 30% by 2 mm D-Ala-D-Ser or UDP-MurNAc-pentapeptide[Ser]. Therefore preferential hydrolysis of substrates terminating in D-Ala would occur during peptidoglycan synthesis in E. gallinarum BM4174, leaving precursors ending in D-Ser with a lower affinity for glycopeptides to be incorporated into peptidoglycan. Mutation of an aspartate residue (Asp59) of His-tagged VanXY(C) corresponding to Asp68 in VanX to Ser or Ala, resulted in a 50% increase and 73% decrease, respectively, of the specificity constant (k(cat)/K(m)) for D-Ala-D-Ala. This situation is in contrast to VanX in which mutation of Asp68-->Ala produced a greater than 200,000-fold decrease in the substrate specificity constant. This suggests that Asp59, unlike Asp68 in VanX, does not have a pivotal role in catalysis. PMID:12047383

  7. CRN13 candidate effectors from plant and animal eukaryotic pathogens are DNA-binding proteins which trigger host DNA damage response.

    PubMed

    Ramirez-Garcés, Diana; Camborde, Laurent; Pel, Michiel J C; Jauneau, Alain; Martinez, Yves; Néant, Isabelle; Leclerc, Catherine; Moreau, Marc; Dumas, Bernard; Gaulin, Elodie

    2016-04-01

    To successfully colonize their host, pathogens produce effectors that can interfere with host cellular processes. Here we investigated the function of CRN13 candidate effectors produced by plant pathogenic oomycetes and detected in the genome of the amphibian pathogenic chytrid fungus Batrachochytrium dendrobatidis (BdCRN13). When expressed in Nicotiana, AeCRN13, from the legume root pathogen Aphanomyces euteiches, increases the susceptibility of the leaves to the oomycete Phytophthora capsici. When transiently expressed in amphibians or plant cells, AeCRN13 and BdCRN13 localize to the cell nuclei, triggering aberrant cell development and eventually causing cell death. Using Förster resonance energy transfer experiments in plant cells, we showed that both CRN13s interact with nuclear DNA and trigger plant DNA damage response (DDR). Mutating key amino acid residues in a predicted HNH-like endonuclease motif abolished the interaction of AeCRN13 with DNA, the induction of DDR and the enhancement of Nicotiana susceptibility to P. capsici. Finally, H2AX phosphorylation, a marker of DNA damage, and enhanced expression of genes involved in the DDR were observed in A. euteiches-infected Medicago truncatula roots. These results show that CRN13 from plant and animal eukaryotic pathogens promotes host susceptibility by targeting nuclear DNA and inducing DDR. PMID:26700936

  8. Binding discrimination of MutS to a set of lesions and compound lesions (base damage and mismatch) reveals its potential role as a cisplatin-damaged DNA sensing protein.

    PubMed

    Fourrier, Laurence; Brooks, Peter; Malinge, Jean-Marc

    2003-06-01

    The DNA mismatch repair (MMR) system plays a critical role in sensitizing both prokaryotic and eukaryotic cells to the clinically potent anticancer drug cisplatin. It is thought to mediate cytotoxicity through recognition of cisplatin DNA lesions. This drug generates a range of lesions that may also give rise to compound lesions resulting from the misincorporation of a base during translesion synthesis. Using gel mobility shift competition assays and surface plasmon resonance, we have analyzed the interaction of Escherichia coli MutS protein with site-specifically modified DNA oligonucleotides containing each of the four cisplatin cross-links or a set of compound lesions. The major 1,2-d(GpG) cisplatin intrastrand cross-link was recognized with only a 1.5-fold specificity, whereas a 47-fold specificity was found with a natural G/T containing DNA substrate. The rate of association, kon, for binding to the 1,2-d(GpG) adduct was 3.1 x 104 m-1 s-1 and the specificity of binding was essentially dependent on koff. DNA duplexes containing a single 1,2-d(ApG), 1,3-d(GpCpG) adduct, and an interstrand cross-link of cisplatin were not preferentially recognized. Among 12 DNA substrates, each containing a different cisplatin compound lesion derived from replicative misincorporation of one base opposite either of the 1,2-intrastrand adducts, 10 were specifically recognized including those that are more likely formed in vivo based on cisplatin mutation spectra. Moreover, among these lesions, two compound lesions formed when an adenine was misincorporated opposite a 1,2-d(GpG) adduct were not substrates for the MutY-dependent mismatch repair pathway. The ability of MutS to sense differentially various platinated DNA substrates suggests that cisplatin compound lesions formed during misincorporation of a base opposite either adducted base of both 1,2-intrastrand cross-links are more plausible critical lesions for MMR-mediated cisplatin cytotoxicity. PMID:12654906

  9. Central Role of the Copper-Binding Motif in the Complex Mechanism of Action of Ixosin: Enhancing Oxidative Damage and Promoting Synergy with Ixosin B.

    PubMed

    Libardo, M Daben J; Gorbatyuk, Vitaliy Y; Angeles-Boza, Alfredo M

    2016-01-01

    Ticks transmit multiple pathogens to different hosts without compromising their health. Their ability to evade microbial infections is largely a result of their effective innate immune response including various antimicrobial peptides. Therefore, a deep understanding of how ticks (and other arthropod vectors) control microbial loads could lead to the design of broad-spectrum antimicrobial agents. In this paper we study the role of the amino-terminal copper and nickel (ATCUN)-binding sequence in the peptide ixosin, isolated from the salivary glands of the hard tick Ixodes sinensis. Our results indicate that the ATCUN motif is not essential to the potency of ixosin, but is indispensable to its oxidative mechanism of action. Specifically, the ATCUN motif promotes dioxygen- and copper-dependent lipid (per)oxidation of bacterial membranes in a temporal fashion coinciding with the onset of bacterial death. Microscopy and studies on model membranes indicate that the oxidized phospholipids are utilized as potential targets of ixosin B (another tick salivary gland peptide) involving its delocalization to the bacterial membrane, thus resulting in a synergistic effect. Our proposed mechanism of action highlights the centrality of the ATCUN motif to ixosin's mechanism of action and demonstrates a novel way in which (tick) antimicrobial peptides (AMPs) utilize metal ions in its activity. This study suggests that ticks employ a variety of effectors to generate an amplified immune response, possibly justifying its vector competence. PMID:27622949

  10. Heart-type fatty acid-binding protein and its relation with morphological changes in rat myocardial damage model induced by isoproterenol.

    PubMed

    Hasić, Sabaheta; Jadrić, Radivoj; Cosović, Esad; Kiseljaković, Emina; Mornjaković, Zakira; Winterhalter-Jadrić, Mira

    2011-11-01

    We have investigated heart type fatty acid binding protein (H-FABP) rat serum values at different time point following subcutaneous (s.c) isoproterenol (ISO) administration and their correlation with severity of myocardial lesion. Thirty adult, male, Wistar rats were used for this study. Six rats per group were treated with a single dose of either ISO (ISO groups, dose 100 mg/kg, s.c.) at different time point (30', 60', 120', 240') or with saline (control group). Serum H-FABP was determined by enzyme-linked immunosorbent assay (ELISA) and histological analysis was performed by hematoxylin-eosin (HE) method of staining. The first serum H-FABP increase was obtained 30' following ISO administration, but maximal value was reached after 240'. Myocardial histological changes were time-dependent and correlated with serum H-FABP values (p<0.001). The results of the study suggest that H-FABP is sensitive marker for acute rat myocardial injury and its possible inclusion in myocardial injury screening studies in rats. PMID:22117831

  11. Antioxidant, metal-binding and DNA-damaging properties of flavonolignans: a joint experimental and computational highlight based on 7-O-galloylsilybin.

    PubMed

    Vacek, Jan; Zatloukalová, Martina; Desmier, Thomas; Nezhodová, Veronika; Hrbáč, Jan; Kubala, Martin; Křen, Vladimír; Ulrichová, Jitka; Trouillas, Patrick

    2013-10-01

    Besides the well-known chemoprotective effects of polyphenols, their prooxidant activities via interactions with biomacromolecules as DNA and proteins are of the utmost importance. Current research focuses not only on natural polyphenols but also on synthetically prepared analogs with promising biological activities. In the present study, the antioxidant and prooxidant properties of a semi-synthetic flavonolignan 7-O-galloylsilybin (7-GSB) are described. The presence of the galloyl moiety significantly enhances the antioxidant capacity of 7-GSB compared to that of silybin (SB). These findings were supported by electrochemistry, DPPH (2,2-diphenyl-1-picrylhydrazyl) scavenging activity, total antioxidant capacity (CL-TAC) and DFT (density functional theory) calculations. A three-step oxidation mechanism of 7-GSB is proposed at pH 7.4, in which the galloyl moiety is first oxidized at Ep,1=+0.20V (vs. Ag/AgCl3M KCl) followed by oxidation of the 20-OH (Ep,2=+0.55V) and most probably 5-OH (Ep,3=+0.95V) group of SB moiety. The molecular orbital analysis and the calculation of O-H bond dissociation enthalpies (BDE) fully rationalize the electrooxidation processes. The metal (Cu(2+)) complexation of 7-GSB was studied, which appeared to involve both the galloyl moiety and the 5-OH group. The prooxidant effects of the metal-complexes were then studied according to their capacity to oxidatively induce DNA modification and cleavage. These results paved the way towards the conclusion that 7-O-galloyl substitution to SB concomitantly (i) enhances antioxidant (ROS scavenging) capacity and (ii) decreases prooxidant effect/DNA damage after Cu complexation. This multidisciplinary approach provides a comprehensive mechanistic picture of the antioxidant vs. metal-induced prooxidant effects of flavonolignans at the molecular level, under ex vivo conditions. PMID:23872255

  12. Haptoglobin binding to apolipoprotein A-I prevents damage from hydroxyl radicals on its stimulatory activity of the enzyme lecithin-cholesterol acyl-transferase.

    PubMed

    Salvatore, Alfonso; Cigliano, Luisa; Bucci, Enrico M; Corpillo, Davide; Velasco, Silvia; Carlucci, Alessandro; Pedone, Carlo; Abrescia, Paolo

    2007-10-01

    Apolipoprotein A-I (ApoA-I), a major component of HDL, binds haptoglobin, a plasma protein transporting to liver or macrophages free Hb for preventing hydroxyl radical production. This work aimed to assess whether haptoglobin protects ApoA-I against this radical. Human ApoA-I structure, as analyzed by electrophoresis and MS, was found severely altered by hydroxyl radicals in vitro. Lower alteration of ApoA-I was found when HDL was oxidized in the presence of haptoglobin. ApoA-I oxidation was limited also when the complex of haptoglobin with both high-density lipoprotein and Hb, immobilized on resin beads, was exposed to hydroxyl radicals. ApoA-I function to stimulate cholesterol esterification was assayed in vitro by using ApoA-I-containing liposomes. Decreased stimulation was observed when liposomes oxidized without haptoglobin were used. Conversely, after oxidative stress in the presence of haptoglobin (0.5 microM monomer), the liposome activity did not change. Plasma of carrageenan-treated mice was analyzed by ELISA for the levels of haptoglobin and ApoA-I, and used to isolate HDL for MS analysis. Hydroxyproline-containing fragments of ApoA-I were found associated with low levels of haptoglobin (18 microM monomer), whereas they were not detected when the haptoglobin level increased (34-70 microM monomer). Therefore haptoglobin, when circulating at enhanced levels with free Hb during the acute phase of inflammation, might protect ApoA-I structure and function against hydroxyl radicals. PMID:17824618

  13. Extracellular DNA Impedes the Transport of Vancomycin in Staphylococcus epidermidis Biofilms Preexposed to Subinhibitory Concentrations of Vancomycin

    PubMed Central

    Tseng, Boo Shan; Howlin, Robert P.; Deacon, Jill; Wharton, Julian A.; Thurner, Philipp J.; Gilmore, Brendan F.; Parsek, Matthew R.; Stoodley, Paul

    2014-01-01

    Staphylococcus epidermidis biofilm formation is responsible for the persistence of orthopedic implant infections. Previous studies have shown that exposure of S. epidermidis biofilms to sub-MICs of antibiotics induced an increased level of biofilm persistence. BODIPY FL-vancomycin (a fluorescent vancomycin conjugate) and confocal microscopy were used to show that the penetration of vancomycin through sub-MIC-vancomycin-treated S. epidermidis biofilms was impeded compared to that of control, untreated biofilms. Further experiments showed an increase in the extracellular DNA (eDNA) concentration in biofilms preexposed to sub-MIC vancomycin, suggesting a potential role for eDNA in the hindrance of vancomycin activity. Exogenously added, S. epidermidis DNA increased the planktonic vancomycin MIC and protected biofilm cells from lethal vancomycin concentrations. Finally, isothermal titration calorimetry (ITC) revealed that the binding constant of DNA and vancomycin was 100-fold higher than the previously reported binding constant of vancomycin and its intended cellular d-Ala-d-Ala peptide target. This study provides an explanation of the eDNA-based mechanism of antibiotic tolerance in sub-MIC-vancomycin-treated S. epidermidis biofilms, which might be an important factor for the persistence of biofilm infections. PMID:25267673

  14. Heart-type fatty acid binding protein and high-sensitivity troponin T are myocardial damage markers that could predict adverse clinical outcomes in patients with peripheral artery disease

    PubMed Central

    Otaki, Yoichiro; Takahashi, Hiroki; Watanabe, Tetsu; Yamaura, Gensai; Funayama, Akira; Arimoto, Takanori; Shishido, Tetsuro; Miyamoto, Takuya; Kubota, Isao

    2015-01-01

    Background Despite many recent advances in endovascular therapy (EVT), peripheral artery disease (PAD) is an increasing health problem with high mortality. Heart-type fatty acid-binding protein (H-FABP) and high-sensitivity troponin T (hsTnT) are markers of ongoing myocardial damage and have been reported to be useful indicators of future cardiovascular events. However, it remains to be determined whether H-FABP and hsTnT can predict adverse clinical outcomes in patients with PAD. Methods and results We enrolled 208 de novo PAD patients who underwent EVT. Serum H-FABP and hsTnT were measured in all patients before EVT. During the median follow-up period of 694 days, there were 40 major adverse cardiovascular and cerebrovascular events (MACCEs) including all-cause deaths, and re-hospitalizations due to cardiovascular and cerebrovascular diseases and amputations. H-FABP and hsTnT were found to be higher in patients with critical limb ischemia (CLI) compared to those without this condition. Multivariate Cox proportional hazard regression analysis revealed that both H-FABP and hsTnT were independent predictors of MACCEs after adjustment for confounding factors. Kaplan–Meier analysis demonstrated that patients in the highest tertile according to H-FABP levels, as well as those in the highest hsTnT tertile, were at greatest risk for MACCEs. The net reclassification index was significantly improved by the addition of H-FABP as well as the addition of hsTnT to traditional risk factors. Conclusion The myocardial damage markers H-FABP and hsTnT were increased in PAD patients with CLI and could predict MACCEs in PAD patients. PMID:26673681

  15. Radiation abolishes inducer binding to lactose repressor.

    PubMed

    Gillard, Nathalie; Spotheim-Maurizot, Mélanie; Charlier, Michel

    2005-04-01

    The lactose operon functions under the control of the repressor-operator system. Binding of the repressor to the operator prevents the expression of the structural genes. This interaction can be destroyed by the binding of an inducer to the repressor. If ionizing radiations damage the partners, a dramatic dysfunction of the regulation system may be expected. We showed previously that gamma irradiation hinders repressor-operator binding through protein damage. Here we show that irradiation of the repressor abolishes the binding of the gratuitous inducer isopropyl-1-beta-D-thiogalactoside (IPTG) to the repressor. The observed lack of release of the repressor from the complex results from the loss of the ability of the inducer to bind to the repressor due to the destruction of the IPTG binding site. Fluorescence measurements show that both tryptophan residues located in or near the IPTG binding site are damaged. Since tryptophan damage is strongly correlated with the loss of IPTG binding ability, we conclude that it plays a critical role in the effect. A model was built that takes into account the kinetic analysis of damage production and the observed protection of its binding site by IPTG. This model satisfactorily accounts for the experimental results and allows us to understand the radiation-induced effects. PMID:15799700

  16. Right Hemisphere Brain Damage

    MedlinePlus

    ... Language and Swallowing / Disorders and Diseases Right Hemisphere Brain Damage [ en Español ] What is right hemisphere brain ... right hemisphere brain damage ? What is right hemisphere brain damage? Right hemisphere brain damage (RHD) is damage ...

  17. Structure of the Bacteriophage [phi]KZ Lytic Transglycosylase gp144

    SciTech Connect

    Fokine, Andrei; Miroshnikov, Konstantin A.; Shneider, Mikhail M.; Mesyanzhinov, Vadim V.; Rossmann, Michael G.

    2008-04-02

    Lytic transglycosylases are enzymes that act on the peptidoglycan of bacterial cell walls. They cleave the glycosidic linkage between N-acetylmuramoyl and N-acetylglucosaminyl residues with the concomitant formation of a 1,6-anhydromuramoyl product. The x-ray structure of the lytic transglycosylase gp144 from the Pseudomonas bacteriophage {phi}KZ has been determined to 2.5-{angstrom} resolution. This protein is probably employed by the bacteriophage in the late stage of the virus reproduction cycle to destroy the bacterial cell wall to release the phage progeny. {phi}KZ gp144 is a 260-residue {alpha}-helical protein composed of a 70-residue N-terminal cell wall-binding domain and a C-terminal catalytic domain. The fold of the N-terminal domain is similar to the peptidoglycan-binding domain from Streptomyces albus G d-Ala-d-Ala carboxypeptidase and to the N-terminal prodomain of human metalloproteinases that act on extracellular matrices. The C-terminal catalytic domain of gp144 has a structural similarity to the catalytic domain of the transglycosylase Slt70 from Escherichia coli and to lysozymes. The gp144 catalytic domain has an elongated groove that can bind at least five sugar residues at sites A-E. As in other lysozymes, the peptidoglycan cleavage (catalyzed by Glu{sup 115} in gp144) occurs between sugar-binding subsites D and E. The x-ray structure of the {phi}KZ transglycosylase complexed with the chitotetraose (N-acetylglucosamine){sub 4} has been determined to 2.6-{angstrom} resolution. The N-acetylglucosamine residues of the chitotetraose bind in sites A-D.

  18. Binding Procurement

    NASA Technical Reports Server (NTRS)

    Rao, Gopalakrishna M.; Vaidyanathan, Hari

    2007-01-01

    This viewgraph presentation reviews the use of the binding procurement process in purchasing Aerospace Flight Battery Systems. NASA Engineering and Safety Center (NESC) requested NASA Aerospace Flight Battery Systems Working Group to develop a set of guideline requirements document for Binding Procurement Contracts.

  19. Influence of the Charge State on the Structures and Interactions of Vancomycin Antibiotics with Cell-Wall Analogue Peptides: Experimental and Theoretical Studies

    SciTech Connect

    Yang, Zhibo; Vorpagel, Erich R.; Laskin, Julia

    2009-02-16

    In this study we examined the effect of the charge state on the energetics and dynamics of dissociation of the non-covalent complex between the vancomycin and the cell wall peptide analogue Nα,Nε-diacetyl-L-Lys-D-Ala-D-Ala (V-Ac2KDADA). The binding energies between the vancomycin and the peptide were obtained from the RRKM modeling of the time- and energy resolved surface-induced dissociation (SID) experiments. Our results demonstrate that the stability of the complex toward fragmentation increases in the order: [V+Ac2KDADA+H]+2 < [V+Ac2KDADA+H]+ < [V+Ac2KDADA-H]-. Dissociation of the singly protonated and singly deprotonated complex is characterized by very large entropy effects indicating substantial increase in the conformational flexibility of the resulting products. The experimental threshold energies of 1.75 eV and 1.34 eV obtained for the [V+Ac2KDADA-H]- and [V+Ac2KDADA+H]+ , respectively, are in excellent agreement with the results of density functional theory (DFT) calculations. The increased stability of the deprotonated complex observed experimentally is attributed to the presence of three charged sites in the deprotonated complex as compared to only one charged site in the singly protonated complex. The low binding energy of 0.93 eV obtained for the doubly protonated complex suggests that this ion is destabilized by Coulomb repulsion between the singly protonated vancomycin and the singly protonated peptide comprising the complex.

  20. Characterization of serine hydroxymethyltransferase GlyA as a potential source of D-alanine in Chlamydia pneumoniae

    PubMed Central

    De Benedetti, Stefania; Bühl, Henrike; Gaballah, Ahmed; Klöckner, Anna; Otten, Christian; Schneider, Tanja; Sahl, Hans-Georg; Henrichfreise, Beate

    2014-01-01

    For intracellular Chlamydiaceae, there is no need to withstand osmotic challenges, and a functional cell wall has not been detected in these pathogens so far. Nevertheless, penicillin inhibits cell division in Chlamydiaceae resulting in enlarged aberrant bodies, a phenomenon known as chlamydial anomaly. D-alanine is a unique and essential component in the biosynthesis of bacterial cell walls. In free-living bacteria like Escherichia coli, penicillin-binding proteins such as monofunctional transpeptidases PBP2 and PBP3, the putative targets of penicillin in Chlamydiaceae, cross-link adjacent peptidoglycan strands via meso-diaminopimelic acid and D-Ala-D-Ala moieties of pentapeptide side chains. In the absence of genes coding for alanine racemase Alr and DadX homologs, the source of D-Ala and thus the presence of substrates for PBP2 and PBP3 activity in Chlamydiaceae has puzzled researchers for years. Interestingly, Chlamydiaceae genomes encode GlyA, a serine hydroxymethyltransferase that has been shown to exhibit slow racemization of D- and L-alanine as a side reaction in E. coli. We show that GlyA from Chlamydia pneumoniae can serve as a source of D-Ala. GlyA partially reversed the D-Ala auxotrophic phenotype of an E. coli racemase double mutant. Moreover, purified chlamydial GlyA had racemase activity on L-Ala in vitro and was inhibited by D-cycloserine, identifying GlyA, besides D-Ala ligase MurC/Ddl, as an additional target of this competitive inhibitor in Chlamydiaceae. Proof of D-Ala biosynthesis in Chlamydiaceae helps to clarify the structure of cell wall precursor lipid II and the role of chlamydial penicillin-binding proteins in the development of non-dividing aberrant chlamydial bodies and persistence in the presence of penicillin. PMID:24616885

  1. Penicillin Binding Protein 1 Is Important in the Compensatory Response of Staphylococcus aureus to Daptomycin-Induced Membrane Damage and Is a Potential Target for β-Lactam–Daptomycin Synergy

    PubMed Central

    Berti, Andrew D.; Theisen, Erin; Sauer, John-Demian; Nonejuie, Poochit; Olson, Joshua; Pogliano, Joseph; Sakoulas, George; Nizet, Victor; Proctor, Richard A.

    2015-01-01

    The activity of daptomycin (DAP) against methicillin-resistant Staphylococcus aureus (MRSA) is enhanced in the presence of β-lactam antibiotics. This effect is more pronounced with β-lactam antibiotics that exhibit avid binding to penicillin binding protein 1 (PBP1). Here, we present evidence that PBP1 has a significant role in responding to DAP-induced stress on the cell. Expression of the pbpA transcript, encoding PBP1, was specifically induced by DAP exposure whereas expression of pbpB, pbpC, and pbpD, encoding PBP2, PBP3, and PBP4, respectively, remained unchanged. Using a MRSA COL strain with pbpA under an inducible promoter, increased pbpA transcription was accompanied by reduced susceptibility to, and killing by, DAP in vitro. Exposure to β-lactams that preferentially inactivate PBP1 was not associated with increased DAP binding, suggesting that synergy in the setting of anti-PBP1 pharmacotherapy results from increased DAP potency on a per-molecule basis. Combination exposure in an in vitro pharmacokinetic/pharmacodynamic model system with β-lactams that preferentially inactivate PBP1 (DAP-meropenem [MEM] or DAP-imipenem [IPM]) resulted in more-rapid killing than did combination exposure with DAP-nafcillin (NAF) (nonselective), DAP-ceftriaxone (CRO) or DAP-cefotaxime (CTX) (PBP2 selective), DAP-cefaclor (CEC) (PBP3 selective), or DAP-cefoxitin (FOX) (PBP4 selective). Compared to β-lactams with poor PBP1 binding specificity, exposure of S. aureus to DAP plus PBP1-selective β-lactams resulted in an increased frequency of septation and cell wall abnormalities. These data suggest that PBP1 activity may contribute to survival during DAP-induced metabolic stress. Therefore, targeted inactivation of PBP1 may enhance the antimicrobial efficiency of DAP, supporting the use of DAP–β-lactam combination therapy for serious MRSA infections, particularly when the β-lactam undermines the PBP1-mediated compensatory response. PMID:26525797

  2. DNA damage and sequence specificity of DNA binding of the new anti-cancer agent 1,4-bis(2'-chloroethyl)-1,4-diazabicyclo-[2.2.1] heptane dimaleate (Dabis maleate)

    PubMed Central

    Broggini, M.; Hartley, J. A.; Mattes, W. B.; Ponti, M.; Kohn, K. W.; D'Incalci, M.

    1990-01-01

    The DNA damage and the sequence specificity of guanine-N7 alkylation produced by the novel, positively charged, antineoplastic agent 1,4-bis(2'-chloroethyl)-1,4-diazabicyclo-[2.2.1] heptane dimaleate (Dabis maleate) and its uncharged tertiary amine analogue 1,4-bis(2'-chloroethyl)-1,4-diazacyclohexane (Dabis analogue) were investigated in L1210 cells and isolated DNA. Both compounds are cytotoxic in vitro causing an arrest of L1210 cells in G2/M phase of the cell cycle. In isolated DNA, Dabis maleate alkylates guanine at the N7-position with some differences in specificity compared to other alkylating agents (e.g. nitrogen mustard). Significant differences are also evident between Dabis maleate and Dabis analogue, suggesting that Dabis analogue is not the sole alkylating species of Dabis maleate. Using the alkaline elution technique a moderate number of DNA interstrand cross-links were detected in L1210 cells treated with both compounds, which were completely repaired within 24 h. Dabis maleate and Dabis analogue do not cause DNA single strand breaks or DNA protein cross-links at the doses at which DNA interstrand cross-links were detected. PMID:2393411

  3. Inflammation-induced DNA damage and damage-induced inflammation: a vicious cycle.

    PubMed

    Pálmai-Pallag, Timea; Bachrati, Csanád Z

    2014-10-01

    Inflammation is the ultimate response to the constant challenges of the immune system by microbes, irritants or injury. The inflammatory cascade initiates with the recognition of microorganism-derived pathogen associated molecular patterns (PAMPs) and host cell-derived damage associated molecular patterns (DAMPs) by the pattern recognition receptors (PRRs). DNA as a molecular PAMP or DAMP is sensed directly or via specific binding proteins to instigate pro-inflammatory response. Some of these DNA binding proteins also participate in canonical DNA repair pathways and recognise damaged DNA to initiate DNA damage response. In this review we aim to capture the essence of the complex interplay between DNA damage response and the pro-inflammatory signalling through representative examples. PMID:25449753

  4. Femoral nerve damage (image)

    MedlinePlus

    The femoral nerve is located in the leg and supplies the muscles that assist help straighten the leg. It supplies sensation ... leg. One risk of damage to the femoral nerve is pelvic fracture. Symptoms of femoral nerve damage ...

  5. DNA Damage and Pulmonary Hypertension

    PubMed Central

    Ranchoux, Benoît; Meloche, Jolyane; Paulin, Roxane; Boucherat, Olivier; Provencher, Steeve; Bonnet, Sébastien

    2016-01-01

    Pulmonary hypertension (PH) is defined by a mean pulmonary arterial pressure over 25 mmHg at rest and is diagnosed by right heart catheterization. Among the different groups of PH, pulmonary arterial hypertension (PAH) is characterized by a progressive obstruction of distal pulmonary arteries, related to endothelial cell dysfunction and vascular cell proliferation, which leads to an increased pulmonary vascular resistance, right ventricular hypertrophy, and right heart failure. Although the primary trigger of PAH remains unknown, oxidative stress and inflammation have been shown to play a key role in the development and progression of vascular remodeling. These factors are known to increase DNA damage that might favor the emergence of the proliferative and apoptosis-resistant phenotype observed in PAH vascular cells. High levels of DNA damage were reported to occur in PAH lungs and remodeled arteries as well as in animal models of PH. Moreover, recent studies have demonstrated that impaired DNA-response mechanisms may lead to an increased mutagen sensitivity in PAH patients. Finally, PAH was linked with decreased breast cancer 1 protein (BRCA1) and DNA topoisomerase 2-binding protein 1 (TopBP1) expression, both involved in maintaining genome integrity. This review aims to provide an overview of recent evidence of DNA damage and DNA repair deficiency and their implication in PAH pathogenesis. PMID:27338373

  6. DNA Damage and Pulmonary Hypertension.

    PubMed

    Ranchoux, Benoît; Meloche, Jolyane; Paulin, Roxane; Boucherat, Olivier; Provencher, Steeve; Bonnet, Sébastien

    2016-01-01

    Pulmonary hypertension (PH) is defined by a mean pulmonary arterial pressure over 25 mmHg at rest and is diagnosed by right heart catheterization. Among the different groups of PH, pulmonary arterial hypertension (PAH) is characterized by a progressive obstruction of distal pulmonary arteries, related to endothelial cell dysfunction and vascular cell proliferation, which leads to an increased pulmonary vascular resistance, right ventricular hypertrophy, and right heart failure. Although the primary trigger of PAH remains unknown, oxidative stress and inflammation have been shown to play a key role in the development and progression of vascular remodeling. These factors are known to increase DNA damage that might favor the emergence of the proliferative and apoptosis-resistant phenotype observed in PAH vascular cells. High levels of DNA damage were reported to occur in PAH lungs and remodeled arteries as well as in animal models of PH. Moreover, recent studies have demonstrated that impaired DNA-response mechanisms may lead to an increased mutagen sensitivity in PAH patients. Finally, PAH was linked with decreased breast cancer 1 protein (BRCA1) and DNA topoisomerase 2-binding protein 1 (TopBP1) expression, both involved in maintaining genome integrity. This review aims to provide an overview of recent evidence of DNA damage and DNA repair deficiency and their implication in PAH pathogenesis. PMID:27338373

  7. Cell Wall Polymers of Bacillus sphaericus: Activities of Enzymes Involved in Peptidoglycan Precursor Synthesis During Sporulation

    PubMed Central

    Linnett, Paul E.; Tipper, Donald J.

    1974-01-01

    In synchronously sporulating cells of Bacillus sphaericus 9602, the specific activities of those enzymes specifically required for the synthesis of the UDP-N-acetyl-muramyl-pentapeptide precursor of vegetative cell wall peptidoglycan decay by 50% after the end of exponential cell division, probably as a consequence of dilution by newly synthesized protein. The meso-diaminopimelate ligase is the only new activity whose synthesis is required for synthesis of the nucleotide-pentapeptide precursor of spore cortex peptidoglycan. The addition of d-Ala-d-Ala to the nucleotide tripeptide is catalyzed by an enzyme present in both vegetative and sporulating cells, which apparently does not discriminate between lysine- and diaminopimelate-containing acceptors. The activities of the l-Ala and d-Ala-d-Ala ligases and of the d-Ala-d-Ala synthetase increases in parallel with the appearance of the diaminopimelate ligase, indicating coordinate derepression and suggesting operon-like organization of the appropriate structural genes. PMID:4417383

  8. Fault damage zones

    NASA Astrophysics Data System (ADS)

    Kim, Young-Seog; Peacock, David C. P.; Sanderson, David J.

    2004-03-01

    Damage zones show very similar geometries across a wide range of scales and fault types, including strike-slip, normal and thrust faults. We use a geometric classification of damage zones into tip-, wall-, and linking-damage zones, based on their location around faults. These classes can be sub-divided in terms of fault and fracture patterns within the damage zone. A variety of damage zone structures can occur at mode II tips of strike-slip faults, including wing cracks, horsetail fractures, antithetic faults, and synthetic branch faults. Wall damage zones result from the propagation of mode II and mode III fault tips through a rock, or from damage associated with the increase in slip on a fault. Wall damage zone structures include extension fractures, antithetic faults, synthetic faults, and rotated blocks with associated triangular openings. The damage formed at the mode III tips of strike-slip faults (e.g. observed in cliff sections) are classified as wall damage zones, because the damage zone structures are distributed along a fault trace in map view. Mixed-mode tips are likely to show characteristics of both mode II and mode III tips. Linking damage zones are developed at steps between two sub-parallel faults, and the structures developed depend on whether the step is extensional or contractional. Extension fractures and pull-aparts typically develop in extensional steps, whilst solution seams, antithetic faults and synthetic faults commonly develop in contractional steps. Rotated blocks, isolated lenses or strike-slip duplexes may occur in both extensional and contractional steps. Damage zone geometries and structures are strongly controlled by the location around a fault, the slip mode at a fault tip, and by the evolutionary stage of the fault. Although other factors control the nature of damage zones (e.g. lithology, rheology and stress system), the three-dimensional fault geometry and slip mode at each tip must be considered to gain an understanding of

  9. DNA Binding Hydroxyl Radical Probes

    PubMed Central

    Tang, Vicky J; Konigsfeld, Katie M; Aguilera, Joe A; Milligan, Jamie R

    2011-01-01

    The hydroxyl radical is the primary mediator of DNA damage by the indirect effect of ionizing radiation. It is a powerful oxidizing agent produced by the radiolysis of water and is responsible for a significant fraction of the DNA damage associated with ionizing radiation. There is therefore an interest in the development of sensitive assays for its detection. The hydroxylation of aromatic groups to produce fluorescent products has been used for this purpose. We have examined four different chromophores which produce fluorescent products when hydroxylated. Of these, the coumarin system suffers from the fewest disadvantages. We have therefore examined its behavior when linked to a cationic peptide ligand designed to bind strongly to DNA. PMID:22125376

  10. CHARACTERIZATION OF DAMAGED MATERIALS

    SciTech Connect

    Hsu, P C; Dehaven, M; McClelland, M; Chidester, S; Maienschein, J L

    2006-06-23

    Thermal damage experiments were conducted on LX-04, LX-10, and LX-17 at high temperatures. Both pristine and damaged samples were characterized for their material properties. A pycnometer was used to determine sample true density and porosity. Gas permeability was measured in a newly procured system (diffusion permeameter). Burn rate was measured in the LLNL strand burner. Weight losses upon thermal exposure were insignificant. Damaged pressed parts expanded, resulting in a reduction of bulk density by up to 10%. Both gas permeabilities and burn rates of the damaged samples increased by several orders of magnitude due to higher porosity and lower density. Moduli of the damaged materials decreased significantly, an indication that the materials became weaker mechanically. Damaged materials were more sensitive to shock initiation at high temperatures. No significant sensitization was observed when the damaged samples were tested at room temperature.

  11. Damage Control Mechanisms in Articular Cartilage

    PubMed Central

    Martin, James A; Scherb, MB; Lembke, Lois A; Buckwalter, Joseph

    2000-01-01

    Articular chondrocytes maintain cartilage throughout life by replacing lost or damaged matrix with freshly synthesized material. Synthesis activity is regulated, rapidly increasing to well above basal levels in response to cartilage injury. Such responses suggest that synthesis activity is linked to the rate of matrix loss by endogenous "damage control" mechanisms. As a major stimulator of matrix synthesis in cartilage, insulin-like growth factor I (IGF-I) is likely to play a role in such mechanisms. Although IGF-I is nearly ubiquitous, its bioavailability in cartilage is controlled by IGF-I binding proteins (IGFBPs) secreted by chondrocytes. IGFBPs are part of a complex system, termed the IGF-I axis, that tightly regulates IGF-I activities. For the most part, IGFBPs block IGF-I activity by sequestering IGF-I from its cell surface receptor. We recently found that the expression of one binding protein, IGFBP-3, increases with chondrocyte age, paralleling an age-related decline in synthesis activity. In addition, IGFBP-3 is overexpressed in osteoarthritic cartilage, leading to metabolic disturbances that contribute to cartilage degeneration. These observations indicate that IGFBP-3 plays a crucial role in regulating matrix synthesis in cartilage, and suggest that cartilage damage control mechanisms may fail due to age-related changes in IGFBP-3 expression or distribution. Our investigation of this hypothesis began with immunolocalization studies to determine the tissue distribution of IGFBP-3 in human cartilage. We found that IGFBP-3 accumulated around chondrocytes in the pericellular/territorial matrix, where it co-localized with fibronectin, but not with the other matrix proteins tenascin-C and type VI collagen. This result suggested that the IGFBP-3 distribution is determined by binding to fibronectin. Binding studies using purified proteins demonstrated that IGFBP-3 does in fact bind to fibronectin, but not to tenascin-C or type VI collagen. Finally, we

  12. DNA damage may drive nucleosomal reorganization to facilitate damage detection

    NASA Astrophysics Data System (ADS)

    LeGresley, Sarah E.; Wilt, Jamie; Antonik, Matthew

    2014-03-01

    One issue in genome maintenance is how DNA repair proteins find lesions at rates that seem to exceed diffusion-limited search rates. We propose a phenomenon where DNA damage induces nucleosomal rearrangements which move lesions to potential rendezvous points in the chromatin structure. These rendezvous points are the dyad and the linker DNA between histones, positions in the chromatin which are more likely to be accessible by repair proteins engaged in a random search. The feasibility of this mechanism is tested by considering the statistical mechanics of DNA containing a single lesion wrapped onto the nucleosome. We consider lesions which make the DNA either more flexible or more rigid by modeling the lesion as either a decrease or an increase in the bending energy. We include this energy in a partition function model of nucleosome breathing. Our results indicate that the steady state for a breathing nucleosome will most likely position the lesion at the dyad or in the linker, depending on the energy of the lesion. A role for DNA binding proteins and chromatin remodelers is suggested based on their ability to alter the mechanical properties of the DNA and DNA-histone binding, respectively. We speculate that these positions around the nucleosome potentially serve as rendezvous points where DNA lesions may be encountered by repair proteins which may be sterically hindered from searching the rest of the nucleosomal DNA. The strength of the repositioning is strongly dependent on the structural details of the DNA lesion and the wrapping and breathing of the nucleosome. A more sophisticated evaluation of this proposed mechanism will require detailed information about breathing dynamics, the structure of partially wrapped nucleosomes, and the structural properties of damaged DNA.

  13. Damage Tolerance of Composites

    NASA Technical Reports Server (NTRS)

    Hodge, Andy

    2007-01-01

    Fracture control requirements have been developed to address damage tolerance of composites for manned space flight hardware. The requirements provide the framework for critical and noncritical hardware assessment and testing. The need for damage threat assessments, impact damage protection plans, and nondestructive evaluation are also addressed. Hardware intended to be damage tolerant have extensive coupon, sub-element, and full-scale testing requirements in-line with the Building Block Approach concept from the MIL-HDBK-17, Department of Defense Composite Materials Handbook.

  14. The RNA Splicing Response to DNA Damage.

    PubMed

    Shkreta, Lulzim; Chabot, Benoit

    2015-01-01

    The number of factors known to participate in the DNA damage response (DDR) has expanded considerably in recent years to include splicing and alternative splicing factors. While the binding of splicing proteins and ribonucleoprotein complexes to nascent transcripts prevents genomic instability by deterring the formation of RNA/DNA duplexes, splicing factors are also recruited to, or removed from, sites of DNA damage. The first steps of the DDR promote the post-translational modification of splicing factors to affect their localization and activity, while more downstream DDR events alter their expression. Although descriptions of molecular mechanisms remain limited, an emerging trend is that DNA damage disrupts the coupling of constitutive and alternative splicing with the transcription of genes involved in DNA repair, cell-cycle control and apoptosis. A better understanding of how changes in splice site selection are integrated into the DDR may provide new avenues to combat cancer and delay aging. PMID:26529031

  15. The RNA Splicing Response to DNA Damage

    PubMed Central

    Shkreta, Lulzim; Chabot, Benoit

    2015-01-01

    The number of factors known to participate in the DNA damage response (DDR) has expanded considerably in recent years to include splicing and alternative splicing factors. While the binding of splicing proteins and ribonucleoprotein complexes to nascent transcripts prevents genomic instability by deterring the formation of RNA/DNA duplexes, splicing factors are also recruited to, or removed from, sites of DNA damage. The first steps of the DDR promote the post-translational modification of splicing factors to affect their localization and activity, while more downstream DDR events alter their expression. Although descriptions of molecular mechanisms remain limited, an emerging trend is that DNA damage disrupts the coupling of constitutive and alternative splicing with the transcription of genes involved in DNA repair, cell-cycle control and apoptosis. A better understanding of how changes in splice site selection are integrated into the DDR may provide new avenues to combat cancer and delay aging. PMID:26529031

  16. Guest Editorial: Laser Damage

    SciTech Connect

    Vitaly Gruzdev, Michelle D. Shinn

    2012-12-01

    Laser damage of optical materials, first reported in 1964, continues to limit the output energy and power of pulsed and continuous-wave laser systems. In spite of some 48 years of research in this area, interest from the international laser community to laser damage issues remains at a very high level and does not show any sign of decreasing. Moreover, it grows with the development of novel laser systems, for example, ultrafast and short-wavelength lasers that involve new damage effects and specific mechanisms not studied before. This interest is evident from the high level of attendance and presentations at the annual SPIE Laser Damage Symposium (aka, Boulder Damage Symposium) that has been held in Boulder, Colorado, since 1969. This special section of Optical Engineering is the first one devoted to the entire field of laser damage rather than to a specific part. It is prepared in response to growing interest from the international laser-damage community. Some papers in this special section were presented at the Laser Damage Symposium; others were submitted in response to the general call for papers for this special section. The 18 papers compiled into this special section represent many sides of the broad field of laser-damage research. They consider theoretical studies of the fundamental mechanisms of laser damage including laser-driven electron dynamics in solids (O. Brenk and B. Rethfeld; A. Nikiforov, A. Epifanov, and S. Garnov; T. Apostolova et al.), modeling of propagation effects for ultrashort high-intensity laser pulses (J. Gulley), an overview of mechanisms of inclusion-induced damage (M. Koldunov and A. Manenkov), the formation of specific periodic ripples on a metal surface by femtosecond laser pulses (M. Ahsan and M. Lee), and the laser-plasma effects on damage in glass (Y. Li et al). Material characterization is represented by the papers devoted to accurate and reliable measurements of absorption with special emphasis on thin films (C. Mühlig and S

  17. Endobronchial Ultrasound Bronchoscope Damage.

    PubMed

    Patil, Monali; Harris, Kassem; Krishnan, Amita; Alraiyes, Abdul H; Dhillon, Samjot S

    2016-07-01

    Endobronchial ultrasound (EBUS)-guided transbronchial needle aspiration is an effective, safe, and cost-effective diagnostic bronchoscopy technique for the work-up of mediastinal lymphadenopathy. Concern has been raised, however, about the high cost of convex-probe EBUS bronchoscope repairs. The damage is usually due to breakage of the insertion tube (the flexible part that is advanced into the airways), moisture invasion and damages to the working channel, image guide bundle, or umbilical cord. Understanding the root cause of EBUS scope damage is important for its prevention. We describe 2 unusual cases of EBUS scope damage. In the first case, the distal black rubber covering of the EBUS scope insertion tube was damaged due to friction with the edge of an endotracheal tube and in the second case, the EBUS scope insertion tube was angulating laterally instead of vertically during the flexion maneuver, probably due to scope manipulation while wedged tightly in a segmental bronchus. PMID:27077640

  18. RNA protects a nucleoprotein complex against radiation damage.

    PubMed

    Bury, Charles S; McGeehan, John E; Antson, Alfred A; Carmichael, Ian; Gerstel, Markus; Shevtsov, Mikhail B; Garman, Elspeth F

    2016-05-01

    Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of radiation-induced structural and conformation changes, the so-called specific damage, within crystalline macromolecules can lead to false interpretations of biological mechanisms. Although this has been well characterized within protein crystals, far less is known about specific damage effects within the larger class of nucleoprotein complexes. Here, a methodology has been developed whereby per-atom density changes could be quantified with increasing dose over a wide (1.3-25.0 MGy) range and at higher resolution (1.98 Å) than the previous systematic specific damage study on a protein-DNA complex. Specific damage manifestations were determined within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein. Over a large dose range, the RNA was found to be far less susceptible to radiation-induced chemical changes than the protein. The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility. The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule. Additionally, the method enabled a quantification of the reduction in radiation-induced Lys and Phe disordering upon RNA binding directly from the electron density. PMID:27139628

  19. RNA protects a nucleoprotein complex against radiation damage

    PubMed Central

    Bury, Charles S.; McGeehan, John E.; Antson, Alfred A.; Carmichael, Ian; Gerstel, Markus; Shevtsov, Mikhail B.; Garman, Elspeth F.

    2016-01-01

    Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of radiation-induced structural and conformation changes, the so-called specific damage, within crystalline macromolecules can lead to false interpretations of biological mechanisms. Although this has been well characterized within protein crystals, far less is known about specific damage effects within the larger class of nucleoprotein complexes. Here, a methodology has been developed whereby per-atom density changes could be quantified with increasing dose over a wide (1.3–25.0 MGy) range and at higher resolution (1.98 Å) than the previous systematic specific damage study on a protein–DNA complex. Specific damage manifestations were determined within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein. Over a large dose range, the RNA was found to be far less susceptible to radiation-induced chemical changes than the protein. The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility. The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule. Additionally, the method enabled a quantification of the reduction in radiation-induced Lys and Phe disordering upon RNA binding directly from the electron density. PMID:27139628

  20. Metabolite Damage and Metabolite Damage Control in Plants.

    PubMed

    Hanson, Andrew D; Henry, Christopher S; Fiehn, Oliver; de Crécy-Lagard, Valérie

    2016-04-29

    It is increasingly clear that (a) many metabolites undergo spontaneous or enzyme-catalyzed side reactions in vivo, (b) the damaged metabolites formed by these reactions can be harmful, and (c) organisms have biochemical systems that limit the buildup of damaged metabolites. These damage-control systems either return a damaged molecule to its pristine state (metabolite repair) or convert harmful molecules to harmless ones (damage preemption). Because all organisms share a core set of metabolites that suffer the same chemical and enzymatic damage reactions, certain damage-control systems are widely conserved across the kingdoms of life. Relatively few damage reactions and damage-control systems are well known. Uncovering new damage reactions and identifying the corresponding damaged metabolites, damage-control genes, and enzymes demands a coordinated mix of chemistry, metabolomics, cheminformatics, biochemistry, and comparative genomics. This review illustrates the above points using examples from plants, which are at least as prone to metabolite damage as other organisms. PMID:26667673

  1. Cumulative fatigue damage models

    NASA Technical Reports Server (NTRS)

    Mcgaw, Michael A.

    1988-01-01

    The problem of calculating expected component life under fatigue loading conditions is complicated by the fact that component loading histories contain, in many cases, cyclic loads of widely varying amplitudes. In such a case a cumulative damage model is required, in addition to a fatigue damage criterion, or life relationship, in order to compute the expected fatigue life. The traditional cumulative damage model used in design is the linear damage rule. This model, while being simple to use, can yield grossly unconservative results under certain loading conditions. Research at the NASA Lewis Research Center has led to the development of a nonlinear cumulative damage model, named the double damage curve approach (DDCA), that has greatly improved predictive capability. This model, which considers the life (or loading) level dependence of damage evolution, was applied successfully to two polycrystalline materials, 316 stainless steel and Haynes 188. The cumulative fatigue behavior of the PWA 1480 single-crystal material is currently being measured to determine the applicability of the DDCA for this material.

  2. Laser Damage Lab

    NASA Technical Reports Server (NTRS)

    1993-01-01

    Optical Damage Threshold Testing Instrumentation at NASA Langley Research Center. This work was sanctioned and funded by Code Q, R, & AE to develop a new standard for damage testing various types of optical materials and coatings. Laser Induced Damage Threshold (LIDT) testing is a destructive test procedure to determine the minimum applied laser energy level that will result in damage and is referred to as the damage threshold. The damage threshold is often the critical limitation in the section of optical materials for use in high-energy laser systems.The test station consists of diagnostic equipment, beam conditioning optical elements, an inspection microscope and three lasers: a high energy pulsed ND: Yag, which develops 650mJ at 10 hz and outputs three wavelengths which include 1.06m, 532nm and 355 nm; a Ti:sapphire laser which produces a continuum of laser output from 790nm to 900nm; and a alignment HeNe, which looks yellow when mixed with the 2nd harmonic ND:Yag laser. Laser sources are used to perform damage threshold testing at the specific wavelength of interest.

  3. War Damage Assessment

    NASA Technical Reports Server (NTRS)

    1994-01-01

    During and after the Persian Gulf war, hundreds of "oil lakes" were created in Kuwait by oil released from damaged wells. The lakes are a hazard to the Kuwait atmosphere, soil and ground water and must be carefully monitored. Boston University Center for Remote Sensing, assisted by other organizations, has accurately mapped the lakes using Landsat and Spot imagery. The war damage included the formation of over 300 oil lakes, oil pollution and sand dune movement. Total damage area is over 5,400 square kilometers - 30 percent of Kuwait's total surface area.

  4. DNA Damage Response

    PubMed Central

    Giglia-Mari, Giuseppina; Zotter, Angelika; Vermeulen, Wim

    2011-01-01

    Structural changes to DNA severely affect its functions, such as replication and transcription, and play a major role in age-related diseases and cancer. A complicated and entangled network of DNA damage response (DDR) mechanisms, including multiple DNA repair pathways, damage tolerance processes, and cell-cycle checkpoints safeguard genomic integrity. Like transcription and replication, DDR is a chromatin-associated process that is generally tightly controlled in time and space. As DNA damage can occur at any time on any genomic location, a specialized spatio-temporal orchestration of this defense apparatus is required. PMID:20980439

  5. Composites Damage Tolerance Workshop

    NASA Technical Reports Server (NTRS)

    Gregg, Wayne

    2006-01-01

    The Composite Damage Tolerance Workshop included participants from NASA, academia, and private industry. The objectives of the workshop were to begin dialogue in order to establish a working group within the Agency, create awareness of damage tolerance requirements for Constellation, and discuss potential composite hardware for the Crew Launch Vehicle (CLV) Upper Stage (US) and Crew Module. It was proposed that a composites damage tolerance working group be created that acts within the framework of the existing NASA Fracture Control Methodology Panel. The working group charter would be to identify damage tolerance gaps and obstacles for implementation of composite structures into manned space flight systems and to develop strategies and recommendations to overcome these obstacles.

  6. LSD and Genetic Damage

    ERIC Educational Resources Information Center

    Dishotsky, Norman I.; And Others

    1971-01-01

    Reviews studies of the effects of lysergic acid diethylamide (LSD) on man and other organisms. Concludes that pure LSD injected in moderate doses does not cause chromosome or detectable genetic damage and is not a teratogen or carcinogen. (JM)

  7. Composite heat damage assessment

    SciTech Connect

    Janke, C.J.; Wachter, E.A.; Philpot, H.E.; Powell, G.L.

    1993-12-31

    The effects of heat damage were determined on the residual mechanical, physical, and chemical properties of IM6/3501-6 laminates, and potential nondestructive techniques to detect and assess material heat damage were evaluated. About one thousand preconditioned specimens were exposed to elevated temperatures, then cooled to room temperature and tested in compression, flexure, interlaminar shear, shore-D hardness, weight loss, and change in thickness. Specimens experienced significant and irreversible reduction in their residual properties when exposed to temperatures exceeding the material upper service temperature of this material (350{degrees}F). The Diffuse Reflectance Infrared Fourier Transform and Laser-Pumped Fluorescence techniques were found to be capable of rapid, in-service, nondestructive detection and quantitation of heat damage in IM6/3501- 6. These techniques also have the potential applicability to detect and assess heat damage effects in other polymer matrix composites.

  8. Diabetes and nerve damage

    MedlinePlus

    ... hot or cold When the nerves that control digestion are affected, you may have trouble digesting food. ... harder to control. Damage to nerves that control digestion almost always occurs in people with severe nerve ...

  9. Assessing Tropical Cyclone Damage

    NASA Astrophysics Data System (ADS)

    Done, J.; Czajkowski, J.

    2012-12-01

    Landfalling tropical cyclones impact large coastal and inland areas causing direct damage due to winds, storm-surge flooding, tornadoes, and precipitation; as well as causing substantial indirect damage such as electrical outages and business interruption. The likely climate change impact of increased tropical cyclone intensity, combined with increases in exposure, bring the possibility of increased damage in the future. A considerable amount of research has focused on modeling economic damage due to tropical cyclones, and a series of indices have been developed to assess damages under climate change. We highlight a number of ways this research can be improved through a series of case study analyses. First, historical loss estimates are revisited to properly account for; time, impacted regions, the source of damage by type, and whether the damage was direct/indirect and insured/uninsured. Second, the drivers of loss from both the socio-economic and physical side are examined. A case is made to move beyond the use of maximum wind speed to more stable metrics and the use of other characteristics of the wind field such as direction, degree of gustiness, and duration is explored. A novel approach presented here is the potential to model losses directly as a function of climate variables such as sea surface temperature, greenhouse gases, and aerosols. This work is the first stage in the development of a tropical cyclone loss model to enable projections of losses under scenarios of both socio-economic change (such as population migration or altered policy) and physical change (such as shifts in tropical cyclone activity one from basin to another or within the same basin).

  10. Peptidoglycan synthesis and structure in Staphylococcus haemolyticus expressing increasing levels of resistance to glycopeptide antibiotics.

    PubMed Central

    Billot-Klein, D; Gutmann, L; Bryant, D; Bell, D; Van Heijenoort, J; Grewal, J; Shlaes, D M

    1996-01-01

    The structures of cytoplasmic peptidoglycan precursor and mature peptidoglycan of an isogenic series of Staphylococcus haemolyticus strains expressing increasing levels of resistance to the glycopeptide antibiotics teicoplanin and vancomycin (MICs, 8 to 32 and 4 to 16 microg/ml, respectively) were determined. High-performance liquid chromatography, mass spectrometry, amino acid analysis, digestion by R39 D,D-carboxypeptidase, and N-terminal amino acid sequencing were utilized. UDP-muramyl-tetrapeptide-D-lactate constituted 1.7% of total cytoplasmic peptidoglycan precursors in the most resistant strain. It is not clear if this amount of depsipeptide precursor can account for the levels of resistance achieved by this strain. Detailed structural analysis of mature peptidoglycan, examined for the first time for this species, revealed that the peptidoglycan of these strains, like that of other staphylococci, is highly cross-linked and is composed of a lysine muropeptide acceptor containing a substitution at its epsilon-amino position of a glycine-containing cross bridge to the D-Ala 4 of the donor, with disaccharide-pentapeptide frequently serving as an acceptor for transpeptidation. The predominant cross bridges were found to be COOH-Gly-Gly-Ser-Gly-Gly-NH2 and COOH-Ala-Gly-Ser-Gly-Gly-NH2. Liquid chromatography-mass spectrometry analysis of the peptidoglycan of resistant strains revealed polymeric muropeptides bearing cross bridges containing an additional serine in place of glycine (probable structures, COOH-Gly-Ser-Ser-Gly-Gly-NH2 and COOH-Ala-Gly-Ser-Ser-Gly-NH2). Muropeptides bearing an additional serine in their cross bridges are estimated to account for 13.6% of peptidoglycan analyzed from resistant strains of S. haemolyticus. A soluble glycopeptide target (L-Ala-gamma-D-iso-glutamyl-L-Lys-D-Ala-D-Ala) was able to more effectively compete for vancomycin when assayed in the presence of resistant cells than when assayed in the presence of susceptible cells

  11. Protein Binding Pocket Dynamics.

    PubMed

    Stank, Antonia; Kokh, Daria B; Fuller, Jonathan C; Wade, Rebecca C

    2016-05-17

    The dynamics of protein binding pockets are crucial for their interaction specificity. Structural flexibility allows proteins to adapt to their individual molecular binding partners and facilitates the binding process. This implies the necessity to consider protein internal motion in determining and predicting binding properties and in designing new binders. Although accounting for protein dynamics presents a challenge for computational approaches, it expands the structural and physicochemical space for compound design and thus offers the prospect of improved binding specificity and selectivity. A cavity on the surface or in the interior of a protein that possesses suitable properties for binding a ligand is usually referred to as a binding pocket. The set of amino acid residues around a binding pocket determines its physicochemical characteristics and, together with its shape and location in a protein, defines its functionality. Residues outside the binding site can also have a long-range effect on the properties of the binding pocket. Cavities with similar functionalities are often conserved across protein families. For example, enzyme active sites are usually concave surfaces that present amino acid residues in a suitable configuration for binding low molecular weight compounds. Macromolecular binding pockets, on the other hand, are located on the protein surface and are often shallower. The mobility of proteins allows the opening, closing, and adaptation of binding pockets to regulate binding processes and specific protein functionalities. For example, channels and tunnels can exist permanently or transiently to transport compounds to and from a binding site. The influence of protein flexibility on binding pockets can vary from small changes to an already existent pocket to the formation of a completely new pocket. Here, we review recent developments in computational methods to detect and define binding pockets and to study pocket dynamics. We introduce five

  12. Crumpling Damaged Graphene

    NASA Astrophysics Data System (ADS)

    Giordanelli, I.; Mendoza, M.; Andrade, J. S., Jr.; Gomes, M. A. F.; Herrmann, H. J.

    2016-05-01

    Through molecular mechanics we find that non-covalent interactions modify the fractality of crumpled damaged graphene. Pristine graphene membranes are damaged by adding random vacancies and carbon-hydrogen bonds. Crumpled membranes exhibit a fractal dimension of 2.71 ± 0.02 when all interactions between carbon atoms are considered, and 2.30 ± 0.05 when non-covalent interactions are suppressed. The transition between these two values, obtained by switching on/off the non-covalent interactions of equilibrium configurations, is shown to be reversible and independent on thermalisation. In order to explain this transition, we propose a theoretical model that is compatible with our numerical findings. Finally, we also compare damaged graphene membranes with other crumpled structures, as for instance polymerised membranes and paper sheets, that share similar scaling properties.

  13. Crumpling Damaged Graphene.

    PubMed

    Giordanelli, I; Mendoza, M; Andrade, J S; Gomes, M A F; Herrmann, H J

    2016-01-01

    Through molecular mechanics we find that non-covalent interactions modify the fractality of crumpled damaged graphene. Pristine graphene membranes are damaged by adding random vacancies and carbon-hydrogen bonds. Crumpled membranes exhibit a fractal dimension of 2.71 ± 0.02 when all interactions between carbon atoms are considered, and 2.30 ± 0.05 when non-covalent interactions are suppressed. The transition between these two values, obtained by switching on/off the non-covalent interactions of equilibrium configurations, is shown to be reversible and independent on thermalisation. In order to explain this transition, we propose a theoretical model that is compatible with our numerical findings. Finally, we also compare damaged graphene membranes with other crumpled structures, as for instance polymerised membranes and paper sheets, that share similar scaling properties. PMID:27173442

  14. Damage Tolerance Assessment Branch

    NASA Technical Reports Server (NTRS)

    Walker, James L.

    2013-01-01

    The Damage Tolerance Assessment Branch evaluates the ability of a structure to perform reliably throughout its service life in the presence of a defect, crack, or other form of damage. Such assessment is fundamental to the use of structural materials and requires an integral blend of materials engineering, fracture testing and analysis, and nondestructive evaluation. The vision of the Branch is to increase the safety of manned space flight by improving the fracture control and the associated nondestructive evaluation processes through development and application of standards, guidelines, advanced test and analytical methods. The Branch also strives to assist and solve non-aerospace related NDE and damage tolerance problems, providing consultation, prototyping and inspection services.

  15. Crumpling Damaged Graphene

    PubMed Central

    Giordanelli, I.; Mendoza, M.; Andrade Jr., J. S.; Gomes, M. A. F.; Herrmann, H. J.

    2016-01-01

    Through molecular mechanics we find that non-covalent interactions modify the fractality of crumpled damaged graphene. Pristine graphene membranes are damaged by adding random vacancies and carbon-hydrogen bonds. Crumpled membranes exhibit a fractal dimension of 2.71 ± 0.02 when all interactions between carbon atoms are considered, and 2.30 ± 0.05 when non-covalent interactions are suppressed. The transition between these two values, obtained by switching on/off the non-covalent interactions of equilibrium configurations, is shown to be reversible and independent on thermalisation. In order to explain this transition, we propose a theoretical model that is compatible with our numerical findings. Finally, we also compare damaged graphene membranes with other crumpled structures, as for instance polymerised membranes and paper sheets, that share similar scaling properties. PMID:27173442

  16. Subrupture Tendon Fatigue Damage

    PubMed Central

    Laudier, Damien M.; Shine, Jean H.; Basta-Pljakic, Jelena; Jepsen, Karl J.; Schaffler, Mitchell B.; Flatow, Evan L.

    2016-01-01

    The mechanical and microstructural bases of tendon fatigue, by which damage accumulates and contributes to degradation, are poorly understood. To investigate the tendon fatigue process, rat flexor digitorum longus tendons were cyclically loaded (1–16 N) until reaching one of three levels of fatigue damage, defined as peak clamp-to-clamp strain magnitudes representing key intervals in the fatigue life: i) Low (6.0%–7.0%); ii) Moderate (8.5%–9.5%); and iii) High (11.0%–12.0%). Stiffness, hysteresis, and clamp-to-clamp strain were assessed diagnostically (by cyclic loading at 1–8 N) before and after fatigue loading and following an unloaded recovery period to identify mechanical parameters as measures of damage. Results showed that tendon clamp-to-clamp strain increased from pre- to post-fatigue loading significantly and progressively with the fatigue damage level (p≤0.010). In contrast, changes in both stiffness and hysteresis were significant only at the High fatigue level (p≤0.043). Correlative microstructural analyses showed that Low level of fatigue was characterized by isolated, transverse patterns of kinked fiber deformations. At higher fatigue levels, tendons exhibited fiber dissociation and localized ruptures of the fibers. Histomorphometric analysis showed that damage area fraction increased significantly with fatigue level (p≤0.048). The current findings characterized the sequential, microstructural events that underlie the tendon fatigue process and indicate that tendon deformation can be used to accurately assess the progression of damage accumulation in tendons. PMID:18683881

  17. Evolving nucleotide binding surfaces

    NASA Technical Reports Server (NTRS)

    Kieber-Emmons, T.; Rein, R.

    1981-01-01

    An analysis is presented of the stability and nature of binding of a nucleotide to several known dehydrogenases. The employed approach includes calculation of hydrophobic stabilization of the binding motif and its intermolecular interaction with the ligand. The evolutionary changes of the binding motif are studied by calculating the Euclidean deviation of the respective dehydrogenases. Attention is given to the possible structural elements involved in the origin of nucleotide recognition by non-coded primordial polypeptides.

  18. ON VASCULAR STENOSIS, RESTENOSIS AND MANNOSE BINDING LECTIN.

    PubMed

    Kahlow, Barbara Stadler; Nery, Rodrigo Araldi; Skare, Thelma L; Ribas, Carmen Australia Paredes Marcondes; Ramos, Gabriela Piovezani; Petisco, Roberta Dombroski

    2016-03-01

    Mannose binding lectin is a lectin instrumental in the innate immunity. It recognizes carbohydrate patterns found on the surface of a large number of pathogenic micro-organisms, activating the complement system. However, this protein seems to increase the tissue damage after ischemia. In this paper is reviewed some aspects of harmful role of the mannose binding lectin in ischemia/reperfusion injury. PMID:27120743

  19. ON VASCULAR STENOSIS, RESTENOSIS AND MANNOSE BINDING LECTIN

    PubMed Central

    KAHLOW, Barbara Stadler; NERY, Rodrigo Araldi; SKARE, Thelma L; RIBAS, Carmen Australia Paredes Marcondes; RAMOS, Gabriela Piovezani; PETISCO, Roberta Dombroski

    2016-01-01

    Mannose binding lectin is a lectin instrumental in the innate immunity. It recognizes carbohydrate patterns found on the surface of a large number of pathogenic micro-organisms, activating the complement system. However, this protein seems to increase the tissue damage after ischemia. In this paper is reviewed some aspects of harmful role of the mannose binding lectin in ischemia/reperfusion injury. PMID:27120743

  20. Ubiquitin-family modifications in the replication of DNA damage.

    PubMed

    Lehmann, Alan R

    2011-09-16

    The cell uses specialised Y-family DNA polymerases or damage avoidance mechanisms to replicate past damaged sites in DNA. These processes are under complex regulatory systems, which employ different types of post-translational modification. All the Y-family polymerases have ubiquitin binding domains that bind to mono-ubiquitinated PCNA to effect the switching from replicative to Y-family polymerase. Ubiquitination and de-ubiquitination of PCNA are tightly regulated. There is also evidence for another as yet unidentified ubiquitinated protein being involved in recruitment of Y-family polymerases to chromatin. Poly-ubiquitination of PCNA stimulates damage avoidance, and, at least in yeast, PCNA is SUMOylated to prevent unwanted recombination events at the replication fork. The Y-family polymerases themselves can be ubiquitinated and, in the case of DNA polymerase η, this results in the polymerase being excluded from chromatin. PMID:21704031

  1. Repairing damaged platforms

    SciTech Connect

    Moore, R.E.; Kwok, P.H.; Wang, S.S.

    1995-10-01

    This paper introduces a unique method for strengthening of platforms and replacing damaged members. Extending the life of existing infrastructure is approved means of decreasing cash expenditures for new platforms and facilities. Platforms can be affected by corrosion, overloading and fatigue. The renovation and repair of existing offshore installations is an important part of offshore engineering. The basis behind this paper is an April, 1993 incident in the Arabian Gulf. A vessel broke loose from its moorings in a severe storm and collided with a wellhead platform. The collision severely damaged the platform buckling seven major support members and cracking joints throughout the structure. In view of the significant damage, there was an urgent need to repair the structure to avoid any further damage from potentially sever winter storm conditions. Various means of repair and their associated costs were evaluated: traditional dry hyperbaric welding, adjacent platforms, grouted clamped connections, and mechanical pipe connectors. The repair was completed using an innovative combination of clamps and wet welding to attach external braces to the structure.

  2. Courtside: A Damaging Lesson

    ERIC Educational Resources Information Center

    Zirkel, Perry A.

    2004-01-01

    This case presents a costly lesson for teachers and for districts that include a liquidated, or stipulated, damages clause in their teacher employment contracts. Although the court enforced the clause in this case, in this well-reasoned recent decision and in most of the much older, canvassed case law from other jurisdictions, the answer to the…

  3. Modifying Radiation Damage

    PubMed Central

    Kim, Kwanghee; McBride, William H.

    2011-01-01

    Radiation leaves a fairly characteristic footprint in biological materials, but this is rapidly all but obliterated by the canonical biological responses to the radiation damage. The innate immune recognition systems that sense “danger” through direct radiation damage and through associated collateral damage set in motion a chain of events that, in a tissue compromised by radiation, often unwittingly result in oscillating waves of molecular and cellular responses as tissues attempt to heal. Understanding “nature’s whispers” that inform on these processes will lead to novel forms of intervention targeted more precisely towards modifying them in an appropriate and timely fashion so as to improve the healing process and prevent or mitigate the development of acute and late effects of normal tissue radiation damage, whether it be accidental, as a result of a terrorist incident, or of therapeutic treatment of cancer. Here we attempt to discuss some of the non-free radical scavenging mechanisms that modify radiation responses and comment on where we see them within a conceptual framework of an evolving radiation-induced lesion. PMID:20583981

  4. Loss and damage

    NASA Astrophysics Data System (ADS)

    Huq, Saleemul; Roberts, Erin; Fenton, Adrian

    2013-11-01

    Loss and damage is a relative newcomer to the climate change agenda. It has the potential to reinvigorate existing mitigation and adaptation efforts, but this will ultimately require leadership from developed countries and enhanced understanding of several key issues, such as limits to adaptation.

  5. Laryngeal nerve damage

    MedlinePlus

    Laryngeal nerve damage is injury to one or both of the nerves that are attached to the voice box. ... Injury to the laryngeal nerves is uncommon. When it does occur, it can be from: A complication of neck or chest surgery (especially thyroid, lung, ...

  6. Coping with brain damage

    NASA Technical Reports Server (NTRS)

    Waring, W.

    1974-01-01

    Two neurological disorders, cerebral palsy, and traumatic brain damage as from an accident, are considered. The discussion covers the incidence of disabilities, their characteristics, and what is now being done to deal with them, particularly in reference to areas in which the capabilities of the engineer can be effectively applied.

  7. Melanin-binding radiopharmaceuticals

    SciTech Connect

    Packer, S; Fairchild, R G; Watts, K P; Greenberg, D; Hannon, S J

    1980-01-01

    The scope of this paper is limited to an analysis of the factors that are important to the relationship of radiopharmaceuticals to melanin. While the authors do not attempt to deal with differences between melanin-binding vs. melanoma-binding, a notable variance is assumed. (PSB)

  8. Damage mechanics in engineering materials

    SciTech Connect

    Voyiadjis, G.Z.; Woody Ju, J.W.; Chaboche, J.L.

    1998-12-31

    This book contains thirty peer-reviewed papers that are based on the presentations made at the symposium on Damage Mechanics in Engineering Materials on the occasion of the Joint ASME/ASCE/SES Mechanics Conference (McNU97), held in Evanston, Illinois, June 28--July 2, 1997. The key area of discussion was on the constitutive modeling of damage mechanics in engineering materials encompassing the following topics: macromechanics/micromechanical constitutive modeling, experimental procedures, numerical modeling, inelastic behavior, interfaces, damage, fracture, failure, computational methods. The book is divided into six parts: study of damage mechanics; localization and damage; damage in brittle materials; damage in metals and metal matrix composites; computational aspects of damage models; damage in polymers and elastomers.

  9. DNA damage tolerance.

    PubMed

    Branzei, Dana; Psakhye, Ivan

    2016-06-01

    Accurate chromosomal DNA replication is fundamental for optimal cellular function and genome integrity. Replication perturbations activate DNA damage tolerance pathways, which are crucial to complete genome duplication as well as to prevent formation of deleterious double strand breaks. Cells use two general strategies to tolerate lesions: recombination to a homologous template, and trans-lesion synthesis with specialized polymerases. While key players of these processes have been outlined, much less is known on their choreography and regulation. Recent advances have uncovered principles by which DNA damage tolerance is regulated locally and temporally - in relation to replication timing and cell cycle stage -, and are beginning to elucidate the DNA dynamics that mediate lesion tolerance and influence chromosome structure during replication. PMID:27060551

  10. Hypertension and cerebrovascular damage.

    PubMed

    Veglio, Franco; Paglieri, Cristina; Rabbia, Franco; Bisbocci, Daniela; Bergui, Mauro; Cerrato, Paolo

    2009-08-01

    Hypertension is the most important modifiable factor for cerebrovascular disease. Stroke and dementia are growing health problems that have considerable social and economical consequences. Hypertension causes brain lesions by several mechanisms predisposing to lacunar infarctions, leucoaraiosis, and white matter changes as well as to intracerebral haemorrhages. These parenchymal damages determine evident or silent neurological alterations that often precede the onset of cognitive decline. It is important to recognize cerebrovascular disease and, above all, to correlate typical lesions to hypertension. Antihypertensive therapy has shown clinical benefits in primary and secondary prevention of stroke. These drugs represent important instruments against cerebrovascular disease but their effects on cognition are still matter of debate. Cerebral parenchymal and functional damages have to be considered together to make medical intervention more incisive. PMID:19100549

  11. Tornado damage risk assessment

    SciTech Connect

    Reinhold, T.A.; Ellingwood, B.

    1982-09-01

    Several proposed models were evaluated for predicting tornado wind speed probabilities at nuclear plant sites as part of a program to develop statistical data on tornadoes needed for probability-based load combination analysis. A unified model was developed which synthesized the desired aspects of tornado occurrence and damage potential. The sensitivity of wind speed probability estimates to various tornado modeling assumptions are examined, and the probability distributions of tornado wind speed that are needed for load combination studies are presented.

  12. Chimeric Proteins to Detect DNA Damage and Mismatches

    SciTech Connect

    McCutchen-Maloney, S; Malfatti, M; Robbins, K M

    2002-01-14

    The goal of this project was to develop chimeric proteins composed of a DNA mismatch or damage binding protein and a nuclease, as well as methods to detect DNA mismatches and damage. We accomplished this through protein engineering based on using polymerase chain reactions (PCRs) to create chimeras with novel functions for damage and mismatch detection. This project addressed fundamental questions relating to disease susceptibility and radiation-induced damage in cells. It also supported and enhanced LLNL's competency in the emerging field of proteomics. In nature, DNA is constantly being subjected to damaging agents such as exposure to ultraviolet (UV) radiation and various environmental and dietary carcinogens. If DNA damage is not repaired however, mutations in DNA result that can eventually manifest in cancer and other diseases. In addition to damage-induced DNA mutations, single nucleotide polymorphisms (SNPs), which are variations in the genetic sequence between individuals, may predispose some to disease. As a result of the Human Genome Project, the integrity of a person's DNA can now be monitored. Therefore, methods to detect DNA damage, mutations, and SNPs are useful not only in basic research but also in the health and biotechnology industries. Current methods of detection often use radioactive labeling and rely on expensive instrumentation that is not readily available in many research settings. Our methods to detect DNA damage and mismatches employ simple gel electrophoresis and flow cytometry, thereby alleviating the need for radioactive labeling and expensive equipment. In FY2001, we explored SNP detection by developing methods based on the ability of the chimeric proteins to detect mismatches. Using multiplex assays with flow cytometry and fluorescent beads to which the DNA substrates where attached, we showed that several of the chimeras possess greater affinity for damaged and mismatched DNA than for native DNA. This affinity was demonstrated in

  13. Positron binding to molecules

    NASA Astrophysics Data System (ADS)

    Danielson, J. R.

    2011-05-01

    While there is theoretical evidence that positrons can bind to atoms, calculations for molecules are much less precise. Unfortunately, there have been no measurements of positron-atom binding, due primarily to the difficulty in forming positron-atom bound states in two-body collisions. In contrast, positrons attach to molecules via Feshbach resonances (VFR) in which a vibrational mode absorbs the excess energy. Using a high-resolution positron beam, this VFR process has been studied to measure binding energies for more than 40 molecules. New measurements will be described in two areas: positron binding to relatively simple molecules, for which theoretical calculations appear to be possible; and positron binding to molecules with large permanent dipole moments, which can be compared to analogous, weakly bound electron-molecule (negative-ion) states. Binding energies range from 75 meV for CS2 (no dipole moment) to 180 meV for acetonitrile (CH3CN). Other species studied include aldehydes and ketones, which have permanent dipole moments in the range 2.5 - 3.0 debye. The measured binding energies are surprisingly large (by a factor of 10 to 100) compared to those for the analogous negative ions, and these differences will be discussed. New theoretical calculations for positron-molecule binding are in progress, and a recent result for acetonitrile will be discussed. This ability to compare theory and experiment represents a significant step in attempts to understand positron binding to matter. In collaboration with A. C. L. Jones, J. J. Gosselin, and C. M. Surko, and supported by NSF grant PHY 07-55809.

  14. Memory binding and white matter integrity in familial Alzheimer's disease.

    PubMed

    Parra, Mario A; Saarimäki, Heini; Bastin, Mark E; Londoño, Ana C; Pettit, Lewis; Lopera, Francisco; Della Sala, Sergio; Abrahams, Sharon

    2015-05-01

    Binding information in short-term and long-term memory are functions sensitive to Alzheimer's disease. They have been found to be affected in patients who meet criteria for familial Alzheimer's disease due to the mutation E280A of the PSEN1 gene. However, only short-term memory binding has been found to be affected in asymptomatic carriers of this mutation. The neural correlates of this dissociation are poorly understood. The present study used diffusion tensor magnetic resonance imaging to investigate whether the integrity of white matter structures could offer an account. A sample of 19 patients with familial Alzheimer's disease, 18 asymptomatic carriers and 21 non-carrier controls underwent diffusion tensor magnetic resonance imaging, neuropsychological and memory binding assessment. The short-term memory binding task required participants to detect changes across two consecutive screens displaying arrays of shapes, colours, or shape-colour bindings. The long-term memory binding task was a Paired Associates Learning Test. Performance on these tasks were entered into regression models. Relative to controls, patients with familial Alzheimer's disease performed poorly on both memory binding tasks. Asymptomatic carriers differed from controls only in the short-term memory binding task. White matter integrity explained poor memory binding performance only in patients with familial Alzheimer's disease. White matter water diffusion metrics from the frontal lobe accounted for poor performance on both memory binding tasks. Dissociations were found in the genu of corpus callosum which accounted for short-term memory binding impairments and in the hippocampal part of cingulum bundle which accounted for long-term memory binding deficits. The results indicate that white matter structures in the frontal and temporal lobes are vulnerable to the early stages of familial Alzheimer's disease and their damage is associated with impairments in two memory binding functions known to

  15. The cellular response to DNA damage: A focus on MDC1 and its interacting proteins

    PubMed Central

    Coster, Gideon

    2010-01-01

    The DNA damage response (DDR) is comprised of a network of proteins that respond to DNA damage. Mediator of DNA Damage Checkpoint 1 (MDC1) plays an early and important role in the DDR. Recent data show that MDC1 binds multiple proteins that participate in various aspects of the DDR, positioning it at the core of the DDR. Furthermore, interactions with non-DDR proteins were also revealed, suggesting novel roles for MDC1. In this review we provide a comprehensive overview of all known MDC1-binding proteins and discuss their role. We present these binding partners according to their function, thereby providing the reader with a detailed and updated overview of the cellular response to DNA damage. We discuss more recent findings in detail and conclude by presenting the challenges the field faces in the future. PMID:21326949

  16. Oxidative damage in chemical teratogenesis.

    PubMed

    Wells, P G; Kim, P M; Laposa, R R; Nicol, C J; Parman, T; Winn, L M

    1997-12-12

    The teratogenicity of many xenobiotics is thought to depend at least in part upon their bioactivation by embryonic cytochromes P450, prostaglandin H synthase (PHS) and lipoxygenases (LPOs) to electrophilic and/or free radical reactive intermediates that covalently bind to or oxidize cellular macromolecules such as DNA, protein and lipid, resulting in in utero death or teratogenesis. Using as models the tobacco carcinogens benzo[a]pyrene (B[a]P) and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), the anticonvulsant drug phenytoin, structurally related anticonvulsants (e.g. mephenytoin, nirvanol, trimethadione, dimethadione) and the sedative drug thalidomide, we have examined the potential teratologic relevance of free radical-initiated, reactive oxygen species (ROS)-mediated oxidative molecular target damage, genotoxicity (micronucleus formation) and DNA repair in mouse and rabbit models in vivo and in embryo culture, and in vitro using purified enzymes or cultured rat skin fibroblasts. These teratogens were bioactivated by PHS and LPOs to free radical reactive intermediary metabolites, characterized by electron spin resonance spectrometry, that initiated ROS formation, including hydroxyl radicals, which were characterized by salicylate hydroxylation. ROS-initiated oxidation of DNA (8-hydroxy-2'-deoxyguanosine formation), protein (carbonyl formation), glutathione (GSH) and lipid (peroxidation), and embryotoxicity were shown for phenytoin, its major hydroxylated metabolite 5-(p-hydroxyphenyl)-5-phenylhydantoin [HPPH], thalidomide, B[a]P and NNK in vivo and/or in embryo culture, the latter indicating a teratologically critical role for embryonic, as distinct from maternal, processes. DNA oxidation and teratogenicity of phenytoin and thalidomide were reduced by PHS inhibitors. Oxidative macromolecular lesions and teratogenicity also were reduced by the free radical trapping agent phenylbutylnitrone (PBN), and the antioxidants caffeic acid and vitamin E. In embryo

  17. Metallochaperones: bind and deliver

    SciTech Connect

    Rosenzweig, A.C.

    2010-03-08

    Metallochaperones deliver metal ions directly to target proteins via specific protein-protein interactions. Recent research has led to a molecular picture of how some metallochaperones bind metal ions, recognize their partner proteins, and accomplish metal ion transfer.

  18. New DNA-binding radioprotectors

    NASA Astrophysics Data System (ADS)

    Martin, Roger

    The normal tissue damage associated with cancer radiotherapy has motivated the development at Peter Mac of a new class of DNA-binding radioprotecting drugs that could be applied top-ically to normal tissues at risk. Methylproamine (MP), the lead compound, reduces radiation induced cell kill at low concentrations. For example, experiments comparing the clonogenic survival of transformed human keratinocytes treated with 30 micromolar MP before and dur-ing various doses of ionising radiation, with the radiation dose response for untreated cells, indicate a dose reduction factor (DRF) of 2. Similar survival curve experiments using various concentrations of MP, with parallel measurements of uptake of MP into cell nuclei, have en-abled the relationship between drug uptake and extent of radioprotection to be established. Radioprotection has also been demonstrated after systemic administration to mice, for three different endpoints, namely lung, jejunum and bone marrow (survival at 30 days post-TBI). The results of pulse radiolysis studies indicated that the drugs act by reduction of transient radiation-induced oxidative species on DNA. This hypothesis was substantiated by the results of experiments in which MP radioprotection of radiation-induced DNA double-strand breaks, assessed as -H2AX foci, in the human keratinocyte cell line. For both endpoints, the extent of radioprotection increased with MP concentration up to a maximal value. These results are consistent with the hypothesis that radioprotection by MP is mediated by attenuation of the extent of initial DNA damage. However, although MP is a potent radioprotector, it becomes cytotoxic at higher concentrations. This limitation has been addressed in an extensive program of lead optimisation and some promising analogues have emerged from which the next lead will be selected. Given the clinical potential of topical radioprotection, the new analogues are being assessed in terms of delivery to mouse oral mucosa. This is

  19. The Sunscreen Octyl Methoxycinnamate Binds to DNA

    NASA Astrophysics Data System (ADS)

    Norrell, Johannes; Vohra, Shikhar; Nordlund, T. M.

    2000-03-01

    Sunscreens are designed to prevent skin cancer by absorbing ultraviolet radiation from the sun before it gets to the DNA in skin cells. The purpose of this work is to determine whether or not octyl methoxycinnamate, an active ingredient in many sunscreens, will bind to DNA. If so, the sunscreen could transfer the energy it absorbed from the sun to the DNA and cause damage. To determine this, we prepared samples with varying concentrations of cinnamate added to herring sperm DNA, sonicating the mixture to disperse the hydrophobic sunscreen into solution. Absorption and fluorescence spectra of the mixtures showed (i) much more sunscreen was dispersed into solution when DNA was present, and (ii) the spectra of both DNA and sunscreen differed from those of the separate solutions. We conclude that the octyl methoxycinnamate can indeed bind to DNA in aqueous solution. Energy transfer experiments from DNA to sunscreen and from sunscreen to 2-aminopurine- (a fluorescent DNA base) labeled DNA will be presented.

  20. The XRCC1 phosphate-binding pocket binds poly (ADP-ribose) and is required for XRCC1 function

    PubMed Central

    Breslin, Claire; Hornyak, Peter; Ridley, Andrew; Rulten, Stuart L.; Hanzlikova, Hana; Oliver, Antony W.; Caldecott, Keith W.

    2015-01-01

    Poly (ADP-ribose) is synthesized at DNA single-strand breaks and can promote the recruitment of the scaffold protein, XRCC1. However, the mechanism and importance of this process has been challenged. To address this issue, we have characterized the mechanism of poly (ADP-ribose) binding by XRCC1 and examined its importance for XRCC1 function. We show that the phosphate-binding pocket in the central BRCT1 domain of XRCC1 is required for selective binding to poly (ADP-ribose) at low levels of ADP-ribosylation, and promotes interaction with cellular PARP1. We also show that the phosphate-binding pocket is required for EGFP-XRCC1 accumulation at DNA damage induced by UVA laser, H2O2, and at sites of sub-nuclear PCNA foci, suggesting that poly (ADP-ribose) promotes XRCC1 recruitment both at single-strand breaks globally across the genome and at sites of DNA replication stress. Finally, we show that the phosphate-binding pocket is required following DNA damage for XRCC1-dependent acceleration of DNA single-strand break repair, DNA base excision repair, and cell survival. These data support the hypothesis that poly (ADP-ribose) synthesis promotes XRCC1 recruitment at DNA damage sites and is important for XRCC1 function. PMID:26130715

  1. The XRCC1 phosphate-binding pocket binds poly (ADP-ribose) and is required for XRCC1 function.

    PubMed

    Breslin, Claire; Hornyak, Peter; Ridley, Andrew; Rulten, Stuart L; Hanzlikova, Hana; Oliver, Antony W; Caldecott, Keith W

    2015-08-18

    Poly (ADP-ribose) is synthesized at DNA single-strand breaks and can promote the recruitment of the scaffold protein, XRCC1. However, the mechanism and importance of this process has been challenged. To address this issue, we have characterized the mechanism of poly (ADP-ribose) binding by XRCC1 and examined its importance for XRCC1 function. We show that the phosphate-binding pocket in the central BRCT1 domain of XRCC1 is required for selective binding to poly (ADP-ribose) at low levels of ADP-ribosylation, and promotes interaction with cellular PARP1. We also show that the phosphate-binding pocket is required for EGFP-XRCC1 accumulation at DNA damage induced by UVA laser, H2O2, and at sites of sub-nuclear PCNA foci, suggesting that poly (ADP-ribose) promotes XRCC1 recruitment both at single-strand breaks globally across the genome and at sites of DNA replication stress. Finally, we show that the phosphate-binding pocket is required following DNA damage for XRCC1-dependent acceleration of DNA single-strand break repair, DNA base excision repair, and cell survival. These data support the hypothesis that poly (ADP-ribose) synthesis promotes XRCC1 recruitment at DNA damage sites and is important for XRCC1 function. PMID:26130715

  2. Serum prostacyclin binding defects in thrombotic thrombocytopenic purpura.

    PubMed Central

    Wu, K K; Hall, E R; Rossi, E C; Papp, A C

    1985-01-01

    To understand the pathophysiologic significance of abnormal serum prostacyclin (PGI2) binding activities in thrombotic thrombocytopenic purpura (TTP), we evaluated the PGI2 binding characteristics in three chronic TTP sera and 19 normal sera. PGI2 binding by serum was rapid and reversible. The binding activity in TTP sera (22.1 +/- SD, 4.4%) was significantly lower than that of normal sera (42.2 +/- 6.2%). Moreover, the antiaggregating activity and 6-keto-prostaglandin F1 alpha (6KPGF1 alpha) content in the gel filtrates representing the binding peak was proportionally lower in a TTP serum than normal serum. Although normal and TTP sera bound [14C]arachidonate with similar activity, and neither bound [3H]6KPGF1 alpha, there was a difference in prostaglandin E1 (PGE1) binding. Binding of [3H]PGE1 was subnormal in two TTP sera (W.J. and T.G.) and normal in the third (H.S.). Normal serum corrected the binding defects of TTP serum. Interestingly, the mixture of two TTP sera (W.J. and H.S.) mutually corrected their PGI2 binding defects. In addition, although in vivo plasma transfusions improved the PGI2 binding activity of W.J. and H.S., there existed a striking difference in the nature of their response. These observations indicate that there is at least two types of PGI2 binding defects in TTP. Our data indicate that TTP is associated with diminished serum binding of PGI2. This defect may reduce the availability of PGI2 to damaged vascular sites and decrease an important modulator of platelet thrombus formation at times of severe vascular insult. Images PMID:3880771

  3. Damage tolerance for commuter aircraft

    NASA Technical Reports Server (NTRS)

    Lincoln, John W.

    1992-01-01

    The damage tolerance experience in the United States Air Force with military aircraft and in the commercial world with large transport category aircraft indicates that a similar success could be achieved in commuter aircraft. The damage tolerance process is described for the purpose of defining the approach that could be used for these aircraft to ensure structural integrity. Results of some of the damage tolerance assessments for this class of aircraft are examined to illustrate the benefits derived from this approach. Recommendations are given for future damage tolerance assessment of existing commuter aircraft and on the incorporation of damage tolerance capability in new designs.

  4. DNA damage checkpoint, damage repair, and genome stability.

    PubMed

    Liu, Wei-Feng; Yu, Shan-Shan; Chen, Guan-Jun; Li, Yue-Zhong

    2006-05-01

    Genomic DNA is under constant attack from both endogenous and exogenous sources of DNA damaging agents. Without proper care, the ensuing DNA damages would lead to alteration of genomic structure thus affecting the faithful transmission of genetic information. During the process of evolution, organisms have acquired a series of mechanisms responding to and repairing DNA damage, thus assuring the maintenance of genome stability and faithful transmission of genetic information. DNA damage checkpoint is one such important mechanism by which, in the face of DNA damage, a cell can respond to amplified damage signals, either by actively halting the cell cycle until it ensures that critical processes such as DNA replication or mitosis are complete or by initiating apoptosis as a last resort. Over the last decade, complex hierarchical interactions between the key components like ATM/ATR in the checkpoint pathway and various other mediators, effectors including DNA damage repair proteins have begun to emerge. In the meantime, an intimate relationship between mechanisms of damage checkpoint pathway, DNA damage repair, and genome stability was also uncovered. Reviewed herein are the recent findings on both the mechanisms of activation of checkpoint pathways and their coordination with DNA damage repair machinery as well as their effect on genomic integrity. PMID:16722332

  5. NBS1 and multiple regulations of DNA damage response

    PubMed Central

    Komatsu, Kenshi

    2016-01-01

    DNA damage response is finely tuned, with several pathways including those for DNA repair, chromatin remodeling and cell cycle checkpoint, although most studies to date have focused on single pathways. Genetic diseases characterized by genome instability have provided novel insights into the underlying mechanisms of DNA damage response. NBS1, a protein responsible for the radiation-sensitive autosomal recessive disorder Nijmegen breakage syndrome, is one of the first factors to accumulate at sites of DNA double-strand breaks (DSBs). NBS1 binds to at least five key proteins, including ATM, RPA, MRE11, RAD18 and RNF20, in the conserved regions within a limited span of the C terminus, functioning in the regulation of chromatin remodeling, cell cycle checkpoint and DNA repair in response to DSBs. In this article, we reviewed the functions of these binding proteins and their comprehensive association with NBS1. PMID:27068998

  6. Damage scenarios and an onboard support system for damaged ships

    NASA Astrophysics Data System (ADS)

    Choi, Jin; Lee, Dongkon; Kang, Hee Jin; Kim, Soo-Young; Shin, Sung-Chul

    2014-06-01

    Although a safety assessment of damaged ships, which considers environmental conditions such as waves and wind, is important in both the design and operation phases of ships, in Korea, rules or guidelines to conduct such assessments are not yet developed. However, NATO and European maritime societies have developed guidelines for a safety assessment. Therefore, it is required to develop rules or guidelines for safety assessments such as the Naval Ship Code (NSC) of NATO. Before the safety assessment of a damaged ship can be performed, the available damage scenarios must be developed and the safety assessment criteria must be established. In this paper, the parameters related to damage by accidents are identified and categorized when developing damage scenarios. The need for damage safety assessment criteria is discussed, and an example is presented. In addition, a concept and specifications for the DB-based supporting system, which is used in the operation phases, are proposed.

  7. Radiation Damage Workshop

    NASA Technical Reports Server (NTRS)

    Stella, P. M.

    1984-01-01

    The availability of data regarding the radiation behavior of GaAs and silicon solar cells is discussed as well as efforts to provide sufficient information. Other materials are considered too immature for reasonable radiation evaluation. The lack of concern over the possible catastrophic radiation degradation in cascade cells is a potentially serious problem. Lithium counterdoping shows potential for removing damage in irradiated P-type material, although initial efficiencies are not comparable to current state of the art. The possibility of refining the lithium doping method to maintain high initial efficiencies and combining it with radiation tolerant structures such as thin BSF cells or vertical junction cells could provide a substantial improvement in EOL efficiencies. Laser annealing of junctions, either those formed ion implantation or diffusion, may not only improve initial cell performance but might also reduce the radiation degradation rate.

  8. Damage control resuscitation.

    PubMed

    Pohlman, Timothy H; Walsh, Mark; Aversa, John; Hutchison, Emily M; Olsen, Kristen P; Lawrence Reed, R

    2015-07-01

    The early recognition and management of hemorrhage shock are among the most difficult tasks challenging the clinician during primary assessment of the acutely bleeding patient. Often with little time, within a chaotic setting, and without sufficient clinical data, a decision must be reached to begin transfusion of blood components in massive amounts. The practice of massive transfusion has advanced considerably and is now a more complete and, arguably, more effective process. This new therapeutic paradigm, referred to as damage control resuscitation (DCR), differs considerably in many important respects from previous management strategies for catastrophic blood loss. We review several important elements of DCR including immediate correction of specific coagulopathies induced by hemorrhage and management of several extreme homeostatic imbalances that may appear in the aftermath of resuscitation. We also emphasize that the foremost objective in managing exsanguinating hemorrhage is always expedient and definitive control of the source of bleeding. PMID:25631636

  9. Multivariate pluvial flood damage models

    SciTech Connect

    Van Ootegem, Luc; Verhofstadt, Elsy; Van Herck, Kristine; Creten, Tom

    2015-09-15

    Depth–damage-functions, relating the monetary flood damage to the depth of the inundation, are commonly used in the case of fluvial floods (floods caused by a river overflowing). We construct four multivariate damage models for pluvial floods (caused by extreme rainfall) by differentiating on the one hand between ground floor floods and basement floods and on the other hand between damage to residential buildings and damage to housing contents. We do not only take into account the effect of flood-depth on damage, but also incorporate the effects of non-hazard indicators (building characteristics, behavioural indicators and socio-economic variables). By using a Tobit-estimation technique on identified victims of pluvial floods in Flanders (Belgium), we take into account the effect of cases of reported zero damage. Our results show that the flood depth is an important predictor of damage, but with a diverging impact between ground floor floods and basement floods. Also non-hazard indicators are important. For example being aware of the risk just before the water enters the building reduces content damage considerably, underlining the importance of warning systems and policy in this case of pluvial floods. - Highlights: • Prediction of damage of pluvial floods using also non-hazard information • We include ‘no damage cases’ using a Tobit model. • The damage of flood depth is stronger for ground floor than for basement floods. • Non-hazard indicators are especially important for content damage. • Potential gain of policies that increase awareness of flood risks.

  10. Inhibition of selectin binding

    DOEpatents

    Nagy, Jon O.; Spevak, Wayne R.; Dasgupta, Falguni; Bertozzi, Caroline

    1999-01-01

    This invention provides compositions for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, these composition scan be used to palliate certain inflammatory and immunological conditions.

  11. Inhibition of selectin binding

    DOEpatents

    Nagy, Jon O.; Spevak, Wayne R.; Dasgupta, Falguni; Bertozzi, Carolyn

    1999-10-05

    This invention provides a system for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, this system can be used to palliate certain inflammatory and immunological conditions.

  12. Inhibition of selectin binding

    DOEpatents

    Nagy, Jon O.; Spevak, Wayne R.; Dasgupta, Falguni; Bertozzi, Caroline

    2001-10-09

    This invention provides compositions for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, these composition scan be used to palliate certain inflammatory and immunological conditions.

  13. Glycosylases utilize ``stop and go'' motion to locate DNA damage

    NASA Astrophysics Data System (ADS)

    Nelson, Shane

    2015-03-01

    Oxidative damage to DNA results in alterations that are mutagenic or even cytotoxic. Base excision repair is a mechanism that functions to identify and correct these lesions, and is present in organisms ranging from bacteria to humans. DNA glycosylases are the first enzymes in this pathway and function to locate and remove oxidatively damaged bases, and do so utilizing only thermal energy. However, the question remains of how these enzymes locate and recognize a damaged base among millions of undamaged bases. Utilizing fluorescence video microscopy with high spatial and temporal resolution, we have observed a number of different fluorescently labeled glycosylases (including bacterial FPG, NEI, and NTH as well as mammalian MutyH and OGG). These enzymes diffuse along DNA tightropes at approximately 0.01 +/- 0.005 μm2/s with binding lifetimes ranging from one second to several minutes. Chemically induced damage to the DNA substrate causes a ~ 50% reduction in diffusion coefficients and a ~ 400% increase in binding lifetimes, while mutation of the key ``wedge residue'' - which has been shown to be responsible for damage detection - results in a 200% increase in the diffusion coefficient. Utilizing a sliding window approach to measure diffusion coefficients within individual trajectories, we observe that distributions of diffusion coefficients are bimodal, consistent with periods of diffusive motion interspersed with immobile periods. Utilizing a unique chemo-mechanical simulation approach, we demonstrate that the motion of these glycosylases can be explained as free diffusion along the helical pitch of the DNA, punctuated with two different types of pauses: 1) rapid, short-lived pauses as the enzyme rapidly probes DNA bases to interrogate for damage and, 2) less frequent, longer lived pauses that reflect the enzyme bound to and catalytically removing a damaged base. These simulations also indicate that the wedge residue is critical for interrogation and recognition of

  14. Cellulose binding domain proteins

    DOEpatents

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.; Doi, R.

    1998-11-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  15. Cellulose binding domain proteins

    DOEpatents

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  16. MD-2 binds cholesterol.

    PubMed

    Choi, Soo-Ho; Kim, Jungsu; Gonen, Ayelet; Viriyakosol, Suganya; Miller, Yury I

    2016-02-19

    Cholesterol is a structural component of cellular membranes, which is transported from liver to peripheral cells in the form of cholesterol esters (CE), residing in the hydrophobic core of low-density lipoprotein. Oxidized CE (OxCE) is often found in plasma and in atherosclerotic lesions of subjects with cardiovascular disease. Our earlier studies have demonstrated that OxCE activates inflammatory responses in macrophages via toll-like receptor-4 (TLR4). Here we demonstrate that cholesterol binds to myeloid differentiation-2 (MD-2), a TLR4 ancillary molecule, which is a binding receptor for bacterial lipopolysaccharide (LPS) and is indispensable for LPS-induced TLR4 dimerization and signaling. Cholesterol binding to MD-2 was competed by LPS and by OxCE-modified BSA. Furthermore, soluble MD-2 in human plasma and MD-2 in mouse atherosclerotic lesions carried cholesterol, the finding supporting the biological significance of MD-2 cholesterol binding. These results help understand the molecular basis of TLR4 activation by OxCE and mechanisms of chronic inflammation in atherosclerosis. PMID:26806306

  17. Sequential memory: Binding dynamics

    NASA Astrophysics Data System (ADS)

    Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

    2015-10-01

    Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories—episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities.

  18. Sequential memory: Binding dynamics.

    PubMed

    Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

    2015-10-01

    Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories-episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities. PMID:26520084

  19. Prediction of tissue thermal damage.

    PubMed

    Li, Xin; Zhong, Yongmin; Subic, Aleksandar; Jazar, Reza; Smith, Julian; Gu, Chengfan

    2016-04-29

    This paper presents a method to characterize tissue thermal damage by taking into account the thermal-mechanical effect of soft tissues for thermal ablation. This method integrates the bio-heating conduction and non-rigid motion dynamics to describe thermal-mechanical behaviors of soft tissues and further extends the traditional tissue damage model to characterize thermal-mechanical damage of soft tissues. Simulations and comparison analysis demonstrate that the proposed method can effectively predict tissue thermal damage and it also provides reliable guidelines for control of the thermal ablation procedure. PMID:27163325

  20. Use of Fluorescent Dyes for Readily Recognizing Sperm Damage

    PubMed Central

    Farah, Omar Ibrahim; Cuiling, Li; Jiaojiao, Wang; Huiping, Zhang

    2013-01-01

    Sperm is produced by the testis and mature in the epididymis. For having a successful conception, the fertilizing sperm should have functional competent membranes, intact acrosome, functional mitochondria and an intact haploid genome. The effects of genetic and environmental factors result in sperm vulnerability to damage in the process of spermatogenesis and maturation. In recent years, the feasibility of detecting sperm damage is enhanced through the advances in technologies like fluoscerent staining techniques assisted with fluorescence microscope, flow cytometry and computer analysis systems. Fluoscerent staining techniques involve the use of fluorescent dyes, either directly or indirectly for binding them with some ingredients of sperm and evaluating the damage of the structure or function of the sperm, i.e. membrane, acrosome, mitochondria, chromosome or DNA. PMID:24163795

  1. Protein Damage by Reactive Electrophiles: Targets and Consequences

    PubMed Central

    Liebler, Daniel C.

    2008-01-01

    It has been sixty years since the Millers first described the covalent binding of carcinogens to tissue proteins. Protein covalent binding was gradually overshadowed by the emergence of DNA adduct formation as the dominant paradigm in chemical carcinogenesis, but re-emerged in the early 1970s as a critical mechanism of drug and chemical toxicity. Technology limitations hampered the characterization of protein adducts until the emergence of mass spectrometry-based proteomics in the late 1990s. The time since has seen rapid progress in the characterization of the protein targets of electrophiles and the consequences of protein damage. Recent integration of novel affinity chemistries for electrophile probes, shotgun proteomics methods and systems modeling tools has led to the identification of hundreds of protein targets of electrophiles in mammalian systems. The technology now exists to map the targets of damage to critical components of signaling pathways and metabolic networks and to understand mechanisms of damage at a systems level. The implementation of sensitive, specific analyses for protein adducts from both xenobiotic-derived and endogenous electrophiles offers a means to link protein damage to clinically relevant health effects of both chemical exposures and disease processes. PMID:18052106

  2. Ribonucleotide triggered DNA damage and RNA-DNA damage responses

    PubMed Central

    Wallace, Bret D; Williams, R Scott

    2014-01-01

    Research indicates that the transient contamination of DNA with ribonucleotides exceeds all other known types of DNA damage combined. The consequences of ribose incorporation into DNA, and the identity of protein factors operating in this RNA-DNA realm to protect genomic integrity from RNA-triggered events are emerging. Left unrepaired, the presence of ribonucleotides in genomic DNA impacts cellular proliferation and is associated with chromosome instability, gross chromosomal rearrangements, mutagenesis, and production of previously unrecognized forms of ribonucleotide-triggered DNA damage. Here, we highlight recent findings on the nature and structure of DNA damage arising from ribonucleotides in DNA, and the identification of cellular factors acting in an RNA-DNA damage response (RDDR) to counter RNA-triggered DNA damage. PMID:25692233

  3. Treatment of anisotropic damage development within a scalar damage formulation

    NASA Astrophysics Data System (ADS)

    Chan, K. S.; Bodner, S. R.; Munson, D. E.

    This paper is concerned with describing a damage mechanics formulation which provides for non-isotropic effects using a scalar damage variable. An investigation has been in progress for establishing the constitutive behavior of rock salt at long times and low to moderate confining pressures in relation to the possible use of excavated rooms in rock salt formations as repositories for nuclear waste. An important consideration is the effect of damage manifested principally by the formation of shear induced wing cracks which have a stress dependent orientation. The analytical formulation utilizes a scalar damage parameter, but is capable of indicating the non-isotropic dependence of inelastic straining on the stress state and the confining pressure. Also, the equations indicate the possibility of volumetric expansions leading to the onset of tertiary creep and eventually rupture if the damage variable reaches a critical value.

  4. Road Damage Following Earthquake

    NASA Technical Reports Server (NTRS)

    1989-01-01

    Ground shaking triggered liquefaction in a subsurface layer of water-saturated sand, producing differential lateral and vertical movement in a overlying carapace of unliquified sand and slit, which moved from right to left towards the Pajaro River. This mode of ground failure, termed lateral spreading, is a principal cause of liquefaction-related earthquake damage caused by the Oct. 17, 1989, Loma Prieta earthquake. Sand and soil grains have faces that can cause friction as they roll and slide against each other, or even cause sticking and form small voids between grains. This complex behavior can cause soil to behave like a liquid under certain conditions such as earthquakes or when powders are handled in industrial processes. Mechanics of Granular Materials (MGM) experiments aboard the Space Shuttle use the microgravity of space to simulate this behavior under conditons that carnot be achieved in laboratory tests on Earth. MGM is shedding light on the behavior of fine-grain materials under low effective stresses. Applications include earthquake engineering, granular flow technologies (such as powder feed systems for pharmaceuticals and fertilizers), and terrestrial and planetary geology. Nine MGM specimens have flown on two Space Shuttle flights. Another three are scheduled to fly on STS-107. The principal investigator is Stein Sture of the University of Colorado at Boulder. Credit: S.D. Ellen, U.S. Geological Survey

  5. Shock Initiation of Damaged Explosives

    SciTech Connect

    Chidester, S K; Vandersall, K S; Tarver, C M

    2009-10-22

    Explosive and propellant charges are subjected to various mechanical and thermal insults that can increase their sensitivity over the course of their lifetimes. To quantify this effect, shock initiation experiments were performed on mechanically and thermally damaged LX-04 (85% HMX, 15% Viton by weight) and PBX 9502 (95% TATB, 5% Kel-F by weight) to obtain in-situ manganin pressure gauge data and run distances to detonation at various shock pressures. We report the behavior of the HMX-based explosive LX-04 that was damaged mechanically by applying a compressive load of 600 psi for 20,000 cycles, thus creating many small narrow cracks, or by cutting wedge shaped parts that were then loosely reassembled, thus creating a few large cracks. The thermally damaged LX-04 charges were heated to 190 C for long enough for the beta to delta solid - solid phase transition to occur, and then cooled to ambient temperature. Mechanically damaged LX-04 exhibited only slightly increased shock sensitivity, while thermally damaged LX-04 was much more shock sensitive. Similarly, the insensitive explosive PBX 9502 was mechanically damaged using the same two techniques. Since PBX 9502 does not undergo a solid - solid phase transition but does undergo irreversible or 'rachet' growth when thermally cycled, thermal damage to PBX 9502 was induced by this procedure. As for LX-04, the thermally damaged PBX 9502 demonstrated a greater shock sensitivity than mechanically damaged PBX 9502. The Ignition and Growth reactive flow model calculated the increased sensitivities by igniting more damaged LX-04 and PBX 9502 near the shock front based on the measured densities (porosities) of the damaged charges.

  6. Ionization induced damage in crystalline silicon

    NASA Technical Reports Server (NTRS)

    Meulenberg, A., Jr.

    1977-01-01

    Close examination of the interaction of the energetic knock-on atoms with the local lattice environment reveals a damage mechanism which does satisfy the experimental data on proton irradiation of silicon. A proton-atom interaction with high energy transfer is considered where the proton path is delineated by a trail of ionization, and the silicon ion path is characterized by much heavier ionization terminating in a dense displacement cluster. At collision, many of the silicon electrons are stripped off, and the resulting energetic ion subsequently loses energy rapidly by Coulomb interaction with bound electrons. The rate of energy loss depends on the charge state and velocity of the knock-on ion. For ion energies in excess of 1 MeV, the intensity of ionization is sufficient to permit lattice atoms, stripped of their binding electrons, to reorient randomly before having an opportunity to recombine with electrons and re-establish the lattice. The path of a knock-on ion thus becomes a thin cylinder of amorphous material within the crystal. Amorphous silicon has a Fermi level closer to mid-band than does single crystal silicon, and a strong field therefore, results around this damaged region. The field produces a large depletion region, representing a very large capture cross section for minority carriers.

  7. Cellular Concentrations of DDB2 Regulate Dynamic Binding of DDB1 at UV-Induced DNA Damage▿

    PubMed Central

    Alekseev, Sergey; Luijsterburg, Martijn S.; Pines, Alex; Geverts, Bart; Mari, Pierre-Olivier; Giglia-Mari, Giuseppina; Lans, Hannes; Houtsmuller, Adriaan B.; Mullenders, Leon H. F.; Hoeijmakers, Jan H. J.; Vermeulen, Wim

    2008-01-01

    Nucleotide excision repair (NER) is the principal pathway for counteracting cytotoxic and mutagenic effects of UV irradiation. To provide insight into the in vivo regulation of the DNA damage recognition step of global genome NER (GG-NER), we constructed cell lines expressing fluorescently tagged damaged DNA binding protein 1 (DDB1). DDB1 is a core subunit of a number of cullin 4-RING ubiquitin ligase complexes. UV-activated DDB1-DDB2-CUL4A-ROC1 ubiquitin ligase participates in the initiation of GG-NER and triggers the UV-dependent degradation of its subunit DDB2. We found that DDB1 rapidly accumulates on DNA damage sites. However, its binding to damaged DNA is not static, since DDB1 constantly dissociates from and binds to DNA lesions. DDB2, but not CUL4A, was indispensable for binding of DDB1 to DNA damage sites. The residence time of DDB1 on the damage site is independent of the main damage-recognizing protein of GG-NER, XPC, as well as of UV-induced proteolysis of DDB2. The amount of DDB1 that is temporally immobilized on damaged DNA critically depends on DDB2 levels in the cell. We propose a model in which UV-dependent degradation of DDB2 is important for the release of DDB1 from continuous association to unrepaired DNA and makes DDB1 available for its other DNA damage response functions. PMID:18936169

  8. Targeted DNA damage at individual telomeres disrupts their integrity and triggers cell death

    PubMed Central

    Sun, Luxi; Tan, Rong; Xu, Jianquan; LaFace, Justin; Gao, Ying; Xiao, Yanchun; Attar, Myriam; Neumann, Carola; Li, Guo-Min; Su, Bing; Liu, Yang; Nakajima, Satoshi; Levine, Arthur S.; Lan, Li

    2015-01-01

    Cellular DNA is organized into chromosomes and capped by a unique nucleoprotein structure, the telomere. Both oxidative stress and telomere shortening/dysfunction cause aging-related degenerative pathologies and increase cancer risk. However, a direct connection between oxidative damage to telomeric DNA, comprising <1% of the genome, and telomere dysfunction has not been established. By fusing the KillerRed chromophore with the telomere repeat binding factor 1, TRF1, we developed a novel approach to generate localized damage to telomere DNA and to monitor the real time damage response at the single telomere level. We found that DNA damage at long telomeres in U2OS cells is not repaired efficiently compared to DNA damage in non-telomeric regions of the same length in heterochromatin. Telomeric DNA damage shortens the average length of telomeres and leads to cell senescence in HeLa cells and cell death in HeLa, U2OS and IMR90 cells, when DNA damage at non-telomeric regions is undetectable. Telomere-specific damage induces chromosomal aberrations, including chromatid telomere loss and telomere associations, distinct from the damage induced by ionizing irradiation. Taken together, our results demonstrate that oxidative damage induces telomere dysfunction and underline the importance of maintaining telomere integrity upon oxidative damage. PMID:26082495

  9. Molecular Evolution of the Oxygen-Binding Hemerythrin Domain

    PubMed Central

    Alvarez-Carreño, Claudia; Becerra, Arturo; Lazcano, Antonio

    2016-01-01

    Background The evolution of oxygenic photosynthesis during Precambrian times entailed the diversification of strategies minimizing reactive oxygen species-associated damage. Four families of oxygen-carrier proteins (hemoglobin, hemerythrin and the two non-homologous families of arthropodan and molluscan hemocyanins) are known to have evolved independently the capacity to bind oxygen reversibly, providing cells with strategies to cope with the evolutionary pressure of oxygen accumulation. Oxygen-binding hemerythrin was first studied in marine invertebrates but further research has made it clear that it is present in the three domains of life, strongly suggesting that its origin predated the emergence of eukaryotes. Results Oxygen-binding hemerythrins are a monophyletic sub-group of the hemerythrin/HHE (histidine, histidine, glutamic acid) cation-binding domain. Oxygen-binding hemerythrin homologs were unambiguously identified in 367/2236 bacterial, 21/150 archaeal and 4/135 eukaryotic genomes. Overall, oxygen-binding hemerythrin homologues were found in the same proportion as single-domain and as long protein sequences. The associated functions of protein domains in long hemerythrin sequences can be classified in three major groups: signal transduction, phosphorelay response regulation, and protein binding. This suggests that in many organisms the reversible oxygen-binding capacity was incorporated in signaling pathways. A maximum-likelihood tree of oxygen-binding hemerythrin homologues revealed a complex evolutionary history in which lateral gene transfer, duplications and gene losses appear to have played an important role. Conclusions Hemerythrin is an ancient protein domain with a complex evolutionary history. The distinctive iron-binding coordination site of oxygen-binding hemerythrins evolved first in prokaryotes, very likely prior to the divergence of Firmicutes and Proteobacteria, and spread into many bacterial, archaeal and eukaryotic species. The later

  10. Binding energy effects in cascade evolution and sputtering

    SciTech Connect

    Robinson, M.T.

    1995-06-01

    The MARLOWE model was extended to include a binding energy dependent on the local crystalline order, so that atoms are bound less strongly to their lattice sites near surfaces or associated damage. Sputtering and cascade evolution were studied on the examples of self-ion irradiations of Cu and Au monocrystals. In cascades, the mean binding energy is reduced {approximately}8% in Cu with little dependence on the initial recoil energy; in Au, it is reduced {approximately}9% at 1 keV and {approximately}15% at 100 keV. In sputtering, the mean binding energy is reduced {approximately}8% in Cu and {approximately}15% in Au with little energy dependence; the yields are increased about half as much. Most sites from which sputtered atoms originate are isolated in both metals. Small clusters of such sites occur in Cu, but there are some large clusters in Au, especially in [111] targets. There are always more large clusters with damage-dependent binding than with a constant binding energy, but only a few clusters are compact enough to be regarded as pits.

  11. Cell permeable vanX inhibitors as vancomycin re-sensitizing agents.

    PubMed

    Muthyala, Ramaiah; Rastogi, Namrata; Shin, Woo Shik; Peterson, Marnie L; Sham, Yuk Yin

    2014-06-01

    VanX is an induced zinc metallo d-Ala-d-Ala dipeptidase involved in the viable remodeling of bacterial cell wall that is essential for the development of VREF. Here we report two cyclic thiohydroxamic acid-based peptide analogs that were designed, synthesized and investigated as vancomycin re-sensitizing agents. These compounds exhibit low micromolar inhibitory activity against vanX, with low cytotoxicity and were shown to increase vancomycin sensitivity against VREF. The improved pharmacological properties of these novel inhibitors over previous transition state mimics should provide an enhanced platform for designing potent vanX inhibitors for overcoming vancomycin resistance. PMID:24751446

  12. The oxidative damage initiation hypothesis for meiosis.

    PubMed

    Hörandl, Elvira; Hadacek, Franz

    2013-12-01

    The maintenance of sexual reproduction in eukaryotes is still a major enigma in evolutionary biology. Meiosis represents the only common feature of sex in all eukaryotic kingdoms, and thus, we regard it a key issue for discussing its function. Almost all asexuality modes maintain meiosis either in a modified form or as an alternative pathway, and facultatively apomictic plants increase frequencies of sexuality relative to apomixis after abiotic stress. On the physiological level, abiotic stress causes oxidative stress. We hypothesize that repair of oxidative damage on nuclear DNA could be a major driving force in the evolution of meiosis. We present a hypothetical model for the possible redox chemistry that underlies the binding of the meiosis-specific protein Spo11 to DNA. During prophase of meiosis I, oxidized sites at the DNA molecule are being targeted by the catalytic tyrosine moieties of Spo11 protein, which acts like an antioxidant reducing the oxidized target. The oxidized tyrosine residues, tyrosyl radicals, attack the phosphodiester bonds of the DNA backbone causing DNA double strand breaks that can be repaired by various mechanisms. Polyploidy in apomictic plants could mitigate oxidative DNA damage and decrease Spo11 activation. Our hypothesis may contribute to explaining various enigmatic phenomena: first, DSB formation outnumbers crossovers and, thus, effective recombination events by far because the target of meiosis may be the removal of oxidative lesions; second, it offers an argument for why expression of sexuality is responsive to stress in many eukaryotes; and third, repair of oxidative DNA damage turns meiosis into an essential characteristic of eukaryotic reproduction. PMID:23995700

  13. Damage Progression in Bolted Composites

    NASA Technical Reports Server (NTRS)

    Minnetyan, Levon; Chamis, Christos C.; Gotsis, Pascal K.

    1998-01-01

    Structural durability, damage tolerance, and progressive fracture characteristics of bolted graphite/epoxy composite laminates are evaluated via computational simulation. Constituent material properties and stress and strain limits are scaled up to the structure level to evaluate the overall damage and fracture propagation for bolted composites. Single and double bolted composite specimens with various widths and bolt spacings are evaluated. The effect of bolt spacing is investigated with regard to the structural durability of a bolted joint. Damage initiation, growth, accumulation, and propagation to fracture are included in the simulations. Results show the damage progression sequence and structural fracture resistance during different degradation stages. A procedure is outlined for the use of computational simulation data in the assessment of damage tolerance, determination of sensitive parameters affecting fracture, and interpretation of experimental results with insight for design decisions.

  14. Damage Progression in Bolted Composites

    NASA Technical Reports Server (NTRS)

    Minnetyan, Levon; Chamis, Christos; Gotsis, Pascal K.

    1998-01-01

    Structural durability,damage tolerance,and progressive fracture characteristics of bolted graphite/epoxy composite laminates are evaluated via computational simulation. Constituent material properties and stress and strain limits are scaled up to the structure level to evaluate the overall damage and fracture propagation for bolted composites. Single and double bolted composite specimens with various widths and bolt spacings are evaluated. The effect of bolt spacing is investigated with regard to the structural durability of a bolted joint. Damage initiation, growth, accumulation, and propagation to fracture are included in the simulations. Results show the damage progression sequence and structural fracture resistance during different degradation stages. A procedure is outlined for the use of computational simulation data in the assessment of damage tolerance, determination of sensitive parameters affecting fracture, and interpretation of experimental results with insight for design decisions.

  15. A systematic analysis of factors localized to damaged chromatin reveals PARP-dependent recruitment of transcription factors

    PubMed Central

    Izhar, Lior; Adamson, Britt; Ciccia, Alberto; Lewis, Jedd; Pontano-Vaites, Laura; Leng, Yumei; Liang, Anthony C.; Westbrook, Thomas F.; Harper, J. Wade; Elledge, Stephen J.

    2015-01-01

    Localization to sites of DNA damage is a hallmark of DNA damage response (DDR) proteins. To identify new DDR factors, we screened epitope-tagged proteins for localization to sites of chromatin damaged by UV laser microirradiation and found >120 proteins that localize to damaged chromatin. These include the BAF tumor suppressor complex and the ALS candidate protein TAF15. TAF15 contains multiple domains that bind damaged chromatin in a PARP-dependent manner, suggesting a possible role as glue that tethers multiple PAR chains together. Many positives were transcription factors and >70% of randomly tested transcription factors localized to sites of DNA damage and approximately 90% were PARP-dependent for localization. Mutational analyses showed that localization to damaged chromatin is DNA-binding domain-dependent. By examining Hoechst staining patterns at damage sites, we see evidence of chromatin decompaction that is PARP-dependent. We propose that PARP-regulated chromatin remodeling at sites of damage allows transient accessibility of DNA-binding proteins. PMID:26004182

  16. Clostridium perfringens Type A Enterotoxin Damages the Rabbit Colon

    PubMed Central

    Garcia, Jorge P.; Li, Jihong; Shrestha, Archana; Freedman, John C.; Beingesser, Juliann; McClane, Bruce A.

    2014-01-01

    Clostridium perfringens enterotoxin causes the gastrointestinal (GI) symptoms of C. perfringens type A food poisoning and CPE-associated non-food-borne human GI diseases. It is well established that CPE induces fluid accumulation and severe tissue damage in ligated small intestinal loops of rabbits and other animals. However, a previous study had also reported that CPE binds to rabbit colonic cells yet does not significantly affect rabbit colonic loops. To the contrary, the current study determined that treatment with 50 or 100 μg/ml of CPE causes significant histologic lesions and luminal fluid accumulation in rabbit colonic loops. Interestingly, a CPE-neutralizing monoclonal antibody blocked the development of CPE-induced histologic damage but not luminal fluid accumulation in these loops. Similar luminal fluid accumulation, without significant histologic damage, also occurred after treatment of colonic loops with heat-inactivated CPE, antibody alone, or bovine serum albumin (BSA), indicating that increased osmolarity was causing or contributing to fluid accumulation in CPE-treated colonic loops. Comparative studies revealed the similar development of histologic damage and luminal fluid accumulation in both small intestinal loops and colonic loops after as little as a 1-h treatment with 50 μg/ml of CPE. Consistent with the CPE sensitivity of the small intestine and colon, Western blotting detected CPE binding and large-complex formation in both organs. In addition, Western blotting demonstrated the presence of the high-affinity CPE receptors claudin-3 and -4 in both organs of rabbits, consistent with the observed toxin binding. Collectively, these results offer support for the possible involvement of the colon in CPE-mediated GI disease. PMID:24643537

  17. Library Binding Manual. Revised Edition.

    ERIC Educational Resources Information Center

    Lakhanpal, S. K.

    This procedural manual is designed to be used in bindery sections in public, university and special libraries. It briefly discusses these general matters: administrative control; selection of a binder; when and what to bind; conventional binding; routines; missing issues; schedule for shipments; temporary binding; rare books, maps and newspapers;…

  18. 3(omega) Damage: Growth Mitigation

    SciTech Connect

    Kozlowski, M; Demos, S; Wu, Z-L; Wong, J; Penetrante, B; Hrubesh, L

    2001-02-22

    The design of high power UV laser systems is limited to a large extent by the laser-initiated damage performance of transmissive fused silica optical components. The 3{omega} (i.e., the third harmonic of the primary laser frequency) damage growth mitigation LDRD effort focused on understanding and reducing the rapid growth of laser-initiated surface damage on fused silica optics. Laser-initiated damage can be discussed in terms of two key issues: damage initiated at some type of precursor and rapid damage growth of the damage due to subsequent laser pulses. The objective of the LDRD effort has been the elucidation of laser-induced damage processes in order to quantify and potentially reduce the risk of damage to fused silica surfaces. The emphasis of the first two years of this effort was the characterization and reduction of damage initiation. In spite of significant reductions in the density of damage sites on polished surfaces, statistically some amount of damage initiation should always be expected. The early effort therefore emphasized the development of testing techniques that quantified the statistical nature of damage initiation on optical surfaces. This work led to the development of an optics lifetime modeling strategy that has been adopted by the NIF project to address damage-risk issues. During FY99 interest shifted to the damage growth issue which was the focus of the final year of this project. The impact of the remaining damage sites on laser performance can be minimized if the damage sites did not continue to grow following subsequent illumination. The objectives of the final year of the LDRD effort were to apply a suite of state-of-the-art characterization tools to elucidate the nature of the initiated damage sites, and to identify a method that effectively mitigates further damage growth. Our specific goal is to understand the cause for the rapid growth of damage sites so that we can develop and apply an effective means to mitigate it. The

  19. Equivalent damage: A critical assessment

    NASA Technical Reports Server (NTRS)

    Laflen, J. R.; Cook, T. S.

    1982-01-01

    Concepts in equivalent damage were evaluated to determine their applicability to the life prediction of hot path components of aircraft gas turbine engines. Equivalent damage was defined as being those effects which influence the crack initiation life-time beyond the damage that is measured in uniaxial, fully-reversed sinusoidal and isothermal experiments at low homologous temperatures. Three areas of equivalent damage were examined: mean stress, cumulative damage, and multiaxiality. For each area, a literature survey was conducted to aid in selecting the most appropriate theories. Where possible, data correlations were also used in the evaluation process. A set of criteria was developed for ranking the theories in each equivalent damage regime. These criteria considered aspects of engine utilization as well as the theoretical basis and correlative ability of each theory. In addition, consideration was given to the complex nature of the loading cycle at fatigue critical locations of hot path components; this loading includes non-proportional multiaxial stressing, combined temperature and strain fluctuations, and general creep-fatigue interactions. Through applications of selected equivalent damage theories to some suitable data sets it was found that there is insufficient data to allow specific recommendations of preferred theories for general applications. A series of experiments and areas of further investigations were identified.

  20. Estimating bird damage from damage incidence in wine grape vineyards

    USGS Publications Warehouse

    DeHaven, R.W.; Hothem, R.L.

    1981-01-01

    Bird damage was measured during 1977 and 1978 at 32 wine grape vineyards in the San Joaquin Valley and North Coastal Region of California. Both the percentage bird loss (PBL) and the percentage of bunches damaged (BDI = bird damage incidence) were determined during 55 total-damage assessments, and the resulting data pairs were used to develop a regression of PBL on BDI. The final prediction equation was loge (PBL + 1) = 0.0385 BDI, for which the SE = 9.6297 10-4, and it accounted for 97% of the observed variation. We conclude that by using that equation, reasonably accurate predictions of PBL can be obtained from relatively quick and inexpensive estimates of BDI. Guidelines for the use of the prediction method and the accuracy of some PBL predictions are discussed.

  1. MERIT40 facilitates BRCA1 localization and DNA damage repair

    PubMed Central

    Feng, Lin; Huang, Jun; Chen, Junjie

    2009-01-01

    The product of breast cancer susceptibility gene 1, BRCA1, plays pivotal roles in the maintenance of genomic integrity. Mounting evidence indicates that BRCA1 associates with many proteins or protein complexes to regulate diverse processes important for the cellular response to DNA damage. One of these complexes, which mediates the accumulation of BRCA1 at sites of DNA breaks, involves the ubiquitin-binding motif (UIM)-containing protein RAP80, a coiled-coil domain protein CCDC98/Abraxas, and a deubiquitinating enzyme BRCC36. Here we describe the characterization of a novel component of this complex, MERIT40 (Mediator of Rap80 Interactions and Targeting 40 kd), which together with an adaptor protein BRE/BRCC45, enforces the BRCA1-dependent DNA damage response. MERIT40 is assembled into this RAP80/CCDC98-containing complex via its direct interaction with BRE/BRCC45. Importantly, MERIT40 regulates BRCA1 retention at DNA breaks and checkpoint function primarily via a role in maintaining the stability of BRE and this five-subunit protein complex at sites of DNA damage. Together, our study reveals that a stable complex containing MERIT40 acts early in DNA damage response and regulates damage-dependent BRCA1 localization. PMID:19261748

  2. Oxidative DNA damage stalls the human mitochondrial replisome

    PubMed Central

    Stojkovič, Gorazd; Makarova, Alena V.; Wanrooij, Paulina H.; Forslund, Josefin; Burgers, Peter M.; Wanrooij, Sjoerd

    2016-01-01

    Oxidative stress is capable of causing damage to various cellular constituents, including DNA. There is however limited knowledge on how oxidative stress influences mitochondrial DNA and its replication. Here, we have used purified mtDNA replication proteins, i.e. DNA polymerase γ holoenzyme, the mitochondrial single-stranded DNA binding protein mtSSB, the replicative helicase Twinkle and the proposed mitochondrial translesion synthesis polymerase PrimPol to study lesion bypass synthesis on oxidative damage-containing DNA templates. Our studies were carried out at dNTP levels representative of those prevailing either in cycling or in non-dividing cells. At dNTP concentrations that mimic those in cycling cells, the replication machinery showed substantial stalling at sites of damage, and these problems were further exacerbated at the lower dNTP concentrations present in resting cells. PrimPol, the translesion synthesis polymerase identified inside mammalian mitochondria, did not promote mtDNA replication fork bypass of the damage. This argues against a conventional role for PrimPol as a mitochondrial translesion synthesis DNA polymerase for oxidative DNA damage; however, we show that Twinkle, the mtDNA replicative helicase, is able to stimulate PrimPol DNA synthesis in vitro, suggestive of an as yet unidentified role of PrimPol in mtDNA metabolism. PMID:27364318

  3. Pneumococcal Pneumolysin Induces DNA Damage and Cell Cycle Arrest.

    PubMed

    Rai, Prashant; He, Fang; Kwang, Jimmy; Engelward, Bevin P; Chow, Vincent T K

    2016-01-01

    Streptococcus pneumoniae produces pneumolysin toxin as a key virulence factor against host cells. Pneumolysin is a cholesterol-dependent cytolysin (CDC) toxin that forms lytic pores in host membranes and mediates pneumococcal disease pathogenesis by modulating inflammatory responses. Here, we show that pneumolysin, which is released during bacterial lysis, induces DNA double strand breaks (DSBs), as indicated by ataxia telangiectasia mutated (ATM)-mediated H2AX phosphorylation (γH2AX). Pneumolysin-induced γH2AX foci recruit mediator of DNA damage checkpoint 1 (MDC1) and p53 binding protein 1 (53BP1), to sites of DSBs. Importantly, results show that toxin-induced DNA damage precedes cell cycle arrest and causes apoptosis when DNA-dependent protein kinase (DNA-PK)-mediated non-homologous end joining is inhibited. Further, we observe that cells that were undergoing DNA replication harbored DSBs in greater frequency during pneumolysin treatment. This observation raises the possibility that DSBs might be arising as a result of replication fork breakdown. Additionally, neutralizing the oligomerization domain of pneumolysin with monoclonal antibody suppresses DNA damage and also cell cycle arrest, indicating that pneumolysin oligomerization is important for causing DNA damage. Taken together, this study reveals a previously unidentified ability of pneumolysin to induce cytotoxicity via DNA damage, with implications in the pathophysiology of S. pneumoniae infection. PMID:27026501

  4. Unmyelinated type II afferent neurons report cochlear damage

    PubMed Central

    Liu, Chang; Glowatzki, Elisabeth; Fuchs, Paul Albert

    2015-01-01

    In the mammalian cochlea, acoustic information is carried to the brain by the predominant (95%) large-diameter, myelinated type I afferents, each of which is postsynaptic to a single inner hair cell. The remaining thin, unmyelinated type II afferents extend hundreds of microns along the cochlear duct to contact many outer hair cells. Despite this extensive arbor, type II afferents are weakly activated by outer hair cell transmitter release and are insensitive to sound. Intriguingly, type II afferents remain intact in damaged regions of the cochlea. Here, we show that type II afferents are activated when outer hair cells are damaged. This response depends on both ionotropic (P2X) and metabotropic (P2Y) purinergic receptors, binding ATP released from nearby supporting cells in response to hair cell damage. Selective activation of P2Y receptors increased type II afferent excitability by the closure of KCNQ-type potassium channels, a potential mechanism for the painful hypersensitivity (that we term “noxacusis” to distinguish from hyperacusis without pain) that can accompany hearing loss. Exposure to the KCNQ channel activator retigabine suppressed the type II fiber’s response to hair cell damage. Type II afferents may be the cochlea’s nociceptors, prompting avoidance of further damage to the irreparable inner ear. PMID:26553995

  5. Glimepiride protects neurons against amyloid-β-induced synapse damage.

    PubMed

    Osborne, Craig; West, Ewan; Nolan, William; McHale-Owen, Harriet; Williams, Alun; Bate, Clive

    2016-02-01

    Alzheimer's disease is associated with the accumulation within the brain of amyloid-β (Aβ) peptides that damage synapses and affect memory acquisition. This process can be modelled by observing the effects of Aβ on synapses in cultured neurons. The addition of picomolar concentrations of soluble Aβ derived from brain extracts triggered the loss of synaptic proteins including synaptophysin, synapsin-1 and cysteine string protein from cultured neurons. Glimepiride, a sulphonylurea used for the treatment of diabetes, protected neurons against synapse damage induced by Aβ. The protective effects of glimepiride were multi-faceted. Glimepiride treatment was associated with altered synaptic membranes including the loss of specific glycosylphosphatidylinositol (GPI)-anchored proteins including the cellular prion protein (PrP(C)) that acts as a receptor for Aβ42, increased synaptic gangliosides and altered cell signalling. More specifically, glimepiride reduced the Aβ-induced increase in cholesterol and the Aβ-induced activation of cytoplasmic phospholipase A2 (cPLA2) in synapses that occurred within cholesterol-dense membrane rafts. Aβ42 binding to glimepiride-treated neurons was not targeted to membrane rafts and less Aβ42 accumulated within synapses. These studies indicate that glimepiride modified the membrane micro-environments in which Aβ-induced signalling leads to synapse damage. In addition, soluble PrP(C), released from neurons by glimepiride, neutralised Aβ-induced synapse damage. Such observations raise the possibility that glimepiride may reduce synapse damage and hence delay the progression of cognitive decline in Alzheimer's disease. PMID:26432105

  6. Pneumococcal Pneumolysin Induces DNA Damage and Cell Cycle Arrest

    PubMed Central

    Rai, Prashant; He, Fang; Kwang, Jimmy; Engelward, Bevin P.; Chow, Vincent T.K.

    2016-01-01

    Streptococcus pneumoniae produces pneumolysin toxin as a key virulence factor against host cells. Pneumolysin is a cholesterol-dependent cytolysin (CDC) toxin that forms lytic pores in host membranes and mediates pneumococcal disease pathogenesis by modulating inflammatory responses. Here, we show that pneumolysin, which is released during bacterial lysis, induces DNA double strand breaks (DSBs), as indicated by ataxia telangiectasia mutated (ATM)-mediated H2AX phosphorylation (γH2AX). Pneumolysin-induced γH2AX foci recruit mediator of DNA damage checkpoint 1 (MDC1) and p53 binding protein 1 (53BP1), to sites of DSBs. Importantly, results show that toxin-induced DNA damage precedes cell cycle arrest and causes apoptosis when DNA-dependent protein kinase (DNA-PK)-mediated non-homologous end joining is inhibited. Further, we observe that cells that were undergoing DNA replication harbored DSBs in greater frequency during pneumolysin treatment. This observation raises the possibility that DSBs might be arising as a result of replication fork breakdown. Additionally, neutralizing the oligomerization domain of pneumolysin with monoclonal antibody suppresses DNA damage and also cell cycle arrest, indicating that pneumolysin oligomerization is important for causing DNA damage. Taken together, this study reveals a previously unidentified ability of pneumolysin to induce cytotoxicity via DNA damage, with implications in the pathophysiology of S. pneumoniae infection. PMID:27026501

  7. MMOD Impact Damage to ISS

    NASA Technical Reports Server (NTRS)

    Hyde, James L.; Christiansen, Eric; Lear, Dana M.

    2014-01-01

    Paper will describe micrometeoroid and orbital debris (MMOD) damage that has been observed on the International Space Station (ISS). Several hundred documented MMOD damage sites on ISS have been identified through imagery from the windows of ISS modules or docked vehicles. Sites that are observable from ISS or shuttle windows exhibiting distinct features of hypervelocity impact damage are usually greater than 5mm in diameter. Many smaller features are revealed in on-orbit imagery are typically less distinct and difficult to characterize but could be MMOD damage. Additional images of on-orbit damage features have been collected by astronauts during extra vehicular activities. Ground inspection of returned ISS hardware has also contributed to the database of ISS MMOD impact damage. A handful of orbital replacement units (ORU) from the ISS active thermal control and electrical power subsystems were swapped out and returned during the Space Shuttle program. In addition, a reusable logistics module was deployed on ISS for a total 59.4 days on 11 shuttle missions between 2001 and 2011 and then brought back in the shuttle payload bay. All of this returned hardware was subjected to detailed post-flight inspections for MMOD damage, and a database with nearly 1000 impact records has been collected. A description of the largest observed damages will be provided in the paper. In addition, a discussion of significant MMOD impact sites with operational or design aspects will be presented. Some of the ISS modules/subsystems damaged by MMOD to be included in the discussion are (1) Solar Arrays, (2) US and Russian windows, (3) EVA handrails, (4) Radiators, and (5) Russian FGB module.

  8. Impact damage in composite laminates

    NASA Technical Reports Server (NTRS)

    Grady, Joseph E.

    1988-01-01

    Damage tolerance requirements have become an important consideration in the design and fabrication of composite structural components for modern aircraft. The ability of a component to contain a flaw of a given size without serious loss of its structural integrity is of prime concern. Composite laminates are particularly susceptible to damage caused by transverse impact loading. The ongoing program described is aimed at developing experimental and analytical methods that can be used to assess damage tolerance capabilities in composite structures subjected to impulsive loading. Some significant results of this work and the methodology used to obtain them are outlined.

  9. Earthquake damage to transportation systems

    USGS Publications Warehouse

    McCullough, Heather

    1994-01-01

    Earthquakes represent one of the most destructive natural hazards known to man. A large magnitude earthquake near a populated area can affect residents over thousands of square kilometers and cause billions of dollars in property damage. Such an event can kill or injure thousands of residents and disrupt the socioeconomic environment for months, sometimes years. A serious result of a large-magnitude earthquake is the disruption of transportation systems, which limits post-disaster emergency response. Movement of emergency vehicles, such as police cars, fire trucks and ambulances, is often severely restricted. Damage to transportation systems is categorized below by cause including: ground failure, faulting, vibration damage, and tsunamis.

  10. The cardiotoxicity and myocyte damage caused by small molecule anticancer tyrosine kinase inhibitors is correlated with lack of target specificity

    SciTech Connect

    Hasinoff, Brian B.

    2010-04-15

    The use of the new anticancer tyrosine kinase inhibitors (TKI) has revolutionized the treatment of certain cancers. However, the use of some of these results in cardiotoxicity. Large-scale profiling data recently made available for the binding of 7 of the 9 FDA-approved tyrosine kinase inhibitors to a panel of 317 kinases has allowed us to correlate kinase inhibitor binding selectivity scores with TKI-induced damage to neonatal rat cardiac myocytes. The tyrosine kinase selectivity scores, but not the serine-threonine kinase scores, were highly correlated with the myocyte damaging effects of the TKIs. Additionally, we showed that damage to myocytes gave a good rank order correlation with clinical cardiotoxicity. Finally, strength of TKI binding to colony-stimulating factor 1 receptor (CSF1R) was highly correlated with myocyte damage, thus possibly implicating this kinase in contributing to TKI-induced cardiotoxicity.

  11. Alcohol binding to liposomes by 2H NMR and radiolabel binding assays: does partitioning describe binding?

    PubMed Central

    Dubey, A K; Eryomin, V A; Taraschi, T F; Janes, N

    1996-01-01

    Implicit within the concept of membrane-buffer partition coefficients of solutes is a nonspecific solvation mechanism of solute binding. However, (2)H NMR studies of the binding of (2)H(6)-ethanol and [1-(2)H(2)] n-hexanol to phosphatidylcholine vesicles have been interpreted as evidence for two distinct alcohol binding modes. One binding mode was reported to be at the membrane surface. The second mode was reported to be within the bilayer interior. An examination of the (2)H NMR binding studies, together with direct radiolabel binding assays, shows that other interpretations of the data are more plausible. The results are entirely consistent with partitioning (nonspecific binding) as the sole mode of alcohol binding to liposomes, in accord with our previous thermodynamic interpretation of alcohol action in phosphatidylcholine liposomes. PMID:9172754

  12. Types and Consequences of DNA Damage

    EPA Science Inventory

    This review provides a concise overview of the types of DNA damage and the molecular mechanisms by which a cell senses DNA damage, repairs the damage, converts the damage into a mutation, or dies as a consequence of unrepaired DNA damage. Such information is important in consid...

  13. Clinical light damage to the eye

    SciTech Connect

    Miller, D.

    1987-01-01

    This book contains four sections: The Nature of Light and of Light Damage to Biological Tissues; Light Damage to the Eye; Protecting the Eye from Light Damage; and Overview of Light Damage to the Eye. Some of the paper titles are: Ultraviolet-Absorbing Intraocular Lens Implants; Phototoxic Changes in the Retina; Light Damage to the Lens; and Radiation, Light, and Sight.

  14. Carboplatin binding to histidine

    SciTech Connect

    Tanley, Simon W. M.; Diederichs, Kay; Kroon-Batenburg, Loes M. J.; Levy, Colin; Schreurs, Antoine M. M.; Helliwell, John R.

    2014-08-29

    An X-ray crystal structure showing the binding of purely carboplatin to histidine in a model protein has finally been obtained. This required extensive crystallization trials and various novel crystal structure analyses. Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the bromine form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.

  15. Optical detection of DNA damage

    NASA Astrophysics Data System (ADS)

    Rogers, Kim R.; Apostol, A.; Cembrano, J.

    1999-02-01

    A rapid and sensitive fluorescence assay for oxidative damage to calf thymus DNA is reported. A decrease in the transition temperature for strand separation resulted from exposure of the DNA to the reactive decomposition products of 3- morpholinosydnonimine (SIN-1) (i.e., nitric oxide, superoxide, peroxynitrite, hydrogen peroxide, and hydroxyl radicals). A decrease in melting temperature of 12 degrees Celsius was indicative of oxidative damage including single strand chain breaks. Double stranded (ds) and single stranded (ss) forms of DNA were determined using the indicator dyes ethidium bromide and PicoGreen. The change in DNA 'melting' curves was dependant on the concentration of SIN-1 and was most pronounced at 75 degrees Celsius. This chemically induced damage was significantly inhibited by sodium citrate, tris(hydroxymethyl)aminomethane (Tris), and diethylenetriaminepentaacetic acid (DTPA), but was unaffected by superoxide dismutase (SOD), catalase, ethylenediamine tetraacietic acid (EDTA), or deferoxamine. Lowest observable effect level for SIN-1-induced damage was 200 (mu) M.

  16. Probabilistic Fatigue Damage Program (FATIG)

    NASA Technical Reports Server (NTRS)

    Michalopoulos, Constantine

    2012-01-01

    FATIG computes fatigue damage/fatigue life using the stress rms (root mean square) value, the total number of cycles, and S-N curve parameters. The damage is computed by the following methods: (a) traditional method using Miner s rule with stress cycles determined from a Rayleigh distribution up to 3*sigma; and (b) classical fatigue damage formula involving the Gamma function, which is derived from the integral version of Miner's rule. The integration is carried out over all stress amplitudes. This software solves the problem of probabilistic fatigue damage using the integral form of the Palmgren-Miner rule. The software computes fatigue life using an approach involving all stress amplitudes, up to N*sigma, as specified by the user. It can be used in the design of structural components subjected to random dynamic loading, or by any stress analyst with minimal training for fatigue life estimates of structural components.

  17. How to accurately bypass damage

    PubMed Central

    Broyde, Suse; Patel, Dinshaw J.

    2016-01-01

    Ultraviolet radiation can cause cancer through DNA damage — specifically, by linking adjacent thymine bases. Crystal structures show how the enzyme DNA polymerase η accurately bypasses such lesions, offering protection. PMID:20577203

  18. Deciphering the DNA Damage Response.

    PubMed

    Haber, James E

    2015-09-10

    This year's Albert Lasker Basic Medical Research Award honors Evelyn Witkin and Stephen J. Elledge, two pioneers in elucidating the DNA damage response, whose contributions span more than 40 years. PMID:26359974

  19. Loss and damage post Paris

    NASA Astrophysics Data System (ADS)

    Petherick, Anna

    2016-08-01

    The Paris Agreement gave the Warsaw International Mechanism for Loss and Damage a permanent and potentially prominent place in climate negotiations, but beyond that its impact remains wide open for interpretation.

  20. Mitochondrial DNA Damage and Diseases

    PubMed Central

    Singh, Gyanesh; Pachouri, U C; Khaidem, Devika Chanu; Kundu, Aman; Chopra, Chirag; Singh, Pushplata

    2015-01-01

    Various endogenous and environmental factors can cause mitochondrial DNA (mtDNA) damage.  One of the reasons for enhanced mtDNA damage could be its proximity to the source of oxidants, and lack of histone-like protective proteins. Moreover, mitochondria contain inadequate DNA repair pathways, and, diminished DNA repair capacity may be one of the factors responsible for high mutation frequency of the mtDNA. mtDNA damage might cause impaired mitochondrial function, and, unrepaired mtDNA damage has been frequently linked with several diseases. Exploration of mitochondrial perspective of diseases might lead to a better understanding of several diseases, and will certainly open new avenues for detection, cure, and prevention of ailments.

  1. Damaging effects of visible light

    NASA Astrophysics Data System (ADS)

    Williams, T. P.; Baker, B. N.

    1982-02-01

    The right eyes of anesthetized, ten week old albino rats are exposed to constant photon fluxes at 6 wavelengths for 6 hours. The left eye of each animal is patched during the exposure and is used as control. Histologic examination of retinal sections disclosed a region in the superior retina which is more damaged than are other areas. Attempting to ascertain an action spectrum by measuring outer nuclear layer (ONL) lost in this sensitive region fails. However, it is shown that when ONL thickness is integrated over the entire retinal sections, a rhodopsin action-spectrum emerges. It is concluded that retinal light damage in the albina rat under these conditions is rhodopsin mediated; and assessment of the extent of damage is best made by some method which integrates over the entire retinal section. The latter methodology is not routinely incorporated into studies of retinal light-damage but probably should be.

  2. BDS thin film damage competition

    SciTech Connect

    Stolz, C J; Thomas, M D; Griffin, A J

    2008-10-24

    A laser damage competition was held at the 2008 Boulder Damage Symposium in order to determine the current status of thin film laser resistance within the private, academic, and government sectors. This damage competition allows a direct comparison of the current state-of-the-art of high laser resistance coatings since they are all tested using the same damage test setup and the same protocol. A normal incidence high reflector multilayer coating was selected at a wavelength of 1064 nm. The substrates were provided by the submitters. A double blind test assured sample and submitter anonymity so only a summary of the results are presented here. In addition to the laser resistance results, details of deposition processes, coating materials, and layer count will also be shared.

  3. Climate change: Unattributed hurricane damage

    NASA Astrophysics Data System (ADS)

    Hallegatte, Stéphane

    2015-11-01

    In the United States, hurricanes have been causing more and more economic damage. A reanalysis of the disaster database using a statistical method that accounts for improvements in resilience opens the possibility that climate change has played a role.

  4. Chemical Protection Against Radiation Damage

    ERIC Educational Resources Information Center

    Campaigne, Ernest

    1969-01-01

    Discusses potential war time and medical uses for chemical compounds giving protection against radiation damage. Describes compounds known to protect, research aimed at discovering such compounds, and problems of toxicity. (EB)

  5. Excitation optimization for damage detection

    SciTech Connect

    Bement, Matthew T; Bewley, Thomas R

    2009-01-01

    A technique is developed to answer the important question: 'Given limited system response measurements and ever-present physical limits on the level of excitation, what excitation should be provided to a system to make damage most detectable?' Specifically, a method is presented for optimizing excitations that maximize the sensitivity of output measurements to perturbations in damage-related parameters estimated with an extended Kalman filter. This optimization is carried out in a computationally efficient manner using adjoint-based optimization and causes the innovations term in the extended Kalman filter to be larger in the presence of estimation errors, which leads to a better estimate of the damage-related parameters in question. The technique is demonstrated numerically on a nonlinear 2 DOF system, where a significant improvement in the damage-related parameter estimation is observed.

  6. The lack of target specificity of small molecule anticancer kinase inhibitors is correlated with their ability to damage myocytes in vitro

    SciTech Connect

    Hasinoff, Brian B. Patel, Daywin

    2010-12-01

    Many new targeted small molecule anticancer kinase inhibitors are actively being developed. However, the clinical use of some kinase inhibitors has been shown to result in cardiotoxicity. In most cases the mechanisms by which they exert their cardiotoxicity are not well understood. We have used large scale profiling data on 8 FDA-approved tyrosine kinase inhibitors and 10 other kinase inhibitors to a panel of 317 kinases in order to correlate binding constants and kinase inhibitor binding selectivity scores with kinase inhibitor-induced damage to neonatal rat cardiac myocytes. The 18 kinase inhibitors that were the subject of this study were: canertinib, dasatinib, dovitinib, erlotinib, flavopiridol, gefitinib, imatinib, lapatinib, midostaurin, motesanib, pazopanib, sorafenib, staurosporine, sunitinib, tandutinib, tozasertib, vandetanib and vatalanib. The combined tyrosine kinase and serine-threonine kinase selectivity scores were highly correlated with the myocyte-damaging effects of the kinase inhibitors. This result suggests that myocyte damage was due to a lack of target selectivity to binding of both tyrosine kinases and serine-threonine kinases, and was not due to binding to either group specifically. Finally, the strength of kinase inhibitor binding for 290 kinases was examined for correlations with myocyte damage. Kinase inhibitor binding was significantly correlated with myocyte damage for 12 kinases. Thus, myocyte damage may be multifactorial in nature with the inhibition of a number of kinases involved in producing kinase inhibitor-induced myocyte damage.

  7. The lack of target specificity of small molecule anticancer kinase inhibitors is correlated with their ability to damage myocytes in vitro.

    PubMed

    Hasinoff, Brian B; Patel, Daywin

    2010-12-01

    Many new targeted small molecule anticancer kinase inhibitors are actively being developed. However, the clinical use of some kinase inhibitors has been shown to result in cardiotoxicity. In most cases the mechanisms by which they exert their cardiotoxicity are not well understood. We have used large scale profiling data on 8 FDA-approved tyrosine kinase inhibitors and 10 other kinase inhibitors to a panel of 317 kinases in order to correlate binding constants and kinase inhibitor binding selectivity scores with kinase inhibitor-induced damage to neonatal rat cardiac myocytes. The 18 kinase inhibitors that were the subject of this study were: canertinib, dasatinib, dovitinib, erlotinib, flavopiridol, gefitinib, imatinib, lapatinib, midostaurin, motesanib, pazopanib, sorafenib, staurosporine, sunitinib, tandutinib, tozasertib, vandetanib and vatalanib. The combined tyrosine kinase and serine-threonine kinase selectivity scores were highly correlated with the myocyte-damaging effects of the kinase inhibitors. This result suggests that myocyte damage was due to a lack of target selectivity to binding of both tyrosine kinases and serine-threonine kinases, and was not due to binding to either group specifically. Finally, the strength of kinase inhibitor binding for 290 kinases was examined for correlations with myocyte damage. Kinase inhibitor binding was significantly correlated with myocyte damage for 12 kinases. Thus, myocyte damage may be multifactorial in nature with the inhibition of a number of kinases involved in producing kinase inhibitor-induced myocyte damage. PMID:20832415

  8. Damage thresholds for terahertz radiation

    NASA Astrophysics Data System (ADS)

    Dalzell, Danielle R.; McQuade, Jill; Vincelette, Rebecca; Ibey, Bennet; Payne, Jason; Thomas, Robert; Roach, W. P.; Roth, Caleb L.; Wilmink, Gerald J.

    2010-02-01

    Several international organizations establish minimum safety standards to ensure that workers and the general population are protected against adverse health effects associated with electromagnetic radiation. Suitable standards are typically defined using published experimental data. To date, few experimental studies have been conducted at Terahertz (THz) frequencies, and as a result, current THz standards have been defined using extrapolated estimates from neighboring spectral regions. In this study, we used computational modeling and experimental approaches to determine tissue-damage thresholds at THz frequencies. For the computational modeling efforts, we used the Arrhenius damage integral to predict damage-thresholds. We determined thresholds experimentally for both long (minutes) and short (seconds) THz exposures. For the long exposure studies, we used an in-house molecular gas THz laser (υ= 1.89 THz, 189.92 mW/cm2, 10 minutes) and excised porcine skin. For the short exposure studies, we used the Free Electron Laser (FEL) at Jefferson Laboratory (υ= 0.1-1.0 THz, 2.0-14.0 mW/cm2, 2 seconds) and wet chamois cloths. Thresholds were determined using conventional damage score determination and probit analysis techniques, and tissue temperatures were measured using infrared thermographic techniques. We found that the FEL was ideal for tissue damage studies, while our in-house THz source was not suitable to determine tissue damage thresholds. Using experimental data, the tissue damage threshold (ED50) was determined to be 7.16 W/cm2. This value was in well agreement with that predicted using our computational models. We hope that knowledge of tissue-damage thresholds at THz frequencies helps to ensure the safe use of THz radiation.

  9. Replicating Damaged DNA in Eukaryotes

    PubMed Central

    Chatterjee, Nimrat; Siede, Wolfram

    2013-01-01

    DNA damage is one of many possible perturbations that challenge the mechanisms that preserve genetic stability during the copying of the eukaryotic genome in S phase. This short review provides, in the first part, a general introduction to the topic and an overview of checkpoint responses. In the second part, the mechanisms of error-free tolerance in response to fork-arresting DNA damage will be discussed in some detail. PMID:24296172

  10. Nav Channels in Damaged Membranes.

    PubMed

    Morris, C E; Joos, B

    2016-01-01

    Sick excitable cells (ie, Nav channel-expressing cells injured by trauma, ischemia, inflammatory, and other conditions) typically exhibit "acquired sodium channelopathies" which, we argue, reflect bleb-damaged membranes rendering their Nav channels "leaky." The situation is excitotoxic because untreated Nav leak exacerbates bleb damage. Fast Nav inactivation (a voltage-independent process) is so tightly coupled, kinetically speaking, to the inherently voltage-dependent process of fast activation that when bleb damage accelerates and thus left-shifts macroscopic fast activation, fast inactivation accelerates to the same extent. The coupled g(V) and availability(V) processes and their window conductance regions consequently left-shift by the same number of millivolts. These damage-induced hyperpolarizing shifts, whose magnitude increases with damage intensity, are called coupled left shift (CLS). Based on past work and modeling, we discuss how to test for Nav-CLS, emphasizing the virtue of sawtooth ramp clamp. We explain that it is the inherent mechanosensitivity of Nav activation that underlies Nav-CLS. Using modeling of excitability, we show the known process of Nav-CLS is sufficient to predict a wide variety of "sick excitable cell" phenomena, from hyperexcitability through to depolarizing block. When living cells are mimicked by inclusion of pumps, mild Nav-CLS produces a wide array of burst phenomena and subthreshold oscillations. Dynamical analysis of mild damage scenarios shows how these phenomena reflect changes in spike thresholds as the pumps try to counteract the leaky Nav channels. Smart Nav inhibitors designed for sick excitable cells would target bleb-damaged membrane, buying time for cell-mediated removal or repair of Nav-bearing membrane that has become bleb-damaged (ie, detached from the cytoskeleton). PMID:27586295

  11. DNA damage in neurodegenerative diseases.

    PubMed

    Coppedè, Fabio; Migliore, Lucia

    2015-06-01

    Following the observation of increased oxidative DNA damage in nuclear and mitochondrial DNA extracted from post-mortem brain regions of patients affected by neurodegenerative diseases, the last years of the previous century and the first decade of the present one have been largely dedicated to the search of markers of DNA damage in neuronal samples and peripheral tissues of patients in early, intermediate or late stages of neurodegeneration. Those studies allowed to demonstrate that oxidative DNA damage is one of the earliest detectable events in neurodegeneration, but also revealed cytogenetic damage in neurodegenerative conditions, such as for example a tendency towards chromosome 21 malsegregation in Alzheimer's disease. As it happens for many neurodegenerative risk factors the question of whether DNA damage is cause or consequence of the neurodegenerative process is still open, and probably both is true. The research interest in markers of oxidative stress was shifted, in recent years, towards the search of epigenetic biomarkers of neurodegenerative disorders, following the accumulating evidence of a substantial contribution of epigenetic mechanisms to learning, memory processes, behavioural disorders and neurodegeneration. Increasing evidence is however linking DNA damage and repair with epigenetic phenomena, thereby opening the way to a very attractive and timely research topic in neurodegenerative diseases. We will address those issues in the context of Alzheimer's disease, Parkinson's disease, and Amyotrophic Lateral Sclerosis, which represent three of the most common neurodegenerative pathologies in humans. PMID:26255941

  12. DNA damage checkpoints in mammals.

    PubMed

    Niida, Hiroyuki; Nakanishi, Makoto

    2006-01-01

    DNA damage is a common event and probably leads to mutation or deletion within chromosomal DNA, which may cause cancer or premature aging. DNA damage induces several cellular responses including DNA repair, checkpoint activity and the triggering of apoptotic pathways. DNA damage checkpoints are associated with biochemical pathways that end delay or arrest of cell-cycle progression. These checkpoints engage damage sensor proteins, such as the Rad9-Rad1-Hus1 (9-1-1) complex, and the Rad17-RFC complex, in the detection of DNA damage and transduction of signals to ATM, ATR, Chk1 and Chk2 kinases. Chk1 and Chk2 kinases regulate Cdc25, Wee1 and p53 that ultimately inactivate cyclin-dependent kinases (Cdks) which inhibit cell-cycle progression. In this review, we discuss the molecular mechanisms by which DNA damage is recognized by sensor proteins and signals are transmitted to Cdks. We classify the genes involved in checkpoint signaling into four categories, namely sensors, mediators, transducers and effectors, although their proteins have the broad activity, and thus this classification is for convenience and is not definitive. PMID:16314342

  13. A model for damage of microheterogeneous kidney stones

    NASA Astrophysics Data System (ADS)

    Szeri, Andrew J.; Zohdi, Tarek I.; Blake, John R.

    2005-04-01

    In this paper, a theoretical framework is developed for the mechanics of kidney stones with an isotropic, random microstructure-such as those comprised of cystine or struvite. The approach is based on a micromechanical description of kidney stones comprised of crystals in a binding matrix. Stress concentration functions are developed to determine load sharing of the particle phase and the binding matrix phase. As an illustration of the theory, the fatigue of kidney stones subject to shock wave lithotripsy is considered. Stress concentration functions are used to construct fatigue life estimates for each phase, as a function of the volume fraction and of the mechanical properties of the constituents, as well as the loading from SWL. The failure of the binding matrix is determined explicitly in a model for the accumulation of distributed damage. Also considered is the amount of material damaged in a representative non-spherical collapse of a cavitation bubble near the stone surface. The theory can be used to assess the importance of microscale heterogeneity on the comminution of renal calculi and to estimate the number of cycles to failure in terms of measurable material properties.

  14. 48 CFR 236.206 - Liquidated damages.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 3 2013-10-01 2013-10-01 false Liquidated damages. 236... Aspects of Contracting for Construction 236.206 Liquidated damages. See 211.503 for instructions on use of liquidated damages....

  15. 48 CFR 236.206 - Liquidated damages.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 3 2011-10-01 2011-10-01 false Liquidated damages. 236... Aspects of Contracting for Construction 236.206 Liquidated damages. See 211.503 for instructions on use of liquidated damages....

  16. 48 CFR 236.206 - Liquidated damages.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 3 2012-10-01 2012-10-01 false Liquidated damages. 236... Aspects of Contracting for Construction 236.206 Liquidated damages. See 211.503 for instructions on use of liquidated damages....

  17. 48 CFR 236.206 - Liquidated damages.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 3 2010-10-01 2010-10-01 false Liquidated damages. 236... Aspects of Contracting for Construction 236.206 Liquidated damages. See 211.503 for instructions on use of liquidated damages....

  18. 48 CFR 236.206 - Liquidated damages.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 3 2014-10-01 2014-10-01 false Liquidated damages. 236... Aspects of Contracting for Construction 236.206 Liquidated damages. See 211.503 for instructions on use of liquidated damages....

  19. Boulder damage symposium annual thin film laser damage competition

    DOE PAGESBeta

    Stolz, Christopher J.

    2012-11-28

    Optical instruments and laser systems are often fluence-limited by multilayer thin films deposited on the optical surfaces. When comparing publications within the laser damage literature, there can be confusing and conflicting laser damage results. This is due to differences in testing protocols between research groups studying very different applications. In this series of competitions, samples from multiple vendors are compared under identical testing parameters and a single testing service. Unlike a typical study where a hypothesis is tested within a well-controlled experiment with isolated variables, this competition isolates the laser damage testing variables so that trends can be observed betweenmore » different deposition processes, coating materials, cleaning techniques, and multiple coating suppliers. The resulting series of damage competitions has also been designed to observe general trends of damage morphologies and mechanisms over a wide range of coating types (high reflector and antireflector), wavelengths (193 to 1064 nm), and pulse lengths (180 fs to 13 ns). A double blind test assured sample and submitter anonymity were used in each of the competitions so only a summary of the deposition process, coating materials, layer count and spectral results are presented. Laser resistance was strongly affected by substrate cleaning, coating deposition method, and coating material selection whereas layer count and spectral properties had minimal impact.« less

  20. Boulder damage symposium annual thin film laser damage competition

    SciTech Connect

    Stolz, Christopher J.

    2012-11-28

    Optical instruments and laser systems are often fluence-limited by multilayer thin films deposited on the optical surfaces. When comparing publications within the laser damage literature, there can be confusing and conflicting laser damage results. This is due to differences in testing protocols between research groups studying very different applications. In this series of competitions, samples from multiple vendors are compared under identical testing parameters and a single testing service. Unlike a typical study where a hypothesis is tested within a well-controlled experiment with isolated variables, this competition isolates the laser damage testing variables so that trends can be observed between different deposition processes, coating materials, cleaning techniques, and multiple coating suppliers. The resulting series of damage competitions has also been designed to observe general trends of damage morphologies and mechanisms over a wide range of coating types (high reflector and antireflector), wavelengths (193 to 1064 nm), and pulse lengths (180 fs to 13 ns). A double blind test assured sample and submitter anonymity were used in each of the competitions so only a summary of the deposition process, coating materials, layer count and spectral results are presented. Laser resistance was strongly affected by substrate cleaning, coating deposition method, and coating material selection whereas layer count and spectral properties had minimal impact.

  1. Neural networks for damage identification

    SciTech Connect

    Paez, T.L.; Klenke, S.E.

    1997-11-01

    Efforts to optimize the design of mechanical systems for preestablished use environments and to extend the durations of use cycles establish a need for in-service health monitoring. Numerous studies have proposed measures of structural response for the identification of structural damage, but few have suggested systematic techniques to guide the decision as to whether or not damage has occurred based on real data. Such techniques are necessary because in field applications the environments in which systems operate and the measurements that characterize system behavior are random. This paper investigates the use of artificial neural networks (ANNs) to identify damage in mechanical systems. Two probabilistic neural networks (PNNs) are developed and used to judge whether or not damage has occurred in a specific mechanical system, based on experimental measurements. The first PNN is a classical type that casts Bayesian decision analysis into an ANN framework; it uses exemplars measured from the undamaged and damaged system to establish whether system response measurements of unknown origin come from the former class (undamaged) or the latter class (damaged). The second PNN establishes the character of the undamaged system in terms of a kernel density estimator of measures of system response; when presented with system response measures of unknown origin, it makes a probabilistic judgment whether or not the data come from the undamaged population. The physical system used to carry out the experiments is an aerospace system component, and the environment used to excite the system is a stationary random vibration. The results of damage identification experiments are presented along with conclusions rating the effectiveness of the approaches.

  2. Glaucomatous damage of the macula

    PubMed Central

    Hood, Donald C.; Raza, Ali S.; de Moraes, Carlos Gustavo V.; Liebmann, Jeffrey M.; Ritch, Robert

    2012-01-01

    There is a growing body of evidence that early glaucomatous damage involves the macula. The anatomical basis of this damage can be studied using frequency domain optical coherence tomography (fdOCT), by which the local thickness of the retinal nerve fiber layer (RNFL) and local retinal ganglion cell plus inner plexiform (RGC+) layer can be measured. Based upon averaged fdOCT results from healthy controls and patients, we show that: 1. For healthy controls, the average RGC+ layer thickness closely matches human histological data; 2. For glaucoma patients and suspects, the average RGC+ layer shows greater glaucomatous thinning in the inferior retina (superior visual field (VF)); and 3. The central test points of the 6° VF grid (24-2 test pattern) miss the region of greatest RGC+ thinning. Based upon fdOCT results from individual patients, we have learned that: 1. Local RGC+ loss is associated with local VF sensitivity loss as long as the displacement of RGCs from the foveal center is taken into consideration; and 2. Macular damage is typically arcuate in nature and often associated with local RNFL thinning in a narrow region of the disc, which we call the macular vulnerability zone (MVZ). According to our schematic model of macular damage, most of the inferior region of the macula projects to the MVZ, which is located largely in the inferior quadrant of the disc, a region that is particularly susceptible to glaucomatous damage. A small (cecocentral) region of the inferior macula, and all of the superior macula (inferior VF), project to the temporal quadrant, a region that is less susceptible to damage. The overall message is clear; clinicians need to be aware that glaucomatous damage to the macula is common, can occur early in the disease, and can be missed and/or underestimated with standard VF tests that use a 6° grid, such as the 24-2 VF test. PMID:22995953

  3. STS-118 Radiator Impact Damage

    NASA Technical Reports Server (NTRS)

    Lear, Dana M.; Hyde, J.; Christiansen, E.; Herrin, J.; Lyons, F.

    2008-01-01

    During the August 2007 STS-118 mission to the International Space Station, a micro-meteoroid or orbital debris (MMOD) particle impacted and completely penetrated one of shuttle Endeavour s radiator panels and the underlying thermal control system (TCS) blanket, leaving deposits on (but no damage to) the payload bay door. While it is not unusual for shuttle orbiters to be impacted by small MMOD particles, the damage from this impact is larger than any previously seen on the shuttle radiator panels. A close-up photograph of the radiator impact entry hole is shown in Figure 1, and the location of the impact on Endeavour s left-side aft-most radiator panel is shown in Figure 2. The aft radiator panel is 0.5-inches thick and consists of 0.011 inch thick aluminum facesheets on the front and back of an aluminum honeycomb core. The front facesheet is additionally covered by a 0.005 inch thick layer of silver-Teflon thermal tape. The entry hole in the silver-Teflon tape measured 8.1 mm by 6.4 mm (0.32 inches by 0.25 inches). The entry hole in the outer facesheet measured 7.4 mm by 5.3 mm (0.29 inches by 0.21 inches) (0.23 inches). The impactor also perforated an existing 0.012 inch doubler that had been bonded over the facesheet to repair previous impact damage (an example that lightning can strike the same place twice, even for MMOD impact). The peeled-back edge around the entry hole, or lip , is a characteristic of many hypervelocity impacts. High velocity impact with the front facesheet fragmented the impacting particle and caused it to spread out into a debris cloud. The debris cloud caused considerable damage to the internal honeycomb core with 23 honeycomb cells over a region of 28 mm by 26 mm (1.1 inches by 1.0 inches) having either been completely destroyed or partially damaged. Figure 3 is a view of the exit hole in the rear facesheet, and partially shows the extent of the honeycomb core damage and clearly shows the jagged petaled exit hole through the backside

  4. Cold Spots in Protein Binding.

    PubMed

    Shirian, Jason; Sharabi, Oz; Shifman, Julia M

    2016-09-01

    Understanding the energetics and architecture of protein-binding interfaces is important for basic research and could potentially facilitate the design of novel binding domains for biotechnological applications. It is well accepted that a few key residues at binding interfaces (binding hot spots) are responsible for contributing most to the free energy of binding. In this opinion article, we introduce a new concept of 'binding cold spots', or interface positions occupied by suboptimal amino acids. Such positions exhibit a potential for affinity enhancement through various mutations. We give several examples of cold spots from different protein-engineering studies and argue that identification of such positions is crucial for studies of protein evolution and protein design. PMID:27477052

  5. A PP1-binding motif present in BRCA1 plays a role in its DNA repair function

    PubMed Central

    Yu, Young-Mi; Pace, Serena M.; Allen, Susan R.; Deng, Chu-Xia; Hsu, Lih-Ching

    2008-01-01

    Protein phosphatase 1α (PP1α) regulates phosphorylation of BRCA1, which contains a PP1-binding motif 898KVTF901. Mutation of this motif greatly reduces the interaction between BRCA1 and PP1α. Here we show that mutation of the PP1-binding motif abolishes the ability of BRCA1 to enhance survival of Brca1-deficient mouse mammary tumor cells after DNA damage. The Rad51 focus formation and comet assays revealed that the DNA repair function of BRCA1 was impaired when the PP1-binding motif was mutated. Analysis of subnuclear localization of GFP-tagged BRCA1 demonstrated that mutation of the PP1-binding motif affected BRCA1 redistribution in response to DNA damage. BRCA1 is required for the formation of Rad51 subnuclear foci after DNA damage. Mutation of the PP1-binding motif in BRCA1 also affected recruitment of Rad51 to sites of DNA damage. Consistent with these findings, knockdown of PP1α in BRCA1-proficient cells by small interfering RNA also significantly reduced Rad51 focus formation induced by DNA damage. Further analysis indicated that mutation of the PP1-binding motif compromised BRCA1 activities in homologous recombination. Altogether, our data implicate that interaction with PP1α is important for BRCA1 function in DNA repair. PMID:18953404

  6. Cofactor binding protects flavodoxin against oxidative stress.

    PubMed

    Lindhoud, Simon; van den Berg, Willy A M; van den Heuvel, Robert H H; Heck, Albert J R; van Mierlo, Carlo P M; van Berkel, Willem J H

    2012-01-01

    In organisms, various protective mechanisms against oxidative damaging of proteins exist. Here, we show that cofactor binding is among these mechanisms, because flavin mononucleotide (FMN) protects Azotobacter vinelandii flavodoxin against hydrogen peroxide-induced oxidation. We identify an oxidation sensitive cysteine residue in a functionally important loop close to the cofactor, i.e., Cys69. Oxidative stress causes dimerization of apoflavodoxin (i.e., flavodoxin without cofactor), and leads to consecutive formation of sulfinate and sulfonate states of Cys69. Use of 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl) reveals that Cys69 modification to a sulfenic acid is a transient intermediate during oxidation. Dithiothreitol converts sulfenic acid and disulfide into thiols, whereas the sulfinate and sulfonate forms of Cys69 are irreversible with respect to this reagent. A variable fraction of Cys69 in freshly isolated flavodoxin is in the sulfenic acid state, but neither oxidation to sulfinic and sulfonic acid nor formation of intermolecular disulfides is observed under oxidising conditions. Furthermore, flavodoxin does not react appreciably with NBD-Cl. Besides its primary role as redox-active moiety, binding of flavin leads to considerably improved stability against protein unfolding and to strong protection against irreversible oxidation and other covalent thiol modifications. Thus, cofactors can protect proteins against oxidation and modification. PMID:22829943

  7. Disorder and residual helicity alter p53-Mdm2 binding affinity and signaling in cells.

    PubMed

    Borcherds, Wade; Theillet, François-Xavier; Katzer, Andrea; Finzel, Ana; Mishall, Katie M; Powell, Anne T; Wu, Hongwei; Manieri, Wanda; Dieterich, Christoph; Selenko, Philipp; Loewer, Alexander; Daughdrill, Gary W

    2014-12-01

    Levels of residual structure in disordered interaction domains determine in vitro binding affinities, but whether they exert similar roles in cells is not known. Here, we show that increasing residual p53 helicity results in stronger Mdm2 binding, altered p53 dynamics, impaired target gene expression and failure to induce cell cycle arrest upon DNA damage. These results establish that residual structure is an important determinant of signaling fidelity in cells. PMID:25362358

  8. Intramolecular Binding of the Rad9 C Terminus in the Checkpoint Clamp Rad9-Hus1-Rad1 Is Closely Linked with Its DNA Binding.

    PubMed

    Takeishi, Yukimasa; Iwaya-Omi, Rie; Ohashi, Eiji; Tsurimoto, Toshiki

    2015-08-01

    The human checkpoint clamp Rad9-Hus1-Rad1 (9-1-1) is loaded onto chromatin by its loader complex, Rad17-RFC, following DNA damage. The 120-amino acid (aa) stretch of the Rad9 C terminus (C-tail) is unstructured and projects from the core ring structure (CRS). Recent studies showed that 9-1-1 and CRS bind DNA independently of Rad17-RFC. The DNA-binding affinity of mutant 9(ΔC)-1-1, which lacked the Rad9 C-tail, was much higher than that of wild-type 9-1-1, suggesting that 9-1-1 has intrinsic DNA binding activity that manifests in the absence of the C-tail. C-tail added in trans interacted with CRS and prevented it from binding to DNA. We narrowed down the amino acid sequence in the C-tail necessary for CRS binding to a 15-aa stretch harboring two conserved consecutive phenylalanine residues. We prepared 9-1-1 mutants containing the variant C-tail deficient for CRS binding, and we demonstrated that the mutant form restored DNA binding as efficiently as 9(ΔC)-1-1. Furthermore, we mapped the sequence necessary for TopBP1 binding within the same 15-aa stretch, demonstrating that TopBP1 and CRS share the same binding region in the C-tail. Indeed, we observed their competitive binding to the C-tail with purified proteins. The importance of interaction between 9-1-1 and TopBP1 for DNA damage signaling suggests that the competitive interactions of TopBP1 and CRS with the C-tail will be crucial for the activation mechanism. PMID:26088138

  9. Chromatin perturbations during the DNA damage response in higher eukaryotes

    PubMed Central

    Bakkenist, Christopher J.; Kastan, Michael B.

    2016-01-01

    The DNA damage response is a widely used term that encompasses all signaling initiated at DNA lesions and damaged replication forks as it extends to orchestrate DNA repair, cell cycle checkpoints, cell death and senescence. ATM, an apical DNA damage signaling kinase, is virtually instantaneously activated following the introduction of DNA double-strand breaks (DSBs). The MRE11-RAD50-NBS1 (MRN) complex, which has a catalytic role in DNA repair, and the KAT5 (Tip60) acetyltransferase are required for maximal ATM kinase activation in cells exposed to low doses of ionizing radiation. The sensing of DNA lesions occurs within a highly complex and heterogeneous chromatin environment. Chromatin decondensation and histone eviction at DSBs may be permissive for KAT5 binding to H3K9me3 and H3K36me3, ATM kinase acetylation and activation. Furthermore, chromatin perturbation may be a prerequisite for most DNA repair. Nucleosome disassembly during DNA repair was first reported in the 1970s by Smerdon and colleagues when nucleosome rearrangement was noted during the process of nucleotide excision repair of UV-induced DNA damage in human cells. Recently, the multi-functional protein nucleolin was identified as the relevant histone chaperone required for partial nucleosome disruption at DBSs, the recruitment of repair enzymes and for DNA repair. Notably, ATM kinase is activated by chromatin perturbations induced by a variety of treatments that do not directly cause DSBs, including treatment with histone deacetylase inhibitors. Central to the mechanisms that activate ATR, the second apical DNA damage signaling kinase, outside of a stalled and collapsed replication fork in S-phase, is chromatin decondensation and histone eviction associated with DNA end resection at DSBs. Thus, a stress that is common to both ATM and ATR kinase activation is chromatin perturbations, and we argue that chromatin perturbations are both sufficient and required for induction of the DNA damage response

  10. Chromatin perturbations during the DNA damage response in higher eukaryotes.

    PubMed

    Bakkenist, Christopher J; Kastan, Michael B

    2015-12-01

    The DNA damage response is a widely used term that encompasses all signaling initiated at DNA lesions and damaged replication forks as it extends to orchestrate DNA repair, cell cycle checkpoints, cell death and senescence. ATM, an apical DNA damage signaling kinase, is virtually instantaneously activated following the introduction of DNA double-strand breaks (DSBs). The MRE11-RAD50-NBS1 (MRN) complex, which has a catalytic role in DNA repair, and the KAT5 (Tip60) acetyltransferase are required for maximal ATM kinase activation in cells exposed to low doses of ionizing radiation. The sensing of DNA lesions occurs within a highly complex and heterogeneous chromatin environment. Chromatin decondensation and histone eviction at DSBs may be permissive for KAT5 binding to H3K9me3 and H3K36me3, ATM kinase acetylation and activation. Furthermore, chromatin perturbation may be a prerequisite for most DNA repair. Nucleosome disassembly during DNA repair was first reported in the 1970s by Smerdon and colleagues when nucleosome rearrangement was noted during the process of nucleotide excision repair of UV-induced DNA damage in human cells. Recently, the multi-functional protein nucleolin was identified as the relevant histone chaperone required for partial nucleosome disruption at DBSs, the recruitment of repair enzymes and for DNA repair. Notably, ATM kinase is activated by chromatin perturbations induced by a variety of treatments that do not directly cause DSBs, including treatment with histone deacetylase inhibitors. Central to the mechanisms that activate ATR, the second apical DNA damage signaling kinase, outside of a stalled and collapsed replication fork in S-phase, is chromatin decondensation and histone eviction associated with DNA end resection at DSBs. Thus, a stress that is common to both ATM and ATR kinase activation is chromatin perturbations, and we argue that chromatin perturbations are both sufficient and required for induction of the DNA damage response

  11. Quarkonium binding and entropic force

    NASA Astrophysics Data System (ADS)

    Satz, Helmut

    2015-05-01

    A bound state represents a balance between repulsive kinetic and attractive potential energy. In a hot quark-gluon plasma, the interaction potential experiences medium effects. Color screening modifies the attractive binding force between the quarks, while the increase of entropy with separation gives rise to a growing repulsion. We study the role of these phenomena for in-medium binding and dissociation. It is found that the relevant potential for binding is the free energy ; with increasing separation, further binding through the internal energy is compensated by repulsive entropic effects.

  12. Remote detection of forest damage

    NASA Technical Reports Server (NTRS)

    Rock, B. N.; Vogelmann, J. E.; Vogelmann, A. F.; Hoshizaki, T.; Williams, D. L.

    1986-01-01

    The use of remote sensing to discriminate, measure, and map forest damage is evaluated. TM spectal coverage, a helicopter-mounted radiometer, and ground-based surveys were utilized to examine the responses of the spruces and firs of Camels Hump Mountain, Vermont to stresses, such as pollution and trace metals. The basic spectral properties of vegetation are described. Forest damage at the site was estimated as 11.8-76.0 percent for the spruces and 19-43.8 percent for the balsam firs. Shifts in the spectra of the conifers in particular in the near IR region are analyzed, and variations in the mesophyll cell anatomy and pigment content of the spruces and firs are investigated. The relations between canopy moisture and damage is studied. The TM data are compared to aircraft data and found to be well correlated.

  13. A fiber optic damage monitor

    NASA Astrophysics Data System (ADS)

    Jen, C. K.; Cielo, P.; Farnell, G. W.; Parker, M.

    A simplified fiber-optic damage monitoring system for on-line assessments of the condition of composite structural materials in F/A-18 fighters is described. Optical fibers are implanted into the composite mesh in a configuration with horizontal and vertical orientations. When light is pumped into the fibers, and failure of transmittance in either the x- or y-coordinates indicates the location of a defect at that coordinate, as revealed by the fiber damage. Attaching photodiodes to the optic fibers and connecting the entire system to a video camera and computer permits on-line monitoring of the mesh-holding panels. Sample results are provided from a system with multimode step index fibers, a VAX 11/780 computer and a video camera with a 488 x 380 cell photodiode array. Image subtraction is an effective means for fast determination of the identities of broken fibers by comparisons of images of arrays of original and damaged fibers.

  14. Autophagy Induced by Calcium Phosphate Precipitates Targets Damaged Endosomes*

    PubMed Central

    Chen, Xi; Khambu, Bilon; Zhang, Hao; Gao, Wentao; Li, Min; Chen, Xiaoyun; Yoshimori, Tamotsu; Yin, Xiao-Ming

    2014-01-01

    Calcium phosphate precipitates (CPPs) form complexes with DNA, which enter cells via endocytosis. Under this condition CPPs induce autophagy via the canonic autophagy machinery. Here we showed that CPP-induced autophagy was also dependent on endocytosis as the process was significantly inhibited by methyl-β-cyclodextrin and dynasore, which suppress clathrin-dependent endocytosis. Consistently, CPP treatment triggered the formation of filipin-positive intracellular vesicles whose membranes are rich in cholesterol. Unexpectedly, these vesicles were also positive for galectin 3, suggesting that they were damaged and the membrane glycans became accessible to galectins to bind. Endosome damage was caused by endocytosis of CPPs and was reversed by calcium chelators or by endocytosis inhibitors. Notably, CPP-induced LC3-positive autophagosomes were colocalized with galectin 3, ubiquitin, and p62/SQSTM1. Inhibition of galectin 3 reduced p62 puncta and autophagosome formation. Knockdown of p62 additionally inhibited the colocalization of autophagosomes with galectins. Furthermore, most of the galectin 3-positive vesicles were colocalized with Rab7 or LAMP1. Agents that affect endosome/lysosome maturation and function, such as bafilomycin A1, also significantly affected CPP-induced tubulovesicular autophagosome formation. These findings thus indicate that endocytosed CPPs caused endosome damage and recruitment of galectins, particularly at the later endosome stage, which led to the interaction of the autophagosomal membranes with the damaged endosome in the presence of p62. PMID:24619419

  15. NBQX and TCP prevent soman-induced hippocampal damage

    SciTech Connect

    Lallement, G.; Carpentier, P.; Pernot-Marino, I.; Baubichon, D.; Blanchet, G.

    1993-05-13

    In a previous investigation we demonstrated that the measurement of w3 (peripheral-type benzodiazepine) binding site densities could be of widespread applicability in the localization and quantification of soman-induced damage in the central nervous system. We thus used this marker to assess, in mouse hippocampus, the neuroprotective activity against soman-induced brain damage of NBQX and TCP which are respective antagonists of non-NMDA and NMDA glutamatergic receptors. Injection of NBQX at 20 or 40 mg/kg 5 min prior to soman totally prevented the neuronal damage. Comparatively, TCP had neuroprotective efficacy when administered at l mg/kg 5 min prior to soman followed by a reinjection 1 hour after. These results demonstrate that both NBQX and TCP afford a satisfactory neuroprotection against soman-induced brain damage. Since it is known that the neuropathology due to soman is closely seizure-related, it is likely that the neuroprotective activities of NBQX and TCP are related to the respective roles of non-NMDA and NMDA receptors in the onset and maintenance of soman-induced seizures.

  16. Identification of consensus binding sites clarifies FMRP binding determinants.

    PubMed

    Anderson, Bart R; Chopra, Pankaj; Suhl, Joshua A; Warren, Stephen T; Bassell, Gary J

    2016-08-19

    Fragile X mental retardation protein (FMRP) is a multifunctional RNA-binding protein with crucial roles in neuronal development and function. Efforts aimed at elucidating how FMRP target mRNAs are selected have produced divergent sets of target mRNA and putative FMRP-bound motifs, and a clear understanding of FMRP's binding determinants has been lacking. To clarify FMRP's binding to its target mRNAs, we produced a shared dataset of FMRP consensus binding sequences (FCBS), which were reproducibly identified in two published FMRP CLIP sequencing datasets. This comparative dataset revealed that of the various sequence and structural motifs that have been proposed to specify FMRP binding, the short sequence motifs TGGA and GAC were corroborated, and a novel TAY motif was identified. In addition, the distribution of the FCBS set demonstrates that FMRP preferentially binds to the coding region of its targets but also revealed binding along 3' UTRs in a subset of target mRNAs. Beyond probing these putative motifs, the FCBS dataset of reproducibly identified FMRP binding sites is a valuable tool for investigating FMRP targets and function. PMID:27378784

  17. The CATDAT damaging earthquakes database

    NASA Astrophysics Data System (ADS)

    Daniell, J. E.; Khazai, B.; Wenzel, F.; Vervaeck, A.

    2011-08-01

    The global CATDAT damaging earthquakes and secondary effects (tsunami, fire, landslides, liquefaction and fault rupture) database was developed to validate, remove discrepancies, and expand greatly upon existing global databases; and to better understand the trends in vulnerability, exposure, and possible future impacts of such historic earthquakes. Lack of consistency and errors in other earthquake loss databases frequently cited and used in analyses was a major shortcoming in the view of the authors which needed to be improved upon. Over 17 000 sources of information have been utilised, primarily in the last few years, to present data from over 12 200 damaging earthquakes historically, with over 7000 earthquakes since 1900 examined and validated before insertion into the database. Each validated earthquake includes seismological information, building damage, ranges of social losses to account for varying sources (deaths, injuries, homeless, and affected), and economic losses (direct, indirect, aid, and insured). Globally, a slightly increasing trend in economic damage due to earthquakes is not consistent with the greatly increasing exposure. The 1923 Great Kanto (214 billion USD damage; 2011 HNDECI-adjusted dollars) compared to the 2011 Tohoku (>300 billion USD at time of writing), 2008 Sichuan and 1995 Kobe earthquakes show the increasing concern for economic loss in urban areas as the trend should be expected to increase. Many economic and social loss values not reported in existing databases have been collected. Historical GDP (Gross Domestic Product), exchange rate, wage information, population, HDI (Human Development Index), and insurance information have been collected globally to form comparisons. This catalogue is the largest known cross-checked global historic damaging earthquake database and should have far-reaching consequences for earthquake loss estimation, socio-economic analysis, and the global reinsurance field.

  18. Reversible calcitonin binding to solubilized sheep brain binding sites.

    PubMed Central

    Sexton, P M; Schneider, H G; D'Santos, C S; Mendelsohn, F A; Kemp, B E; Moseley, J M; Martin, T J; Findlay, D M

    1991-01-01

    In this study we have solubilized and characterized binding sites for calcitonin (CT) from sheep brainstem. Autoradiography of 125I-labelled salmon CT (125I-sCT) binding to sheep diencephalon revealed a similar pattern of binding to that seen in other species, although the extent of distribution was greater in the sheep. CT binding activity could be extracted from membranes with either CHAPS or digitonin, but not with beta-octyl glucoside, 125I-sCT binding was saturable, with a dissociation constant for CHAPS-solubilized membranes of 2.8 +/- 0.5 nM and a maximum binding site concentration of 6.2 +/- 1.6 pmol/mg of protein. In competition binding studies, various CTs and their analogues demonstrated a similar rank order of potency to that seen in other CT receptor systems, Optimal binding occurred in the pH range 6.5-7.5, and was decreased in the presence of NaCl concentrations greater than 200 mM. In contrast with most other CT receptor binding systems, in which binding is poorly reversible, the binding of 125I-sCT to sheep brain binding sites underwent substantial dissociation upon addition of excess unlabelled sCT, with 40% and 46% dissociation after 2 h at 4 degree C in particulate and solubilized membranes respectively. Photoaffinity labelling of the binding site with the biologically active analogue 125I-[Arg11,18,4-azidobenzoyl-Lys14]sCT and analysis on SDS/PAGE under reducing conditions revealed a specific protein band of Mr approximately solubilized and particulate brain membranes. This is in accordance with the molecular size of CT receptors in other tissues where two species of receptor have been identified. one of Mr approximately 71,000 and another of Mr approximately 88,000. These results demonstrate the presence of high concentrations of CT binding sites in sheep brain which display different kinetic properties to those of CT receptors found in other tissues. Images Fig. 1. Fig. 6. PMID:1846527

  19. Damage kinetics in silicon carbide

    NASA Astrophysics Data System (ADS)

    Pickup, I. M.; Barker, A. K.

    1998-07-01

    Three silicon carbides of similar density and grain size but manufactured via different routes (reaction bonded, pressureless sintered and pressure assisted densification) have been investigated. High speed photography in conjunction with Hopkinson pressure bar compression tests has revealed that not only does the manufacturing route confer a significant difference in failure kinetics but also modifies the phenomenology of failure. Plate impact experiments using lateral and longitudinal manganin stress gauges have been used to study shear strength behaviour of damaged material. Failure waves have been observed in all three materials and characteristically different damaged material shear strength relationships with pressure have been observed.

  20. 7 CFR 51.2129 - Serious damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Serious damage. 51.2129 Section 51.2129 Agriculture... Serious damage. Serious damage means any defect which makes a kernel or piece of kernel unsuitable for human consumption, and includes decay, rancidity, insect injury and damage by mold....

  1. 7 CFR 51.2129 - Serious damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Serious damage. 51.2129 Section 51.2129 Agriculture... Standards for Grades of Shelled Almonds Definitions § 51.2129 Serious damage. Serious damage means any..., rancidity, insect injury and damage by mold....

  2. 7 CFR 51.2129 - Serious damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Serious damage. 51.2129 Section 51.2129 Agriculture... Standards for Grades of Shelled Almonds Definitions § 51.2129 Serious damage. Serious damage means any..., rancidity, insect injury and damage by mold....

  3. 47 CFR 1.722 - Damages.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Damages. 1.722 Section 1.722 Telecommunication... Reports Involving Common Carriers Formal Complaints § 1.722 Damages. (a) If a complainant wishes to recover damages, the complaint must contain a clear and unequivocal request for damages. (b) If...

  4. 7 CFR 51.2293 - Serious damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Serious damage. 51.2293 Section 51.2293 Agriculture... Standards for Shelled English Walnuts (Juglans Regia) Definitions § 51.2293 Serious damage. Serious damage... shall be considered as serious damage: (a) Shriveling when more than one-fourth of the kernel...

  5. 7 CFR 51.2739 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Damage. 51.2739 Section 51.2739 Agriculture... Standards for Grades of Shelled Spanish Type Peanuts Definitions § 51.2739 Damage. Damage means any specific... damage: (a) Rancidity or decay; (b) Mold; (c) Insects, worm cuts, web or frass; (d) Freezing...

  6. 32 CFR 750.33 - Damages.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 5 2013-07-01 2013-07-01 false Damages. 750.33 Section 750.33 National Defense... Claims Act § 750.33 Damages. (a) Generally. The measure of damages is determined by the law of the place... for interest prior to judgment or for punitive damages. In a death case, if the place where the act...

  7. 7 CFR 51.2292 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Damage. 51.2292 Section 51.2292 Agriculture... Standards for Shelled English Walnuts (Juglans Regia) Definitions § 51.2292 Damage. Damage means any defect... considered as damage: (a) Shriveling when more than one-eighth of the portion of kernel is severely...

  8. 47 CFR 1.722 - Damages.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 1 2014-10-01 2014-10-01 false Damages. 1.722 Section 1.722 Telecommunication... Reports Involving Common Carriers Formal Complaints § 1.722 Damages. (a) If a complainant wishes to recover damages, the complaint must contain a clear and unequivocal request for damages. (b) If...

  9. 7 CFR 51.1583 - Damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Damage. 51.1583 Section 51.1583 Agriculture..., CERTIFICATION, AND STANDARDS) United States Consumer Standards for Potatoes Definitions § 51.1583 Damage. Damage... defective area. Loss of outer skin (epidermis) shall not be considered as damage when the potatoes...

  10. 7 CFR 51.1449 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Damage. 51.1449 Section 51.1449 Agriculture... Standards for Grades of Shelled Pecans Definitions § 51.1449 Damage. Damage means any specific defect... should be considered as damage: (a) Adhering material from inside the shell when attached to more...

  11. 7 CFR 51.1449 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Damage. 51.1449 Section 51.1449 Agriculture... Standards for Grades of Shelled Pecans Definitions § 51.1449 Damage. Damage means any specific defect... should be considered as damage: (a) Adhering material from inside the shell when attached to more...

  12. 7 CFR 51.1583 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Damage. 51.1583 Section 51.1583 Agriculture... Consumer Standards for Potatoes Definitions § 51.1583 Damage. Damage means any injury or defect which... (epidermis) shall not be considered as damage when the potatoes are designated as “Early” unless the...

  13. 7 CFR 51.1241 - Damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Damage. 51.1241 Section 51.1241 Agriculture... § 51.1241 Damage. Damage means any injury or defect which materially affects the appearance edible or... damage: (a) Cracked or broken shells which have been broken to the extent that the kernel within...

  14. 7 CFR 51.2090 - Serious damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Serious damage. 51.2090 Section 51.2090 Agriculture... Serious damage. Serious damage means any defect which makes a kernel or piece of kernel unsuitable for human consumption, and includes decay, rancidity, insect injury and damage by mold. The following...

  15. 7 CFR 51.1241 - Damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Damage. 51.1241 Section 51.1241 Agriculture... § 51.1241 Damage. Damage means any injury or defect which materially affects the appearance edible or... damage: (a) Cracked or broken shells which have been broken to the extent that the kernel within...

  16. 32 CFR 750.33 - Damages.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 5 2011-07-01 2011-07-01 false Damages. 750.33 Section 750.33 National Defense... Claims Act § 750.33 Damages. (a) Generally. The measure of damages is determined by the law of the place... for interest prior to judgment or for punitive damages. In a death case, if the place where the act...

  17. 7 CFR 51.2293 - Serious damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Serious damage. 51.2293 Section 51.2293 Agriculture... § 51.2293 Serious damage. Serious damage means any defect, other than color, which seriously affects... exceeds the maximum allowed for any one defect shall be considered as serious damage: (a) Shriveling...

  18. 7 CFR 51.2090 - Serious damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Serious damage. 51.2090 Section 51.2090 Agriculture... Standards for Grades of Almonds in the Shell Definitions § 51.2090 Serious damage. Serious damage means any..., rancidity, insect injury and damage by mold. The following defect shall be considered as serious...

  19. 7 CFR 51.2292 - Damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Damage. 51.2292 Section 51.2292 Agriculture... § 51.2292 Damage. Damage means any defect, other than color, which materially affects the appearance... maximum allowed for any one defect shall be considered as damage: (a) Shriveling when more than...

  20. 7 CFR 51.1586 - Serious damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Serious damage. 51.1586 Section 51.1586 Agriculture... Consumer Standards for Potatoes Definitions § 51.1586 Serious damage. Serious damage means any injury or... maximum allowed for any one defect shall be considered as serious damage: (a) Fairly smooth cuts such...

  1. 47 CFR 1.722 - Damages.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 1 2013-10-01 2013-10-01 false Damages. 1.722 Section 1.722 Telecommunication... Reports Involving Common Carriers Formal Complaints § 1.722 Damages. (a) If a complainant wishes to recover damages, the complaint must contain a clear and unequivocal request for damages. (b) If...

  2. 32 CFR 750.33 - Damages.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 5 2012-07-01 2012-07-01 false Damages. 750.33 Section 750.33 National Defense... Claims Act § 750.33 Damages. (a) Generally. The measure of damages is determined by the law of the place... for interest prior to judgment or for punitive damages. In a death case, if the place where the act...

  3. 47 CFR 1.722 - Damages.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 1 2012-10-01 2012-10-01 false Damages. 1.722 Section 1.722 Telecommunication... Reports Involving Common Carriers Formal Complaints § 1.722 Damages. (a) If a complainant wishes to recover damages, the complaint must contain a clear and unequivocal request for damages. (b) If...

  4. 7 CFR 51.1583 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Damage. 51.1583 Section 51.1583 Agriculture... Consumer Standards for Potatoes Definitions § 51.1583 Damage. Damage means any injury or defect which... (epidermis) shall not be considered as damage when the potatoes are designated as “Early” unless the...

  5. 7 CFR 51.2003 - Damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Damage. 51.2003 Section 51.2003 Agriculture....2003 Damage. Damage means any specific defect described in this section; or an equally objectionable... defects shall be considered as damage: (a) Stains which are dark and materially affect the appearance...

  6. 7 CFR 51.2090 - Serious damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Serious damage. 51.2090 Section 51.2090 Agriculture... Standards for Grades of Almonds in the Shell Definitions § 51.2090 Serious damage. Serious damage means any..., rancidity, insect injury and damage by mold. The following defect shall be considered as serious...

  7. 47 CFR 1.722 - Damages.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 1 2011-10-01 2011-10-01 false Damages. 1.722 Section 1.722 Telecommunication... Reports Involving Common Carriers Formal Complaints § 1.722 Damages. (a) If a complainant wishes to recover damages, the complaint must contain a clear and unequivocal request for damages. (b) If...

  8. 32 CFR 750.33 - Damages.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 5 2014-07-01 2014-07-01 false Damages. 750.33 Section 750.33 National Defense... Claims Act § 750.33 Damages. (a) Generally. The measure of damages is determined by the law of the place... for interest prior to judgment or for punitive damages. In a death case, if the place where the act...

  9. 7 CFR 51.2129 - Serious damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Serious damage. 51.2129 Section 51.2129 Agriculture... Serious damage. Serious damage means any defect which makes a kernel or piece of kernel unsuitable for human consumption, and includes decay, rancidity, insect injury and damage by mold....

  10. 7 CFR 51.2292 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Damage. 51.2292 Section 51.2292 Agriculture... Standards for Shelled English Walnuts (Juglans Regia) Definitions § 51.2292 Damage. Damage means any defect... considered as damage: (a) Shriveling when more than one-eighth of the portion of kernel is severely...

  11. 7 CFR 51.1586 - Serious damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Serious damage. 51.1586 Section 51.1586 Agriculture... Consumer Standards for Potatoes Definitions § 51.1586 Serious damage. Serious damage means any injury or... maximum allowed for any one defect shall be considered as serious damage: (a) Fairly smooth cuts such...

  12. 7 CFR 51.2090 - Serious damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Serious damage. 51.2090 Section 51.2090 Agriculture... Serious damage. Serious damage means any defect which makes a kernel or piece of kernel unsuitable for human consumption, and includes decay, rancidity, insect injury and damage by mold. The following...

  13. 32 CFR 750.33 - Damages.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 5 2010-07-01 2010-07-01 false Damages. 750.33 Section 750.33 National Defense... Claims Act § 750.33 Damages. (a) Generally. The measure of damages is determined by the law of the place... for interest prior to judgment or for punitive damages. In a death case, if the place where the act...

  14. 7 CFR 51.2293 - Serious damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Serious damage. 51.2293 Section 51.2293 Agriculture... Standards for Shelled English Walnuts (Juglans Regia) Definitions § 51.2293 Serious damage. Serious damage... shall be considered as serious damage: (a) Shriveling when more than one-fourth of the kernel...

  15. 7 CFR 51.2090 - Serious damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Serious damage. 51.2090 Section 51.2090 Agriculture... Standards for Grades of Almonds in the Shell Definitions § 51.2090 Serious damage. Serious damage means any..., rancidity, insect injury and damage by mold. The following defect shall be considered as serious...

  16. 7 CFR 51.2960 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.2960 Section 51.2960 Agriculture... Standards for Grades of Walnuts in the Shell Definitions § 51.2960 Damage. Damage means any specific defect... considered as damage: (a) Broken shells when the area from which a portion of the shell is missing is...

  17. 7 CFR 51.1583 - Damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Damage. 51.1583 Section 51.1583 Agriculture..., CERTIFICATION, AND STANDARDS) United States Consumer Standards for Potatoes Definitions § 51.1583 Damage. Damage... defective area. Loss of outer skin (epidermis) shall not be considered as damage when the potatoes...

  18. Lamin A/C-dependent interaction with 53BP1 promotes cellular responses to DNA damage

    PubMed Central

    Gibbs-Seymour, Ian; Markiewicz, Ewa; Bekker-Jensen, Simon; Mailand, Niels; Hutchison, Christopher J

    2015-01-01

    Lamins A/C have been implicated in DNA damage response pathways. We show that the DNA repair protein 53BP1 is a lamin A/C binding protein. In undamaged human dermal fibroblasts (HDF), 53BP1 is a nucleoskeleton protein. 53BP1 binds to lamins A/C via its Tudor domain, and this is abrogated by DNA damage. Lamins A/C regulate 53BP1 levels and consequently lamin A/C-null HDF display a 53BP1 null-like phenotype. Our data favour a model in which lamins A/C maintain a nucleoplasmic pool of 53BP1 in order to facilitate its rapid recruitment to sites of DNA damage and could explain why an absence of lamin A/C accelerates aging. PMID:25645366

  19. Cisplatin-resistant cells express increased levels of a factor that recognizes damaged DNA

    SciTech Connect

    Chu, G.; Chang, E. )

    1990-05-01

    Cancer treatment with the drug cisplatin is often thwarted by the emergence of drug-resistant cells. To study this phenomenon, the authors identified two independent cellular factors that recognize cisplatin-damaged DNA. One of the two factors, designated XPE binding factor, is deficient in complementation group E of xeroderma pigmentosum, an inherited disease characterized by defective repair of DNA damaged by ultraviolet radiation, cisplatin, and other agents. Human tumor cell lines selected for resistance to cisplatin showed more efficient DNA repair and increased expression of XPE binding factor. These results suggest that XPE binding factor may be responsible, at least in part, for the development of cisplatin resistance in human tumors and that the mechanism may be increased DNA repair.

  20. Certification of damage tolerant composite structure

    NASA Technical Reports Server (NTRS)

    Rapoff, Andrew J.; Dill, Harold D.; Sanger, Kenneth B.; Kautz, Edward F.

    1990-01-01

    A reliability based certification testing methodology for impact damage tolerant composite structure was developed. Cocured, adhesively bonded, and impact damaged composite static strength and fatigue life data were statistically analyzed to determine the influence of test parameters on the data scatter. The impact damage resistance and damage tolerance of various structural configurations were characterized through the analysis of an industry wide database of impact test results. Realistic impact damage certification requirements were proposed based on actual fleet aircraft data. The capabilities of available impact damage analysis methods were determined through correlation with experimental data. Probabilistic methods were developed to estimate the reliability of impact damaged composite structures.

  1. Reprogramming cellular events by poly(ADP-ribose)-binding proteins

    PubMed Central

    Pic, Émilie; Ethier, Chantal; Dawson, Ted M.; Dawson, Valina L.; Masson, Jean-Yves; Poirier, Guy G.; Gagné, Jean-Philippe

    2013-01-01

    Poly(ADP-ribosyl)ation is a posttranslational modification catalyzed by the poly(ADP-ribose) polymerases (PARPs). These enzymes covalently modify glutamic, aspartic and lysine amino acid side chains of acceptor proteins by the sequential addition of ADP-ribose (ADPr) units. The poly(ADP-ribose) (pADPr) polymers formed alter the physico-chemical characteristics of the substrate with functional consequences on its biological activities. Recently, non-covalent binding to pADPr has emerged as a key mechanism to modulate and coordinate several intracellular pathways including the DNA damage response, protein stability and cell death. In this review, we describe the basis of non-covalent binding to pADPr that has led to the emerging concept of pADPr-responsive signaling pathways. This review emphasizes the structural elements and the modular strategies developed by pADPr-binding proteins to exert a fine-tuned control of a variety of pathways. Poly(ADP-ribosyl)ation reactions are highly regulated processes, both spatially and temporally, for which at least four specialized pADPr-binding modules accommodate different pADPr structures and reprogram protein functions. In this review, we highlight the role of well-characterized and newly discovered pADPr-binding modules in a diverse set of physiological functions. PMID:23268355

  2. Binding Energy and Enzymatic Catalysis.

    ERIC Educational Resources Information Center

    Hansen, David E.; Raines, Ronald T.

    1990-01-01

    Discussed is the fundamental role that the favorable free energy of binding of the rate-determining transition state plays in catalysis. The principle that all of the catalytic factors discussed are realized by the use of this binding energy is reviewed. (CW)

  3. How Serious Is the Damage?

    ERIC Educational Resources Information Center

    Ellis, John M.

    2007-01-01

    When surveys of faculty tell everyone that politically right-of-center voices are now much reduced or even in certain areas largely absent, people can be sure that the academy is damaged in at least one respect: the campus political and social climate will be unrealistic. Programs where this is central, such as political science and sociology,…

  4. Sulfur Dioxide and Material Damage

    ERIC Educational Resources Information Center

    Gillette, Donald G.

    1975-01-01

    This study relates sulfur dioxide levels with material damage in heavily populated or polluted areas. Estimates of loss were determined from increased maintenance and replacement costs. The data indicate a decrease in losses during the past five years probably due to decline in pollution levels established by air quality standards. (MR)

  5. Compensation for oil pollution damage

    NASA Astrophysics Data System (ADS)

    Matugina, E. G.; Glyzina, T. S.; Kolbysheva, Yu V.; Klyuchnikov, A. S.; Vusovich, O. V.

    2015-11-01

    The commitment of national industries to traditional energy sources, as well as constantly growing energy demand combined with adverse environmental impact of petroleum production and transportation urge to establish and maintain an appropriate legal and administrative framework for oil pollution damage compensation. The article considers management strategies for petroleum companies that embrace not only production benefits but also environmental issues.

  6. Cholinergic influences on feature binding.

    PubMed

    Botly, Leigh C P; De Rosa, Eve

    2007-04-01

    The binding problem refers to the fundamental challenge of the central nervous system to integrate sensory information registered by multiple brain regions to form a unified neural representation of a stimulus. Human behavioral, neuropsychological, and functional neuroimaging evidence suggests a fundamental role for attention in feature binding; however, its neurochemical basis is currently unknown. This study examined whether acetylcholine (ACh), a neuromodulator that has been implicated in attentional processes, plays a critical role in feature binding. Using a within-subjects pharmacological design and the cholinergic muscarinic antagonist scopolamine, the present experiments demonstrate, in a rat model, a critical role for the cortical muscarinic cholinergic system in feature binding. Specifically, ACh and the attentional resources that it supports are essential for the initial feature binding process but are not required to maintain neural representations of bound stimuli. PMID:17469916

  7. Identification of Cell-Binding Adhesins of Leptospira interrogans

    PubMed Central

    Evangelista, Karen V.; Hahn, Beth; Wunder, Elsio A.; Ko, Albert I.; Haake, David A.; Coburn, Jenifer

    2014-01-01

    Leptospirosis is a globally distributed bacterial infectious disease caused by pathogenic members of the genus Leptospira. Infection can lead to illness ranging from mild and non-specific to severe, with jaundice, kidney and liver dysfunction, and widespread endothelial damage. The adhesion of pathogenic Leptospira species (spp.), the causative agent of leptospirosis, to host tissue components is necessary for infection and pathogenesis. While it is well-established that extracellular matrix (ECM) components play a role in the interaction of the pathogen with host molecules, we have shown that pathogenic Leptospira interrogans binds to host cells more efficiently than to ECM components. Using in vitro phage display to select for phage clones that bind to EA.hy926 endothelial cells, we identified the putative lipoproteins LIC10508 and LIC13411, and the conserved hypothetical proteins LIC12341 and LIC11574, as candidate L. interrogans sv. Copenhageni st. Fiocruz L1–130 adhesins. Recombinant LIC11574, but not its L. biflexa homologue LBF1629, exhibited dose-dependent binding to both endothelial and epithelial cells. In addition, LIC11574 and LIC13411 bind to VE-cadherin, an endothelial cell receptor for L. interrogans. Extraction of bacteria with the non-ionic detergent Triton X-114 resulted in partitioning of the candidate adhesins to the detergent fraction, a likely indication that these proteins are outer membrane localized. All candidate adhesins were recognized by sera obtained from leptospirosis patients but not by sera from healthy individuals as assessed by western blot. This work has identified bacterial adhesins that are potentially involved in L. interrogans infection of the mammalian host, and through cadherin binding, may contribute to dissemination and vascular damage. Our findings may be of value in leptospirosis control and prevention, with the bacterial adhesins potentially serving as targets for development of diagnostics, therapeutics, and

  8. The PIN domain of EXO1 recognizes poly(ADP-ribose) in DNA damage response.

    PubMed

    Zhang, Feng; Shi, Jiazhong; Chen, Shih-Hsun; Bian, Chunjing; Yu, Xiaochun

    2015-12-15

    Following DNA double-strand breaks, poly(ADP-ribose) (PAR) is quickly and heavily synthesized to mediate fast and early recruitment of a number of DNA damage response factors to the sites of DNA lesions and facilitates DNA damage repair. Here, we found that EXO1, an exonuclease for DNA damage repair, is quickly recruited to the sites of DNA damage via PAR-binding. With further dissection of the functional domains of EXO1, we report that the PIN domain of EXO1 recognizes PAR both in vitro and in vivo and the interaction between the PIN domain and PAR is sufficient for the recruitment. We also found that the R93G variant of EXO1, generated by a single nucleotide polymorphism, abolishes the interaction and the early recruitment. Moreover, our study suggests that the PAR-mediated fast recruitment of EXO1 facilities early DNA end resection, the first step of homologous recombination repair. We observed that other PIN domains could also recognize DNA damage-induced PAR. Taken together, our study demonstrates a novel class of PAR-binding module that plays an important role in DNA damage response. PMID:26400172

  9. The PIN domain of EXO1 recognizes poly(ADP-ribose) in DNA damage response

    PubMed Central

    Zhang, Feng; Shi, Jiazhong; Chen, Shih-Hsun; Bian, Chunjing; Yu, Xiaochun

    2015-01-01

    Following DNA double-strand breaks, poly(ADP-ribose) (PAR) is quickly and heavily synthesized to mediate fast and early recruitment of a number of DNA damage response factors to the sites of DNA lesions and facilitates DNA damage repair. Here, we found that EXO1, an exonuclease for DNA damage repair, is quickly recruited to the sites of DNA damage via PAR-binding. With further dissection of the functional domains of EXO1, we report that the PIN domain of EXO1 recognizes PAR both in vitro and in vivo and the interaction between the PIN domain and PAR is sufficient for the recruitment. We also found that the R93G variant of EXO1, generated by a single nucleotide polymorphism, abolishes the interaction and the early recruitment. Moreover, our study suggests that the PAR-mediated fast recruitment of EXO1 facilities early DNA end resection, the first step of homologous recombination repair. We observed that other PIN domains could also recognize DNA damage-induced PAR. Taken together, our study demonstrates a novel class of PAR-binding module that plays an important role in DNA damage response. PMID:26400172

  10. Plate tectonics, damage and inheritance.

    PubMed

    Bercovici, David; Ricard, Yanick

    2014-04-24

    The initiation of plate tectonics on Earth is a critical event in our planet's history. The time lag between the first proto-subduction (about 4 billion years ago) and global tectonics (approximately 3 billion years ago) suggests that plates and plate boundaries became widespread over a period of 1 billion years. The reason for this time lag is unknown but fundamental to understanding the origin of plate tectonics. Here we suggest that when sufficient lithospheric damage (which promotes shear localization and long-lived weak zones) combines with transient mantle flow and migrating proto-subduction, it leads to the accumulation of weak plate boundaries and eventually to fully formed tectonic plates driven by subduction alone. We simulate this process using a grain evolution and damage mechanism with a composite rheology (which is compatible with field and laboratory observations of polycrystalline rocks), coupled to an idealized model of pressure-driven lithospheric flow in which a low-pressure zone is equivalent to the suction of convective downwellings. In the simplest case, for Earth-like conditions, a few successive rotations of the driving pressure field yield relic damaged weak zones that are inherited by the lithospheric flow to form a nearly perfect plate, with passive spreading and strike-slip margins that persist and localize further, even though flow is driven only by subduction. But for hotter surface conditions, such as those on Venus, accumulation and inheritance of damage is negligible; hence only subduction zones survive and plate tectonics does not spread, which corresponds to observations. After plates have developed, continued changes in driving forces, combined with inherited damage and weak zones, promote increased tectonic complexity, such as oblique subduction, strike-slip boundaries that are subparallel to plate motion, and spalling of minor plates. PMID:24717430

  11. Peptidase activity of beta-lactamases.

    PubMed Central

    Rhazi, N; Galleni, M; Page, M I; Frère, J M

    1999-01-01

    Although beta-lactamases have generally been considered as being devoid of peptidase activity, a low but significant hydrolysis of various N-acylated dipeptides was observed with representatives of each class of beta-lactamases. The kcat/Km values were below 0.1 M(-1). s(-1), but the enzyme rate enhancement factors were in the range 5000-20000 for the best substrates. Not unexpectedly, the best 'peptidase' was the class C beta-lactamase of Enterobacter cloacae P99, but, more surprisingly, the activity was always higher with the phenylacetyl- and benzoyl-d-Ala-d-Ala dipeptides than with the diacetyl- and alpha-acetyl-l-Lys-d-Ala-d-Ala tripeptides, which are the preferred substrates of the low-molecular-mass, soluble dd-peptidases. A comparison between the beta-lactamases and dd-peptidases showed that it might be as difficult for a dd-peptidase to open the beta-lactam ring as it is for the beta-lactamases to hydrolyse the peptides, an observation which can be explained by geometric and stereoelectronic considerations. PMID:10393100

  12. Moss Chloroplasts Are Surrounded by a Peptidoglycan Wall Containing D-Amino Acids[OPEN

    PubMed Central

    Hirano, Takayuki; Tanidokoro, Koji; Shimizu, Yasuhiro; Kawarabayasi, Yutaka; Ohshima, Toshihisa; Sato, Momo; Tadano, Shinji; Ishikawa, Hayato; Takio, Susumu; Takechi, Katsuaki; Takano, Hiroyoshi

    2016-01-01

    It is believed that the plastids in green plants lost peptidoglycan (i.e., a bacterial cell wall-containing d-amino acids) during their evolution from an endosymbiotic cyanobacterium. Although wall-like structures could not be detected in the plastids of green plants, the moss Physcomitrella patens has the genes required to generate peptidoglycan (Mur genes), and knocking out these genes causes defects in chloroplast division. Here, we generated P. patens knockout lines (∆Pp-ddl) for a homolog of the bacterial peptidoglycan-synthetic gene encoding d-Ala:d-Ala ligase. ∆Pp-ddl had a macrochloroplast phenotype, similar to other Mur knockout lines. The addition of d-Ala-d-Ala (DA-DA) to the medium suppressed the appearance of giant chloroplasts in ∆Pp-ddl, but the addition of l-Ala-l-Ala (LA-LA), DA-LA, LA-DA, or d-Ala did not. Recently, a metabolic method for labeling bacterial peptidoglycan was established using ethynyl-DA-DA (EDA-DA) and click chemistry to attach an azide-modified fluorophore to the ethynyl group. The ∆Pp-ddl line complemented with EDA-DA showed that moss chloroplasts are completely surrounded by peptidoglycan. Our findings strongly suggest that the moss plastids have a peptidoglycan wall containing d-amino acids. By contrast, no plastid phenotypes were observed in the T-DNA tagged ddl mutant lines of Arabidopsis thaliana. PMID:27325639

  13. Expression Profile of DNA Damage Signaling Genes in Proton Exposed Mouse Brain

    NASA Astrophysics Data System (ADS)

    Ramesh, Govindarajan; Wu, Honglu

    Exposure of living systems to radiation results in a wide assortment of lesions, the most signif-icant of is damage to genomic DNA which induce several cellular functions such as cell cycle arrest, repair, apoptosis etc. The radiation induced DNA damage investigation is one of the im-portant area in biology, but still the information available regarding the effects of proton is very limited. In this report, we investigated the differential gene expression pattern of DNA damage signaling genes particularly, damaged DNA binding, repair, cell cycle arrest, checkpoints and apoptosis using quantitative real-time RT-PCR array in proton exposed mouse brain tissues. The expression profiles showed significant changes in DNA damage related genes in 2Gy proton exposed mouse brain tissues as compared with control brain tissues. Furthermore, we also show that significantly increased levels of apoptotic related genes, caspase-3 and 8 activities in these cells, suggesting that in addition to differential expression of DNA damage genes, the alteration of apoptosis related genes may also contribute to the radiation induced DNA damage followed by programmed cell death. In summary, our findings suggest that proton exposed brain tissue undergo severe DNA damage which in turn destabilize the chromatin stability.

  14. New hopes from old drugs: revisiting DNA-binding small molecules as anticancer agents

    PubMed Central

    Gurova, Katerina

    2010-01-01

    Most of the anticancer chemotherapeutic drugs that are broadly and successfully used today are DNA-damaging agents. Targeting of DNA has been proven to cause relatively potent and selective destruction of tumor cells. However, the clinical potential of DNA-damaging agents is limited by the adverse side effects and increased risk of secondary cancers that are consequences of the agents' genotoxicity. In this review, we present evidence that those agents capable of targeting DNA without inducing DNA damage would not be limited in these ways, and may be as potent as DNA-damaging agents in the killing of tumor cells. We use as an example literature data and our own research of the well-known antimalarial drug quinacrine, which binds to DNA without inducing DNA damage, yet modulates a number of cellular pathways that impact tumor cell survival. PMID:20001804

  15. Functional Analysis of p53 Binding under Differential Stresses†

    PubMed Central

    Krieg, Adam J.; Hammond, Ester M.; Giaccia, Amato J.

    2006-01-01

    Hypoxia and DNA damage stabilize the p53 protein, but the subsequent effect that each stress has on transcriptional regulation of known p53 target genes is variable. We have used chromatin immunoprecipitation followed by CpG island (CGI) microarray hybridization to identify promoters bound by p53 under both DNA-damaging and non-DNA-damaging conditions in HCT116 cells. Using gene-specific PCR analysis, we have verified an association with CGIs of the highest enrichment (>2.5-fold) (REV3L, XPMC2H, HNRPUL1, TOR1AIP1, glutathione peroxidase 1, and SCFD2), with CGIs of intermediate enrichment (>2.2-fold) (COX7A2L, SYVN1, and JAG2), and with CGIs of low enrichment (>2.0-fold) (MYC and PCNA). We found little difference in promoter binding when p53 is stabilized by these two distinctly different stresses. However, expression of these genes varies a great deal: while a few genes exhibit classical induction with adriamycin, the majority of the genes are unchanged or are mildly repressed by either hypoxia or adriamycin. Further analysis using p53 mutated in the core DNA binding domain revealed that the interaction of p53 with CGIs may be occurring through both sequence-dependent and -independent mechanisms. Taken together, these experiments describe the identification of novel p53 target genes and the subsequent discovery of distinctly different expression phenomena for p53 target genes under different stress scenarios. PMID:16980608

  16. A small molecule directly inhibits the p53 transactivation domain from binding to replication protein A

    PubMed Central

    Glanzer, Jason G.; Carnes, Katie A.; Soto, Patricia; Liu, Shengqin; Parkhurst, Lawrence J.; Oakley, Gregory G.

    2013-01-01

    Replication protein A (RPA), essential for DNA replication, repair and DNA damage signalling, possesses six ssDNA-binding domains (DBDs), including DBD-F on the N-terminus of the largest subunit, RPA70. This domain functions as a binding site for p53 and other DNA damage and repair proteins that contain amphipathic alpha helical domains. Here, we demonstrate direct binding of both ssDNA and the transactivation domain 2 of p53 (p53TAD2) to DBD-F, as well as DBD-F-directed dsDNA strand separation by RPA, all of which are inhibited by fumaropimaric acid (FPA). FPA binds directly to RPA, resulting in a conformational shift as determined through quenching of intrinsic tryptophan fluorescence in full length RPA. Structural analogues of FPA provide insight on chemical properties that are required for inhibition. Finally, we confirm the inability of RPA possessing R41E and R43E mutations to bind to p53, destabilize dsDNA and quench tryptophan fluorescence by FPA, suggesting that protein binding, DNA modulation and inhibitor binding all occur within the same site on DBD-F. The disruption of p53–RPA interactions by FPA may disturb the regulatory functions of p53 and RPA, thereby inhibiting cellular pathways that control the cell cycle and maintain the integrity of the human genome. PMID:23267009

  17. Detection, purification and characterization of a protein that binds the (6-4) photoproduct-containing DNA in HeLa cells.

    PubMed

    Fujiwara, Y; Masutani, C; Hanaoka, F; Iwai, S

    1997-01-01

    HeLa cell proteins that bind DNA containing the pyrimidine(6-4)pyrimidone photoproduct were detected by the electrophoretic mobility shift assay using synthetic oligonucleotide duplexes as probes. The major species was purified to near homogeneity, and the amino acid sequences of the proteolytic peptides revealed that it was the human damage-specific DNA-binding protein, which was reported previously. The substrate specificity of this protein was determined using damaged or modified DNA duplexes. PMID:9586107

  18. Cooperative binding: a multiple personality.

    PubMed

    Martini, Johannes W R; Diambra, Luis; Habeck, Michael

    2016-06-01

    Cooperative binding has been described in many publications and has been related to or defined by several different properties of the binding behavior of the ligand to the target molecule. In addition to the commonly used Hill coefficient, other characteristics such as a sigmoidal shape of the overall titration curve in a linear plot, a change of ligand affinity of the other binding sites when a site of the target molecule becomes occupied, or complex roots of the binding polynomial have been used to define or to quantify cooperative binding. In this work, we analyze how the different properties are related in the most general model for binding curves based on the grand canonical partition function and present several examples which highlight differences between the cooperativity characterizing properties which are discussed. Our results mainly show that among the presented definitions there are not two which fully coincide. Moreover, this work poses the question whether it can make sense to distinguish between positive and negative cooperativity based on the macroscopic binding isotherm only. This article shall emphasize that scientists who investigate cooperative effects in biological systems could help avoiding misunderstandings by stating clearly which kind of cooperativity they discuss. PMID:26319983

  19. (/sup 3/)tetrahydrotrazodone binding. Association with serotonin binding sites

    SciTech Connect

    Kendall, D.A.; Taylor, D.P.; Enna, S.J.

    1983-05-01

    High (17 nM) and low (603 nM) affinity binding sites for (/sup 3/)tetrahydrotrazodone ((/sup 3/) THT), a biologically active analogue of trazodone, have been identified in rat brain membranes. The substrate specificity, concentration, and subcellular and regional distributions of these sites suggest that they may represent a component of the serotonin transmitter system. Pharmacological analysis of (/sup 3/)THT binding, coupled with brain lesion and drug treatment experiments, revealed that, unlike other antidepressants, (/sup 3/) THT does not attach to either a biogenic amine transporter or serotonin binding sites. Rather, it would appear that (/sup 3/)THT may be an antagonist ligand for the serotonin binding site. This probe may prove of value in defining the mechanism of action of trazodone and in further characterizing serotonin receptors.

  20. Comparative study of radiation damage accumulation in Cu and Fe

    NASA Astrophysics Data System (ADS)

    Caturla, M. J.; Soneda, N.; Alonso, E.; Wirth, B. D.; Díaz de la Rubia, T.; Perlado, J. M.

    2000-01-01

    Bcc and fcc metals exhibit significant differences in behavior when exposed to neutron or heavy ion irradiation. Transmission electron microscopy (TEM) observations reveal that damage in the form of stacking fault tetrahedra (SFT) is visible in copper irradiated to very low doses, but that no damage is visible in iron irradiated to the same total dose. In order to understand and quantify this difference in behavior, we have simulated damage production and accumulation in fcc Cu and bcc Fe. We use 20 keV primary knock-on atoms (PKAs) at a homologous temperature of 0.25 of the melting point. The primary damage state was calculated using molecular dynamics (MD) with empirical, embedded-atom interatomic potentials. Damage accumulation was modeled using a kinetic Monte Carlo (kMC) algorithm to follow the evolution of all defects produced in the cascades. The diffusivities and binding energies of defects are input data for this simulation and were either extracted from experiments, the literature, or calculated using MD. MD simulations reveal that vacancy clusters are produced within the cascade core in the case of copper. In iron, most of the vacancies do not cluster during cooling of the cascade core and are available for diffusion. In addition, self-interstitial atom (SIA) clusters are produced in copper cascades but those observed in iron are smaller in number and size. The combined MD/kMC simulations reveal that the visible cluster densities obtained as a function of dose are at least one order of magnitude lower in Fe than in Cu. We compare the results with experimental measurements of cluster density and find excellent agreement between the simulations and experiments when small interstitial clusters are considered to be mobile as suggested by recent MD simulations.

  1. Benzodiazepine binding to bovine retina.

    PubMed

    Osborne, N N

    1980-02-01

    [3H]Diazepam binds to membrane preparations of the retina, suggesting that benzodiazepine receptors exist in this tissue. The binding characteristics are similar to those known to occur in the brain, with affinity constants in the same range. Unlike the finding in the brain, [3H]diazepam binding in the retina is not stimulated by GABA and other GABA agonists. These findings indicate that benzodiazepine receptors may have a more general function and not only be associated with anxiety or emotional behaviour. PMID:6302572

  2. Mercury binding on activated carbon

    SciTech Connect

    Bihter Padak; Michael Brunetti; Amanda Lewis; Jennifer Wilcox

    2006-11-15

    Density functional theory has been employed for the modeling of activated carbon (AC) using a fused-benzene ring cluster approach. Oxygen functional groups have been investigated for their promotion of effective elemental mercury binding on AC surface sites. Lactone and carbonyl functional groups yield the highest mercury binding energies. Further, the addition of halogen atoms has been considered to the modeled surface, and has been found to increase the AC's mercury adsorption capacity. The mercury binding energies increase with the addition of the following halogen atoms, F {gt} Cl {gt} Br {gt} I, with the fluorine addition being the most promising halogen for increasing mercury adsorption.

  3. PUMA Binding Induces Partial Unfolding within BCL-xL to Disrupt p53 Binding and Promote Apoptosis

    PubMed Central

    Follis, Ariele Viacava; Chipuk, Jerry E.; Fisher, John C.; Yun, Mi-Kyung; Grace, Christy R.; Nourse, Amanda; Baran, Katherine; Ou, Li; Min, Lie; White, Stephen W.; Green, Douglas R.; Kriwacki, Richard W.

    2012-01-01

    Following DNA damage, nuclear p53 induces the expression of PUMA, a BH3-only protein that binds and inhibits the anti-apoptotic BCL-2 repertoire, including BCL-xL. PUMA, unique amongst BH3-only proteins, disrupts the interaction between cytosolic p53 and BCL-xL, allowing p53 to promote apoptosis via direct activation of the BCL-2 effector molecules, BAX and BAK. Structural investigations using nuclear magnetic resonance spectroscopy and X-ray crystallography revealed that PUMA binding induced partial unfolding of two α-helices within BCL-xL. Wild-type PUMA or a PUMA mutant incapable of causing binding-induced unfolding of BCL-xL equivalently inhibited the anti-apoptotic BCL-2 repertoire to sensitize for death receptor (DR)-activated apoptosis, but only wild-type PUMA promoted p53-dependent, DNA damage-induced apoptosis. Our data suggest that PUMA-induced partial unfolding of BCL-xL disrupts interactions between cytosolic p53 and BCL-xL, releasing the bound p53 to initiate apoptosis. We propose that regulated unfolding of BCL-xL provides a mechanism to promote PUMA-dependent signaling within the apoptotic pathways. PMID:23340338

  4. Evidence against the nuclear in situ binding of arsenicals-oxidative stress theory of arsenic carcinogenesis

    EPA Science Inventory

    A large amount of evidence suggests that arsenicals act via oxidative stress in causing cancer in humans and experimental animals. It is possible that arsenicals could bind in situ close to nuclear DNA followed by Haber-Weiss type oxidative DNA damage. Therefore, we tested this...

  5. Analysis of LexA binding sites and transcriptomics in response to genotoxic stress in Leptospira interrogans

    PubMed Central

    Schons-Fonseca, Luciane; da Silva, Josefa B.; Milanez, Juliana S.; Domingos, Renan H.; Smith, Janet L.; Nakaya, Helder I.; Grossman, Alan D.; Ho, Paulo L.; da Costa, Renata MA

    2016-01-01

    We determined the effects of DNA damage caused by ultraviolet radiation on gene expression in Leptospira interrogans using DNA microarrays. These data were integrated with DNA binding in vivo of LexA1, a regulator of the DNA damage response, assessed by chromatin immunoprecipitation and massively parallel DNA sequencing (ChIP-seq). In response to DNA damage, Leptospira induced expression of genes involved in DNA metabolism, in mobile genetic elements and defective prophages. The DNA repair genes involved in removal of photo-damage (e.g. nucleotide excision repair uvrABC, recombinases recBCD and resolvases ruvABC) were not induced. Genes involved in various metabolic pathways were down regulated, including genes involved in cell growth, RNA metabolism and the tricarboxylic acid cycle. From ChIP-seq data, we observed 24 LexA1 binding sites located throughout chromosome 1 and one binding site in chromosome 2. Expression of many, but not all, genes near those sites was increased following DNA damage. Binding sites were found as far as 550 bp upstream from the start codon, or 1 kb into the coding sequence. Our findings indicate that there is a shift in gene expression following DNA damage that represses genes involved in cell growth and virulence, and induces genes involved in mutagenesis and recombination. PMID:26762976

  6. Analysis of LexA binding sites and transcriptomics in response to genotoxic stress in Leptospira interrogans.

    PubMed

    Schons-Fonseca, Luciane; da Silva, Josefa B; Milanez, Juliana S; Domingos, Renan H; Smith, Janet L; Nakaya, Helder I; Grossman, Alan D; Ho, Paulo L; da Costa, Renata M A

    2016-02-18

    We determined the effects of DNA damage caused by ultraviolet radiation on gene expression in Leptospira interrogans using DNA microarrays. These data were integrated with DNA binding in vivo of LexA1, a regulator of the DNA damage response, assessed by chromatin immunoprecipitation and massively parallel DNA sequencing (ChIP-seq). In response to DNA damage, Leptospira induced expression of genes involved in DNA metabolism, in mobile genetic elements and defective prophages. The DNA repair genes involved in removal of photo-damage (e.g. nucleotide excision repair uvrABC, recombinases recBCD and resolvases ruvABC) were not induced. Genes involved in various metabolic pathways were down regulated, including genes involved in cell growth, RNA metabolism and the tricarboxylic acid cycle. From ChIP-seq data, we observed 24 LexA1 binding sites located throughout chromosome 1 and one binding site in chromosome 2. Expression of many, but not all, genes near those sites was increased following DNA damage. Binding sites were found as far as 550 bp upstream from the start codon, or 1 kb into the coding sequence. Our findings indicate that there is a shift in gene expression following DNA damage that represses genes involved in cell growth and virulence, and induces genes involved in mutagenesis and recombination. PMID:26762976

  7. Radiation damage evolution in ceramics

    SciTech Connect

    Devanathan, Ramaswami

    2009-09-15

    A review is presented of recent results on radiation damage production, defect accumulation and dynamic annealing in a number of ceramics, such as silicon carbide, zircon and zirconia. Under energetic particle irradiation, ceramics can undergo amorphization by the accumulation of point defects and defect clusters (silicon carbide) or direct impact amorphization (zircon). Ceramics that resist radiation-induced amorphization have mechanisms to dissipate the primary knock-on atom energy, such as replacement collision sequences that leave the lattice undisturbed and low-energy cation site exchange. The presence of engineered mobile defects, such as structural vacancies in stabilized zirconia, can dynamically anneal radiation damage. Thus, defect engineering is a promising strategy to design radiation tolerance for applications such as nuclear waste disposal.

  8. Radiation damage of germanium detectors

    NASA Technical Reports Server (NTRS)

    Pehl, R. H.

    1978-01-01

    Energetic particles can produce interstitial-vacancy pairs in a crystal by knocking the atoms from their normal positions. Detectors are unique among semiconductor devices in depending on very low concentrations of electrically active impurities, and also on efficient transport of holes and electrons over relatively large distances. Because the dense regions of damage produced by energetic particles may result in donors and/or acceptors, and also provide trapping sites for holes and electrons, detectors are very sensitive to radiation damage. In addition to these effects occurring within the detector, radiation may also change the characteristics of the exposed surfaces causing unpredictable effects on the detector leakage current. Radiation-induced surface degradation has rarely, if ever, been observed for germanium detectors. The possibility of minimizing hole trapping in charge collection by the use of a high-purity germanium coaxial detector configured with the p (+) contact on the coaxial periphery is discussed.

  9. Formation of ion damage tracks

    NASA Astrophysics Data System (ADS)

    Tombrello, T. A.; Wie, C. R.; Itoh, N.; Nakayama, T.

    1984-01-01

    A new model is proposed to explain both localized damage regions and preferential etching of damage tracks caused by the passage of energetic ions in insulators. The formation of each region of extended defects is initiated by the Auger decay of a vacancy produced in an inner electronic shell of an atom of the insulator by an incident ion. This decay produces an intense source of ionization within a small volume around the decaying atom, which causes decomposition of the material in a manner similar to that observed in pulsed laser irradiation. The resulting chemical or crystalline modification of the material is the latent track, which can be preferentially etched due to its changed structure.

  10. Damage of hybrid composite laminates

    NASA Astrophysics Data System (ADS)

    Haery, Haleh A.; Kim, Ho Sung

    2013-08-01

    Hybrid laminates consisting of woven glass fabric/epoxy composite plies and woven carbon fabric/epoxy composite plies are studied for fatigue damage and residual strength. A theoretical framework based on the systems approach is proposed as a guide to deal with the complexity involving uncertainties and a large number of variables in the hybrid composite system. A relative damage sensitivity factor expression was developed for quantitative comparisons between non-hybrid and hybrid composites. Hypotheses derived from the theoretical framework were tested and verified. The first hypothesis was that the difference between two different sets of properties produces shear stress in interface between carbon fibre reinforced plastics (CRP) and glass fibre reinforced plastics (GRP), and eventually become a source for CRP/GRP interfacial delamination or longitudinal cracking. The second hypothesis was that inter-fibre bundle delamination occurs more severely to CRP sub-system than GRP sub-system.

  11. Method for producing damage resistant optics

    DOEpatents

    Hackel, Lloyd A.; Burnham, Alan K.; Penetrante, Bernardino M.; Brusasco, Raymond M.; Wegner, Paul J.; Hrubesh, Lawrence W.; Kozlowski, Mark R.; Feit, Michael D.

    2003-01-01

    The present invention provides a system that mitigates the growth of surface damage in an optic. Damage to the optic is minimally initiated. In an embodiment of the invention, damage sites in the optic are initiated, located, and then treated to stop the growth of the damage sites. The step of initiating damage sites in the optic includes a scan of the optic using a laser to initiate defects. The exact positions of the initiated sites are identified. A mitigation process is performed that locally or globally removes the cause of subsequent growth of the damaged sites.

  12. Cumulative life damage in dermatology

    PubMed Central

    Ibler, Kristina; Jemec, Gregor B.E.

    2011-01-01

    Cumulative life damage is an old concept of considerable face validity, which has attracted more scientific interest in the fields of sociology and psychology than in medicine over the years. The research examines the interconnectivity of the many factors which shape the development of individuals or institutions over time. By focussing on time, context and process, life course research highlights the different effects seemingly similar events may have at different points in time and in different contexts. PMID:25386260

  13. Smart accelerometer. [vibration damage detection

    NASA Technical Reports Server (NTRS)

    Bozeman, Richard J., Jr. (Inventor)

    1994-01-01

    The invention discloses methods and apparatus for detecting vibrations from machines which indicate an impending malfunction for the purpose of preventing additional damage and allowing for an orderly shutdown or a change in mode of operation. The method and apparatus is especially suited for reliable operation in providing thruster control data concerning unstable vibration in an electrical environment which is typically noisy and in which unrecognized ground loops may exist.

  14. Yeast DNA-repair gene RAD14 encodes a zinc metalloprotein with affinity for ultraviolet-damaged DNA

    SciTech Connect

    Guzder, S.N.; Sung, P.; Prakash, S. ); Prakash, L. )

    1993-06-15

    Xeroderma pigmentosum (XP) patients suffer from a high incidence of skin cancers due to a defect in excision repair of UV light-damaged DNA. Of the seven XP complementation groups, A--G, group A represents a severe and frequent form of the disease. The Saccharomyces cerevisiae RAD14 gene is a homolog of the XP-A correcting (XPAC) gene. Like XP-A cells, rad14-null mutants are defective in the incision step of excision repair of UV-damaged DNA. The authors have purified RAD14 protein to homogeneity from extract of a yeast strain genetically tailored to overexpress RAD14. As determined by atomic emission spectroscopy, RAD14 contains one zinc atom. They also show in vitro that RAD14 binds zinc but does not bind other divalent metal ions. In DNA mobility-shift assays, RAD14 binds specifically to UV-damaged DNA. Removal of cyclobutane pyrimidine dimers from damaged DNA by enzymatic photoreactivation has no effect on binding, strongly suggesting that RAD14 recognizes pyrimidine(6-4)pyrimidone photoproduct sites. These findings indicate that RAD14 functions in damage recognition during excision repair. 37 refs., 4 figs.

  15. Economic measurement of environment damages

    SciTech Connect

    Krawiec, F.

    1980-05-01

    The densities, energy consumption, and economic development of the increasing population exacerbate environmental degradation. Air and water pollution is a major environmental problem affecting life and health, outdoor recreation, household soiling, vegetation, materials, and production. The literature review indicated that numerous studies have assessed the physical and monetary damage to populations at risk from excessive concentrations of major air and water pollutants-sulfur dioxide, total suspended particulate matter, oxidants, and carbon monoxide in air; and nutrients, oil, pesticides, and toxic metals and others in water. The measurement of the damages was one of the most controversial issues in pollution abatement. The methods that have been used to estimate the societal value of pollution abatement are: (1) chain of effects, (2) market approaches, and (3) surveys. National gross damages of air pollution of $20.2 billion and of water pollution of $11.1 billion for 1973 are substantial. These best estimates, updated for the economic and demographic conditions, could provide acceptable control totals for estimating and predicting benefits and costs of abating air and water pollution emissions. The major issues to be resolved are: (1) lack of available noneconomic data, (2) theoretical and empirical difficulties of placing a value on human life and health and on benefits such as aesthetics, and (3) lack of available demographic and economic data.

  16. Superresolution microscopy with transient binding.

    PubMed

    Molle, Julia; Raab, Mario; Holzmeister, Susanne; Schmitt-Monreal, Daniel; Grohmann, Dina; He, Zhike; Tinnefeld, Philip

    2016-06-01

    For single-molecule localization based superresolution, the concentration of fluorescent labels has to be thinned out. This is commonly achieved by photophysically or photochemically deactivating subsets of molecules. Alternatively, apparent switching of molecules can be achieved by transient binding of fluorescent labels. Here, a diffusing dye yields bright fluorescent spots when binding to the structure of interest. As the binding interaction is weak, the labeling is reversible and the dye ligand construct diffuses back into solution. This approach of achieving superresolution by transient binding (STB) is reviewed in this manuscript. Different realizations of STB are discussed and compared to other localization-based superresolution modalities. We propose the development of labeling strategies that will make STB a highly versatile tool for superresolution microscopy at highest resolution. PMID:26773299

  17. When is protein binding important?

    PubMed

    Heuberger, Jules; Schmidt, Stephan; Derendorf, Hartmut

    2013-09-01

    The present paper is an ode to a classic citation by Benet and Hoener (2002. Clin Pharm Ther 71(3):115-121). The now classic paper had a huge impact on drug development and the way the issue of protein binding is perceived and interpreted. Although the authors very clearly pointed out the limitations and underlying assumptions for their delineations, these are too often overlooked and the classic paper's message is misinterpreted by broadening to cases that were not intended. Some members of the scientific community concluded from the paper that protein binding is not important. This was clearly not intended by the authors, as they finished their paper with a paragraph entitled: "When is protein binding important?" Misinterpretation of the underlying assumptions in the classic work can result in major pitfalls in drug development. Therefore, we revisit the topic of protein binding with the intention of clarifying when clinically relevant changes should be considered during drug development. PMID:23650013

  18. Detection of damage in axial (membrane) systems

    SciTech Connect

    Duffey, T.A.; Baker, W.E.; Farrar, C.R.; Rhee, W.H.

    1998-12-31

    In a recent paper, two methods of damage identification (Modified Damage Index and Change-in-Flexibility) were applied to detection of damage in an 8-DOF vibrating system. The goal of the work was to detect damage (reduction in stiffness of one or more of the elements) as well as to locate the particular damaged elements (S). However, the investigation was limited to numerical simulations only. In this paper, a physical, spring-mass model of a similar, degenerate 8-DOF system (7 normal modes plus a rigid-body mode) was constructed. Experiments were then performed and the modal properties of the system were determined in undamaged and damaged states. Excitation was provided either by an impact hammer or by an electromechanical shaker. Damage was induced by replacing one of the springs with a spring of lower stiffness. The Modified Damage Index method clearly isolated the location of damage for a variety of damage locations and levels of damage. The Change-in-Flexibility method, however, was found to be less reliable. The ability of the method to locate damage depended strongly on location and the level of damage as well as the number of modes included.

  19. Radiation damage effects in zircon

    NASA Astrophysics Data System (ADS)

    Trachenko, Kostya; Dove, Martin; Salje, Ekhard

    2002-03-01

    Zircon, ZrSiO_4, is important for geology and geochronology, and has been proposed as a host material to immobilize highly radioactive materials from dismantled weapons and nuclear waste from power stations [1]. In these applications zircon is exposed to alpha-irradiation. Computer simulations have started to be employed to simulate radiation damage in zircon [2], but the origin and microscopic mechanisms of the most important structural changes in zircon - unit cell expansion and large macroscopic swelling at higher doses, strong shear deformation of the crystalline lattice, and polymerization of SiOn units [3], remain unknown. Here, we perform the molecular dynamics simulation of highly energetic recoils in zircon. Basing on the simulation results, we propose the simple picture of the density change in the damaged region that consists of the depleted and densified matter. We find that the experimentally observed structural changes originate from the interaction of the damaged region with the surrounding crystalline lattice: the shear of the lattice around the damaged region causes shear deformation and expansion of the unit cells. The polymers of connected SiOn polyhedra are most commonly present in the densified shell at the periphery of the damaged region. [1] R C Ewing et al, J. Mater. Res. 10, 243 (1995); W J Weber et al, B E Burakov et al, in Scientific Basis for Nuclear Waste Management XIX, 25-32 and 33-40 (Plenum, New York, 1996); R C Ewing, et al in Crystalline Ceramics: Waste Forms for the Disposal of Weapons Plutonium, NATO Workshop Proceedings 65 (Academic Publishers, Dordrecht, The Netherlands, 1996). [2] B Park et al, Phys. Rev. B, 64, 174108 (1-16) (2001); J P Crocombette and D Ghaleb, J. Nucl. Mater., 295, 167 (2001); K Trachenko et al, J. Appl. Phys., 87, 7702 (2000); K Trachenko et al, J. Phys.: Cond. Matt., 13, 1947 (2001). [3] T Murakami et al, Am. Min., 76, 1510 (1991); H D Holland and D Gottfried, Acta Cryst. 8, 291 (1955).; W J Weber, J. Am

  20. 7 CFR 51.573 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Standards for Celery Definitions § 51.573 Damage. Damage, unless otherwise specifically defined in this... the celery stalk or the general appearance of the stalks in the container. Any one of the...

  1. 7 CFR 51.573 - Damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ..., CERTIFICATION, AND STANDARDS) United States Standards for Celery Definitions § 51.573 Damage. Damage, unless... the edible or shipping quality of the celery stalk or the general appearance of the stalks in...

  2. 7 CFR 51.586 - Serious damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Standards for Celery Definitions § 51.586 Serious damage. Serious damage, unless otherwise specifically... shipping quality of the celery stalk or the general appearance of the stalks in the container. Any one...

  3. 7 CFR 51.573 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Standards for Celery Definitions § 51.573 Damage. Damage, unless otherwise specifically defined in this... the celery stalk or the general appearance of the stalks in the container. Any one of the...

  4. 7 CFR 51.586 - Serious damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Standards for Celery Definitions § 51.586 Serious damage. Serious damage, unless otherwise specifically... shipping quality of the celery stalk or the general appearance of the stalks in the container. Any one...

  5. Damage Tolerance of Large Shell Structures

    NASA Technical Reports Server (NTRS)

    Minnetyan, L.; Chamis, C. C.

    1999-01-01

    Progressive damage and fracture of large shell structures is investigated. A computer model is used for the assessment of structural response, progressive fracture resistance, and defect/damage tolerance characteristics. Critical locations of a stiffened conical shell segment are identified. Defective and defect-free computer models are simulated to evaluate structural damage/defect tolerance. Safe pressurization levels are assessed for the retention of structural integrity at the presence of damage/ defects. Damage initiation, growth, accumulation, and propagation to fracture are included in the simulations. Damage propagation and burst pressures for defective and defect-free shells are compared to evaluate damage tolerance. Design implications with regard to defect and damage tolerance of a large steel pressure vessel are examined.

  6. 7 CFR 29.3017 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Damage. The effect of mold, must, rot, black rot, or other fungous or bacterial diseases which attack tobacco in its cured state. Tobacco having the odor of mold, must, or rot is considered damaged. (See...

  7. 7 CFR 29.3017 - Damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... Damage. The effect of mold, must, rot, black rot, or other fungous or bacterial diseases which attack tobacco in its cured state. Tobacco having the odor of mold, must, or rot is considered damaged. (See...

  8. 7 CFR 29.3017 - Damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... Damage. The effect of mold, must, rot, black rot, or other fungous or bacterial diseases which attack tobacco in its cured state. Tobacco having the odor of mold, must, or rot is considered damaged. (See...

  9. 7 CFR 29.3017 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Damage. The effect of mold, must, rot, black rot, or other fungous or bacterial diseases which attack tobacco in its cured state. Tobacco having the odor of mold, must, or rot is considered damaged. (See...

  10. 7 CFR 51.1413 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Standards for Grades of Pecans in the Shell 1 Definitions § 51.1413 Damage. Damage means any specific defect... marketing quality of the individual pecan or the general appearance of the pecans in the lot. The...

  11. 7 CFR 51.1413 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Standards for Grades of Pecans in the Shell 1 Definitions § 51.1413 Damage. Damage means any specific defect... marketing quality of the individual pecan or the general appearance of the pecans in the lot. The...

  12. DNA Damage and Repair in Vascular Disease.

    PubMed

    Uryga, Anna; Gray, Kelly; Bennett, Martin

    2016-01-01

    DNA damage affecting both genomic and mitochondrial DNA is present in a variety of both inherited and acquired vascular diseases. Multiple cell types show persistent DNA damage and a range of lesions. In turn, DNA damage activates a variety of DNA repair mechanisms, many of which are activated in vascular disease. Such DNA repair mechanisms either stall the cell cycle to allow repair to occur or trigger apoptosis or cell senescence to prevent propagation of damaged DNA. Recent evidence has indicated that DNA damage occurs early, is progressive, and is sufficient to impair function of cells composing the vascular wall. The consequences of persistent genomic and mitochondrial DNA damage, including inflammation, cell senescence, and apoptosis, are present in vascular disease. DNA damage can thus directly cause vascular disease, opening up new possibilities for both prevention and treatment. We review the evidence for and the causes, types, and consequences of DNA damage in vascular disease. PMID:26442438

  13. ATMOSPHERIC ACID DEPOSITION DAMAGE TO PAINTS

    EPA Science Inventory

    Available data from laboratory and field studies of damage to paints by erosion have been analyzed to develop an atmospheric acid deposition damage function for exterior house paints containing calcium carbonate or silicate extenders. Regression analysis coefficients associated w...

  14. 7 CFR 51.2739 - Damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... § 51.2739 Damage. Damage means any specific defect described in this section; or any other defect, or...) Dirt when the surface of the kernel is heavily smeared, thickly flecked or coated with dirt,...

  15. 7 CFR 51.2739 - Damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... § 51.2739 Damage. Damage means any specific defect described in this section; or any other defect, or...) Dirt when the surface of the kernel is heavily smeared, thickly flecked or coated with dirt,...

  16. Recent Advances in Composite Damage Mechanics

    NASA Technical Reports Server (NTRS)

    Reifsnider, Ken; Case, Scott; Iyengar, Nirmal

    1996-01-01

    The state of the art and recent developments in the field of composite material damage mechanics are reviewed, with emphasis on damage accumulation. The kinetics of damage accumulation are considered with emphasis on the general accumulation of discrete local damage events such as single or multiple fiber fractures or microcrack formation. The issues addressed include: how to define strength in the presence of widely distributed damage, and how to combine mechanical representations in order to predict the damage tolerance and life of engineering components. It is shown that a damage mechanics approach can be related to the thermodynamics of the damage accumulation processes in composite laminates subjected to mechanical loading and environmental conditions over long periods of time.

  17. Protein damage, radiation sensitivity and aging.

    PubMed

    Radman, Miroslav

    2016-08-01

    This paper promotes a concept that protein damage determines radiation resistance and underlies aging and age-related diseases. The first bottleneck in cell recovery from radiation damage is functional (proteome) rather than informational (DNA), since prokaryotic and eukaryotic cell death correlates with incurred protein, but not DNA, damage. Proteome protection against oxidative damage determines survival after ionizing or UV irradiation, since sufficient residual proteome activity is required to turn on the DNA damage response activating DNA repair and protein renewal processes. Extreme radiation and desiccation resistance of rare bacterial and animal species is accounted for by exceptional constitutive proteome protection against oxidative damage. After excessive radiation their well-protected proteome faithfully reconstitutes a transcription-competent genome from hundreds of DNA fragments. The observation that oxidative damage targeted selectively to cellular proteins results in aging-like phenotypes suggests that aging and age-related diseases could be phenotypic consequences of proteome damage patterns progressing with age. PMID:27264559

  18. Non-contact intracellular binding of chloroplasts in vivo

    NASA Astrophysics Data System (ADS)

    Li, Yuchao; Xin, Hongbao; Liu, Xiaoshuai; Li, Baojun

    2015-06-01

    Non-contact intracellular binding and controllable manipulation of chloroplasts in vivo was demonstrated using an optical fiber probe. Launching a 980-nm laser beam into a fiber, which was placed about 3 μm above the surface of a living plant (Hydrilla verticillata) leaf, enabled stable binding of different numbers of chloroplasts, as well as their arrangement into one-dimensional chains and two-dimensional arrays inside the leaf without damaging the chloroplasts. Additionally, the formed chloroplast chains were controllably transported inside the living cells. The optical force exerted on the chloroplasts was calculated to explain the experimental results. This method provides a flexible method for studying intracellular organelle interaction with highly organized organelle-organelle contact in vivo in a non-contact manner.

  19. Pharmacological activity of metal binding agents that alter copper bioavailability

    PubMed Central

    Helsel, Marian E.

    2015-01-01

    Iron, copper and zinc are required nutrients for many organisms but also potent toxins if misappropriated. An overload of any of these metals can be cytotoxic and ultimately lead to organ failure, whereas deficiencies can result in anemia, weakened immune system function, and other medical conditions. Cellular metal imbalances have been implicated in neurodegenerative diseases, cancer and infection. It is therefore critical for living organisms to maintain careful control of both the total levels and subcellular distributions of these metals to maintain healthy function. This perspective explores several strategies envisioned to alter the bioavailability of metal ions by using synthetic metal-binding agents targeted for diseases where misappropriated metal ions are suspected of exacerbating cellular damage. Specifically, we discuss chemical properties that influence the pharmacological outcome of a subset of metal-binding agents known as ionophores, and review several examples that have shown multiple pharmacological activities in metal-related diseases, with a specific focus on copper. PMID:25797044

  20. Rate process analysis of thermal damage in cartilage

    NASA Astrophysics Data System (ADS)

    Díaz, Sergio H.; Nelson, J. Stuart; Wong, Brian J. F.

    2003-01-01

    Cartilage laser thermoforming (CLT) is a new surgical procedure that allows in situ treatment of deformities in the head and neck with less morbidity than traditional approaches. While some animal and human studies have shown promising results, the clinical feasibility of CLT depends on preservation of chondrocyte viability, which has not been extensively studied. The present paper characterizes cellular damage due to heat in rabbit nasal cartilage. Damage was modelled as a first order rate process for which two experimentally derived coefficients, A = 1.2 × 1070 s-1 and Ea = 4.5 × 105 J mole-1, were determined by quantifying the decrease in concentration of healthy chondrocytes in tissue samples as a function of exposure time to constant-temperature water baths. After immersion, chondrocytes were enzymatically isolated from the matrix and stained with a two-component fluorescent dye. The dye binds nuclear DNA differentially depending upon chondrocyte viability. A flow cytometer was used to detect differential cell fluorescence to determine the percentage of live and dead cells in each sample. As a result, a damage kinetic model was obtained that can be used to predict the onset, extent and severity of cellular injury to thermal exposure.

  1. Large area damage testing of optics

    SciTech Connect

    Sheehan, L.; Kozlowski, M.; Stolz, C.

    1996-04-26

    The damage threshold specifications for the National Ignition Facility will include a mixture of standard small-area tests and new large-area tests. During our studies of laser damage and conditioning processes of various materials we have found that some damage morphologies are fairly small and this damage does not grow with further illumination. This type of damage might not be detrimental to the laser performance. We should therefore assume that some damage can be allowed on the optics, but decide on a maximum damage allowance of damage. A new specification of damage threshold termed {open_quotes}functional damage threshold{close_quotes} was derived. Further correlation of damage size and type to system performance must be determined in order to use this measurement, but it is clear that it will be a large factor in the optics performance specifications. Large-area tests have verified that small-area testing is not always sufficient when the optic in question has defect-initiated damage. This was evident for example on sputtered polarizer and mirror coatings where the defect density was low enough that the features could be missed by standard small- area testing. For some materials, the scale-length at which damage non-uniformities occur will effect the comparison of small-area and large-area tests. An example of this was the sub-aperture tests on KD*P crystals on the Beamlet test station. The tests verified the large-area damage threshold to be similar to that found when testing a small-area. Implying that for this KD*P material, the dominate damage mechanism is of sufficiently small scale-length that small-area testing is capable of determining the threshold. The Beamlet test station experiments also demonstrated the use of on-line laser conditioning to increase the crystals damage threshold.

  2. Avionics Box Cold Plate Damage Prevention

    NASA Technical Reports Server (NTRS)

    Stambolian, Damon; Larcher, Steven; Henderson, Gena; Tran, Donald

    2011-01-01

    Over the years there have been several occurrences of damage to Space Shuttle Orbiter cold plates during removal and replacement of avionics boxes. Thus a process improvement team was put together to determine ways to prevent these kinds of damage. From this effort there were many solutions including, protective covers, training, and improved operations instructions. The focus of this paper is to explain the cold plate damage problem and the corrective actions for preventing future damage to aerospace avionics cold plate designs.

  3. Damage experiments in cylindrical geometry update

    SciTech Connect

    Kaul, Anne; Holtkamp, David; Rodriguez, George

    2009-01-01

    Using a cylindrical configuration to study spallation damage allows for a natural recollection of the damaged material under proper driving conditions. Previous experiments provided data about failure initiation in aluminum in a cylindrical geometry and the behavior of material recollected after damage from pressures in the damage initiation regime. The current series of experiments studied the behavior of material recollected after complete failure. Results from the current experiments will be presented.

  4. Putting life on ice: bacteria that bind to frozen water

    PubMed Central

    Bernheim, Reut; Guo, Shuaiqi; Davies, Peter L.; Braslavsky, Ido

    2016-01-01

    Ice-binding proteins (IBPs) are typically small, soluble proteins produced by cold-adapted organisms to help them avoid ice damage by either resisting or tolerating freezing. By contrast, the IBP of the Antarctic bacterium Marinomonas primoryensis is an extremely long, 1.5 MDa protein consisting of five different regions. The fourth region, a 34 kDa domain, is the only part that confers ice binding. Bioinformatic studies suggest that this IBP serves as an adhesin that attaches the bacteria to ice to keep it near the top of the water column, where oxygen and nutrients are available. Using temperature-controlled cells and a microfluidic apparatus, we show that M. primoryensis adheres to ice and is only released when melting occurs. Binding is dependent on the mobility of the bacterium and the functionality of the IBP domain. A polyclonal antibody raised against the IBP region blocks bacterial ice adhesion. This concept may be the basis for blocking biofilm formation in other bacteria, including pathogens. Currently, this IBP is the only known example of an adhesin that has evolved to bind ice. PMID:27534698

  5. Putting life on ice: bacteria that bind to frozen water.

    PubMed

    Bar Dolev, Maya; Bernheim, Reut; Guo, Shuaiqi; Davies, Peter L; Braslavsky, Ido

    2016-08-01

    Ice-binding proteins (IBPs) are typically small, soluble proteins produced by cold-adapted organisms to help them avoid ice damage by either resisting or tolerating freezing. By contrast, the IBP of the Antarctic bacterium Marinomonas primoryensis is an extremely long, 1.5 MDa protein consisting of five different regions. The fourth region, a 34 kDa domain, is the only part that confers ice binding. Bioinformatic studies suggest that this IBP serves as an adhesin that attaches the bacteria to ice to keep it near the top of the water column, where oxygen and nutrients are available. Using temperature-controlled cells and a microfluidic apparatus, we show that M. primoryensis adheres to ice and is only released when melting occurs. Binding is dependent on the mobility of the bacterium and the functionality of the IBP domain. A polyclonal antibody raised against the IBP region blocks bacterial ice adhesion. This concept may be the basis for blocking biofilm formation in other bacteria, including pathogens. Currently, this IBP is the only known example of an adhesin that has evolved to bind ice. PMID:27534698

  6. 7 CFR 51.773 - Damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Damage. 51.773 Section 51.773 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Damage. Damage means any specific defect described in § 51.784, Table I; or an equally...

  7. 7 CFR 51.702 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Damage. 51.702 Section 51.702 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... § 51.702 Damage. Damage means any specific defect described in § 51.713, Table IV; or an...

  8. 7 CFR 51.1560 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Damage. 51.1560 Section 51.1560 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Potatoes 1 Definitions § 51.1560 Damage. Damage means any defect, or any...

  9. 7 CFR 51.708 - Serious damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Serious damage. 51.708 Section 51.708 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... § 51.708 Serious damage. Serious damage means any specific defect described in § 51.713, Table IV;...

  10. 7 CFR 51.777 - Serious damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Serious damage. 51.777 Section 51.777 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Serious damage. Serious damage means any specific defect described in § 51.784, Table I; or an...

  11. 7 CFR 51.1358 - Serious damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Serious damage. 51.1358 Section 51.1358 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Pears for Canning Definitions § 51.1358 Serious damage. Serious damage means any injury...

  12. 7 CFR 51.3749 - Serious damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Serious damage. 51.3749 Section 51.3749 Agriculture... Standards for Grades of Honey Dew and Honey Ball Type Melons Definitions § 51.3749 Serious damage. Serious damage means any defect or any combination of defects which seriously detracts from the appearance,...

  13. 7 CFR 51.1355 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.1355 Section 51.1355 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Pears for Canning Definitions § 51.1355 Damage. Damage means any injury or defect...

  14. 7 CFR 51.1163 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Damage. 51.1163 Section 51.1163 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Florida Oranges and Tangelos Definitions § 51.1163 Damage. Damage means any...

  15. 46 CFR 172.103 - Damage stability.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 7 2013-10-01 2013-10-01 false Damage stability. 172.103 Section 172.103 Shipping COAST... Subchapter O of This Chapter § 172.103 Damage stability. Each tank barge must be shown by design calculations to meet the survival conditions in § 172.110 assuming the damage specified in § 172.104 to the...

  16. 7 CFR 51.702 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Damage. 51.702 Section 51.702 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... § 51.702 Damage. Damage means any specific defect described in § 51.713, Table IV; or an...

  17. 46 CFR 172.205 - Local damage.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 7 2012-10-01 2012-10-01 false Local damage. 172.205 Section 172.205 Shipping COAST... Subchapter O of This Chapter § 172.205 Local damage. (a) Each tankship must be shown by design calculations... operation assuming that local damage extending 30 inches (76 cm) normal to the hull shell is applied at...

  18. 46 CFR 172.050 - Damage stability.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 7 2013-10-01 2013-10-01 false Damage stability. 172.050 Section 172.050 Shipping COAST... This Chapter § 172.050 Damage stability. (a) Each tank barge is assigned a hull type number by the... mm) of positive GM in each condition of loading and operation after assuming the damage specified...

  19. 7 CFR 51.773 - Damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Damage. 51.773 Section 51.773 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Damage. Damage means any specific defect described in § 51.784, Table I; or an equally...

  20. 7 CFR 51.908 - Serious damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Serious damage. 51.908 Section 51.908 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Definitions § 51.908 Serious damage. Serious damage means any defect or any combination of defects...

  1. 7 CFR 51.1874 - Serious damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Serious damage. 51.1874 Section 51.1874 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Fresh Tomatoes 1 Definitions § 51.1874 Serious damage. Serious damage means any...

  2. 7 CFR 51.2763 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Damage. 51.2763 Section 51.2763 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Shelled Virginia Type Peanuts Definitions § 51.2763 Damage. Damage means that the...

  3. 7 CFR 51.708 - Serious damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Serious damage. 51.708 Section 51.708 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... § 51.708 Serious damage. Serious damage means any specific defect described in § 51.713, Table IV;...

  4. 7 CFR 51.2763 - Damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Damage. 51.2763 Section 51.2763 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Damage. Damage means that the peanut kernel is affected by one or more of the following: (a) Rancidity...

  5. 7 CFR 51.1358 - Serious damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Serious damage. 51.1358 Section 51.1358 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Pears for Canning Definitions § 51.1358 Serious damage. Serious damage means any injury...

  6. 7 CFR 51.908 - Serious damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Serious damage. 51.908 Section 51.908 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Definitions § 51.908 Serious damage. Serious damage means any defect or any combination of defects...

  7. 7 CFR 51.1560 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.1560 Section 51.1560 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Potatoes 1 Definitions § 51.1560 Damage. Damage means any defect, or any...

  8. 7 CFR 51.773 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Damage. 51.773 Section 51.773 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Florida Grapefruit Definitions § 51.773 Damage. Damage means any specific...

  9. 7 CFR 51.642 - Damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Damage. 51.642 Section 51.642 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Florida, California, and Arizona) Definitions § 51.642 Damage. Damage means any specific defect...

  10. 7 CFR 51.642 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Damage. 51.642 Section 51.642 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing...) Definitions § 51.642 Damage. Damage means any specific defect described in § 51.652, Table IV; or an...

  11. 7 CFR 51.1833 - Serious damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Serious damage. 51.1833 Section 51.1833 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Serious damage. Serious damage means any specific defect described in § 51.1837, Table I; or an...

  12. 7 CFR 51.1833 - Serious damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Serious damage. 51.1833 Section 51.1833 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Florida Tangerines Definitions § 51.1833 Serious damage. Serious damage means...

  13. 7 CFR 51.1871 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Damage. 51.1871 Section 51.1871 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Fresh Tomatoes 1 Definitions § 51.1871 Damage. Damage means any specific defect described...

  14. 7 CFR 51.1833 - Serious damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Serious damage. 51.1833 Section 51.1833 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Serious damage. Serious damage means any specific defect described in § 51.1837, Table I; or an...

  15. 7 CFR 51.646 - Serious damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Serious damage. 51.646 Section 51.646 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing...) Definitions § 51.646 Serious damage. Serious damage means any specific defect described in § 51.652, Table...

  16. 7 CFR 51.908 - Serious damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Serious damage. 51.908 Section 51.908 Agriculture... Standards for Grades of Table Grapes (European or Vinifera Type) 1 Definitions § 51.908 Serious damage. Serious damage means any defect or any combination of defects which seriously detracts from the...

  17. 7 CFR 51.1163 - Damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Damage. 51.1163 Section 51.1163 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... § 51.1163 Damage. Damage means any specific defect described in § 51.1175, Table I; or an...

  18. 7 CFR 51.1871 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.1871 Section 51.1871 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Fresh Tomatoes 1 Definitions § 51.1871 Damage. Damage means any specific defect described...

  19. 7 CFR 51.702 - Damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Damage. 51.702 Section 51.702 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing..., California, and Arizona) Definitions § 51.702 Damage. Damage means any specific defect described in §...

  20. 7 CFR 51.1826 - Damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Damage. 51.1826 Section 51.1826 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Damage. Damage means any specific defect described in § 51.1837, Table I; or an equally...

  1. 46 CFR 390.12 - Liquidated damages.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 8 2013-10-01 2013-10-01 false Liquidated damages. 390.12 Section 390.12 Shipping... CONSTRUCTION FUND § 390.12 Liquidated damages. (a) Liquidated damages—(1) In general. Each agreement entered into under Chapter 535 shall contain a liquidated damages provision for the purpose of placing...

  2. 7 CFR 51.1449 - Damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Damage. 51.1449 Section 51.1449 Agriculture..., CERTIFICATION, AND STANDARDS) United States Standards for Grades of Shelled Pecans Definitions § 51.1449 Damage. Damage means any specific defect described in this section; or an equally objectionable variation of...

  3. 7 CFR 51.642 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.642 Section 51.642 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing...) Definitions § 51.642 Damage. Damage means any specific defect described in § 51.652, Table IV; or an...

  4. 7 CFR 51.1833 - Serious damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Serious damage. 51.1833 Section 51.1833 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Florida Tangerines Definitions § 51.1833 Serious damage. Serious damage means...

  5. 46 CFR 390.12 - Liquidated damages.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 8 2011-10-01 2011-10-01 false Liquidated damages. 390.12 Section 390.12 Shipping... CONSTRUCTION FUND § 390.12 Liquidated damages. (a) Liquidated damages—(1) In general. Each agreement entered into under Chapter 535 shall contain a liquidated damages provision for the purpose of placing...

  6. 7 CFR 51.1355 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Damage. 51.1355 Section 51.1355 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Pears for Canning Definitions § 51.1355 Damage. Damage means any injury or defect...

  7. 7 CFR 51.3749 - Serious damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Serious damage. 51.3749 Section 51.3749 Agriculture... Standards for Grades of Honey Dew and Honey Ball Type Melons Definitions § 51.3749 Serious damage. Serious damage means any defect or any combination of defects which seriously detracts from the appearance,...

  8. 7 CFR 51.1163 - Damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Damage. 51.1163 Section 51.1163 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... § 51.1163 Damage. Damage means any specific defect described in § 51.1175, Table I; or an...

  9. 7 CFR 51.1826 - Damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Damage. 51.1826 Section 51.1826 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Damage. Damage means any specific defect described in § 51.1837, Table I; or an equally...

  10. 7 CFR 51.1163 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Damage. 51.1163 Section 51.1163 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Florida Oranges and Tangelos Definitions § 51.1163 Damage. Damage means any...

  11. 7 CFR 51.1170 - Serious damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Serious damage. 51.1170 Section 51.1170 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... § 51.1170 Serious damage. Serious damage means any specific defect described in § 51.1175, Table I;...

  12. 7 CFR 51.702 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.702 Section 51.702 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... § 51.702 Damage. Damage means any specific defect described in § 51.713, Table IV; or an...

  13. 7 CFR 51.1358 - Serious damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Serious damage. 51.1358 Section 51.1358 Agriculture..., CERTIFICATION, AND STANDARDS) United States Standards for Pears for Canning Definitions § 51.1358 Serious damage. Serious damage means any injury or defect which cannot be removed during the usual commercial...

  14. 7 CFR 51.646 - Serious damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Serious damage. 51.646 Section 51.646 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing...) Definitions § 51.646 Serious damage. Serious damage means any specific defect described in § 51.652, Table...

  15. 7 CFR 51.2721 - Damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Damage. 51.2721 Section 51.2721 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Damage. Damage means that the peanut kernel is affected by one or more of the following: (a) Rancidity...

  16. 7 CFR 51.777 - Serious damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Serious damage. 51.777 Section 51.777 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Florida Grapefruit Definitions § 51.777 Serious damage. Serious damage means...

  17. 7 CFR 51.777 - Serious damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Serious damage. 51.777 Section 51.777 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Florida Grapefruit Definitions § 51.777 Serious damage. Serious damage means...

  18. 7 CFR 51.642 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Damage. 51.642 Section 51.642 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing...) Definitions § 51.642 Damage. Damage means any specific defect described in § 51.652, Table IV; or an...

  19. 7 CFR 51.773 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Damage. 51.773 Section 51.773 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Florida Grapefruit Definitions § 51.773 Damage. Damage means any specific...

  20. 7 CFR 51.1826 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Damage. 51.1826 Section 51.1826 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Florida Tangerines Definitions § 51.1826 Damage. Damage means any specific...

  1. 7 CFR 51.708 - Serious damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Serious damage. 51.708 Section 51.708 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing..., California, and Arizona) Definitions § 51.708 Serious damage. Serious damage means any specific...

  2. 7 CFR 51.777 - Serious damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Serious damage. 51.777 Section 51.777 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Serious damage. Serious damage means any specific defect described in § 51.784, Table I; or an...

  3. 7 CFR 51.1874 - Serious damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Serious damage. 51.1874 Section 51.1874 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Fresh Tomatoes 1 Definitions § 51.1874 Serious damage. Serious damage means any...

  4. 7 CFR 51.1874 - Serious damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Serious damage. 51.1874 Section 51.1874 Agriculture..., CERTIFICATION, AND STANDARDS) United States Standards for Fresh Tomatoes 1 Definitions § 51.1874 Serious damage. Serious damage means any specific defect described in § 51.1877, table II; or an equally...

  5. 46 CFR 390.12 - Liquidated damages.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 8 2012-10-01 2012-10-01 false Liquidated damages. 390.12 Section 390.12 Shipping... CONSTRUCTION FUND § 390.12 Liquidated damages. (a) Liquidated damages—(1) In general. Each agreement entered into under Chapter 535 shall contain a liquidated damages provision for the purpose of placing...

  6. 7 CFR 51.2003 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Damage. 51.2003 Section 51.2003 Agriculture... Standards for Grades of Filberts in the Shell 1 Definitions § 51.2003 Damage. Damage means any specific... or marketing quality of the filberts. The following specific defects shall be considered as...

  7. 7 CFR 51.2763 - Damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Damage. 51.2763 Section 51.2763 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Damage. Damage means that the peanut kernel is affected by one or more of the following: (a) Rancidity...

  8. 46 CFR 172.050 - Damage stability.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 7 2012-10-01 2012-10-01 false Damage stability. 172.050 Section 172.050 Shipping COAST... This Chapter § 172.050 Damage stability. (a) Each tank barge is assigned a hull type number by the... mm) of positive GM in each condition of loading and operation after assuming the damage specified...

  9. 7 CFR 51.1826 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.1826 Section 51.1826 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Florida Tangerines Definitions § 51.1826 Damage. Damage means any specific...

  10. 7 CFR 51.646 - Serious damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Serious damage. 51.646 Section 51.646 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Florida, California, and Arizona) Definitions § 51.646 Serious damage. Serious damage means any...

  11. 7 CFR 51.1355 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Damage. 51.1355 Section 51.1355 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Pears for Canning Definitions § 51.1355 Damage. Damage means any injury or defect...

  12. 7 CFR 51.2721 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Damage. 51.2721 Section 51.2721 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Shelled Runner Type Peanuts Definitions § 51.2721 Damage. Damage means that the peanut...

  13. 7 CFR 51.1170 - Serious damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Serious damage. 51.1170 Section 51.1170 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... § 51.1170 Serious damage. Serious damage means any specific defect described in § 51.1175, Table I;...

  14. 7 CFR 51.773 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.773 Section 51.773 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Florida Grapefruit Definitions § 51.773 Damage. Damage means any specific...

  15. 7 CFR 51.2721 - Damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Damage. 51.2721 Section 51.2721 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Damage. Damage means that the peanut kernel is affected by one or more of the following: (a) Rancidity...

  16. 46 CFR 172.103 - Damage stability.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 7 2012-10-01 2012-10-01 false Damage stability. 172.103 Section 172.103 Shipping COAST... Subchapter O of This Chapter § 172.103 Damage stability. Each tank barge must be shown by design calculations to meet the survival conditions in § 172.110 assuming the damage specified in § 172.104 to the...

  17. 7 CFR 51.708 - Serious damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Serious damage. 51.708 Section 51.708 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing..., California, and Arizona) Definitions § 51.708 Serious damage. Serious damage means any specific...

  18. 7 CFR 51.1874 - Serious damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Serious damage. 51.1874 Section 51.1874 Agriculture..., CERTIFICATION, AND STANDARDS) United States Standards for Fresh Tomatoes 1 Definitions § 51.1874 Serious damage. Serious damage means any specific defect described in § 51.1877, table II; or an equally...

  19. 7 CFR 51.1826 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Damage. 51.1826 Section 51.1826 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Florida Tangerines Definitions § 51.1826 Damage. Damage means any specific...

  20. 7 CFR 51.2721 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Damage. 51.2721 Section 51.2721 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Shelled Runner Type Peanuts Definitions § 51.2721 Damage. Damage means that the peanut...

  1. 7 CFR 51.908 - Serious damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Serious damage. 51.908 Section 51.908 Agriculture... Standards for Grades of Table Grapes (European or Vinifera Type) 1 Definitions § 51.908 Serious damage. Serious damage means any defect or any combination of defects which seriously detracts from the...

  2. 7 CFR 51.1871 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Damage. 51.1871 Section 51.1871 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Fresh Tomatoes 1 Definitions § 51.1871 Damage. Damage means any specific defect described...

  3. 7 CFR 51.702 - Damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Damage. 51.702 Section 51.702 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing..., California, and Arizona) Definitions § 51.702 Damage. Damage means any specific defect described in §...

  4. 7 CFR 51.2763 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Damage. 51.2763 Section 51.2763 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Shelled Virginia Type Peanuts Definitions § 51.2763 Damage. Damage means that the...

  5. 7 CFR 51.1163 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.1163 Section 51.1163 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Florida Oranges and Tangelos Definitions § 51.1163 Damage. Damage means any...

  6. 46 CFR 172.103 - Damage stability.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 7 2014-10-01 2014-10-01 false Damage stability. 172.103 Section 172.103 Shipping COAST... Subchapter O of This Chapter § 172.103 Damage stability. Each tank barge must be shown by design calculations to meet the survival conditions in § 172.110 assuming the damage specified in § 172.104 to the...

  7. 7 CFR 51.1358 - Serious damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Serious damage. 51.1358 Section 51.1358 Agriculture..., CERTIFICATION, AND STANDARDS) United States Standards for Pears for Canning Definitions § 51.1358 Serious damage. Serious damage means any injury or defect which cannot be removed during the usual commercial...

  8. 46 CFR 172.050 - Damage stability.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 7 2014-10-01 2014-10-01 false Damage stability. 172.050 Section 172.050 Shipping COAST... This Chapter § 172.050 Damage stability. (a) Each tank barge is assigned a hull type number by the... mm) of positive GM in each condition of loading and operation after assuming the damage specified...

  9. 7 CFR 51.646 - Serious damage.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 2 2013-01-01 2013-01-01 false Serious damage. 51.646 Section 51.646 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Florida, California, and Arizona) Definitions § 51.646 Serious damage. Serious damage means any...

  10. 7 CFR 51.642 - Damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Damage. 51.642 Section 51.642 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Florida, California, and Arizona) Definitions § 51.642 Damage. Damage means any specific defect...

  11. 7 CFR 51.1561 - Serious damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Serious damage. 51.1561 Section 51.1561 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Potatoes 1 Definitions § 51.1561 Serious damage. Serious damage means any defect,...

  12. 46 CFR 390.12 - Liquidated damages.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 8 2014-10-01 2014-10-01 false Liquidated damages. 390.12 Section 390.12 Shipping... CONSTRUCTION FUND § 390.12 Liquidated damages. (a) Liquidated damages—(1) In general. Each agreement entered into under Chapter 535 shall contain a liquidated damages provision for the purpose of placing...

  13. 7 CFR 51.777 - Serious damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Serious damage. 51.777 Section 51.777 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Florida Grapefruit Definitions § 51.777 Serious damage. Serious damage means...

  14. 7 CFR 51.1561 - Serious damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Serious damage. 51.1561 Section 51.1561 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Potatoes 1 Definitions § 51.1561 Serious damage. Serious damage means any defect,...

  15. 7 CFR 51.1874 - Serious damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Serious damage. 51.1874 Section 51.1874 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Fresh Tomatoes 1 Definitions § 51.1874 Serious damage. Serious damage means any...

  16. 7 CFR 51.908 - Serious damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Serious damage. 51.908 Section 51.908 Agriculture... Standards for Grades of Table Grapes (European or Vinifera Type) 1 Definitions § 51.908 Serious damage. Serious damage means any defect or any combination of defects which seriously detracts from the...

  17. 7 CFR 51.1833 - Serious damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Serious damage. 51.1833 Section 51.1833 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Florida Tangerines Definitions § 51.1833 Serious damage. Serious damage means...

  18. 7 CFR 51.1358 - Serious damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Serious damage. 51.1358 Section 51.1358 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Pears for Canning Definitions § 51.1358 Serious damage. Serious damage means any injury...

  19. 7 CFR 51.2129 - Serious damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Serious damage. 51.2129 Section 51.2129 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Shelled Almonds Definitions § 51.2129 Serious damage. Serious damage means...

  20. 7 CFR 51.646 - Serious damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Serious damage. 51.646 Section 51.646 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing...) Definitions § 51.646 Serious damage. Serious damage means any specific defect described in § 51.652, Table...

  1. 7 CFR 51.708 - Serious damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Serious damage. 51.708 Section 51.708 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... § 51.708 Serious damage. Serious damage means any specific defect described in § 51.713, Table IV;...

  2. Damage Caused by the Rogue Trustee

    ERIC Educational Resources Information Center

    O'Banion, Terry

    2009-01-01

    Fifty-nine community college presidents and chancellors in 16 states report on the damage caused by rogue trustees. While the damage to presidents, other trustees, and faculty and staff is alarming, the damage these trustees cause the college suggests that the rogue trustee may be the single most destructive force ever to plague an educational…

  3. 7 CFR 51.901 - Damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Standards for Grades of Table Grapes (European or Vinifera Type) 1 Definitions § 51.901 Damage. Damage means... following shall be considered as damage to stems: (1) Active powdery mildew or any other disease when... by mildew or other disease constrict or weaken any part of the main or lateral stems; and,...

  4. 7 CFR 51.901 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Standards for Grades of Table Grapes (European or Vinifera Type) 1 Definitions § 51.901 Damage. Damage means... following shall be considered as damage to stems: (1) Active powdery mildew or any other disease when... by mildew or other disease constrict or weaken any part of the main or lateral stems; and,...

  5. 7 CFR 51.901 - Damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Standards for Grades of Table Grapes (European or Vinifera Type) 1 Definitions § 51.901 Damage. Damage means... following shall be considered as damage to stems: (1) Active powdery mildew or any other disease when... by mildew or other disease constrict or weaken any part of the main or lateral stems; and,...

  6. 7 CFR 51.2293 - Serious damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Serious damage. 51.2293 Section 51.2293 Agriculture... Standards for Shelled English Walnuts (Juglans Regia) Definitions § 51.2293 Serious damage. Serious damage... severely shriveled, or a greater area is affected by lesser degrees of shriveling producing an...

  7. 7 CFR 51.1010 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.1010 Section 51.1010 Agriculture... Standards for Persian (Tahiti) Limes Definitions § 51.1010 Damage. Damage means any defect which materially... area of a circle one-fourth inch in diameter; (c) Exanthema (ammoniation) which materially...

  8. 7 CFR 51.2966 - Serious damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Serious damage. 51.2966 Section 51.2966 Agriculture... Standards for Grades of Walnuts in the Shell Definitions § 51.2966 Serious damage. Serious damage means any... discoloration covering a smaller area if the appearance is equally objectionable; (b) Perforated shells when...

  9. 7 CFR 51.1015 - Serious damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Serious damage. 51.1015 Section 51.1015 Agriculture... Standards for Persian (Tahiti) Limes Definitions § 51.1015 Serious damage. Serious damage means any defect... in the aggregate exceeds the area of a circle one-half inch in diameter; (c) Exanthema...

  10. 7 CFR 51.2293 - Serious damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Serious damage. 51.2293 Section 51.2293 Agriculture... § 51.2293 Serious damage. Serious damage means any defect, other than color, which seriously affects... more than one-fourth of the kernel is severely shriveled, or a greater area is affected by...

  11. 7 CFR 51.2292 - Damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Damage. 51.2292 Section 51.2292 Agriculture... § 51.2292 Damage. Damage means any defect, other than color, which materially affects the appearance... of the portion of kernel is severely shriveled, or a greater area is affected by lesser degrees...

  12. 7 CFR 51.3064 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.3064 Section 51.3064 Agriculture... Standards for Florida Avocados Definitions § 51.3064 Damage. Damage means any defect which materially... area exceeds that of a rectangle 1 inch in length and one-eighth inch in width, or when healed and...

  13. 7 CFR 51.2852 - Serious damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Serious damage. 51.2852 Section 51.2852 Agriculture... Creole Types) Definitions § 51.2852 Serious damage. Serious damage means any specific defect described in... affecting an area equivalent to that of a circle 1 inch in diameter on an onion 23/4 inches in diameter,...

  14. 7 CFR 51.573 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.573 Section 51.573 Agriculture Regulations... Standards for Celery Definitions § 51.573 Damage. Damage, unless otherwise specifically defined in this... of the stalk or 8 inches in length (see §§ 51.587 and 51.588); (e) Dirt when there is caked dirt...

  15. 7 CFR 51.2655 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.2655 Section 51.2655 Agriculture... Standards for Grades for Sweet Cherries 1 Definitions § 51.2655 Damage. Damage means any specific defect... appearance; (c) Hail injury when deep or not well healed, or when the aggregate area exceeds the area of...

  16. 7 CFR 51.1413 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.1413 Section 51.1413 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Pecans in the Shell 1 Definitions § 51.1413 Damage. Damage means any specific...

  17. 7 CFR 51.493 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.493 Section 51.493 Agriculture Regulations... Standards for Grades of Cantaloups 1 Definitions § 51.493 Damage. Damage means any specific defect described... discoloration affects an aggregate area exceeding 20 percent of the surface of the cantaloup; or when...

  18. 7 CFR 51.2128 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.2128 Section 51.2128 Agriculture... Standards for Grades of Shelled Almonds Definitions § 51.2128 Damage. Damage means any defect which... the affected area on an individual kernel aggregates more than the equivalent of a circle...

  19. 7 CFR 51.1586 - Serious damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Serious damage. 51.1586 Section 51.1586 Agriculture... Consumer Standards for Potatoes Definitions § 51.1586 Serious damage. Serious damage means any injury or... of more than 10 percent of the total weight of the potato including peel covering defective area....

  20. 7 CFR 51.1449 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.1449 Section 51.1449 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Shelled Pecans Definitions § 51.1449 Damage. Damage means any specific...

  1. 7 CFR 51.1450 - Serious damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Serious damage. 51.1450 Section 51.1450 Agriculture... Standards for Grades of Shelled Pecans Definitions § 51.1450 Serious damage. Serious damage means any... of two or more spots affect an area of more than 10 percent of the surface of the half-kernel...

  2. 7 CFR 51.2292 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.2292 Section 51.2292 Agriculture... Standards for Shelled English Walnuts (Juglans Regia) Definitions § 51.2292 Damage. Damage means any defect..., or a greater area is affected by lesser degrees of shriveling producing an equally...

  3. 7 CFR 51.2849 - Damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Damage. 51.2849 Section 51.2849 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Creole Types) Definitions § 51.2849 Damage. Damage means any specific defect described in this...

  4. 7 CFR 51.1583 - Damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Damage. 51.1583 Section 51.1583 Agriculture... Consumer Standards for Potatoes Definitions § 51.1583 Damage. Damage means any injury or defect which... of the total weight of the potato including peel covering defective area. Loss of outer...

  5. 7 CFR 51.573 - Damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Damage. 51.573 Section 51.573 Agriculture Regulations..., CERTIFICATION, AND STANDARDS) United States Standards for Celery Definitions § 51.573 Damage. Damage, unless... §§ 51.587 and 51.588); (e) Dirt when there is caked dirt on the stalk, or when dirt is present...

  6. 7 CFR 51.3210 - Serious damage.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Serious damage. 51.3210 Section 51.3210 Agriculture... § 51.3210 Serious damage. Serious damage unless otherwise specifically defined in this section, means... affecting an area equivalent to that of a circle 1 inch in diameter on an onion 23/4 inches in diameter,...

  7. 7 CFR 51.586 - Serious damage.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Serious damage. 51.586 Section 51.586 Agriculture... Standards for Celery Definitions § 51.586 Serious damage. Serious damage, unless otherwise specifically... seedstem exceeds 3 times the diameter of the stalk (see §§ 51.587 and 51.588); (e) Dirt when dirt is...

  8. 7 CFR 51.1911 - Damaged.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... FRESH FRUITS, VEGETABLES AND OTHER PRODUCTS 1,2 (INSPECTION, CERTIFICATION, AND STANDARDS) United States Consumer Standards for Fresh Tomatoes Definitions § 51.1911 Damaged. Damaged means any defect which... the fruit. Such scars damage the tomato when they are rough or deep, or when channels extend into...

  9. 7 CFR 51.1911 - Damaged.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... FRESH FRUITS, VEGETABLES AND OTHER PRODUCTS 1,2 (INSPECTION, CERTIFICATION, AND STANDARDS) United States Consumer Standards for Fresh Tomatoes Definitions § 51.1911 Damaged. Damaged means any defect which... the fruit. Such scars damage the tomato when they are rough or deep, or when channels extend into...

  10. 7 CFR 51.2933 - Serious damage.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Standards for Grades of Apricots Definitions § 51.2933 Serious damage. Serious Damage means any specific... or shipping quality of the apricot. The dimensions given for these defects are based on an apricot... larger or smaller apricots. The following specific defects shall be considered as serious damage:...

  11. 7 CFR 51.2933 - Serious damage.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Standards for Grades of Apricots Definitions § 51.2933 Serious damage. Serious Damage means any specific... or shipping quality of the apricot. The dimensions given for these defects are based on an apricot... larger or smaller apricots. The following specific defects shall be considered as serious damage:...

  12. Targeting DNA damage response in cancer therapy

    PubMed Central

    Hosoya, Noriko; Miyagawa, Kiyoshi

    2014-01-01

    Cancer chemotherapy and radiotherapy are designed to kill cancer cells mostly by inducing DNA damage. DNA damage is normally recognized and repaired by the intrinsic DNA damage response machinery. If the damaged lesions are successfully repaired, the cells will survive. In order to specifically and effectively kill cancer cells by therapies that induce DNA damage, it is important to take advantage of specific abnormalities in the DNA damage response machinery that are present in cancer cells but not in normal cells. Such properties of cancer cells can provide biomarkers or targets for sensitization. For example, defects or upregulation of the specific pathways that recognize or repair specific types of DNA damage can serve as biomarkers of favorable or poor response to therapies that induce such types of DNA damage. Inhibition of a DNA damage response pathway may enhance the therapeutic effects in combination with the DNA-damaging agents. Moreover, it may also be useful as a monotherapy when it achieves synthetic lethality, in which inhibition of a complementary DNA damage response pathway selectively kills cancer cells that have a defect in a particular DNA repair pathway. The most striking application of this strategy is the treatment of cancers deficient in homologous recombination by poly(ADP-ribose) polymerase inhibitors. In this review, we describe the impact of targeting the cancer-specific aberrations in the DNA damage response by explaining how these treatment strategies are currently being evaluated in preclinical or clinical trials. PMID:24484288

  13. A Binary-Encounter-Bethe Approach to Simulate DNA Damage by the Direct Effect

    NASA Technical Reports Server (NTRS)

    Plante, Ianik; Cucinotta, Francis A.

    2013-01-01

    The DNA damage is of crucial importance in the understanding of the effects of ionizing radiation. The main mechanisms of DNA damage are by the direct effect of radiation (e.g. direct ionization) and by indirect effect (e.g. damage by.OH radicals created by the radiolysis of water). Despite years of research in this area, many questions on the formation of DNA damage remains. To refine existing DNA damage models, an approach based on the Binary-Encounter-Bethe (BEB) model was developed[1]. This model calculates differential cross sections for ionization of the molecular orbitals of the DNA bases, sugars and phosphates using the electron binding energy, the mean kinetic energy and the occupancy number of the orbital. This cross section has an analytic form which is quite convenient to use and allows the sampling of the energy loss occurring during an ionization event. To simulate the radiation track structure, the code RITRACKS developed at the NASA Johnson Space Center is used[2]. This code calculates all the energy deposition events and the formation of the radiolytic species by the ion and the secondary electrons as well. We have also developed a technique to use the integrated BEB cross section for the bases, sugar and phosphates in the radiation transport code RITRACKS. These techniques should allow the simulation of DNA damage by ionizing radiation, and understanding of the formation of double-strand breaks caused by clustered damage in different conditions.

  14. Role of the translationally controlled tumor protein in DNA damage sensing and repair.

    PubMed

    Zhang, Jie; de Toledo, Sonia M; Pandey, Badri N; Guo, Guozheng; Pain, Debkumar; Li, Hong; Azzam, Edouard I

    2012-04-17

    The translationally controlled tumor protein (TCTP) is essential for survival by mechanisms that as yet are incompletely defined. Here we describe an important role of TCTP in response to DNA damage. Upon exposure of normal human cells to low-dose γ rays, the TCTP protein level was greatly increased, with a significant enrichment in nuclei. TCTP up-regulation occurred in a manner dependent on ataxia-telangiectasia mutated (ATM) kinase and the DNA-dependent protein kinase and was associated with protective effects against DNA damage. In chromatin of irradiated cells, coimmunoprecipitation experiments showed that TCTP forms a complex with ATM and γH2A.X, in agreement with its distinct localization with the foci of the DNA damage-marker proteins γH2A.X, 53BP1, and P-ATM. In cells lacking TCTP, repair of chromosomal damage induced by γ rays was compromised significantly. TCTP also was shown to interact with p53 and the DNA-binding subunits, Ku70 and Ku80, of DNA-dependent protein kinase. TCTP knockdown led to decreased levels of Ku70 and Ku80 in nuclei of irradiated cells and attenuated their DNA-binding activity. It also attenuated the radiation-induced G(1) delay but prolonged the G(2) delay. TCTP therefore may play a critical role in maintaining genomic integrity in response to DNA-damaging agents. PMID:22451927

  15. Multi-Dimensional Damage Detection

    NASA Technical Reports Server (NTRS)

    Gibson, Tracy L. (Inventor); Williams, Martha K. (Inventor); Lewis, Mark E. (Inventor); Roberson, Luke B. (Inventor); Snyder, Sarah J. (Inventor); Medelius, Pedro J. (Inventor)

    2016-01-01

    Methods and systems may provide for a structure having a plurality of interconnected panels, wherein each panel has a plurality of detection layers separated from one another by one or more non-detection layers. The plurality of detection layers may form a grid of conductive traces. Additionally, a monitor may be coupled to each grid of conductive traces, wherein the monitor is configured to detect damage to the plurality of interconnected panels in response to an electrical property change with respect to one or more of the conductive traces. In one example, the structure is part of an inflatable space platform such as a spacecraft or habitat.

  16. Tetracycline in uranyl nitrate intoxication: Its action on renal damage and U retention in bone

    SciTech Connect

    Guglielmotti, M.B.; Ubios, A.M.; Larumbe, J.; Cabrini, R.L. )

    1989-09-01

    In acute intoxication, uranium (U) not only inhibits bone formation but its excretion in urine also causes renal damage. The former effect is ameliorated by tetracycline (TC), probably due to its chelation property, which might also prevent U deposition in bone. Chemical determination of U incorporated in bone and a histological study of the kidneys were performed on animals injected with U and then treated with TC. The results showed that TC was unable to prevent the binding of U to bone while it exacerbated U-induced renal damage.

  17. Mitochonic Acid 5 Binds Mitochondria and Ameliorates Renal Tubular and Cardiac Myocyte Damage.

    PubMed

    Suzuki, Takehiro; Yamaguchi, Hiroaki; Kikusato, Motoi; Hashizume, Osamu; Nagatoishi, Satoru; Matsuo, Akihiro; Sato, Takeya; Kudo, Tai; Matsuhashi, Tetsuro; Murayama, Kazutaka; Ohba, Yuki; Watanabe, Shun; Kanno, Shin-Ichiro; Minaki, Daichi; Saigusa, Daisuke; Shinbo, Hiroko; Mori, Nobuyoshi; Yuri, Akinori; Yokoro, Miyuki; Mishima, Eikan; Shima, Hisato; Akiyama, Yasutoshi; Takeuchi, Yoichi; Kikuchi, Koichi; Toyohara, Takafumi; Suzuki, Chitose; Ichimura, Takaharu; Anzai, Jun-Ichi; Kohzuki, Masahiro; Mano, Nariyasu; Kure, Shigeo; Yanagisawa, Teruyuki; Tomioka, Yoshihisa; Toyomizu, Masaaki; Tsumoto, Kohei; Nakada, Kazuto; Bonventre, Joseph V; Ito, Sadayoshi; Osaka, Hitoshi; Hayashi, Ken-Ichi; Abe, Takaaki

    2016-07-01

    Mitochondrial dysfunction causes increased oxidative stress and depletion of ATP, which are involved in the etiology of a variety of renal diseases, such as CKD, AKI, and steroid-resistant nephrotic syndrome. Antioxidant therapies are being investigated, but clinical outcomes have yet to be determined. Recently, we reported that a newly synthesized indole derivative, mitochonic acid 5 (MA-5), increases cellular ATP level and survival of fibroblasts from patients with mitochondrial disease. MA-5 modulates mitochondrial ATP synthesis independently of oxidative phosphorylation and the electron transport chain. Here, we further investigated the mechanism of action for MA-5. Administration of MA-5 to an ischemia-reperfusion injury model and a cisplatin-induced nephropathy model improved renal function. In in vitro bioenergetic studies, MA-5 facilitated ATP production and reduced the level of mitochondrial reactive oxygen species (ROS) without affecting activity of mitochondrial complexes I-IV. Additional assays revealed that MA-5 targets the mitochondrial protein mitofilin at the crista junction of the inner membrane. In Hep3B cells, overexpression of mitofilin increased the basal ATP level, and treatment with MA-5 amplified this effect. In a unique mitochondrial disease model (Mitomice with mitochondrial DNA deletion that mimics typical human mitochondrial disease phenotype), MA-5 improved the reduced cardiac and renal mitochondrial respiration and seemed to prolong survival, although statistical analysis of survival times could not be conducted. These results suggest that MA-5 functions in a manner differing from that of antioxidant therapy and could be a novel therapeutic drug for the treatment of cardiac and renal diseases associated with mitochondrial dysfunction. PMID:26609120

  18. Ductile damage model with void coalescence

    SciTech Connect

    Tonks, D.L.

    1995-03-01

    A general model for ductile damage in metals is presented. It includes damage induced by shear stress as well as damage caused by volumetric tension. Spallation is included as a special case. Strain induced damage is also treated. Void nucleation and growth are included and give rise to strain rate effects. Strain rate effects also arise in the model through elastic release wave propagation between damage centers. Underlying physics of the model is the nucleation, growth, and coalescence of voids in a plastically flowing solid. Implementation of the model in hydrocodes is discussed.

  19. Laser damage growth with picosecond pulses.

    PubMed

    Sozet, Martin; Neauport, Jérôme; Lavastre, Eric; Roquin, Nadja; Gallais, Laurent; Lamaignère, Laurent

    2016-05-15

    Laser-induced damage growth has been investigated in the subpicosecond regime at 1030 nm. We have herein studied the growth of damage sites initiated on a high-reflective dielectric coating under subsequent laser irradiations at a constant fluence. We show through an experimental approach that growth can be triggered for fluences as low as 50% of the intrinsic damage threshold of the mirror. Moreover, once growth starts, damage areas increase linearly with the number of laser shots. The behavior of defect-induced damage sites has been observed more extensively, and it appears that their growth probability depends on their initiation fluence. PMID:27176998

  20. Chimeric proteins for detection and quantitation of DNA mutations, DNA sequence variations, DNA damage and DNA mismatches

    DOEpatents

    McCutchen-Maloney, Sandra L.

    2002-01-01

    Chimeric proteins having both DNA mutation binding activity and nuclease activity are synthesized by recombinant technology. The proteins are of the general formula A-L-B and B-L-A where A is a peptide having DNA mutation binding activity, L is a linker and B is a peptide having nuclease activity. The chimeric proteins are useful for detection and identification of DNA sequence variations including DNA mutations (including DNA damage and mismatches) by binding to the DNA mutation and cutting the DNA once the DNA mutation is detected.

  1. Cholesterol binding to ion channels

    PubMed Central

    Levitan, Irena; Singh, Dev K.; Rosenhouse-Dantsker, Avia

    2014-01-01

    Numerous studies demonstrated that membrane cholesterol is a major regulator of ion channel function. The goal of this review is to discuss significant advances that have been recently achieved in elucidating the mechanisms responsible for cholesterol regulation of ion channels. The first major insight that comes from growing number of studies that based on the sterol specificity of cholesterol effects, show that several types of ion channels (nAChR, Kir, BK, TRPV) are regulated by specific sterol-protein interactions. This conclusion is supported by demonstrating direct saturable binding of cholesterol to a bacterial Kir channel. The second major advance in the field is the identification of putative cholesterol binding sites in several types of ion channels. These include sites at locations associated with the well-known cholesterol binding motif CRAC and its reversed form CARC in nAChR, BK, and TRPV, as well as novel cholesterol binding regions in Kir channels. Notably, in the majority of these channels, cholesterol is suggested to interact mainly with hydrophobic residues in non-annular regions of the channels being embedded in between transmembrane protein helices. We also discuss how identification of putative cholesterol binding sites is an essential step to understand the mechanistic basis of cholesterol-induced channel regulation. Clearly, however, these are only the first few steps in obtaining a general understanding of cholesterol-ion channels interactions and their roles in cellular and organ functions. PMID:24616704

  2. Cell damage seen from Chernobyl

    SciTech Connect

    Not Available

    1992-07-24

    The 30 kilometer radius forbidden zone around the Chernobyl atomic plant serves as a sobering reminder of the world's worst nuclear accident. But for former Soviet biologists, it's also a unique natural laboratory. And one scientist, Nadejda Gulaya of Kiev's Pallaguine Institute of Biochemistry, has been doing studies that she claims offer surprising evidence of Chernobyl's after-effects. Prolonged exposure to radioactive fallout from the 1986 accident, she says, has caused damage to cell membranes in both animals and humans. For the past year, Gulaya has been comparing tissues from animals such as mink, pigs, and rodents inhabiting the Chernobyl area with those from other parts of Ukraine. Her conclusion: Exposure to radiation has, in many cases, caused alterations to membrane phospholipids. These changes, are similar to those that disrupt cellular metabolism following exposure to oxidizing free radicals. Gulaya also has preliminary data from human studies. She claims to have found similar alterations in the neurons of people who have died since being exposed to Chernobyl radiation. That leads her to speculate that the frequent psychiatric disorders may not just be from mental stress or radiophobia, but might reflect actual damage to the central nervous system.

  3. [Space flight and peroxidative damage].

    PubMed

    Yang, Tang-bin; Zhong, Ping; Qu, Li-na; Yuan, Yan-hong

    2003-12-01

    Space flight is associated with an increase of peroxidative damage after returning to 1 g. The effect is more pronounced after long-duration space flight and can even last for several weeks after landing. In humans there is increased lipid peroxidation in erythrocyte membranes, reduced blood antioxidants, and increased urinary excretion of 8-iso-prostaglandin F2alpha, and 8-oxo-7, 8 dihydro-2 deoxyguanosine. Isoprostane 8-iso-prostaglandin F2alpha and 8-oxo-7, 8 dihydro-2 deoxyguanosine are markers for oxidative damage to lipids and DNA, respectively. The changes are attributed to a combination of energy deficiency that occurs during flight and substrate competition for amino acids occurring between repleted muscle and other tissues during the recovery phase. The observations in humans have been complemented by studies in rodents, which showed increased production of lipid peroxidation products and decreased antioxidant enzyme activity afterflight. The changes in rodents were attributed to the stress associated with re-entry into Earth's gravity. Reducing the imbalance between the production of endogenous oxidant defenses and oxidant production by increasing the supply antioxidants in diet may lessen the severity of the postflight increase in oxidative stress. PMID:15008196

  4. Lipid peroxidation and tissue damage.

    PubMed

    Mylonas, C; Kouretas, D

    1999-01-01

    In recent years it has become apparent that the oxidation of lipids, or lipid peroxidation, is a crucial step in the pathogenesis of several disease states in adult and infant patients. Lipid peroxidation is a process generated naturally in small amounts in the body, mainly by the effect of several reactive oxygen species (hydroxyl radical, hydrogen peroxide etc.). It can also be generated by the action of several phagocytes. These reactive oxygen species readily attack the polyunsaturated fatty acids of the fatty acid membrane, initiating a self-propagating chain reaction. The destruction of membrane lipids and the end-products of such lipid peroxidation reactions are especially dangerous for the viability of cells, even tissues. Enzymatic (catalase, superoxide dismutasse) and nonenzymatic (vitamins A and E) natural antioxidant defence mechanisms exist; however, these mechanisms may be overcome, causing lipid peroxidation to take place. Since lipid peroxidation is a self-propagating chain-reaction, the initial oxidation of only a few lipid molecules can result in significant tissue damage. Despite extensive research in the field of lipid peroxidation it has not yet been precisely determined if it is the cause or an effect of several pathological conditions. Lipid peroxidation has been implicated in disease states such as atherosclerosis, IBD, ROP, BPD, asthma, Parkinson's disease, kidney damage, preeclampsia and others. PMID:10459507

  5. Brittle damage models in DYNA2D

    SciTech Connect

    Faux, D.R.

    1997-09-01

    DYNA2D is an explicit Lagrangian finite element code used to model dynamic events where stress wave interactions influence the overall response of the system. DYNA2D is often used to model penetration problems involving ductile-to-ductile impacts; however, with the advent of the use of ceramics in the armor-anti-armor community and the need to model damage to laser optics components, good brittle damage models are now needed in DYNA2D. This report will detail the implementation of four brittle damage models in DYNA2D, three scalar damage models and one tensor damage model. These new brittle damage models are then used to predict experimental results from three distinctly different glass damage problems.

  6. Damage experiments in a cylindrical geometry

    SciTech Connect

    Kaul, Ann M

    2010-09-21

    Studying spallation damage with a cylindrical configuration allows for a natural recollection of the damaged material under proper driving conditions. Additionally, the damaged material can come to a complete rest without the application of further stopping forces. Specific areas of research include the damage initiation regime in convergent geometry, behavior of material recollected after damage, and effects of convergent geometry on the material response. Such experiments produce unique strain and shear stress states, motivating improvements in existing computational material models and increasing the predictive capabilities of codes. A LANL/VNIIEF joint experimental series has produced cylindrical aluminum failure initiation data and studied the behavior of material recollected after damage initiation and after complete failure. In addition to post-shot collection of the damaged target material for subsequent metallographic analysis, dynamic in-situ experimental diagnostics include velocimetry and transverse radial radiography. This paper will discuss the current experimental status.

  7. Wiring Damage Analyses for STS OV-103

    NASA Technical Reports Server (NTRS)

    Thomas, Walter, III

    2006-01-01

    This study investigated the Shuttle Program s belief that Space Transportation System (STS) wiring damage occurrences are random, that is, a constant occurrence rate. Using Problem Reporting and Corrective Action (PRACA)-derived data for STS Space Shuttle OV-103, wiring damage was observed to increase over the vehicle s life. Causal factors could include wiring physical deterioration, maintenance and inspection induced damage, and inspection process changes resulting in more damage events being reported. Induced damage effects cannot be resolved with existent data. Growth analysis (using Crow-AMSAA, or CA) resolved maintenance/inspection effects (e.g., heightened awareness) on all wire damages and indicated an overall increase since Challenger Return-to-Flight (RTF). An increasing failure or occurrence rate per flight cycle was seen for each wire damage mode; these (individual) rates were not affected by inspection process effects, within statistical error.

  8. Hypervelocity impact damage assessment for Space Station

    NASA Technical Reports Server (NTRS)

    Coronado, Alex R.; Gibbins, Martin N.; Stern, Paul H.

    1988-01-01

    To inhibit damage and limit the probability of penetration of the Space Station pressure wall by micrometeoroids and orbital debris, a shield placed away from the wall is used to form a double wall. To determine shield effectiveness and assess impact damage, existing test data were reviewed and additional testing was performed for Space Station double wall designs. Empirical spallation and penetration functions derived from the data show that shield thickness and impact angle affect the damage to the wall. Thick shields reduce wall damage for low angle impacts but increase damage for oblique impacts. Multilayer insulation between the shield and wall reduces impact damage to the wall. A relationship between impact velocity and spall damage to the wall is demonstrated. Preliminary test results on Li-Al shield material indicate possible improved effectiveness over Al shields.

  9. Two glycosylase families diffusively scan DNA using a wedge residue to probe for and identify oxidatively damaged bases

    PubMed Central

    Nelson, Shane R.; Dunn, Andrew R.; Kathe, Scott D.; Warshaw, David M.; Wallace, Susan S.

    2014-01-01

    DNA glycosylases are enzymes that perform the initial steps of base excision repair, the principal repair mechanism that identifies and removes endogenous damages that occur in an organism’s DNA. We characterized the motion of single molecules of three bacterial glycosylases that recognize oxidized bases, Fpg, Nei, and Nth, as they scan for damages on tightropes of λ DNA. We find that all three enzymes use a key “wedge residue” to scan for damage because mutation of this residue to an alanine results in faster diffusion. Moreover, all three enzymes bind longer and diffuse more slowly on DNA that contains the damages they recognize and remove. Using a sliding window approach to measure diffusion constants and a simple chemomechanical simulation, we demonstrate that these enzymes diffuse along DNA, pausing momentarily to interrogate random bases, and when a damaged base is recognized, they stop to evert and excise it. PMID:24799677

  10. Water binding in legume seeds

    NASA Technical Reports Server (NTRS)

    Vertucci, C. W.; Leopold, A. C.

    1987-01-01

    The physical status of water in seeds has a pivotal role in determining the physiological reactions that can take place in the dry state. Using water sorption isotherms from cotyledon and axis tissue of five leguminous seeds, the strength of water binding and the numbers of binding sites have been estimated using van't Hoff analyses and the D'Arcy/Watt equation. These parameters of water sorption are calculated for each of the three regions of water binding and for a range of temperatures. Water sorption characteristics are reflective of the chemical composition of the biological materials as well as the temperature at which hydration takes place. Changes in the sorption characteristics with temperature and hydration level may suggest hydration-induced structural changes in cellular components.

  11. Computational Prediction of RNA-Binding Proteins and Binding Sites

    PubMed Central

    Si, Jingna; Cui, Jing; Cheng, Jin; Wu, Rongling

    2015-01-01

    Proteins and RNA interaction have vital roles in many cellular processes such as protein synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and post-transcriptional levels. Approximately 6%–8% of all proteins are RNA-binding proteins (RBPs). Distinguishing these RBPs or their binding residues is a major aim of structural biology. Previously, a number of experimental methods were developed for the determination of protein–RNA interactions. However, these experimental methods are expensive, time-consuming, and labor-intensive. Alternatively, researchers have developed many computational approaches to predict RBPs and protein–RNA binding sites, by combining various machine learning methods and abundant sequence and/or structural features. There are three kinds of computational approaches, which are prediction from protein sequence, prediction from protein structure, and protein-RNA docking. In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and complexes, including data sets used in different approaches, sequence and structural features used in several predictors, prediction method classifications, performance comparisons, evaluation methods, and future directions. PMID:26540053

  12. Unusual monoclonal DNA binding immunoglobulin.

    PubMed

    Sawada, S; Iijima, S; Kuwana, K; Nishinarita, S; Takeuchi, J; Shida, M; Karasaki, M; Amaki, I

    1983-03-01

    The monoclonal antibodies directed against DNA were produced by somatic cell hybridization with parental cells (SP-2) and spleen cells from nonimmunized autoimmune MRL/lpr mice. The immunoglobulins were recovered from the culture supernatant from hybridoma by a solid immunoadsorbent and antibody immunoprecipitation. The results from the specificities of DNA binding monoclonal immunoglobulins suggest that the antibodies to DNA have the antibody combining sites for both epitope of double stranded helix and base of DNA and support the concept of the multiple antigen binding potentials of the hybridoma autoantibodies. PMID:6857646

  13. Projecting global tropical cyclone economic damages with validation of tropical cyclone economic damage model

    NASA Astrophysics Data System (ADS)

    Iseri, Y.; Iwasaki, A.; Miyazaki, C.; Kanae, S.

    2014-12-01

    Tropical cyclones (TCs) sometimes cause serious damages to human society and thus possible changes of TC properties in the future have been concerned. In fact, the Fifth Assessment Report (AR5) by IPCC (Intergovernmental Panel on Climate Change) mentions likely increasing in intensity and rain rate of TCs. In addition, future change of socioeconomic condition (e.g. population growth) might worsen TC impacts in the future. Thereby, in this study, we developed regression models to estimate economic damages by TCs (hereafter TC damage model), and employed those models to project TC economic damages under several future climate and socioeconomic scenarios. We developed the TC damage models for each of 4 regions; western North Pacific, North American, North Indian, and Southern Hemisphere. The inputs for TC damage model are tropical cyclone central pressure, populations in the area exposed by tropical cyclone wind, and GDP (Gross Domestic Product) per capita. The TC damage models we firstly developed tended to overestimate very low damages and also underestimate very high damages. Thereby we modified structure of TC damage models to improve model performance, and then executed extensive validation of the model. The modified model presented better performance in estimating very low and high TC damages. After the modification and validation of the model, we determined the structure of TC damage models and projected TC economic damages. The result indicated increase in TC economic damage in global scale, while TC economic damage against world GDP would decrease in the future, which result is consistent with previous study.

  14. RNA Bind-n-Seq: Measuring the Binding Affinity Landscape of RNA-Binding Proteins.

    PubMed

    Lambert, Nicole J; Robertson, Alex D; Burge, Christopher B

    2015-01-01

    RNA-binding proteins (RBPs) coordinate post-transcriptional control of gene expression, often through sequence-specific recognition of primary transcripts or mature messenger RNAs. Hundreds of RBPs are encoded in the human genome, most with undefined or incompletely defined biological roles. Understanding the function of these factors will require the identification of each RBP's distinct RNA binding specificity. RNA Bind-n-Seq (RBNS) is a high-throughput, cost-effective in vitro method capable of resolving sequence and secondary structure preferences of RBPs. Dissociation constants can also be inferred from RBNS data when provided with additional experimental information. Here, we describe the experimental procedures to perform RBNS and discuss important parameters of the method and ways that the experiment can be tailored to the specific RBP under study. Additionally, we present the conceptual framework and execution of the freely available RBNS computational pipeline and describe the outputs of the pipeline. Different approaches to quantify binding specificity, quality control metrics, and estimation of binding constants are also covered. PMID:26068750

  15. The GOLPH3 pathway regulates Golgi shape and function and is activated by DNA damage

    PubMed Central

    Buschman, Matthew D.; Xing, Mengke; Field, Seth J.

    2015-01-01

    The Golgi protein GOLPH3 binds to PtdIns(4)P and MYO18A, linking the Golgi to the actin cytoskeleton. The GOLPH3 pathway is essential for vesicular trafficking from the Golgi to the plasma membrane. A side effect of GOLPH3-dependent trafficking is to generate the extended ribbon shape of the Golgi. Perturbation of the pathway results in changes to both Golgi morphology and secretion, with functional consequences for the cell. The cellular response to DNA damage provides an example of GOLPH3-mediated regulation of the Golgi. Upon DNA damage, DNA-PK phosphorylation of GOLPH3 increases binding to MYO18A, activating the GOLPH3 pathway, which consequently results in Golgi fragmentation, reduced trafficking, and enhanced cell survival. The PtdIns(4)P/GOLPH3/MYO18A/F-actin pathway provides new insight into the relationship between Golgi morphology and function, and their regulation. PMID:26500484

  16. Synthetic heparin-binding growth factor analogs

    DOEpatents

    Pena, Louis A.; Zamora, Paul; Lin, Xinhua; Glass, John D.

    2007-01-23

    The invention provides synthetic heparin-binding growth factor analogs having at least one peptide chain that binds a heparin-binding growth factor receptor, covalently bound to a hydrophobic linker, which is in turn covalently bound to a non-signaling peptide that includes a heparin-binding domain. The synthetic heparin-binding growth factor analogs are useful as soluble biologics or as surface coatings for medical devices.

  17. Gear Damage Detection Using Oil Debris Analysis

    NASA Technical Reports Server (NTRS)

    Dempsey, Paula J.

    2001-01-01

    The purpose of this paper was to verify, when using an oil debris sensor, that accumulated mass predicts gear pitting damage and to identify a method to set threshold limits for damaged gears. Oil debris data was collected from 8 experiments with no damage and 8 with pitting damage in the NASA Glenn Spur Gear Fatigue Rig. Oil debris feature analysis was performed on this data. Video images of damage progression were also collected from 6 of the experiments with pitting damage. During each test, data from an oil debris sensor was monitored and recorded for the occurrence of pitting damage. The data measured from the oil debris sensor during experiments with damage and with no damage was used to identify membership functions to build a simple fuzzy logic model. Using fuzzy logic techniques and the oil debris data, threshold limits were defined that discriminate between stages of pitting wear. Results indicate accumulated mass combined with fuzzy logic analysis techniques is a good predictor of pitting damage on spur gears.

  18. Rotor damage detection by using piezoelectric impedance

    NASA Astrophysics Data System (ADS)

    Qin, Y.; Tao, Y.; Mao, Y. F.

    2016-04-01

    Rotor is a core component of rotary machinery. Once the rotor has the damage, it may lead to a major accident. Thus the quantitative rotor damage detection method based on piezoelectric impedance is studied in this paper. With the governing equation of piezoelectric transducer (PZT) in a cylindrical coordinate, the displacement along the radius direction is derived. The charge of PZT is calculated by the electric displacement. Then, by the use of the obtained displacement and charge, an analytic piezoelectric impedance model of the rotor is built. Given the circular boundary condition of a rotor, annular elements are used as the analyzed objects and spectral element method is used to set up the damage detection model. The Electro-Mechanical (E/M) coupled impedance expression of an undamaged rotor is deduced with the application of a low-cost impedance test circuit. A Taylor expansion method is used to obtain the approximate E/M coupled impedance expression for the damaged rotor. After obtaining the difference between the undamaged and damaged rotor impedance, a rotor damage detection method is proposed. This method can directly calculate the change of bending stiffness of the structural elements, it follows that the rotor damage can be effectively detected. Finally, a preset damage configuration is used for the numerical simulation. The result shows that the quantitative damage detection algorithm based on spectral element method and piezoelectric impedance proposed in this paper can identify the location and the severity of the damaged rotor accurately.

  19. Nanofoams Response to Radiation Damage

    SciTech Connect

    Fu, Engang; Serrano De Caro, Magdalena; Wang, Yongqiang; Nastasi, Michael; Zepeda-Ruiz, Luis; Bringa, Eduardo M.; Baldwin, Jon K.; Caro, Jose A.

    2012-07-30

    Conclusions of this presentation are: (1) np-Au foams were successfully synthesized by de-alloying process; (2) np-Au foams remain porous structure after Ne ion irradiation to 1 dpa; (3) SFTs were observed in irradiated np-Au foams with highest and intermediate flux, while no SFTs were observed with lowest flux; (4) SFTs were observed in irradiated np-Au foams at RT, whereas no SFTs were observed at LNT irradiation; (5) The diffusivity of vacancies in Au at RT is high enough so that the vacancies have enough time to agglomerate and thus collapse. As a result, SFTs were formed; (6) The high flux created much more damage/time, vacancies don't have enough time to diffuse or recombine. As a result, SFTs were formed.

  20. Radiation damage in MINP cells

    NASA Astrophysics Data System (ADS)

    Minahan, J. A.; Green, M. J.

    Experiments have been carried out to examine the effects of exposure to various fluence levels of 1 MeV electrons on 0.2 ohm-cm MINP silicon solar cell characteristics. Fluence levels ranged from 10 to the 14th e/sq cm to 3 x 10 to the 15th e/sq cm. Minority carrier diffusion lengths, Lbase, were derived from short circuit current calculations that included corrections for surface shadowing, reflection and emitter contribution to the short circuit current. From Lbase and fluences, a damage coefficient for diffusion length was calculated (1.4 x 10 to the -9th/electron) and compared with results obtained for other cell designs and base resistivities.