Reductive cleavage of the peptide bond

NASA Technical Reports Server (NTRS)

Holian, J.; Garrison, W. M.

1973-01-01

In many biological research efforts, long chain organic molecules are studied by breaking large molecules into smaller components. Cleavage technique of recent interest is the use of solvated electrons. These are formed when aqueous solutions are bombarded with gamma radiation. Solvated electron is very reactive and can reduce most any species present, even to form free radicals.

[Cleavage of DNA fragments induced by UV nanosecond laser excitation at 193 nm].

PubMed

Vtiurina, N N; Grokhovskiĭ, S L; Filimonov, I V; Medvedkov, O I; Nechipurenko, D Iu; Vasil'ev, S A; Nechipurenko, Iu D

2011-01-01

The cleavage of dsDNA fragments in aqueous solution after irradiation with UV laser pulses at 193 nm has been studied. Samples were investigated using polyacrylamide gel electrophoresis. The intensity of damage of particular phosphodiester bond after hot alkali treatment was shown to depend on the base pair sequence. It was established that the probability of cleavage is twice higher for sites of DNA containing two or more successively running guanine residues. A possible mechanism of damage to the DNA molecule connected with the migration of holes along the helix is discussed.

Solution structure and backbone dynamics of an endopeptidase HycI from Escherichia coli: implications for mechanism of the [NiFe] hydrogenase maturation.

PubMed

Yang, Fan; Hu, Wei; Xu, Huimin; Li, Congmin; Xia, Bin; Jin, Changwen

2007-02-09

[NiFe] hydrogenases are metalloenzymes involved in many biological processes concerning the metabolism of hydrogen. The maturation of the large subunit of these hydrogenases requires the cleavage of a peptide at the C terminus by an endopeptidase before the final formation of the [NiFe] metallocenter. HycI is an endopeptidase of the M52 family and responsible for the C-terminal cleavage of the large subunit of hydrogenase 3 in Escherichia coli. Although extensive studies were performed, the molecular mechanism of recognition and cleavage of hydrogenase 3 remains elusive. Herein, we report the solution structure of E. coli HycI determined by high resolution nuclear magnetic resonance spectroscopy. This is the first solution structure of the apo form of endopeptidase of the M52 family reported thus far. The overall structure is similar to the crystal structure of holo-HybD in the same family. However, significant diversity was observed between the two structures. Especially, HycI shows an open conformation at the putative nickel-binding site, whereas HybD adopts a closed conformation. In addition, we performed backbone dynamic studies to probe the motional properties of the apo form of HycI. Furthermore, the metal ion titration experiments provide insightful information on the substrate recognition and cleavage processes. Taken together, our current structural, biochemical, and dynamic studies extend the knowledge of the M52 family proteins and provide novel insights into the biological function of HycI.

In situ coupling of chitosan onto polypropylene foils by an Atmospheric Pressure Air Glow Discharge with a liquid cathode.

PubMed

Nikitin, D; Choukourov, A; Titov, V; Kuzmicheva, L; Lipatova, I; Mezina, E; Aleksandriiskii, V; Shelemin, A; Khalakhan, I; Slavinska, D; Biederman, H

2016-12-10

Atmospheric air plasma treatment of chitosan solutions leads to degradation of chitosan molecules by OH radicals and is accompanied by a predominant cleavage of glycosidic linkages and by a decrease of the molecular weight. The degradation proceeds via first order kinetics with the rate constant of (5.73±0.22)×10(-6)s(-1) and the energetic yield of chitosan bond scission of (2.4±0.2)×10(-8)mol/J. Products of degradation together with intact chitosan molecules adsorb and form coatings on polypropylene foils immersed into the solution that is being plasma treated. The plasma treatment results in strong binding of chitosan to polypropylene due to the formation of covalent bonds between the activated polymer surface and chitosan molecules. Plasma-driven crosslinking is responsible for the accumulation of compressive stress which leads to the development of buckling instabilities in the chitosan coatings. Copyright © 2016 Elsevier Ltd. All rights reserved.

Cleavage reaction of HDV ribozymes in the presence of Mg2+ is accompanied by a conformational change.

PubMed

Tanaka, Yoichiro; Tagaya, Mitsuhiro; Hori, Tamaki; Sakamoto, Taiichi; Kurihara, Yasuyuki; Katahira, Masato; Uesugi, Seiichi

2002-06-01

Hepatitis delta virus (HDV) ribozymes cleave RNA in the presence of divalent metal ions. We have previously elucidated the solution conformation of a minimized trans-acting HDV ribozyme and obtained evidence by NMR study that an Mg2+ ion binds to a site close to the cleavage site. We examined two ribozyme systems: a pre-cleavage complex with a non-cleavable substrate analogue (mS8) and a post-cleavage complex with a 3' cleavage product (P7). Upon titration with MgCl2, the complex with P7 showed a profound spectral change, while that with mS8 showed broadening of the signals. Analysis of the NOESY spectra of the P7 complex at high Mg2+ concentration revealed that a G:U pair is formed within the L3 loop, and the P1 and P4 stems are stabilized with respect to those of the pre-cleavage complex. The present analysis indicates that the cleavage reaction of the HDV ribozyme produces a big conformational change. Furthermore, presence of the 5'-terminal cytidine residue prevents this conformational change and its absence stabilizes the product-ribozyme complex in the presence of Mg2+. The structure of the Mg2+-bound P7 complex is similar to the crystal structure found for a product-ribozyme complex but is different from the pre-cleavage structure.

Hydrogen storage and delivery: the carbon dioxide - formic acid couple.

PubMed

Laurenczy, Gábor

2011-01-01

Carbon dioxide and the carbonates, the available natural C1 sources, can be easily hydrogenated into formic acid and formates in water; the rate of this reduction strongly depends on the pH of the solution. This reaction is catalysed by ruthenium(II) pre-catalyst complexes with a large variety of water-soluble phosphine ligands; high conversions and turnover numbers have been realised. Although ruthenium(II) is predominant in these reactions, the iron(II) - tris[(2-diphenylphosphino)-ethyl]phosphine (PP3) complex is also active, showing a new perspective to use abundant and inexpensive iron-based compounds in the CO2 reduction. In the catalytic hydrogenation cycles the in situ formed metal hydride complexes play a key role, their structures with several other intermediates have been proven by multinuclear NMR spectroscopy. In the other hand safe and convenient hydrogen storage and supply is the fundamental question for the further development of the hydrogen economy; and carbon dioxide has been recognised to be a viable H2 vector. Formic acid--containing 4.4 weight % of H2, that is 53 g hydrogen per litre--is suitable for H2 storage; we have shown that in aqueous solutions it can be selectively decomposed into CO-free (CO < 10 ppm) CO2 and H2. The reaction takes place under mild experimental conditions and it is able to generate high pressure H2 (up to 600 bar). The cleavage of HCOOH is catalysed by several hydrophilic Ru(II) phosphine complexes (meta-trisulfonated triphenylphosphine, mTPPTS, being the most efficient one), either in homogeneous systems or as immobilised catalysts. We have also shown that the iron(II)--hydrido tris[(2-diphenylphosphino)ethyl]phosphine complex catalyses with an exceptionally high rate and efficiency (turnover frequency, TOF = 9425 h(-1)mol(-1); turnover number, TON = 92400) the formic acid cleavage, in environmentally friendly propylene carbonate solution, opening the way to use cheap, non-noble metal based catalysts for this reaction, too.

Oxidative cleavage of erucic acid for the synthesis of brassylic acid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mohammed J. Nasrullah; Pooja Thapliyal; Erica N. Pfarr

2010-10-29

The main focus of this work is to synthesize Brassylic Acid (BA) using oxidative cleavage of Erucic Acid (EA). Crambe (Crambe abyssinica) is an industrial oilseed grown in North Dakota. Crambe has potential as an industrial fatty acid feedstock as a source of Erucic acid (EA). It has approximately 50-60 % of EA, a C{sub 22} monounsaturated fatty acid. Oxidative cleavage of unsaturated fatty acids derived from oilseeds produces long chain (9, 11, and 13 carbon atoms) dibasic and monobasic acids. These acids are known commercial feedstocks for the preparation of nylons, polyesters, waxes, surfactants, and perfumes. Other sources ofmore » EA are Rapeseed seed oil which 50-60 % of EA. Rapeseed is grown outside USA. The oxidative cleavage of EA was done using a high throughput parallel pressure reactor system. Kinetics of the reaction shows that BA yields reach a saturation at 12 hours. H{sub 2}WO{sub 4} was found to be the best catalyst for the oxidative cleavage of EA. High yields of BA were obtained at 80 C with bubbling of O{sub 2} or 10 bar of O{sub 2} for 12 hours.« less

An ultraviolet crosslink in the hammerhead ribozyme dependent on 2-thiocytidine or 4-thiouridine substitution.

PubMed Central

Wang, L; Ruffner, D E

1997-01-01

The hammerhead domain is one of the smallest known ribozymes. Like other ribozymes it catalyzes site-specific cleavage of a phosphodiester bond. The hammerhead ribozyme has been the subject of a vast number of biochemical and structural studies aimed at determining the structure and mechanism of cleavage. Recently crystallographic analysis has produced a structure for the hammerhead. As the hammerhead is capable of undergoing cleavage within the crystal, it would appear that the crystal structure is representative of the catalytically active solution structure. However, the crystal structure conflicts with much of the biochemical data and reveals a catalytic metal ion binding site expected to be of very low affinity. Clearly, additional studies are needed to reconcile the discrepancies and provide a clear understanding of the structure and mechanism of the hammerhead ribozyme. Here we demonstrate that a unique crosslink can be induced in the hammerhead with 2-thiocytidine or 4-thiouridine substitution at different locations within the conserved core. Generation of the same crosslink with different modifications at different positions suggests that the structure trapped by the crosslink may be relevant to the catalytically active solution structure of the hammerhead ribozyme. As this crosslink appears to be incompatible with the crystal structure, this provides yet another indication that the active solution and crystal structures may differ significantly. PMID:9336468

Quantitative separation of murine leukemia virus proteins by reversed-phase high-pressure liquid chromatography reveals newly described gag and env cleavage products.

PubMed Central

Henderson, L E; Sowder, R; Copeland, T D; Smythers, G; Oroszlan, S

1984-01-01

The structural proteins of murine type C retroviruses are proteolytic cleavage products of two different precursor polyproteins coded by the viral gag and env genes. To further investigate the nature and number of proteolytic cleavages involved in virus maturation, we quantitatively isolated the structural proteins of the Rauscher and Moloney strains of type C murine leukemia virus (R-MuLV and M-MuLV, respectively) by reversed-phase high-pressure liquid chromatography. Proteins and polypeptides isolated from R-MuLV included p10, p12, p15, p30, p15(E), gp69, and gp71 and three previously undescribed virus components designated here as p10', p2(E), and p2(E). Homologous proteins and polypeptides were isolated from M-MuLV. Complete or partial amino acid sequences of all the proteins listed above were either determined in this study or were available in previous reports from this laboratory. These data were compared with those from the translation of the M-MuLV proviral DNA sequence (Shinnick et al., Nature [London] 293:543-548, 1981) to determine the exact nature of proteolytic cleavages for all the structural proteins described above and to determine the origin of p10' and p2(E)s. The results showed that, during proteolytic processing of gp80env from M-MuLV (M-gp 80env), a single Arg residue was excised between gp70 and p15(E) and a single peptide bond was cleaved between p15(E) and p2(E). The structure of M-gPr80env is gp70-(Arg)-p15(E)-p2(E). The data suggest that proteolytic cleavage sites in R-gp85env are identical to corresponding cleavage sites in M-gp80env. The p2(E)s are shown to be different genetic variants of p2(E) present in the uncloned-virus preparations. The data for R- and M-p10's shows that they are cleavage products of the gag precursor with the structure p10-Thr-Leu-Asp-Asp-OH. The complete structure of Pr65gag is p15-p12-p30-p10'. Stoichiometries of the gag and env cleavage products in mature R- and M-MuLV were determined. In each virus, gag cleavage products (p15, p12, p30, and p10 plus p10') were found in equimolar amounts and p15(E)s were equimolar with p2(E)s. The stoichiometry of gag to env cleavage products was 4:1. These data are consistent with the proposal that proteolytic processing of precursor polyproteins occurs after virus assembly and that the C-terminal portion of Pr15(E) [i.e., p15(E)-p2(E)] is located on the inner side of the lipid bilayer of the virus. Images PMID:6333515

The chemical stability of abasic RNA compared to abasic DNA

PubMed Central

Küpfer, Pascal A.; Leumann, Christian J.

2007-01-01

We describe the synthesis of an abasic RNA phosphoramidite carrying a photocleavable 1-(2-nitrophenyl)ethyl (NPE) group at the anomeric center and a triisopropylsilyloxymethyl (TOM) group as 2′-O-protecting group together with the analogous DNA and the 2′-OMe RNA abasic building blocks. These units were incorporated into RNA-, 2′-OMe-RNA- and DNA for the purpose of studying their chemical stabilities towards backbone cleavage in a comparative way. Stability measurements were performed under basic conditions (0.1 M NaOH) and in the presence of aniline (pH 4.6) at 37°C. The kinetics and mechanisms of strand cleavage were followed by High pressure liquid chromotography and ESI-MS. Under basic conditions, strand cleavage at abasic RNA sites can occur via β,δ-elimination and 2′,3′-cyclophosphate formation. We found that β,δ-elimination was 154-fold slower compared to the same mechanism in abasic DNA. Overall strand cleavage of abasic RNA (including cyclophosphate formation) was still 16.8 times slower compared to abasic DNA. In the presence of aniline at pH 4.6, where only β,δ-elimination contributes to strand cleavage, a 15-fold reduced cleavage rate at the RNA abasic site was observed. Thus abasic RNA is significantly more stable than abasic DNA. The higher stability of abasic RNA is discussed in the context of its potential biological role. PMID:17151071

The preparation and application of white graphene

NASA Astrophysics Data System (ADS)

Zhou, Chenghong

2014-12-01

In this article, another thin film named white graphene is introduced, containing its properties, preparation and potential applications. White graphene, which has the same structure with graphene but quite different electrical properties, can be exfoliated from its layered crystal, hexagonal boron nitride. Here two preparation methods of white graphene including supersonic cleavage and supercritical cleavage are presented. Inspired by the cleavage of graphene oxide, supersonic is applied to BN and few-layered films are obtained. Compared with supersonic cleavage, supercritical cleavage proves to be more successful. As supercritical fluid can diffuse into interlayer space of the layered hexagonal boron nitride easily, once reduce the pressure of the supercritical system fast, supercritical fluid among layers expands and escapes form interlayer, consequently exfoliating the hexagonal boron nitride into few layered structure. A series of characterization demonstrate that the monolayer white graphene prepared in the process matches its theoretical thickness 0.333nm and has lateral sizes at the order of 10μm. Supercritical cleavage proves to be successful and shows many advantages, such as good production quality and fast production cycle. Furthermore, the band energy of white graphene, which shows quite different from graphene, is simulated via tight-bonding in theory. The excellent properties will lead to extensive applications of white graphene. As white graphene has not received enough concern and exploration, it's potential to play a significant role in the fields of industry and science.

Catalyst system and process for benzyl ether fragmentation and coal liquefaction

DOEpatents

Zoeller, Joseph Robert

1998-04-28

Dibenzyl ether can be readily cleaved to form primarily benzaldehyde and toluene as products, along with minor amounts of bibenzyl and benzyl benzoate, in the presence of a catalyst system comprising a Group 6 metal, preferably molybdenum, a salt, and an organic halide. Although useful synthetically for the cleavage of benzyl ethers, this cleavage also represents a key model reaction for the liquefaction of coal; thus this catalyst system and process should be useful in coal liquefaction with the advantage of operating at significantly lower temperatures and pressures.

X-ray diffraction study of the molecular propolis films deposited from an alcohol solution onto the cleavage surfaces of layered V2VI3 compounds

NASA Astrophysics Data System (ADS)

Drapak, S. I.; Gavrylyuk, S. V.; Kaminskii, V. M.; Kovalyuk, Z. D.

2008-09-01

The structures of the molecular propolis films deposited from an alcohol solution on the (0001) cleavage surface of layered bismuth selenide and telluride are studied by X-ray diffraction. Despite the chemical interaction between the semiconductor substrates and the organic-substance components, the molecular structural ordering of the propolis films is shown to be identical to that in the films of this substance on the surface of amorphous glass substrates. The chemical and deformation interaction between the organic substance and the layered V2VI3 compounds is found to result in the formation of an organic-inorganic sandwich nanostructure at a distance of ˜0.3 μm from the layered crystal-propolis film interface.

The effects and regulatory mechanism of RIP3 on RGC-5 necroptosis following elevated hydrostatic pressure.

PubMed

Shang, Lei; Ding, Wei; Li, Na; Liao, Lvshuang; Chen, Dan; Huang, Jufang; Xiong, Kun

2017-02-06

Necroptosis is a type of regulated cell death that has been implicated in various diseases. Receptor-interacting protein 3 (RIP3), a member of the RIP family, is an important mediator of the necroptotic pathway. Cleavage of RIP3 at Asp328 by caspase-8 abolishes the kinase activity of RIP3, which is critical for necroptosis. Moreover, RIP3 is significantly upregulated during the early stages of acute high intra-ocular pressure and oxygen glucose deprivation. In this study, the effects of RIP3 during elevated hydrostatic pressure (EHP) were investigated and the possible mechanism through which caspase-8 regulated RIP3 cleavage was explored. Flow cytometry analysis revealed that the number of EHP-induced necrotic retinal ganglion cell 5 (RGC-5) cells was reduced after RIP3-knockdown. Furthermore, malondialdehyde (MDA) levels and glycogen phosphorylase (PYGL) activity in normal RGC-5 cells were much higher than those in RIP3-knockdown cells after EHP. EHP-induced RGC-5 necrosis was significantly reduced after treatment with butylated hydroxyanisole (BHA), a reactive oxygen species (ROS) scavenger. MDA levels and PYGL activity were lower in normal RGC-5 cells than those in cells with caspase-8 inhibition after EHP. Western blot analysis demonstrated that the RIP3 cleavage product was upregulated in cells with caspase-8 inhibition. Additionally, flow cytometry analysis revealed that the number of EHP-induced necrotic RGC-5 cells was increased after caspase-8 inhibition. Our results suggested that RGC-5 necroptosis following EHP was mediated by RIP3 through induction of PYGL activity and subsequent ROS accumulation. Thus, caspase-8 may participate in the regulation of RGC-5 necroptosis via RIP3 cleavage. © The Author 2016. Published by Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Familial Alzheimer’s mutations within APPTM increase Aβ42 production by enhancing accessibility of ɛ-cleavage site

NASA Astrophysics Data System (ADS)

Chen, Wen; Gamache, Eric; Rosenman, David J.; Xie, Jian; Lopez, Maria M.; Li, Yue-Ming; Wang, Chunyu

2014-01-01

The high Aβ42/Aβ40 production ratio is a hallmark of familial Alzheimer’s disease, which can be caused by mutations in the amyloid precursor protein (APP). The C-terminus of Aβ is generated by γ-secretase cleavage within the transmembrane domain of APP (APPTM), a process that is primed by an initial ɛ-cleavage at either T48 or L49, resulting in subsequent production of Aβ42 or Aβ40, respectively. Here we solve the dimer structures of wild-type APPTM (AAPTM WT) and mutant APPTM (FAD mutants V44M) with solution NMR. The right-handed APPTM helical dimer is mediated by GXXXA motif. From the NMR structural and dynamic data, we show that the V44M and V44A mutations can selectively expose the T48 site by weakening helical hydrogen bonds and increasing hydrogen-deuterium exchange rate (kex). We propose a structural model in which FAD mutations (V44M and V44A) can open the T48 site γ-secretase for the initial ɛ-cleavage, and consequently shift cleavage preference towards Aβ42.

Synthesis, structure, and DNA cleavage properties of copper(II) complexes of 1,4,7-triazacyclononane ligands featuring pairs of guanidine pendants.

PubMed

Tjioe, Linda; Joshi, Tanmaya; Brugger, Joël; Graham, Bim; Spiccia, Leone

2011-01-17

Two new ligands, L(1) and L(2), have been prepared via N-functionalization of 1,4,7-triazacyclononane (tacn) with pairs of ethyl- or propyl-guanidine pendants, respectively. The X-ray crystal structure of [CuL(1)](ClO4)2 (C1) isolated from basic solution (pH 9) indicates that a secondary amine nitrogen from each guanidine pendants coordinates to the copper(II) center in addition to the nitrogen atoms in the tacn macrocycle, resulting in a five-coordinate complex with intermediate square-pyramidal/trigonal bipyramidal geometry. The guanidines adopt an unusual coordination mode in that their amine nitrogen nearest to the tacn macrocycle binds to the copper(II) center, forming very stable five-membered chelate rings. A spectrophotometric pH titration established the pK(app) for the deprotonation and coordination of each guanidine group to be 3.98 and 5.72, and revealed that [CuL(1)](2+) is the only detectable species present in solution above pH ∼ 8. The solution speciation of the CuL(2) complex (C2) is more complex, with at least 5 deprotonation steps over the pH range 4-12.5, and mononuclear and binuclear complexes coexisting. Analysis of the spectrophotometric data provided apparent deprotonation constants, and suggests that solutions at pH ∼ 7.5 contain the maximum proportion of polynuclear complexes. Complex C1 exhibits virtually no cleavage activity toward the model phosphate diesters, bis(p-nitrophenyl)phosphate (BNPP) and 2-hydroxypropyl-p-nitrophenyl phosphate (HPNPP), while C2 exhibits moderate activity. For C2, the respective kobs values measured at pH 7.0 (7.24 (± 0.08) × 10(-5) s(-1) (BNPP at 50 °C) and 3.2 (± 0.3) × 10(-5) s(-1) (HPNPP at 25 °C)) are 40- and 10-times faster than [Cu(tacn)(OH2)2](2+) complex. Both complexes cleave supercoiled pBR 322 plasmid DNA, indicating that the guanidine pendants of [CuL(1)](2+) may have been displaced from the copper coordination sphere to allow for DNA binding and subsequent cleavage. The rate of DNA cleavage by C2 is twice that measured for [Cu(tacn)(OH2)2](2+), suggesting some degree of cooperativity between the copper center and guanidinium pendants in the hydrolysis of the phosphate ester linkages of DNA. A predominantly hydrolytic cleavage mechanism was confirmed through experiments performed either in the presence of various radical scavengers or under anaerobic conditions.

The catalytic chain of human complement subcomponent C1r. Purification and N-terminal amino acid sequences of the major cyanogen bromide-cleavage fragments.

PubMed

Arlaud, G J; Gagnon, J; Porter, R R

1982-01-01

1. The a- and b-chains of reduced and alkylated human complement subcomponent C1r were separated by high-pressure gel-permeation chromatography and isolated in good yield and in pure form. 2. CNBr cleavage of C1r b-chain yielded eight major peptides, which were purified by gel filtration and high-pressure reversed-phase chromatography. As determined from the sum of their amino acid compositions, these peptides accounted for a minimum molecular weight of 28 000, close to the value 29 100 calculated from the whole b-chain. 3. N-Terminal sequence determinations of C1r b-chain and its CNBr-cleavage peptides allowed the identification of about two-thirds of the amino acids of C1r b-chain. From our results, and on the basis of homology with other serine proteinases, an alignment of the eight CNBr-cleavage peptides from C1r b-chain is proposed. 4. The residues forming the 'charge-relay' system of the active site of serine proteinases (His-57, Asp-102 and Ser-195 in the chymotrypsinogen numbering) are found in the corresponding regions of C1r b-chain, and the amino acid sequence around these residues has been determined. 5. The N-terminal sequence of C1r b-chain has been extended to residue 60 and reveals that C1r b-chain lacks the 'histidine loop', a disulphide bond that is present in all other known serine proteinases.

Low-stress pressure solution experiments on halite single-crystals

NASA Astrophysics Data System (ADS)

Martin, Brigitte; Röller, Klaus; Stöckhert, Bernhard

1999-07-01

Pressure solution experiments on halite single-crystals in saturated solution were carried out at atmospheric pressure under uniaxial stress ranging from 0.1 to 2.0 MPa and at temperatures of 303 and 323 K. The experiments were performed in ceramic loading rigs with damp-proofed sample chambers. The low uniaxial stress is applied by loading the piston with steel weights ranging from 0.5 to 5.0 kg. The position of the piston is measured by an electronic displacement transducer, connected to a data acquisition system. Deviations caused by fluctuations of temperature and output voltage of the power supply are corrected after data acquisition. The halite cubes {100} with edge dimensions of 3-9 mm are prepared by cleaving and placed with a (100) cleavage face on the (001) face of a muscovite single-crystal (10×10×0.1 mm), a polished quartz (0001) plate, or another halite crystal oriented to form a 45° twist boundary. The four free (100) faces of the halite cube are in contact with the surrounding NaCl solution. The initial displacement rate of the piston after flooding of the system and loading is up to 50.0 μm/day, attributed to smoothing of the halite face and elimination of point contacts with high stress concentration. Within 2 to 3 days this stage grades into steady-state displacement with rates of 0.1-2.0 μm/day. In some experiments stages of higher displacement rates (2.0-5.0 μm/day) lasting for 3-5 days are observed episodically, with intervals of 10-15 days. These cycles appear not to be triggered by external events. Experiments with a dry mica-halite interface, carried out for comparison at the same temperature and at an uniaxial stress of 2 MPa, result in a displacement rate below the limits of detection. This rules out a significant contribution of crystal plastic deformation in the wet experiments. The experimental results show no simple correlation between displacement rate and magnitude of uniaxial stress, crystal size, type of the interface, and temperature. At the given conditions, convergence at a single interface due to pressure solution is apparently not a steady-state process. The alternating stages of lower and higher displacement rates observed in many experiments suggest that the mechanisms of transport or dissolution may change spontaneously during the experiment. It is possible that the process itself leads to an unstable configuration causing episodic changes.

Activation energies for dissociation of double strand oligonucleotide anions: evidence for watson-crick base pairing in vacuo.

PubMed

Schnier, P D; Klassen, J S; Strittmatter, E F; Williams, E R

1998-09-23

The dissociation kinetics of a series of complementary and noncomplementary DNA duplexes, (TGCA)(2) (3-), (CCGG)(2) (3-), (AATTAAT)(2) (3-), (CCGGCCG)(2) (3-), A(7)*T(7) (3-), A(7)*A(7) (3-), T(7)*T(7) (3-), and A(7)*C(7) (3-) were investigated using blackbody infrared radiative dissociation in a Fourier transform mass spectrometer. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained. Activation energies range from 1.2 to 1.7 eV, and preexponential factors range from 10(13) to 10(19) s(-1). Dissociation of the duplexes results in cleavage of the noncovalent bonds and/or cleavage of covalent bonds leading to loss of a neutral nucleobase followed by backbone cleavage producing sequence-specific (a - base) and w ions. Four pieces of evidence are presented which indicate that Watson-Crick (WC) base pairing is preserved in complementary DNA duplexes in the gas phase: i. the activation energy for dissociation of the complementary dimer, A(7)*T(7) (3-), to the single strands is significantly higher than that for the related noncomplementary A(7)*A(7) (3-) and T(7)*T(7) (3-) dimers, indicating a stronger interaction between strands with a specific base sequence, ii. extensive loss of neutral adenine occurs for A(7)*A(7) (3-) and A(7)*C(7) (3-) but not for A(7)*T(7) (3-) consistent with this process being shut down by WC hydrogen bonding, iii. a correlation is observed between the measured activation energy for dissociation to single strands and the dimerization enthalpy (-DeltaH(d)) in solution, and iv. molecular dynamics carried out at 300 and 400 K indicate that WC base pairing is preserved for A(7)*T(7) (3-) duplex, although the helical structure is essentially lost. In combination, these results provide strong evidence that WC base pairing can exist in the complete absence of solvent.

In vivo administration of calpeptin attenuates calpain activation and cardiomyocyte loss in pressure-overloaded feline myocardium

PubMed Central

Mani, Santhosh K.; Shiraishi, Hirokazu; Balasubramanian, Sundaravadivel; Yamane, Kentaro; Chellaiah, Meenakshi; Cooper, George; Banik, Naren; Zile, Michael R.; Kuppuswamy, Dhandapani

2008-01-01

Calpain activation is linked to the cleavage of several cytoskeletal proteins and could be an important contributor to the loss of cardiomyocytes and contractile dysfunction during cardiac pressure overload (PO). Using a feline right ventricular (RV) PO model, we analyzed calpain activation during the early compensatory period of cardiac hypertrophy. Calpain enrichment and its increased activity with a reduced calpastatin level were observed in 24- to 48-h-PO myocardium, and these changes returned to basal level by 1 wk of PO. Histochemical studies in 24-h-PO myocardium revealed the presence of TdT-mediated dUTP nick-end label (TUNEL)-positive cardiomyocytes, which exhibited enrichment of calpain and gelsolin. Biochemical studies showed an increase in histone H2B phosphorylation and cytoskeletal binding and cleavage of gelsolin, which indicate programmed cardiomyocyte cell death. To test whether calpain inhibition could prevent these changes, we administered calpeptin (0.6 mg/kg iv) by bolus injections twice, 15 min before and 6 h after induction of 24-h PO. Calpeptin blocked the following PO-induced changes: calpain enrichment and activation, decreased calpastatin level, caspase-3 activation, enrichment and cleavage of gelsolin, TUNEL staining, and histone H2B phosphorylation. Although similar administration of a caspase inhibitor, N-benzoylcarbonyl-Val-Ala-Asp-fluoromethylketone (Z-VD-fmk), blocked caspase-3 activation, it did not alleviate other aforementioned changes. These results indicate that biochemical markers of cardiomyocyte cell death, such as sarcomeric disarray, gelsolin cleavage, and TUNEL-positive nuclei, are mediated, at least in part, by calpain and that calpeptin may serve as a potential therapeutic agent to prevent cardiomyocyte loss and preserve myocardial structure and function during cardiac hypertrophy. PMID:18487434

Selective Cleavage of the Aryl Ether Bonds in Lignin for Depolymerization by Acidic Lithium Bromide Molten Salt Hydrate under Mild Conditions.

PubMed

Yang, Xiaohui; Li, Ning; Lin, Xuliang; Pan, Xuejun; Zhou, Yonghong

2016-11-09

The present study demonstrates that the concentrated lithium bromide (LiBr) solution with acid as catalyst was able to selectively cleave the β-O-4 aryl ether bond and lead to lignin depolymerization under mild conditions (e.g., in 60% LiBr with 0.3 M HCl at 110 °C for 2 h). Four industrial lignins from different pulping and biorefining processes, including softwood kraft lignin (SKL), hardwood kraft lignin (HKL), softwood ethanol organosolv lignin (EOL), and acid corncob lignin (ACL), were treated in the LiBr solution. The molecular weight, functional group, and interunit linkages of the lignins were characterized using GPC, FTIR, and NMR. The results indicated that the β-O-4 aryl ether bonds of the lignins were selectively cleaved, and both LiBr and HCl played crucial roles in catalyzing the cleavage of the ether bonds.

Solution structure of conserved AGNN tetraloops: insights into Rnt1p RNA processing

PubMed Central

Lebars, Isabelle; Lamontagne, Bruno; Yoshizawa, Satoko; Abou Elela, Sherif; Fourmy, Dominique

2001-01-01

Rnt1p, the yeast orthologue of RNase III, cleaves rRNAs, snRNAs and snoRNAs at a stem capped with conserved AGNN tetraloop. Here we show that 9 bp long stems ending with AGAA or AGUC tetraloops bind to Rnt1p and direct specific but sequence-independent RNA cleavage when provided with stems longer than 13 bp. The solution structures of these two tetraloops reveal a common fold for the terminal loop stabilized by non-canonical A–A or A–C pairs and extensive base stacking. The conserved nucleotides are stacked at the 5′ side of the loop, exposing their Watson–Crick and Hoogsteen faces for recognition by Rnt1p. These results indicate that yeast RNase III recognizes the fold of a conserved single-stranded tetraloop to direct specific dsRNA cleavage. PMID:11743001

Papain cleavage of the 38,000-dalton fragment inhibits the binding of 4, 4'-diisothiocyanostilbene-2, 2'-disulfonate to lys-539 on the 60,000-dalton fragment in human band 3.

PubMed

Yamaguchi, Takeo; Kojima, Hideaki; Kawaguchi, Shiori; Shimada, Maiko; Aso, Haruka

2017-08-01

Human band 3 is a 98-kDa transmembrane (TM) protein comprising 14 TM segments. Papain cleavages band 3 into 38- and 60-kDa fragments. Under vigorous conditions, the cleavage of the loop region between the TM 7 of gate domain and the TM 8 of core domain in the 38-kDa fragment produces 7- and 31-kDa fragments. Conformational changes of the TM 5 segment containing Lys-539 by cleavage of the 38-kDa fragment remain unclear. Pressure-induced haemolysis of erythrocytes was suppressed by binding of 4, 4'-diisothiocyanostilbene-2, 2'-disulfonate (DIDS) to Lys-539. Such effect of DIDS was not observed upon cleavage of the 38-kDa fragment, because of inhibition of DIDS binding to Lys-539. Using fluorescence of DIDS labelled to Lys-539, conformational changes of band 3 were examined. Fluorescence spectra demonstrated that the molecular motion of DIDS is more restricted upon digestion of the 38-kDa fragment. Interestingly, the quenching of DIDS fluorescence showed that Hg2+ is less accessible to DIDS upon digestion of the 38-kDa fragment. Taken together, we propose that the conformational changes of the TM 5 segment characterized by the sequestration and restricted motion of Lys-539 are induced by the cleavage of the loop region between the TM 7 and the TM 8. © The Authors 2017. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Mechanism of the mutagenic action of hydroxylamine. IX. The UV-induced cleavage of the N-O bond in N4-hydroxy-and N4-methoxycytidine and N6-methoxyadenosine.

PubMed Central

Simukova, N A; Yakovlev, D Y; Budowsky, E I

1975-01-01

The principal UV-induced (lambda = 2546nm) reaction of N4-hydroxy- and N4methoxycytidines and N6-methoxyadenosine in neutral aqueous solutions is cleavage of the exocyclic N-O bond with the respective formation of cytidine and adenosine. Quantum yields are 2.8x10(-3) and 2.2x10(-3) M/E for the first two compounds and 9.1x10(-3) M/E for N6-methoxyadenosine. PMID:1052542

Characterization of the Trans Watson-Crick GU Base Pair Located in the Catalytic Core of the Antigenomic HDV Ribozyme

PubMed Central

Lévesque, Dominique; Reymond, Cédric; Perreault, Jean-Pierre

2012-01-01

The HDV ribozyme’s folding pathway is, by far, the most complex folding pathway elucidated to date for a small ribozyme. It includes 6 different steps that have been shown to occur before the chemical cleavage. It is likely that other steps remain to be discovered. One of the most critical of these unknown steps is the formation of the trans Watson-Crick GU base pair within loop III. The U23 and G28 nucleotides that form this base pair are perfectly conserved in all natural variants of the HDV ribozyme, and therefore are considered as being part of the signature of HDV-like ribozymes. Both the formation and the transformation of this base pair have been studied mainly by crystal structure and by molecular dynamic simulations. In order to obtain physical support for the formation of this base pair in solution, a set of experiments, including direct mutagenesis, the site-specific substitution of chemical groups, kinetic studies, chemical probing and magnesium-induced cleavage, were performed with the specific goal of characterizing this trans Watson-Crick GU base pair in an antigenomic HDV ribozyme. Both U23 and G28 can be substituted for nucleotides that likely preserve some of the H-bond interactions present before and after the cleavage step. The formation of the more stable trans Watson-Crick base pair is shown to be a post-cleavage event, while a possibly weaker trans Watson-Crick/Hoogsteen interaction seems to form before the cleavage step. The formation of this unusually stable post-cleavage base pair may act as a driving force on the chemical cleavage by favouring the formation of a more stable ground state of the product-ribozyme complex. To our knowledge, this represents the first demonstration of a potential stabilising role of a post-cleavage conformational switch event in a ribozyme-catalyzed reaction. PMID:22768274

Effects of the bradykinin antagonist B4310 on smooth muscles and blood pressure in the rat, and its enzymatic degradation.

PubMed Central

Griesbacher, T.; Lembeck, F.; Saria, A.

1989-01-01

1. Six competitive bradykinin (Bk) antagonists were tested for their agonistic properties on the rat uterus. Five of these peptides showed agonistic effects only at concentrations at least two orders of magnitude higher than those of bradykinin. 2. The antagonistic potency of Lys-Lys-3-Hyp-5,8-Thi-7-DPhe-Bk (B4310) in the rat uterus (pA2 = 7.24) and in the rat duodenum (pA2 = 7.31) was very similar to that determined in an earlier study for the antagonism of the bradykinin-induced stimulation of the trigeminal nerve in the rabbit iris sphincter muscle preparation (pA2 = 7.59). 3. The fall in mean arterial blood pressure induced by i.a. injections of bradykinin was greatly reduced during an i.a. infusion of B4310, but not 10 min thereafter, which indicates a rapid inactivation of B4310 in vivo. Bacitracin possibly interferes with the enzymatic cleavage of B4310 but seems to have no effect on the degradation of bradykinin. 4. An i.a. infusion of captopril greatly enhanced the potency of bradykinin in inducing a fall in arterial blood pressure, confirming the important role of angiotensin converting enzyme in the cleavage of bradykinin. However, the design of this experiment did not allow conclusions about the effect of captopril on the degradation of B4310. 5. B4310 incubated with rat lung tissue disappeared from the incubation medium within a few minutes, i.e. as fast as bradykinin, which explains its short duration of action in vivo. Captopril partially inhibited the cleavage of both bradykinin and B4310.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2655805

Investigation of a new thermosensitive block copolymer micelle: hydrolysis, disruption, and release.

PubMed

Pelletier, Maxime; Babin, Jérôme; Tremblay, Luc; Zhao, Yue

2008-11-04

Thermosensitive polymer micelles are generally obtained with block copolymers in which one block exhibits a lower critical solution temperature in aqueous solution. We investigate a different design that is based on the use of one block bearing a thermally labile side group, whose hydrolysis upon heating shifts the hydrophilic-hydrophobic balance toward the destabilization of block copolymer micelles. Atom transfer radical polymerization was utilized to synthesize a series of diblock copolymers composed of hydrophilic poly(ethylene oxide) (PEO) and hydrophobic poly(2-tetrahydropyranyl methacrylate) (PTHPMA). We show that micelles of PEO-b-PTHPMA in aqueous solution can be destabilized as a result of the thermosensitive hydrolytic cleavage of tetrahydropyranyl (THP) groups that transforms PTHPMA into hydrophilic poly(methacrylic acid). The three related processes occurring in aqueous solution, namely, hydrolytic cleavage of THP, destabilization of micelles, and release of loaded Nile Red (NR), were investigated simultaneously using 1H NMR, dynamic light scattering, and fluorescence spectroscopy, respectively. At 80 degrees C, the results suggest that the three events proceed with a similar kinetics. Although slower than at elevated temperatures, the disruption of PEO-b-PTHPMA micelles can take place at the body temperature (approximately 37 degrees C), and the release kinetics of NR can be adjusted by changing the relative lengths of the two blocks or the pH of the solution.

Molecular dynamics simulation of siderite-hematite-quartz flotation with sodium oleate

NASA Astrophysics Data System (ADS)

Li, Lixia; Hao, Haiqing; Yuan, Zhitao; Liu, Jiongtian

2017-10-01

Models of sodium oleate adsorption on siderite, hematite and quartz were investigated by molecular dynamic simulation, respectively. Surface energy was calculated to confirm the cleavage plan of hematite and quartz. Both natural cleavage plane of siderite and calculated plane were used to investigate the flotation of the three minerals. Based on the molecular simulation in solution with water as medium, adsorption quantity and interaction capability of oleate ions on the three minerals indicated that siderite could be collected efficiently by sodium oleate at neutral pH. Results of flotation experiments were further demonstrated by analysis of relative concentration of carbon atoms and oxygen atoms.

Hydrogen-assisted stable crack growth in iron-3 wt% silicon steel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marrow, T.J.; Prangnell, P.; Aindow, M.

1996-08-01

Observations of internal hydrogen cleavage in Fe-3Si are reported. Hydrogen-assisted stable crack growth (H-SCG) is associated with cleavage striations of a 300 nm spacing, observed using scanning electron microscopy (SEM) and atomic force microscopy (AFM). High resolution SEM revealed finer striations, previously undetected, with a spacing of approximately 30 nm. These were parallel to the coarser striations. Scanning tunneling microscopy (STM) also showed the fine striation spacing, and gave a striation height of approximately 15 nm. The crack front was not parallel to the striations. Transmission electron microscopy (TEM) of crack tip plastic zones showed {l_brace}112{r_brace} and {l_brace}110{r_brace} slip, withmore » a high dislocation density (around 10{sup 14}m{sup {minus}2}). The slip plane spacing was approximately 15--30 nm. Parallel arrays of high dislocation density were observed in the wake of the hydrogen cleavage crack. It is concluded that H-ScG in Fe-3Si occurs by periodic brittle cleavage on the {l_brace}001{r_brace} planes. This is preceded by dislocation emission. The coarse striations are produced by crack tip blunting and the fine striations by dislocations attracted by image forces to the fracture surface after cleavage. The effects of temperature, pressure and yield strength on the kinetics of H-SCG can be predicted using a model for diffusion of hydrogen through the plastic zone.« less

Oxidation of aniline aerofloat in flotation wastewater by sodium hypochlorite solution.

PubMed

Lin, Weixiong; Tian, Jing; Ren, Jie; Xu, Pingting; Dai, Yongkang; Sun, Shuiyu; Wu, Chun

2016-01-01

Aniline aerofloat (dianilinodithiophosphoric acid (C6H5NH)2PSSH) is a widely used phosphorodithioic organic flotation collector that contains aniline groups and dithiophosphate groups. In the present study, sodium hypochlorite solution was used to oxidize aniline aerofloat. The effect of operational parameters and optimum oxidation conditions on aniline aerofloat was studied, and the oxidation pathway of aniline aerofloat was proposed by analyzing its main oxidation intermediates. The results showed that NaOCl concentration had a significant influence on aniline aerofloat oxidation and at 100 mg/L aniline aerofloat, 84.54% was removed under the following optimal conditions: NaOCl concentration = 1.25 g/L, pH = 4, and reaction time = 60 min. The main reaction of aniline aerofloat by NaOCl included N-P bond cleavage, aniline group oxidation, aniline group chlorination, and dithiophosphate group oxidation. The initial reaction was the N-P bond cleavage and the anilines and dithiophosphate was further oxidized to other intermediates by five parallel reaction pathways.

Enzymatic production and in situ separation of natural β-ionone from β-carotene.

PubMed

Nacke, Christoph; Hüttmann, Sonja; Etschmann, Maria M W; Schrader, Jens

2012-12-01

A biotechnological process concept for generation and in situ separation of natural β-ionone from β-carotene is presented. The process employs carotenoid cleavage dioxygenases (CCDs), a plant-derived iron-containing nonheme enzyme family requiring only dissolved oxygen as cosubstrate and no additional cofactors. Organophilic pervaporation was found to be very well suited for continuous in situ separation of β-ionone. Its application led to a highly pure product despite the complexity of the reaction solution containing cell homogenates. Among three different pervaporation membrane types tested, a polyoctylmethylsiloxane active layer on a porous polyetherimide support led to the best results. A laboratory-scale demonstration plant was set up, and a highly pure aqueous-ethanolic solution of β-ionone was produced from β-carotene. The described process permits generation of high-value flavor and fragrance compounds bearing the desired label "natural" according to US and European food and safety regulations and demonstrates the potential of CCD enzymes for selective oxidative cleavage of carotenoids.

Real-time observation of DNA target interrogation and product release by the RNA-guided endonuclease CRISPR Cpf1 (Cas12a).

PubMed

Singh, Digvijay; Mallon, John; Poddar, Anustup; Wang, Yanbo; Tippana, Ramreddy; Yang, Olivia; Bailey, Scott; Ha, Taekjip

2018-05-22

CRISPR-Cas9, which imparts adaptive immunity against foreign genomic invaders in certain prokaryotes, has been repurposed for genome-engineering applications. More recently, another RNA-guided CRISPR endonuclease called Cpf1 (also known as Cas12a) was identified and is also being repurposed. Little is known about the kinetics and mechanism of Cpf1 DNA interaction and how sequence mismatches between the DNA target and guide-RNA influence this interaction. We used single-molecule fluorescence analysis and biochemical assays to characterize DNA interrogation, cleavage, and product release by three Cpf1 orthologs. Our Cpf1 data are consistent with the DNA interrogation mechanism proposed for Cas9. They both bind any DNA in search of protospacer-adjacent motif (PAM) sequences, verify the target sequence directionally from the PAM-proximal end, and rapidly reject any targets that lack a PAM or that are poorly matched with the guide-RNA. Unlike Cas9, which requires 9 bp for stable binding and ∼16 bp for cleavage, Cpf1 requires an ∼17-bp sequence match for both stable binding and cleavage. Unlike Cas9, which does not release the DNA cleavage products, Cpf1 rapidly releases the PAM-distal cleavage product, but not the PAM-proximal product. Solution pH, reducing conditions, and 5' guanine in guide-RNA differentially affected different Cpf1 orthologs. Our findings have important implications on Cpf1-based genome engineering and manipulation applications.

Fast cleavage of phycocyanobilin from phycocyanin for use in food colouring.

PubMed

Roda-Serrat, Maria Cinta; Christensen, Knud Villy; El-Houri, Rime Bahij; Fretté, Xavier; Christensen, Lars Porskjær

2018-02-01

Phycocyanins from cyanobacteria are possible sources for new natural blue colourants. Their chromophore, phycocyanobilin (PCB), was cleaved from the apoprotein by solvolysis in alcohols and alcoholic aqueous solutions. In all cases two PCB isomers were obtained, while different solvent adducts were formed upon the use of different reagents. The reaction is believed to take place via two competing pathways, a concerted E2 elimination and a S N 2 nucleophilic substitution. Three cleavage methods were compared in terms of yield and purity: conventional reflux, sealed vessel heated in an oil bath, and microwave assisted reaction. The sealed vessel method is a new approach for fast cleavage of PCB from phycocyanin and gave at 120°C the same yield within 30min compared to 16h by the conventional reflux method (P<0.05). In addition the sealed vessel method resulted in improved purity compared to the other methods. Microwave irradiation increased product degradation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Halogeno-substituted 2-aminobenzoic acid derivatives for negative ion fragmentation studies of N-linked carbohydrates.

PubMed

Harvey, David J

2005-01-01

Negative ion electrospray mass spectra of high-mannose N-linked glycans derivatised with 2-aminobenzoic acids and ionised from solutions containing ammonium hydroxide gave prominent [M-H](-) ions accompanied by weaker [M-2H](2-) ions. Fragmentation of both types of ions gave prominent singly charged glycosidic cleavage ions containing the derivatised reducing terminus and ions from the non-reducing terminus that appeared to be products of cross-ring cleavages. Differentiation of these two groups of ions was conveniently achieved in a single spectrum by use of chloro- or bromo-substituted benzoic acids in order to label ions containing the derivative with an atom with a distinctive isotope pattern. Fragmentation of the doubly charged ions gave more abundant fragments, both singly and doubly charged, than did fragmentation of the singly charged ions, but information of chain branching was masked by the appearance of prominent ions produced by internal cleavages. Copyright (c) 2005 John Wiley & Sons, Ltd.

Photosensitized cleavage of some olefins as potential linkers to be used in drug delivery

NASA Astrophysics Data System (ADS)

Dinache, Andra; Smarandache, Adriana; Simon, Agota; Nastasa, Viorel; Tozar, Tatiana; Pascu, Alexandru; Enescu, Mironel; Khatyr, Abderrahim; Sima, Felix; Pascu, Mihail-Lucian; Staicu, Angela

2017-09-01

A study of photosensitized cleavage of different olefins as potential linkers for drug carrier complexes is reported. The role of singlet oxygen and the kinetic rates for light induced reactions were estimated by time-resolved measurements of singlet oxygen phosphorescence (at 1270 nm) obtained via 532 nm pulse laser excitation of a photosensitizer. The mixture of each studied olefin with verteporfin (used as photosensitizer) were exposed to low energy visible radiation. The rate constants for singlet oxygen quenching by studied olefins were determined. The irradiated solutions were investigated by FTIR spectroscopy and potential photoproducts were suggested. The experimental results were compared with simulations made by DFT method.

Labeled Nucleoside Triphosphates with Reversibly Terminating Aminoalkoxyl Groups

PubMed Central

Hutter, Daniel; Kim, Myong-Jung; Karalkar, Nilesh; Leal, Nicole A.; Chen, Fei; Guggenheim, Evan; Visalakshi, Visa; Olejnik, Jerzy; Gordon, Steven; Benner, Steven A.

2013-01-01

Nucleoside triphosphates having a 3′-ONH2 blocking group have been prepared with and without fluorescent tags on their nucleobases. DNA polymerases were identified that accepted these, adding a single nucleotide to the 3′-end of a primer in a template-directed extension reaction that then stops. Nitrite chemistry was developed to cleave the 3′-ONH2 group under mild conditions to allow continued primer extension. Extension-cleavage-extension cycles in solution were demonstrated with untagged nucleotides and mixtures of tagged and untagged nucleotides. Multiple extension-cleavage-extension cycles were demonstrated on an Intelligent Bio-Systems Sequencer, showing the potential of the 3′-ONH2 blocking group in “next generation sequencing”. PMID:21128174

Activation Energies for Dissociation of Double Strand Oligonucleotide Anions: Evidence for Watson–Crick Base Pairing in Vacuo

PubMed Central

Schnier, Paul D.; Klassen, John S.; Strittmatter, Eric F.; Williams*, Evan R.

2005-01-01

The dissociation kinetics of a series of complementary and noncomplementary DNA duplexes, (TGCA)23−, (CCGG)23−, (AATTAAT)23−, (CCGGCCG)23−, A7·T73−, A7·A73−, T7·T73−, and A7·C73− were investigated using blackbody infrared radiative dissociation in a Fourier transform mass spectrometer. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained. Activation energies range from 1.2 to 1.7 eV, and preexponential factors range from 1013 to 1019 s−1. Dissociation of the duplexes results in cleavage of the noncovalent bonds and/or cleavage of covalent bonds leading to loss of a neutral nucleobase followed by backbone cleavage producing sequence-specific (a – base) and w ions. Four pieces of evidence are presented which indicate that Watson–Crick (WC) base pairing is preserved in complementary DNA duplexes in the gas phase: i. the activation energy for dissociation of the complementary dimer, A7·T73−, to the single strands is significantly higher than that for the related noncomplementary A7·A73− and T7·T73− dimers, indicating a stronger interaction between strands with a specific base sequence, ii. extensive loss of neutral adenine occurs for A7·A73− and A7·C73− but not for A7·T73− consistent with this process being shut down by WC hydrogen bonding, iii. a correlation is observed between the measured activation energy for dissociation to single strands and the dimerization enthalpy (−ΔHd) in solution, and iv. molecular dynamics carried out at 300 and 400 K indicate that WC base pairing is preserved for A7·T73− duplex, although the helical structure is essentially lost. In combination, these results provide strong evidence that WC base pairing can exist in the complete absence of solvent. PMID:16498487

Both positional and chemical variables control in vitro proteolytic cleavage of a presenilin ortholog

PubMed Central

Naing, Swe-Htet; Kalyoncu, Sibel; Smalley, David M.; Kim, Hyojung; Tao, Xingjian; George, Josh B.; Jonke, Alex P.; Oliver, Ryan C.; Urban, Volker S.; Torres, Matthew P.; Lieberman, Raquel L.

2018-01-01

Mechanistic details of intramembrane aspartyl protease (IAP) chemistry, which is central to many biological and pathogenic processes, remain largely obscure. Here, we investigated the in vitro kinetics of a microbial intramembrane aspartyl protease (mIAP) fortuitously acting on the renin substrate angiotensinogen and the C-terminal transmembrane segment of amyloid precursor protein (C100), which is cleaved by the presenilin subunit of γ-secretase, an Alzheimer disease (AD)-associated IAP. mIAP variants with substitutions in active-site and putative substrate-gating residues generally exhibit impaired, but not abolished, activity toward angiotensinogen and retain the predominant cleavage site (His–Thr). The aromatic ring, but not the hydroxyl substituent, within Tyr of the catalytic Tyr–Asp (YD) motif plays a catalytic role, and the hydrolysis reaction incorporates bulk water as in soluble aspartyl proteases. mIAP hydrolyzes the transmembrane region of C100 at two major presenilin cleavage sites, one corresponding to the AD-associated Aβ42 peptide (Ala–Thr) and the other to the non-pathogenic Aβ48 (Thr–Leu). For the former site, we observed more favorable kinetics in lipid bilayer–mimicking bicelles than in detergent solution, indicating that substrate–lipid and substrate–enzyme interactions both contribute to catalytic rates. High-resolution MS analyses across four substrates support a preference for threonine at the scissile bond. However, results from threonine-scanning mutagenesis of angiotensinogen demonstrate a competing positional preference for cleavage. Our results indicate that IAP cleavage is controlled by both positional and chemical factors, opening up new avenues for selective IAP inhibition for therapeutic interventions. PMID:29382721

Effect of holding pressure on microstructure and fracture behavior of low-pressure die cast A356-T6 alloy

NASA Astrophysics Data System (ADS)

Wu, Xiaoyan; Yun, Ying; Zhang, Huarui; Ma, Zhen; Jia, Lina; Tao, Tongxiang; Zhang, Hu

2017-12-01

The effect of different holding pressures on microstructure, tensile properties and fracture behavior of A356-T6 aluminum alloy was investigated. It was observed that the ultimate strength, yield strength and elongation of A356-T6 aluminum alloy increased with the increasing of holding pressure from 85 kPa to 300 kPa. This was attributed to the finer microstructure and the elimination of porosity defects caused by high holding pressure. The fractographs of specimens obtained under lower holding pressure displayed mixed quasi-cleavage and dimple type morphology with flat dimples and large amount of porosities. However, the fractographs of specimens obtained under high holding pressure of 300 kPa clearly exhibited a dimple morphology with small and deep dimples. The differences in the tensile fracture were attributed to the different shape of eutectic Si particle and different amount of porosity defects.

HIV-1 protease-substrate coevolution in nelfinavir resistance.

PubMed

Kolli, Madhavi; Ozen, Ayşegül; Kurt-Yilmaz, Nese; Schiffer, Celia A

2014-07-01

Resistance to various human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. The virus accumulates mutations within the protease (PR) that render the PIs less potent. Occasionally, Gag sequences also coevolve with mutations at PR cleavage sites contributing to drug resistance. In this study, we investigated the structural basis of coevolution of the p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations by determining crystal structures of wild-type and NFV-resistant HIV-1 protease in complex with p1-p6 substrate peptide variants with L449F and/or S451N. Alterations of residue 30's interaction with the substrate are compensated by the coevolving L449F and S451N cleavage site mutations. This interdependency in the PR-p1-p6 interactions enhances intermolecular contacts and reinforces the overall fit of the substrate within the substrate envelope, likely enabling coevolution to sustain substrate recognition and cleavage in the presence of PR resistance mutations. Resistance to human immunodeficiency virus type 1 (HIV-1) protease inhibitors challenges the effectiveness of therapies in treating HIV-1-infected individuals and AIDS patients. Mutations in HIV-1 protease selected under the pressure of protease inhibitors render the inhibitors less potent. Occasionally, Gag sequences also mutate and coevolve with protease, contributing to maintenance of viral fitness and to drug resistance. In this study, we investigated the structural basis of coevolution at the Gag p1-p6 cleavage site with the nelfinavir (NFV) resistance D30N/N88D protease mutations. Our structural analysis reveals the interdependency of protease-substrate interactions and how coevolution may restore substrate recognition and cleavage in the presence of protease drug resistance mutations. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Gene Encoding the Hydrolase for the Product of the meta-Cleavage Reaction in Testosterone Degradation by Comamonas testosteroni

PubMed Central

Horinouchi, Masae; Hayashi, Toshiaki; Koshino, Hiroyuki; Yamamoto, Takako; Kudo, Toshiaki

2003-01-01

In a previous study we isolated the meta-cleavage enzyme gene, tesB, that encodes an enzyme that carries out a meta-cleavage reaction in the breakdown of testosterone by Comamonas testeroni TA441 (M. Horinouchi et al., Microbiology 147:3367-3375, 2001). Here we report the isolation of a gene, tesD, that encodes a hydrolase which acts on the product of the meta-cleavage reaction. We isolated tesD by using a Tn5 mutant of TA441 that showed limited growth on testosterone. TesD exhibited ca. 40% identity in amino acid sequence with BphDs, known hydrolases of biphenyl degradation in Pseudomonas spp. The TesD-disrupted mutant showed limited growth on testosterone, and the culture shows an intense yellow color. High-pressure liquid chromatography analysis of the culture of TesD-disrupted mutant incubated with testosterone detected five major intermediate compounds, one of which, showing yellow color under neutral conditions, was considered to be the product of the meta-cleavage reaction. The methylation product was analyzed and identified as methyl-4,5-9,10-diseco-3-methoxy-5,9,17-trioxoandrosta-1(10),2-dien-4-oate, indicating that the substrate of TesD in testosterone degradation is 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-dien-4-oic acid. 4,5-9,10-Diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-dien-4-oic acid was transformed by Escherichia coli-expressed TesD. Downstream of tesD, we identified tesE, F, and G, which encode for enzymes that degrade one of the products of 4,5-9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-dien-4-oic acid converted by TesD. PMID:12676694

Nuclei fluorescence microscopic observation on early embryonic development of mitogynogenetic diploid induced by hydrostatic pressure treatment in olive flounder (Paralichthys olivaceus).

PubMed

Lin, Zhengmei; Zhu, Xiangping; You, Feng; Wu, Zhihao; Cao, Yuanshui

2015-05-01

Sperm genetic material of olive flounder (Paralichthys olivaceus) was inactivated by ultraviolet irradiation. The nuclear phase changes during early embryonic development of diploid, haploid, and mitogynogenetic diploid induced by hydrostatic pressure treatment were observed under fluorescent microscope with 4',6-diamidino-2-phenylindole staining. The parameters of hydrostatic pressure treatment were 600 kg/cm(2) for 6 minutes at prometaphase stage. The data showed that developmental timing sequence of diploid and haploid fertilized eggs was similar. The cell cycle was about 48 minutes, including interphase (about 21 minutes), prophase (about 3 minutes), prometaphase (about 6 minutes), metaphase (about 6 minutes), anaphase (around 9 minutes), and telophase (about 3 minutes). After entering the fertilized egg, ultraviolet-inactivated sperm formed a male pronucleus and became a dense chromatin body in the cytoplasm. Dense chromatin body did not participate in nuclear division and unchanged all the time. For hydrostatic pressure-treated embryos, the first nuclear division and cytokinesis after treatment proceeded normally after about 15 minutes recovery. During the second mitosis, having undergone interphase, prophase, and prometaphase stage, chromosomes began to slowly spread around and scattered in the cell but not entered into metaphase and anaphase. The second nuclear division and cytokinesis was inhibited. The occurrence frequency of developmentally delayed embryos also showed that the second cleavage of about 80% treated eggs was inhibited. The inhibition of the second cleavage resulted to chromosome set doubling. So chromosome set doubling for mitogynogenetic flounder diploid induced by hydrostatic pressure treatment, performed at prometaphase stage, was mainly due to inhibition of the second mitosis rather than the first one. Copyright © 2015 Elsevier Inc. All rights reserved.

Further biochemical characterization of human pancreatic lipase-related protein 2 expressed in yeast cells.

PubMed

Eydoux, Cécilia; De Caro, Josiane; Ferrato, Francine; Boullanger, Paul; Lafont, Dominique; Laugier, René; Carrière, Frédéric; De Caro, Alain

2007-07-01

Recombinant human pancreatic lipase-related protein 2 (rHPLRP2) was produced in the protease A-deficient yeast Pichia pastoris. A major protein with a molecular mass of 50 kDa was purified from the culture medium using SP-Sepharose and Mono Q chromatography. The protein was found to be highly sensitive to the proteolytic cleavage of a peptide bond in the lid domain. The proteolytic cleavage process occurring in the lid affected both the lipase and phospholipase activities of rHPLRP2. The substrate specificity of the nonproteolyzed rHPLRP2 was investigated using pH-stat and monomolecular film techniques and various substrates (glycerides, phospholipids, and galactolipids). All of the enzyme activities were maximum at alkaline pH values and decreased in the pH 5-7 range corresponding to the physiological conditions occurring in the duodenum. rHPLRP2 was found to act preferentially on substrates forming small aggregates in solution (monoglycerides, egg phosphatidylcholine, and galactolipids) rather than on emulsified substrates such as triolein and diolein. The activity of rHPLRP2 on monogalactosyldiglyceride and digalactosyldiglyceride monomolecular films was determined and compared with that of guinea pig pancreatic lipase-related protein 2, which shows a large deletion in the lid domain. The presence of a full-length lid domain in rHPLRP2 makes it possible for enzyme activity to occur at higher surface pressures. The finding that the inhibition of nonproteolyzed rHPLRP2 by tetrahydrolipstatin and diethyl-p-nitrophenyl phosphate does not involve any bile salt requirements suggests that the rHPLRP2 lid adopts an open conformation in aqueous media.

Ab initio study of the operating mechanisms of tris(trimethylsilyl) phosphite as a multifunctional additive for Li-ion batteries

NASA Astrophysics Data System (ADS)

Kim, Dong Young; Park, Hosang; Choi, Woon Ih; Roy, Basab; Seo, Jinah; Park, Insun; Kim, Jin Hae; Park, Jong Hwan; Kang, Yoon-Sok; Koh, Meiten

2017-07-01

Tris(trimethylsilyl) phosphite (P(OSi(CH3)3)3) is a multifunctional electrolyte additive for scavenging HF and forming a cathode electrolyte interphase (CEI). Systematic analysis of the HF reaction pathways and redox potentials of P(OSi(CH3)3)3, OP(OSi(CH3)3)3, P(OSiF3)3, and OP(OSiF3)3, and their reaction products, using ab initio calculations allowed us to elucidate the operating mechanism of P(OSi(CH3)3)3 and verify the rules that determine its HF reaction pathways and electrochemical stability. While Osbnd Si cleavage is the predominant HF scavenging pathway for P(OSi(CH3)3)3, Osbnd P cleavage is stabilized by replacing CH3 with an electron-withdrawing group. Thus, P(OSiF3)3 scavenges HF mainly through Osbnd P cleavage to produce PF3, which has high oxidation stability. However, the Osbnd Si cleavage pathway produces P(OSi(CH3)3)2OH, P(OSi(CH3)3) (OH)2, and P(OH)3 sequentially, along with Si(CH3)3F. These PO3 systems, which are oxidized earlier than carbonate solutions and form tightly bonded units following oxidation, act as seed units for compact CEI growth. Moreover, the HF scavenging ability of PO3 systems is maintained during oxidation until all Osbnd Si bonds are broken. As a strategy for developing additives with enhanced functionality, modifying P(OSi(CH3)3)3 by replacing CH3 with an electron-donating group to exclusively utilize the Osbnd Si cleavage pathway for HF scavenging is recommended.

A ReaxFF-based molecular dynamics study of the mechanisms of interactions between reactive oxygen plasma species and the Candida albicans cell wall

NASA Astrophysics Data System (ADS)

Zhao, T.; Shi, L.; Zhang, Y. T.; Zou, L.; Zhang, L.

2017-10-01

Atmospheric pressure non-equilibrium plasmas have attracted significant attention and have been widely used to inactivate pathogens, yet the mechanisms underlying the interactions between plasma-generated species and bio-organisms have not been elucidated clearly. In this paper, reactive molecular dynamics simulations are employed to investigate the mechanisms of interactions between reactive oxygen plasma species (O, OH, and O2) and β-1,6-glucan (a model for the C. albicans cell wall) from a microscopic point of view. Our simulations show that O and OH species can break structurally important C-C and C-O bonds, while O2 molecules exhibit only weak, non-bonded interactions with β-1,6-glucan. Hydrogen abstraction from hydroxyl or CH groups occurs first in all bond cleavage mechanisms. This is followed by a cascade of bond cleavage and double bond formation events. These lead to the destruction of the fungal cell wall. O and OH have similar effects related to their bond cleavage mechanisms. Our simulation results provide fundamental insights into the mechanisms underlying the interactions between reactive oxygen plasma species and the fungal cell wall of C. albicans at the atomic level.

Effects of polyethylene glycol and a synthetic ice blocker during vitrification of immature porcine oocytes on survival and subsequent embryo development.

PubMed

Santos, Elisa Caroline da Silva; Somfai, Tamas; Appeltant, Ruth; Dang-Nguyen, Thanh Quang; Noguchi, Junko; Kaneko, Hiroyuki; Kikuchi, Kazuhiro

2017-08-01

We evaluated the effects of polyethylene glycol (PEG) and Supercool X-1000 (SC) as supplements during the vitrification of immature cumulus-enclosed porcine oocytes in a solution based on 17.5% ethylene glycol + 17.5% propylene glycol. After warming, the oocytes were subjected to in vitro maturation, fertilization and embryo culture. In Experiment 1, equilibration and vitrification solutions were supplemented with or without 2% (w/v) PEG (PEG+ and PEG-, respectively). The survival rate, cleavage and blastocyst development were similar between PEG+ and PEG- groups; however, all values were lower than those in the non-vitrified control. In Experiment 2, vitrification solution was supplemented with or without 1% (v/v) SC (SC+ and SC-, respectively). The percentages of survival and blastocyst development were similar between SC+ and SC- groups but lower than those in the non-vitrified control. The percentage of cleavage in the SC- group was significantly lower than the control and the SC+ groups, which were in turn similar to one another. In both experiments, the cell numbers in blastocysts were not significantly different among the non-vitrified and vitrified groups. In conclusion, PEG did not improve oocyte survival and embryo development, whereas SC improved the ability of surviving oocytes to cleave but not to develop into blastocysts. © 2016 Japanese Society of Animal Science.

NMR solution structure of the mitochondrial F1beta presequence from Nicotiana plumbaginifolia.

PubMed

Moberg, Per; Nilsson, Stefan; Ståhl, Annelie; Eriksson, Anna-Carin; Glaser, Elzbieta; Mäler, Lena

2004-03-05

We have isolated, characterized and determined the three-dimensional NMR solution structure of the presequence of ATPsynthase F1beta subunit from Nicotiana plumbaginifolia. A general method for purification of presequences is presented. The method is based on overexpression of a mutant precursor containing a methionine residue introduced at the processing site, followed by CNBr-cleavage and purification of the presequence on a cation-exchange column. The F1beta presequence, 53 amino acid residues long, retained its native properties as evidenced by inhibition of in vitro mitochondrial import and processing at micromolar concentrations. CD spectroscopy revealed that the F1beta presequence formed an alpha-helical structure in membrane mimetic environments such as SDS and DPC micelles (approximately 50% alpha-helix), and in acidic phospholipid bicelles (approximately 60% alpha-helix). The NMR solution structure of the F1beta presequence in SDS micelles was determined on the basis of 518 distance and 21 torsion angle constraints. The structure was found to contain two helices, an N-terminal amphipathic alpha-helix (residues 4-15) and a C-terminal alpha-helix (residues 43-53), separated by a largely unstructured 27 residue long internal domain. The N-terminal amphipathic alpha-helix forms the putative Tom20 receptor binding site, whereas the C-terminal alpha-helix is located upstream of the mitochondrial processing peptidase cleavage site.

The dehydroalanine effect in the fragmentation of ions derived from polypeptides

PubMed Central

Pilo, Alice L.; Peng, Zhou; McLuckey, Scott A.

2016-01-01

The fragmentation of peptides and proteins upon collision-induced dissociation (CID) is highly dependent on sequence and ion type (e.g. protonated, deprotonated, sodiated, odd electron, etc.). Some amino acids, for example aspartic acid and proline, have been found to enhance certain cleavages along the backbone. Here, we show that peptides and proteins containing dehydroalanine, a non-proteinogenic amino acid with an unsaturated side-chain, undergo enhanced cleavage of the N—Cα bond of the dehydroalanine residue to generate c- and z-ions. Because these fragment ion types are not commonly observed upon activation of positively charged even-electron species, they can be used to identify dehydroalanine residues and localize them within the peptide or protein chain. While dehydroalanine can be generated in solution, it can also be generated in the gas phase upon CID of various species. Oxidized S-alkyl cysteine residues generate dehydroalanine upon activation via highly efficient loss of the alkyl sulfenic acid. Asymmetric cleavage of disulfide bonds upon collisional activation of systems with limited proton mobility also generates dehydroalanine. Furthermore, we show that gas-phase ion/ion reactions can be used to facilitate the generation of dehydroalanine residues via, for example, oxidation of S-alkyl cysteine residues and conversion of multiply-protonated peptides to radical cations. In the latter case, loss of radical side-chains to generate dehydroalanine from some amino acids gives rise to the possibility for residue-specific backbone cleavage of polypeptide ions. PMID:27484024

Oxidative Metabolites of Curcumin Poison Human Type II Topoisomerases†

PubMed Central

Ketron, Adam C.; Gordon, Odaine N.; Schneider, Claus; Osheroff, Neil

2013-01-01

The polyphenol curcumin is the principal flavor and color component of the spice turmeric. Beyond its culinary uses, curcumin is believed to positively impact human health and displays antioxidant, anti-inflammatory, antibacterial, and chemopreventive properties. It also is in clinical trials as an anticancer agent. In aqueous solution at physiological pH, curcumin undergoes spontaneous autoxidation that is enhanced by oxidizing agents. The reaction proceeds through a series of quinone methide and other reactive intermediates to form a final dioxygenated bicyclopentadione product. Several naturally occurring polyphenols that can form quinones have been shown to act as topoisomerase II poisons (i.e., increase levels of topoisomerase II-mediated DNA cleavage). Because several of these compounds have chemopreventive properties, we determined the effects of curcumin, its oxidative metabolites, and structurally related degradation products (vanillin, ferulic acid, and feruloylmethane), on the DNA cleavage activities of human topoisomerase IIα and IIβ. Intermediates in the curcumin oxidation pathway increased DNA scission mediated by both enzymes ~4-5–fold. In contrast, curcumin and the bicyclopentadione, as well as vanillin, ferulic acid, and feruloylmethane, had no effect on DNA cleavage. As found for other quinone-based compounds, curcumin oxidation intermediates acted as redox-dependent (as opposed to interfacial) topoisomerase II poisons. Finally, under conditions that promote oxidation, the dietary spice turmeric enhanced topoisomerase II-mediated DNA cleavage. Thus, even within the more complex spice formulation, oxidized curcumin intermediates appear to function as topoisomerase II poisons. PMID:23253398

Synthesis and Base Hydrolysis of a Cobalt(III) Complex Coordinated by a Thioether Ligand

ERIC Educational Resources Information Center

Roecker, Lee

2008-01-01

A two-week laboratory experiment for students in advanced inorganic chemistry is described. Students prepare and characterize a cobalt(III) complex coordinated by a thioether ligand during the first week of the experiment and then study the kinetics of Co-S bond cleavage in basic solution during the second week. The synthetic portion of the…

Two-Dimensional NMR Evidence for Cleavage of Lignin and Xylan Substituents in Wheat Straw Through Hydrothermal Pretreatment and Enzymatic Hydrolysis

Treesearch

Daniel J. Yelle; Prasad Kaparaju; Christopher G. Hunt; Kolby Hirth; Hoon Kim; John Ralph; Claus Felby

2012-01-01

Solution-state two-dimensional (2D) nuclear magnetic resonance (NMR) spectroscopy of plant cell walls is a powerful tool for characterizing changes in cell wall chemistry during the hydrothermal pretreatment process of wheat straw for second-generation bioethanol production. One-bond 13C-1H NMR correlation spectroscopy, via...

Improving off-line accelerated tryptic digestion. Towards fast-lane proteolysis of complex biological samples.

PubMed

Vukovic, Jadranka; Loftheim, Håvard; Winther, Bjørn; Reubsaet, J Léon E

2008-06-27

Off-line digestion of proteins using immobilized trypsin beads is studied with respect to the format of the digestion reactor, the digestion conditions, the comparison with in-solution digestion and its use in complex biological samples. The use of the filter vial as the most appropriate digestion reactor enables simple, efficient and easy-to-handle off-line digestion of the proteins on trypsin beads. It was shown that complex proteins like bovine serum albumin (BSA) need much longer time (89 min) and elevated temperature (37 degrees C) to be digested to an acceptable level compared to smaller proteins like cytochrome c (5 min, room temperature). Comparing the BSA digestion using immobilized trypsin beads with conventional in-solution digestion (overnight at 37 degrees C), it was shown that comparable results were obtained with respect to sequence coverage (>90%) and amount of missed cleavages (in both cases around 20 peptides with 1 or 2 missed cleavages were detected). However, the digestion using immobilized trypsin beads was considerable less time consuming. Good reproducibility and signal intensities were obtained for the digestion products of BSA in a complex urine sample. In addition to this, peptide products of proteins typically present in urine were identified.

Isolation of an oxomanganese(V) porphyrin intermediate in the reaction of a manganese(III) porphyrin complex and H2O2 in aqueous solution.

PubMed

Nam, Wonwoo; Kim, Inwoo; Lim, Mi Hee; Choi, Hye Jin; Lee, Je Seung; Jang, Ho G

2002-05-03

The reaction of [Mn(TF(4)TMAP)](CF(3)SO(3))(5) (TF(4)TMAP=meso-tetrakis(2,3,5,6-tetrafluoro-N,N,N-trimethyl-4-aniliniumyl)porphinato dianion) with H(2)O(2) (2 equiv) at pH 10.5 and 0 degrees C yielded an oxomanganese(V) porphyrin complex 1 in aqueous solution, whereas an oxomanganese(IV) porphyrin complex 2 was generated in the reactions of tert-alkyl hydroperoxides such as tert-butyl hydroperoxide and 2-methyl-1-phenyl-2-propyl hydroperoxide. Complex 1 was capable of epoxidizing olefins and exchanging its oxygen with H(2) (18)O, whereas 2 did not epoxidize olefins. From the reactions of [Mn(TF(4)TMAP)](5+) with various oxidants in the pH range 3-11, the O-O bond cleavage of hydroperoxides was found to be sensitive to the hydroperoxide substituent and the pH of the reaction solution. Whereas the O-O bond of hydroperoxides containing an electron-donating tert-alkyl group is cleaved homolytically, an electron-withdrawing substituent such as an acyl group in m-chloroperoxybenzoic acid (m-CPBA) facilitates O-O bond heterolysis. The mechanism of the O-O bond cleavage of H(2)O(2) depends on the pH of the reaction solution: O-O bond homolysis prevails at low pH and O-O bond heterolysis becomes a predominant pathway at high pH. The effect of pH on (18)O incorporation from H(2) (18)O into oxygenated products was examined over a wide pH range, by carrying out the epoxidation of carbamazepine (CBZ) with [Mn(TF(4)TMAP)](5+) and KHSO(5) in buffered H(2) (18)O solutions. A high proportion of (18)O was incorporated into the CBZ-10,11-oxide product at all pH values but this proportion was not affected significantly by the pH of the reaction solution.

Dynamic plasticity and failure of high-purity alumina under shock loading.

PubMed

Chen, M W; McCauley, J W; Dandekar, D P; Bourne, N K

2006-08-01

Most high-performance ceramics subjected to shock loading can withstand high failure strength and exhibit significant inelastic strain that cannot be achieved under conventional loading conditions. The transition point from elastic to inelastic response prior to failure during shock loading, known as the Hugoniot elastic limit (HEL), has been widely used as an important parameter in the characterization of the dynamic mechanical properties of ceramics. Nevertheless, the underlying micromechanisms that control HEL have been debated for many years. Here we show high-resolution electron microscopy of high-purity alumina, soft-recovered from shock-loading experiments. The change of deformation behaviour from dislocation activity in the vicinity of grain boundaries to deformation twinning has been observed as the impact pressures increase from below, to above HEL. The evolution of deformation modes leads to the conversion of material failure from an intergranular mode to transgranular cleavage, in which twinning interfaces serve as the preferred cleavage planes.

Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis

PubMed Central

Lu, Duo; Silhan, Jan; MacDonald, James T.; Carpenter, Elisabeth P.; Jensen, Kirsten; Tang, Christoph M.; Baldwin, Geoff S.; Freemont, Paul S.

2012-01-01

Base excision repair (BER) is a highly conserved DNA repair pathway throughout all kingdoms from bacteria to humans. Whereas several enzymes are required to complete the multistep repair process of damaged bases, apurinic-apyrimidic (AP) endonucleases play an essential role in enabling the repair process by recognizing intermediary abasic sites cleaving the phosphodiester backbone 5′ to the abasic site. Despite extensive study, there is no structure of a bacterial AP endonuclease bound to substrate DNA. Furthermore, the structural mechanism for AP-site cleavage is incomplete. Here we report a detailed structural and biochemical study of the AP endonuclease from Neisseria meningitidis that has allowed us to capture structural intermediates providing more complete snapshots of the catalytic mechanism. Our data reveal subtle differences in AP-site recognition and kinetics between the human and bacterial enzymes that may reflect different evolutionary pressures. PMID:23035246

Tibiofemoral Contact Mechanics with Horizontal Cleavage Tear and Resection of the Medial Meniscus in the Human Knee.

PubMed

Koh, Jason L; Yi, Seung Jin; Ren, Yupeng; Zimmerman, Todd A; Zhang, Li-Qun

2016-11-02

The meniscus is known to increase the contact area and decrease contact pressure in the tibiofemoral compartments of the knee. Radial tears of the meniscal root attachment along with partial resections of the torn meniscal tissue decrease the contact area and increase pressure; however, there is a lack of information on the effects of a horizontal cleavage tear (HCT) and partial leaf meniscectomy of such tears on tibiofemoral contact pressure and contact area. Twelve fresh-frozen human cadaveric knees were tested under 10 conditions: 5 serial conditions of posterior medial meniscectomy (intact meniscus, HCT, repaired HCT, inferior leaf resection, and resection of both inferior and superior leaves), each at 2 knee flexion angles (0° and 60°) under an 800-N axial load. Tekscan sensors (model 4000) were used to measure the contact pressure and contact area. HCT and HCT repair resulted in small changes in the contact area and an increase in contact pressure compared with the intact condition. Resection of the inferior leaf resulted in significantly decreased contact area (to a mean 82.3% of the intact condition at 0° of flexion and 81.8% at 60° of flexion; p < 0.05) and increased peak contact pressure (a mean 36.3% increase at 0° flexion and 43.2% increase at 60° flexion; p < 0.05) in the medial compartment. Further resection of the remaining superior leaf resulted in additional significant decreases in contact area (to a mean 60.1% of the intact condition at 0° of flexion and 49.7% at 60° of flexion; p < 0.05) and increases in peak contact pressure (a mean 79.2% increase at 0° of flexion and 74.9% increase at 60° of flexion; p < 0.05). Resection of meniscal tissue forming the inferior leaf of an HCT resulted in substantially decreased contact area and increased contact pressure. Additional resection of the superior leaf resulted in a further significant decrease in contact area and increase in contact pressure in the medial compartment. Repair or minimal resection of meniscal tissue of an HCT may be preferred to complete leaf resection to maintain knee tibiofemoral contact mechanics. Copyright © 2016 by The Journal of Bone and Joint Surgery, Incorporated.

Supercritical fluid molecular spray film deposition and powder formation

DOEpatents

Smith, Richard D.

1986-01-01

Solid films are deposited, or fine powders formed, by dissolving a solid material into a supercritical fluid solution at an elevated pressure and then rapidly expanding the solution through a short orifice into a region of relatively low pressure. This produces a molecular spray which is directed against a substrate to deposit a solid thin film thereon, or discharged into a collection chamber to collect a fine powder. Upon expansion and supersonic interaction with background gases in the low pressure region, any clusters of solvent are broken up and the solvent is vaporized and pumped away. Solute concentration in the solution is varied primarily by varying solution pressure to determine, together with flow rate, the rate of deposition and to control in part whether a film or powder is produced and the granularity of each. Solvent clustering and solute nucleation are controlled by manipulating the rate of expansion of the solution and the pressure of the lower pressure region. Solution and low pressure region temperatures are also controlled.

Behavior of a hammerhead ribozyme in aqueous solution at medium to high temperatures

NASA Astrophysics Data System (ADS)

El-Murr, Nizar; Maurel, Marie-Christine; Rihova, Martina; Vergne, Jacques; Hervé, Guy; Kato, Mikio; Kawamura, Kunio

2012-09-01

The "RNA world" hypothesis proposes that—early in the evolution of life—RNA molecules played important roles both in information storage and in enzymatic functions. However, this hypothesis seems to be inconsistent with the concept that life may have emerged under hydrothermal conditions since RNA molecules are considered to be labile under such extreme conditions. Presently, the possibility that the last common ancestor of the present organisms was a hyperthermophilic organism which is important to support the hypothesis of the hydrothermal origin of life has been subject of strong discussions. Consequently, it is of importance to study the behavior of RNA molecules under hydrothermal conditions from the viewpoints of stability, catalytic functions, and storage of genetic information of RNA molecules and determination of the upper limit of temperature where life could have emerged. In the present work, self-cleavage of a natural hammerhead ribozyme was examined at temperatures 10-200 °C. Self-cleavage was investigated in the presence of Mg2+, which facilitates and accelerates this reaction. Self-cleavage of the hammerhead ribozyme was clearly observed at temperatures up to 60 °C, but at higher temperatures self-cleavage occurs together with hydrolysis and with increasing temperature hydrolysis becomes dominant. The influence of the amount of Mg2+ on the reaction rate was also investigated. In addition, we discovered that the reaction proceeds in the presence of high concentrations of monovalent cations (Na+ or K+), although very slowly. Furthermore, at high temperatures (above 60 °C), monovalent cations protect the ribozyme against degradation.

Corrosion behavior of stainless steel weldments in physiological solutions

NASA Astrophysics Data System (ADS)

Farooq, A.; Azam, M.; Deen, K. M.

2018-01-01

In this study corrosion behavior of TIG welded 316L stainless steel plates in simulated biological solutions is investigated. The mechanical testing results showed slight decrease in ductility after welding and the fracture surface represented mixed cleavage and inclusions containing dimple structure. The heat affected and weld zone (WZ) demonstrated higher corrosion potential and relatively large pitting tendency than base metal (BM) in both Hank’s and Ringer’s solution. The formation of delta (δ) ferrite in the heat affected and WZ decreased the corrosion resistance as confirmed from potentiodynamic Tafel scans. The decrease in pitting resistance and lower protection tendency of the WZ compared to BM and heat affected zone was also quantified from the cyclic polarization trends.

Changes in solvation during DNA binding and cleavage are critical to altered specificity of the EcoRI endonuclease

PubMed Central

Robinson, Clifford R.; Sligar, Stephen G.

1998-01-01

Restriction endonucleases such as EcoRI bind and cleave DNA with great specificity and represent a paradigm for protein–DNA interactions and molecular recognition. Using osmotic pressure to induce water release, we demonstrate the participation of bound waters in the sequence discrimination of substrate DNA by EcoRI. Changes in solvation can play a critical role in directing sequence-specific DNA binding by EcoRI and are also crucial in assisting site discrimination during catalysis. By measuring the volume change for complex formation, we show that at the cognate sequence (GAATTC) EcoRI binding releases about 70 fewer water molecules than binding at an alternate DNA sequence (TAATTC), which differs by a single base pair. EcoRI complexation with nonspecific DNA releases substantially less water than either of these specific complexes. In cognate substrates (GAATTC) kcat decreases as osmotic pressure is increased, indicating the binding of about 30 water molecules accompanies the cleavage reaction. For the alternate substrate (TAATTC), release of about 40 water molecules accompanies the reaction, indicated by a dramatic acceleration of the rate when osmotic pressure is raised. These large differences in solvation effects demonstrate that water molecules can be key players in the molecular recognition process during both association and catalytic phases of the EcoRI reaction, acting to change the specificity of the enzyme. For both the protein–DNA complex and the transition state, there may be substantial conformational differences between cognate and alternate sites, accompanied by significant alterations in hydration and solvent accessibility. PMID:9482860

A Serendipitous Discover that in situ Proteolysis is Essential for the Crystallization of Yeast CPSF-100 (Ydh1p)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mandel,C.; Gebauer, D.; Zhang, H.

2006-01-01

The cleavage and polyadenylation specificity factor (CPSF) complex is required for the cleavage and polyadenylation of the 3'-end of messenger RNA precursors in eukaryotes. During structural studies of the 100 kDa subunit (CPSF-100, Ydh1p) of the yeast CPSF complex, it was serendipitously discovered that a solution that is infected by a fungus (subsequently identified as Penicillium) is crucial for the crystallization of this protein. Further analyses suggest that the protein has undergone partial proteolysis during crystallization, resulting in the deletion of an internal segment of about 200 highly charged and hydrophilic residues, very likely catalyzed by a protease secreted bymore » the fungus. With the removal of this segment, yeast CPSF-100 (Ydh1p) has greatly reduced solubility and can be crystallized in the presence of a minute amount of precipitant.« less

AB INITIO STUDY OF GRAIN BOUNDARY PROPERTIES OF TUNGSTEN ALLOYS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Setyawan, Wahyu; Kurtz, Richard J.

2012-04-17

Density functional theory was employed to investigate the grain boundary (GB) property of W-TM alloys (TM: fifth and sixth row transition metals). GB strengthening was found for Hf, Ta, Nb, Ru, Re, Os and Ir for 27{l_brace}525{r_brace} and to a lesser degree for 11{l_brace}323{r_brace}. Lower valence solutes strengthen the GB at certain substitutional sites, while higher valence elements enforce it at other positions. For 3{l_brace}112{r_brace}, the alloys exhibit reduced cleavage energies. Hence, allowing with TMs increases the GB cohesion more effectively for large-angle GBs whose cleavage energy is, in general, inherently lower than the low-angle ones. Electron density analysis elucidatesmore » the mechanism of charge addition or depletion of the GB bonding region upon TM substitution at various positions leading to stronger or weaker intergranular cohesion, respectively.« less

Aerobic Oxidation of Xylose to Xylaric acid in Water over Pt Catalysts.

PubMed

Saha, Basudeb; Sadula, Sunitha

2018-05-02

Energy-efficient catalytic conversion of biomass intermediates to functional chemicals can enable bio-products viable. Herein, we report an efficient and low temperature aerobic oxidation of xylose to xylaric acid, a promising bio-based chemical for the production of glutaric acid, over commercial catalysts in water. Among several heterogeneous catalysts investigated, Pt/C exhibits the best activity. Systematic variation of reaction parameters in the pH range of 2.5 to 10 suggests that the reaction is fast at higher temperatures but high C-C scission of intermediate C5-oxidized products to low carbon carboxylic acids undermines xylaric acid selectivity. The C-C cleavage is also high in basic solution. The oxidation at neutral pH and 60 C achieves the highest xylaric acid yield (64%). O2 pressure and Pt-amount have significant influence on the reactivity. Decarboxylation of short chain carboxylic acids results in formation of CO2, causing some carbon loss; however such decarboxylation is slow in the presence of xylose. The catalyst retained comparable activity, in terms of product selectivity, after five cycles with no sign of Pt leaching. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular Mechanism of Processive 3' to 5' RNA Translocation in the Active Subunit of the RNA Exosome Complex.

PubMed

Vuković, Lela; Chipot, Christophe; Makino, Debora L; Conti, Elena; Schulten, Klaus

2016-03-30

Recent experimental studies revealed structural details of 3' to 5' degradation of RNA molecules, performed by the exosome complex. ssRNA is channeled through its multisubunit ring-like core into the active site tunnel of its key exonuclease subunit Rrp44, which acts both as an enzyme and a motor. Even in isolation, Rrp44 can pull and sequentially cleave RNA nucleotides, one at a time, without any external energy input and release a final 3-5 nucleotide long product. Using molecular dynamics simulations, we identify the main factors that control these processes. Our free energy calculations reveal that RNA transfer from solution into the active site of Rrp44 is highly favorable, but dependent on the length of the RNA strand. While RNA strands formed by 5 nucleotides or more correspond to a decreasing free energy along the translocation coordinate toward the cleavage site, a 4-nucleotide RNA experiences a free energy barrier along the same direction, potentially leading to incomplete cleavage of ssRNA and the release of short (3-5) nucleotide products. We provide new insight into how Rrp44 catalyzes a localized enzymatic reaction and performs an action distributed over several RNA nucleotides, leading eventually to the translocation of whole RNA segments into the position suitable for cleavage.

Hydrogen generation systems and methods utilizing sodium silicide and sodium silica gel materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wallace, Andrew P.; Melack, John M.; Lefenfeld, Michael

Systems, devices, and methods combine thermally stable reactant materials and aqueous solutions to generate hydrogen and a non-toxic liquid by-product. The reactant materials can sodium silicide or sodium silica gel. The hydrogen generation devices are used in fuels cells and other industrial applications. One system combines cooling, pumping, water storage, and other devices to sense and control reactions between reactant materials and aqueous solutions to generate hydrogen. Springs and other pressurization mechanisms pressurize and deliver an aqueous solution to the reaction. A check valve and other pressure regulation mechanisms regulate the pressure of the aqueous solution delivered to the reactantmore » fuel material in the reactor based upon characteristics of the pressurization mechanisms and can regulate the pressure of the delivered aqueous solution as a steady decay associated with the pressurization force. The pressure regulation mechanism can also prevent hydrogen gas from deflecting the pressure regulation mechanism.« less

Hydrogen generation systems and methods utilizing sodium silicide and sodium silica gel materials

DOEpatents

Wallace, Andrew P.; Melack, John M.; Lefenfeld, Michael

2015-08-11

Systems, devices, and methods combine thermally stable reactant materials and aqueous solutions to generate hydrogen and a non-toxic liquid by-product. The reactant materials can sodium silicide or sodium silica gel. The hydrogen generation devices are used in fuels cells and other industrial applications. One system combines cooling, pumping, water storage, and other devices to sense and control reactions between reactant materials and aqueous solutions to generate hydrogen. Springs and other pressurization mechanisms pressurize and deliver an aqueous solution to the reaction. A check valve and other pressure regulation mechanisms regulate the pressure of the aqueous solution delivered to the reactant fuel material in the reactor based upon characteristics of the pressurization mechanisms and can regulate the pressure of the delivered aqueous solution as a steady decay associated with the pressurization force. The pressure regulation mechanism can also prevent hydrogen gas from deflecting the pressure regulation mechanism.

Influence of phase type and solute structure on changes in retention with pressure in reversed-phase high performance liquid chromatography.

PubMed

Fallas, Morgane M; Tanaka, Nobuo; Buckenmaier, Stephan M C; McCalley, David V

2013-07-05

The influence of pressure on the retention of several types of solute, including acids, bases and neutrals, was studied by the use of restriction capillaries added to the end of various monomeric and polymeric octadecylsilyl-modified 5μm particle size columns. Although it appeared that certain polymeric columns could give somewhat greater increases in retention with pressure, differences in behaviour between these different C18 columns were rather small. Differences in solute molecular size were most important in determining increases in retention with pressure. However, solute structure such as polarity and planarity were also influential. A prototype C30 column gave interesting selectivity changes between planar and non-planar solutes as a function of pressure. Considerable selectivity differences with pressure were shown when diverse mixtures of solutes were analysed. For the solutes studied, only minor effects of increased pressure on column efficiency and peak shape were noted. Copyright © 2013 Elsevier B.V. All rights reserved.

Fracture toughness of Ti-Al3Ti-Al-Al3Ti laminate composites under static and cyclic loading conditions

NASA Astrophysics Data System (ADS)

Patselov, A. M.; Gladkovskii, S. V.; Lavrikov, R. D.; Kamantsev, I. S.

2015-10-01

The static and cyclic fracture toughnesses of a Ti-Al3Ti-Al-Al3Ti laminate composite material containing at most 15 vol % intermetallic compound are studied. Composite specimens are prepared by terminating reaction sintering of titanium and aluminum foils under pressure. The fracture of the titanium layers is quasi-cleavage during cyclic crack growth and is ductile during subsequent static loading.

Osmosis and solute-solvent drag: fluid transport and fluid exchange in animals and plants.

PubMed

Hammel, H T; Schlegel, Whitney M

2005-01-01

In 1903, George Hulett explained how solute alters water in an aqueous solution to lower the vapor pressure of its water. Hulett also explained how the same altered water causes osmosis and osmotic pressure when the solution is separated from liquid water by a membrane permeable to the water only. Hulett recognized that the solute molecules diffuse toward all boundaries of the solution containing the solute. Solute diffusion is stopped at all boundaries, at an open-unopposed surface of the solution, at a semipermeable membrane, at a container wall, or at the boundary of a solid or gaseous inclusion surrounded by solution but not dissolved in it. At each boundary of the solution, the solute molecules are reflected, they change momentum, and the change of momentum of all reflected molecules is a pressure, a solute pressure (i.e., a force on a unit area of reflecting boundary). When a boundary of the solution is open and unopposed, the solute pressure alters the internal tension in the force bonding the water in its liquid phase, namely, the hydrogen bond. All altered properties of the water in the solution are explained by the altered internal tension of the water in the solution. We acclaim Hulett's explanation of osmosis, osmotic pressure, and lowering of the vapor pressure of water in an aqueous solution. His explanation is self-evident. It is the necessary, sufficient, and inescapable explanation of all altered properties of the water in the solution relative to the same property of pure liquid water at the same externally applied pressure and the same temperature. We extend Hulett's explanation of osmosis to include the osmotic effects of solute diffusing through solvent and dragging on the solvent through which it diffuses. Therein lies the explanations of (1) the extravasation from and return of interstitial fluid to capillaries, (2) the return of luminal fluid in the proximal and distal convoluted tubules of a kidney nephron to their peritubular capillaries, (3) the return of interstitial fluid to the vasa recta, (4) return of aqueous humor to the episcleral veins, and (5) flow of phloem from source to sink in higher plants and many more examples of fluid transport and fluid exchange in animal and plant physiology. When a membrane is permeable to water only and when it separates differing aqueous solutions, the flow of water is from the solution with the lower osmotic pressure to the solution with the higher osmotic pressure.

Unexpected Hydrolytic Instability of N-Acylated Amino Acid Amides and Peptides

PubMed Central

2015-01-01

Remote amide bonds in simple N-acyl amino acid amide or peptide derivatives 1 can be surprisingly unstable hydrolytically, affording, in solution, variable amounts of 3 under mild acidic conditions, such as trifluoroacetic acid/water mixtures at room temperature. This observation has important implications for the synthesis of this class of compounds, which includes N-terminal-acylated peptides. We describe the factors contributing to this instability and how to predict and control it. The instability is a function of the remote acyl group, R2CO, four bonds away from the site of hydrolysis. Electron-rich acyl R2 groups accelerate this reaction. In the case of acyl groups derived from substituted aromatic carboxylic acids, the acceleration is predictable from the substituent’s Hammett σ value. N-Acyl dipeptides are also hydrolyzed under typical cleavage conditions. This suggests that unwanted peptide truncation may occur during synthesis or prolonged standing in solution when dipeptides or longer peptides are acylated on the N-terminus with electron-rich aromatic groups. When amide hydrolysis is an undesired secondary reaction, as can be the case in the trifluoroacetic acid-catalyzed cleavage of amino acid amide or peptide derivatives 1 from solid-phase resins, conditions are provided to minimize that hydrolysis. PMID:24617596

In-Situ Atomic Force Microscope Imaging of Calcite Etch Pit Morphology Changes in Undersaturated and 1-Hydroxyethylidene-1,1-diphosphonic Acid Poisoned Solutions

PubMed Central

Britt, David W.

2012-01-01

Morphology changes in etch pits formed on the (1014) cleavage plane of calcite were induced by varying the ratio of [Ca2+] to [CO32−] in the bulk solution as well as through the addition of the crystal poison 1-hydroxyethylidene-1,1-diphosphonic acid (HEDP). Three distinct morphologies were noted: symmetric rhombic, asymmetric rhombic, and triangular with a rough curved hypotenuse. The latter represents a transient morphology which is only observed during the actual dissolution process, while the former morphologies persist after dissolution is halted. PMID:25125794

Pd-loaded carbon felt as the cathode for selective dechlorination of 2,4-dichlorophenoxyacetic acid in aqueous solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsyganok, A.I.; Yamanaka, Ichiro; Otsuka, Kiyoshi

1998-11-01

Electrocatalytic reductive dehalogenation of 2,4-dichlorophenoxyacetic acid (2,4-D) to phenoxyacetic acid in aqueous solution containing MeOH, trifluoroacetic acid, and tetraalkylammonium salt was studied. A Teflon-made two-compartment flow-through cell with a permeable carbon felt cathode and a platinum foil anode was employed. Several noble metals were tested as electrocatalysts. Palladium-loaded carbon felt was found to be the most suitable significantly enhanced its electrocatalytic activity toward 2,4-D dechlorination. The reaction was hypothesized to proceed at carbon-palladium interface areas through 4-chlorine cleavage to form 2-chlorophenoxyacetic acid as the main reaction intermediate.

Supercooling of aqueous dimethylsulfoxide solution at normal and high pressures: Evidence for the coexistence of phase-separated aqueous dimethylsulfoxide solutions of different water structures.

PubMed

Kanno, H; Kajiwara, K; Miyata, K

2010-05-21

Supercooling behavior of aqueous dimethylsulfoxide (DMSO) solution was investigated as a function of DMSO concentration and at high pressures. A linear relationship was observed for T(H) (homogeneous ice nucleation temperature) and T(m) (melting temperature) for the supercooling of aqueous DMSO solution at normal pressure. Analysis of the DTA (differential thermal analysis) traces for homogeneous ice crystallization in the bottom region of the T(H) curve for a DMSO solution of R=20 (R: moles of water/moles of DMSO) at high pressures supported the contention that the second critical point (SCP) of liquid water should exist at P(c2)= approximately 200 MPa and at T(c2)<-100 degrees C (P(c2): pressure of SCP, T(c2): temperature of SCP). The presence of two T(H) peaks for DMSO solutions (R=15, 12, and 10) suggests that phase separation occurs in aqueous DMSO solution (R

Supercooling of aqueous dimethylsulfoxide solution at normal and high pressures: Evidence for the coexistence of phase-separated aqueous dimethylsulfoxide solutions of different water structures

NASA Astrophysics Data System (ADS)

Kanno, H.; Kajiwara, K.; Miyata, K.

2010-05-01

Supercooling behavior of aqueous dimethylsulfoxide (DMSO) solution was investigated as a function of DMSO concentration and at high pressures. A linear relationship was observed for TH (homogeneous ice nucleation temperature) and Tm (melting temperature) for the supercooling of aqueous DMSO solution at normal pressure. Analysis of the DTA (differential thermal analysis) traces for homogeneous ice crystallization in the bottom region of the TH curve for a DMSO solution of R =20 (R: moles of water/moles of DMSO) at high pressures supported the contention that the second critical point (SCP) of liquid water should exist at Pc2=˜200 MPa and at Tc2<-100 °C (Pc2: pressure of SCP, Tc2: temperature of SCP). The presence of two TH peaks for DMSO solutions (R =15, 12, and 10) suggests that phase separation occurs in aqueous DMSO solution (R ≤15) at high pressures and low temperatures (<-90 °C). The pressure dependence of the two TH curves for DMSO solutions of R =10 and 12 indicates that the two phase-separated components in the DMSO solution of R =10 have different liquid water structures [LDL-like and HDL-like structures (LDL: low-density liquid water, HDL: high-density liquid water)] in the pressure range of 120-230 MPa.

Elucidating Direct Photolysis Mechanisms of Different Dissociation Species of Norfloxacin in Water and Mg2+ Effects by Quantum Chemical Calculations.

PubMed

Wang, Se; Wang, Zhuang

2017-11-11

The study of pollution due to combined antibiotics and metals is urgently needed. Photochemical processes are an important transformation pathway for antibiotics in the environment. The mechanisms underlying the effects of metal-ion complexation on the aquatic photochemical transformation of antibiotics in different dissociation forms are crucial problems in science, and beg solutions. Herein, we investigated the mechanisms of direct photolysis of norfloxacin (NOR) in different dissociation forms in water and metal ion Mg 2+ effects using quantum chemical calculations. Results show that different dissociation forms of NOR had different maximum electronic absorbance wavelengths (NOR 2+ < NOR⁰ < NOR⁺) and showed different photolysis reactivity. Analysis of transition states (TS) and reaction activation energies ( E a ) indicated NOR⁺ generally underwent loss of the piperazine ring (C10-N13 bond cleavage) and damage to piperazine ring (N13-C14 bond cleavage). For NOR 2+ , the main direct photolysis pathways were de-ethylation (N7-C8 bond cleavage) and decarboxylation (C2-C5 bond cleavage). Furthermore, the presence of Mg 2+ changed the order of the wavelength at maximum electronic absorbance (NOR⁺-Mg 2+ < NOR⁰-Mg 2+ < NOR 2+ -Mg 2+ ) and increased the intensities of absorbance peaks of all three dissociation species of NOR, implying that Mg 2+ played an important role in the direct photolysis of NOR⁰, NOR⁺, and NOR 2+ . The calculated TS results indicated that the presence of Mg 2+ increased E a for most direct photolysis pathways of NOR, while it decreased E a for some direct photolysis pathways such as the loss of the piperazine ring and the damage of the piperazine ring of NOR⁰ and the defluorination of NOR⁺.

Structural characterization by both positive and negative electrospray ion trap mass spectrometry of oligogalacturonates purified by high-performance anion-exchange chromatography.

PubMed

Quéméner, Bernard; Désiré, Cédric; Debrauwer, Laurent; Rathahao, Estelle

2003-01-17

The off-line coupling of high-performance anion-exchange chromatography to electrospray ion trap mass spectrometry (ESI-IT-MS) is described. Two sets of isocratic conditions were optimised for the semi-preparative purification of oligogalacturonates of degree of polymerisation from 4 to 6 by monitoring eluates with either pulsed amperometric detection or evaporative light scattering detection in the presence of an online Dionex Carbohydrate Membrane Desalter (CMD). In these conditions, purified oligogalacturonate solutions were suitable, without further desalting steps, for infusion ESI-IT-MS experiments. This paper provides some interesting features of positive and negative ESI-IT-multiple MS (MSn) of these acidic oligosaccharides. The spectra acquired in both ion modes show characteristic fragments resulting from glycosidic bond and cross-ring cleavages. Under negative ionization conditions, the fragmentation of the singly-charged [M-H]- ions, as well as the Ci-, and Zi-, fragment ions through sequential MSn experiments, was always dominated by product ions from C- and Z-type glycosidic cleavages. All spectra also displayed 0.2 A-type cross-ring cleavage ions which carry linkage information. Collision-induced dissociation (CID) spectra of sodium-cationized species obtained under positive ionization conditions were more complex. Successive MSn experiments also led to the 0.2 A-type cross-ring cleavage ions observed together with B- and Y-type ions. The presence of the 0.2 A ion series was related to Mr 60 (C2H4O2) losses. Combined with the absence of the Mr 30 (CH2O) and the Mr 90 (C3H6O3) ions, these ions were indicative of 1-4 type glycosidic linkage.

Overexpression of soluble Fas ligand following AAV gene therapy prevents retinal ganglion cell death in chronic and acute murine models of glaucoma

PubMed Central

Krishnan, Anitha; Fei, Fei; Jones, Alexander; Busto, Patricia; Marshak-Rothstein, Ann; Ksander, Bruce R.; Gregory-Ksander, Meredith

2016-01-01

Glaucoma is a multifactorial disease resulting in the death of retinal ganglion cells (RGCs) and irreversible blindness. Glaucoma-associated RGC cell death depends on the pro-apoptotic and proinflammatory activity of membrane-bound FasL (mFasL). In contrast to mFasL, the natural soluble FasL cleavage product (sFasL) inhibits mFasL-mediated apoptosis and inflammation and is therefore a mFasL antagonist. DBA/2J (D2) mice spontaneously develop glaucoma and predictably RGC destruction is exacerbated by expression of a mutated membrane-only FasL (mFasL) gene that lacks the extracellular cleavage site. Remarkably, one time intraocular adeno-associated virus-mediated gene delivery of sFasL (AAV2.sFasL) provides complete and sustained neuroprotection in both the chronic D2 and acute microbead-induced models of glaucoma, even in the presence of elevated intraocular pressure (IOP). This protection correlated with inhibition of glial activation, reduced production of TNFα, and decreased apoptosis of RGCs and loss of axons. These data indicate that cleavage of FasL under homeostatic conditions, and the ensuing release of sFasL, normally limits the neurodestructive activity of FasL. The data further support the notion that sFasL, and not mFasL, contributes to the immune privileged status of the eye. PMID:27849168

Effects of reactive oxygen species levels in prepared culture media on embryo development: a comparison of two media.

PubMed

Shih, Ying-Fu; Lee, Tsung-Hsien; Liu, Chung-Hsien; Tsao, Hui-Mei; Huang, Chun-Chia; Lee, Maw-Sheng

2014-12-01

This study determined the correlation between the levels of reactive oxygen species (ROS) in prepared culture media and the early development of human embryos. This was an autocontrolled comparison study. A total of 159 patients undergoing in vitro fertilization/intracytoplasmic sperm injection treatment were recruited in this study. The pH values, osmolarity pressures, and ROS levels of 15 batches of two culture media were measured. Sibling oocytes or embryos from individual patients were randomly assigned to two culture groups with Quinn's Advantage Cleavage and Blastocyst media (QAC/QAB) or GIII series cleavage and blastocyst media (G1.3/G2.3). The difference between the two culture groups was analyzed using one-sample t test. The QAC/QAB and G1.3/G2.3 media exhibited similar pH values and osmolarity pressures. However, the prepared QAC/QAB media were characterized to contain lower amounts of ROS than the G1.3/G2.3 media. Furthermore, the blastocysts that developed under the QAC/QAB media were morphologically superior to those that developed under the G1.3/G2.3 media. The elevated ROS levels in culture media were associated with poor development of blastocyst-stage embryos. Measurement of ROS levels may be a valuable process for medium selection or modification. Copyright © 2014. Published by Elsevier B.V.

Blackbody infrared radiative dissociation of oligonucleotide anions.

PubMed

Klassen, J S; Schnier, P D; Williams, E R

1998-11-01

The dissociation kinetics of a series of doubly deprotonated oligonucleotide 7-mers [d(A)7(2-), d(AATTAAT)2-, d(TTAATTA)2-, and d(CCGGCCG)2-] were measured using blackbody infrared radiative dissociation in a Fourier-transform mass spectrometer. The oligonucleotides dissociate first by cleavage at the glycosidic bond leading to the loss of a neutral nucleobase, followed by cleavage at the adjacent (5') phosphodiester bond to produce structurally informative a-base and w type ions. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained for the loss of base. The measured Arrhenius parameters are dependent on the identity of the nucleobase. The process involving the loss of an adenine base from the dianions, d(A)7(2-), d(AATTAAT)2-, and d(TTAATTA)2- has an average activation energy (Ea) of approximately 1.0 eV and a preexponential factor (A) of 10(10) s-1. Both guanine and cytosine base loss occurs for d(CCGGCCG)2-. The average Arrhenius parameters for the loss of cytosine and guanine are Ea = 1.32 +/- 0.03 eV and A = 10(13.3 +/- 0.3) s-1. No loss of thymine was observed for mixed adenine-thymine oligonucleotides. Neither base loss nor any other fragmentation reactions occur for d(T)7(2-) over a 600 s reaction delay at 207 degrees C, a temperature close to the upper limit accessible with our instrument. The Arrhenius parameters indicate that the preferred cleavage sites for mixed oligonucleotides of similar mass-to-charge ratio will be strongly dependent on the internal energy of the precursor ions. At low internal energies (effective temperatures below 475 K), loss of adenine and subsequent cleavage of the adjacent phosphoester bonds will dominate, whereas at higher energies, preferential cleavage at C and G residues will occur. The magnitude of the A factors < or = 10(13) s-1 measured for the loss of the three nucleobases (A, G, and C) is indicative of an entropically neutral or disfavored process as the rate limiting step for this reaction.

Blackbody Infrared Radiative Dissociation of Oligonucleotide Anions

PubMed Central

Klassen, John S.; Schnier, Paul D.; Williams, Evan R.

2005-01-01

The dissociation kinetics of a series of doubly deprotonated oligonucleotide 7-mers [ d(A)72-, d(AATTAAT)2−, d(TTAATTA)2−, and d(CCGGCCG)2−] were measured using blackbody infrared radiative dissociation in a Fourier-transform mass spectrometer. The oligonucleotides dissociate first by cleavage at the glycosidic bond leading to the loss of a neutral nucleobase, followed by cleavage at the adjacent (5′) phosphodiester bond to produce structurally informative a-base and w type ions. From the temperature dependence of the unimolecular dissociation rate constants, Arrhenius activation parameters in the zero-pressure limit are obtained for the loss of base. The measured Arrhenius parameters are dependent on the identity of the nucleobase. The process involving the loss of an adenine base from the dianions, d(A)72-, d(AATTAAT)2−, and d(TTAATTA)2− has an average activation energy (Ea) of ~1.0 eV and a preexponential factor (A) of 1010 s−1. Both guanine and cytosine base loss occurs for d(CCGGCCG)2−. The average Arrhenius parameters for the loss of cytosine and guanine are Ea = 1.32 ± 0.03 eV and A = 1013.3±0.3 s−1. No loss of thymine was observed for mixed adenine–thymine oligonucleotides. Neither base loss nor any other fragmentation reactions occur for d(T)72- over a 600 s reaction delay at 207 °C, a temperature close to the upper limit accessible with our instrument. The Arrhenius parameters indicate that the preferred cleavage sites for mixed oligonucleotides of similar mass-to-charge ratio will be strongly dependent on the internal energy of the precursor ions. At low internal energies (effective temperatures below 475 K), loss of adenine and subsequent cleavage of the adjacent phosphoester bonds will dominate, whereas at higher energies, preferential cleavage at C and G residues will occur. The magnitude of the A factors ≤1013 s−1 measured for the loss of the three nucleobases (A, G, and C) is indicative of an entropically neutral or disfavored process as the rate limiting step for this reaction. PMID:9794082

Telescoping metamorphic isograds: Evidence from 40Ar/39A dating in the Orange-Milford belt, southern Connecticut

USGS Publications Warehouse

Kunk, Michael J.; Walsh, Gregory J.; Growdon, Martha L.; Wintsch, Robert P.

2013-01-01

New 40Ar/39Ar ages for hornblende and muscovite from the Orange-Milford belt in southern Connecticut reflect cooling from Acadian amphibolite facies metamorphism between ∼380 to 360 Ma followed by retrograde recrystallization of fabric-forming muscovite and chlorite during lower greenschist facies Alleghanian transpression at ∼280 Ma. Reported field temperature and pressure gradients are improbably high for these rocks and a NW metamorphic field gradient climbing from chlorite-grade to staurolite-grade occurs over less than 5 km. Simple tilting cannot account for this compressed isograd spacing given the geothermal gradient of ∼20 °C/km present at the time of regional metamorphism. However, post-metamorphic transpression could effectively telescope the isograds by stretching the belt at an oblique angle to the isograd traces. Textures in the field and in thin section reveal several older prograde schistosities overprinted by lower greenschist facies fabrics. The late cleavages commonly occur at the scale of ∼100 μm and these samples contain multiple age populations of white mica. 40Ar/39Ar analysis of these poly-metamorphic samples with mixed muscovite populations yield climbing or U-shaped age spectra. The ages of the low temperature steps are late Paleozoic, while the ages of the older steps are late Devonian. These results support our petrologic interpretation that the younger cleavage developed under metamorphic conditions below the closure temperature for Ar diffusion in muscovite, that is, in the lower greenschist facies. The correlation of a younger regionally reproducible age population with a pervasive retrograde muscovite ± chlorite cleavage reveals an Alleghanian (∼280 Ma) overprint on the Acadian metamorphic gradient (∼380 Ma). Outcrop-scale structures including drag folds and imbricate boudins suggest that Alleghanian deformation and cleavage development occurred in response to dextral transpression along a northeast striking boundary. Alleghanian oblique collision of accreting terranes from the northeast would have resulted in northeast-southwest dextral transpression against the New York promontory. This deformation was responsible for crystallization of pervasive retrograde muscovite + chlorite cleavages and associated telescoping of the Acadian metamorphic isograds in southern Connecticut at ∼280 Ma.

Experimental Study of Hybrid Fractures and the Transition From Joints to Faults

NASA Astrophysics Data System (ADS)

Ramsey, J. M.; Chester, F. M.

2003-12-01

Joints and faults are end members of a continuous spectrum of brittle fractures including the hybrid fractures, hypothesized to form under mixed compressive and tensile stress. However, unequivocal evidence for the existence of hybrid fractures has not been presented. To investigate this transition, we have conducted triaxial extension experiments on dog-bone shaped cylindrical samples of Carrara marble at room temperature, an axial extension rate of 2x10-2 mm s-1, and confining pressures between 7.5 and 170 MPa. Two parallel suites of experiments were completed, one using very weak, latex jacketing to obtain accurate failure strength, and another using copper foil jacketing to preserve fracture surfaces. The combined data set provides strong evidence for the existence of hybrid fractures on the basis of the progressive change in failure strength, fracture orientation, and fracture surface morphology from joints to faults. At the lowest confining pressures (7.5 to 60 MPa), fractures are oriented approximately parallel to the maximum principal compressive stress, form at a tensile axial stress of approximately -7.75 MPa (i.e. the uniaxial tensile strength), and display fracture surfaces characterized by many reflective grain-scale cleavage faces, consistent with jointing. At the highest confining pressures (130 to 170 MPa), fractures are oriented from 13.4 to 21.6 degrees to the maximum principal compressive stress, form under completely compressive stress states where the axial stress is between 0 and 4.3 MPa, and are characterized by short slip lineations and powdery, finely comminuted grains consistent with faulting. At intermediate confining pressures (70 to 120 MPa), fractures are oriented from 3.7 to 12.4 degrees to the maximum principal compressive stress, form under mixed stress conditions with the axial stress ranging from -10.6 to -3.0 MPa, and display both reflective cleavage faces and short slip lineations with comminuted grains, consistent with hybrid fracturing.

Prediction of ice content in biological model solutions when frozen under high pressure.

PubMed

Guignon, B; Aparicio, C; Otero, L; Sanz, P D

2009-01-01

High pressure is, at least, as effective as cryoprotective agents (CPAs) and are used for decreasing both homogenous nucleation and freezing temperatures. This fact gives rise to a great variety of possible cryopreservation processes under high pressure. They have not been optimized yet, since they are relatively recent and are mainly based on the pressure-temperature phase diagram of pure water. Very few phase diagrams of biological material are available under pressure. This is owing to the lack of suitable equipment and to the difficulties encountered in carrying out the measurements. Different aqueous solutions of salt and CPAs as biological models are studied in the range of 0 degrees C down to -35 degrees C, 0.1 up to 250 MPa, and 0-20% w/w total solute concentration. The phase transition curves of glycerol and of sodium chloride with either glycerol or sucrose in aqueous solutions are determined in a high hydrostatic pressure vessel. The experimental phase diagrams of binary solutions were well described by a third-degree polynomial equation. It was also shown that Robinson and Stokes' equation at high pressure succeeds in predicting the phase diagrams of both binary and ternary solutions. The solute cryoconcentration and the ice content were calculated as a function of temperature and pressure conditions during the freezing of a binary solution. This information should provide a basis upon which high-pressure cryopreservation processes may be performed and the damages derived from ice formation evaluated. (c) 2009 American Institute of Chemical Engineers Biotechnol.

Multispectral Photoacoustic Imaging of Tumor Protease Activity with a Gold Nanocage-Based Activatable Probe.

PubMed

Liu, Cheng; Li, Shiying; Gu, Yanjuan; Xiong, Huahua; Wong, Wing-Tak; Sun, Lei

2018-05-07

Tumor proteases have been recognized as significant regulators in the tumor microenvironment, but the current strategies for in vivo protease imaging have tended to focus on the development of a probe design rather than the investigation of a novel imaging strategy by leveraging the imaging technique and probe. Herein, it is the first report to investigate the ability of multispectral photoacoustic imaging (PAI) to estimate the distribution of protease cleavage sites inside living tumor tissue by using an activatable photoacoustic (PA) probe. The protease MMP-2 is selected as the target. In this probe, gold nanocages (GNCs) with an absorption peak at ~ 800 nm and fluorescent dye molecules with an absorption peak at ~ 680 nm are conjugated via a specific enzymatic peptide substrate. Upon enzymatic activation by MMP-2, the peptide substrate is cleaved and the chromophores are released. Due to the different retention speeds of large GNCs and small dye molecules, the probe alters its intrinsic absorption profile and produces a distinct change in the PA signal. A multispectral PAI technique that can distinguish different chromophores based on intrinsic PA spectral signatures is applied to estimate the signal composition changes and indicate the cleavage interaction sites. Finally, the multispectral PAI technique with the activatable probe is tested in solution, cultured cells, and a subcutaneous tumor model in vivo. Our experiment in solution with enzyme ± inhibitor, cell culture ± inhibitor, and in vivo tumor model with administration of the developed probe ± inhibitor demonstrated the probe was cleaved by the targeted enzyme. Particularly, the in vivo estimation of the cleavage site distribution was validated with the result of ex vivo immunohistochemistry analysis. This novel synergy of the multispectral PAI technique and the activatable probe is a potential strategy for the distribution estimation of tumor protease activity in vivo.

Multidisciplinary exploratory study of a geothermal resource in the active volcanic arc of Basse-Terre (Guadeloupe, Lesser Antilles)

NASA Astrophysics Data System (ADS)

Navelot, Vivien; Favier, Alexiane; Géraud, Yves; Diraison, Marc; Corsini, Michel; Verati, Chrystèle; Lardeaux, Jean-Marc; Mercier de Lépinay, Jeanne; Munschy, Marc

2017-04-01

The GEOTREF project (high enthalpy geothermal energy in fractured reservoirs), supported by the French government program, "Investissements d'avenir" develops a sustainable geothermal resource in the Vieux Habitants area, 8-km south of the currently exploited Bouillante geothermal field. The Basse Terre Island is a recent volcanic arc (< 3 Myr) belonging to the Lesser Antilles subduction zone. It is composed of arc typical calc-alkaline volcanic rocks. Outcrops of the studied area consist either of andesitic lava flows, volcanic sedimentary facies or dikes. Field studies allow to propose a structural framework and highlight three major directions N000˚ E, N050˚ E and N090˚ E, which are consistent with the regional tectonic trends of the arc. Petrographical and petrophysical studies displayed that the major part of outcropping facies in the Vieux-Habitants area are not altered. Andesitic lava flows have poor reservoir properties with porosity and permeability lower than 5 % and 10-15m2 respectively. These results are in contrast with measurements performed in volcano-sedimentary rocks, which have heterogeneous petrophysical properties ranging from 15 to 50 % for porosity and from 10-15to 10-9m2 for permeability. Such surface data would probably change and decrease when depth increases. As there is a lack of underground data under the Vieux-Habitants area (wireline, drill core), exhumated rocks outcropping in the northern part of Basse-Terre Island (Basal Complex) have been studied. Such rocks have been identified in the Basal Complex (2.5 - 3 Myr) located in the northern part of the Basse-Terre Island. Previous works have demonstrated a 1000 m/Myr erosional rate, which corresponds at least to a 2 - 3 km exhumation. The petrography study of the Basal Complex reveals sub-greenschist type mineralogical transformations (chlorite, white mica, quartz...) changing the andesitic protolith in a meta-andesite. This metamorphism forms cleavage plans thanks to a pressure-solution mechanism. Mineralogical transformations associated with these cleavage planes have an impact on petrophysical properties. The solid phase density and porosity decrease. An anisotropy of permeability develops due to cleavage plans. Thermodynamics modelling based on the rock chemical composition and petrography observations emphasizes a steady-state mineral assemblage between 1.5 - 2 kbar and 280 - 320˚ C. This is consistent with an in situ measured volcanic arc conductive geothermal gradient of 70 ˚ C/km.

Thermal Motion and Forced Migration of Colloidal Particles Generate Hydrostatic Pressure in Solvent

PubMed Central

Hammel, H. T.; Scholander, P. F.

1973-01-01

A colloidal solution of ferrite particles in an osmometer has been used to demonstrate that the property that propels water across the semipermeable membrane is the decrease in hydrostatic pressure in the water of the solution. A magnetic field gradient directed so as to force the ferrite particles away from the semipermeable membrane of the osmometer and toward the free surface of the solution enhanced the colloidal osmotic pressure. The enhancement of this pressure was always exactly equal to the augmentation of the pressure as measured by the outward force of the particles, against the area of the free surface. Contrariwise, directing the magnetic field gradient so as to force the ferrite particles away from the free surface and toward the semipermeable membrane diminished the colloidal osmotic pressure of the solution. For a sufficiently forceful field gradient, the initial colloidal osmotic pressure could be negative, followed by an equilibrium pressure approaching zero regardless of the force of the particles against the membrane. Thus, the osmotic pressure of a solution is to be attributed to the pressure in the solvent generated in opposition to the pressure of the solute particles caused by their interaction with the free surface (Brownian motion and/or an external field force), or by their viscous shear when they migrate through the solvent, or both. PMID:16592046

Zinc-dependent cleavage in the catalytic core of the hammerhead ribozyme: evidence for a pH-dependent conformational change

PubMed Central

Borda, Emily J.; Markley, John C.; Sigurdsson, Snorri Th.

2003-01-01

We have characterized a novel Zn2+-catalyzed cleavage site between nucleotides C3 and U4 in the catalytic core of the hammerhead ribozyme. In contrast to previously described divalent metal-ion-dependent cleavage of RNA, U4 cleavage is only observed in the presence of Zn2+. This new cleavage site has an unusual pH dependence, in that U4 cleavage products are only observed above pH 7.9 and reach a maximum yield at about pH 8.5. These data, together with the fact that no metal ion-binding site is observed in proximity to the U4 cleavage site in either of the crystal structures, point toward a pH-dependent conformational change in the hammerhead ribozyme. We have described previously Zn2+-dependent cleavage between G8 and A9 in the hammerhead ribozyme and have discovered that U4 cleavage occurs only after A9 cleavage. To our knowledge, this is the first example of sequential cleavage events as a possible regulatory mechanism in ribozymes. PMID:12736309

[Effects of choledochal perfusion with biliary acid solutions on activity of the sphincter of Oddi (author's transl)].

PubMed

Bevilacqua, R G; Margarido, N F; Soares, L A; Mansur, R; Koch, V; Gonçalves, E L

1979-06-01

The changes of sphincter of Oddi's resistance, induced by choledochal perfusion of conjugated (taurocolic) and non-conjugated (colic) biliary acid solutions, in anesthetized dogs, were studied. The perfusions were made at a constant flow and intracholedochal pressures were registered. The mean number of contractions per minute, the mean maximal pressures and the mean minimal pressures in each study periods were analysed. The choledochal perfusion with the biliary acids solutions induced a slight but significative increase in sphincteric resistance. After 15 minutes, the perfusion with colic acid solution induced maximal pressures significantly more elevated than the ones observed with taurocolic acid solution. The non-conjugated solution induced a pressure tracing significantly distinct from the tracing observed with the conjugated acid solution. No changes in resistance were observed with a 2% NaCl solution. This implies that the observed changes in resistance were not related to osmotic stimulation of the sphincter of Oddi.

Method for growth of crystals by pressure reduction of supercritical or subcritical solution

NASA Technical Reports Server (NTRS)

Shlichta, P. J. (Inventor)

1985-01-01

Crystals of high morphological quality are grown by dissolution of a substance to be grown into the crystal in a suitable solvent under high pressure, and by subsequent slow, time-controlled reduction of the pressure of the resulting solution. During the reduction of the pressure interchange of heat between the solution and the environment is minimized by performing the pressure reduction either under isothermal or adiabatic conditions.

Cleavage crystallography of liquid metal embrittled aluminum alloys

NASA Technical Reports Server (NTRS)

Reynolds, A. P.; Stoner, G. E.

1991-01-01

The crystallography of liquid metal-induced transgranular cleavage in six aluminum alloys having a variety of microstructures has been determined via Laue X-ray back reflection. The cleavage crystallography was independent of alloy microstructure, and the cleavage plane was 100-plane oriented in all cases. It was further determined that the cleavage crystallography was not influenced by alloy texture. Examination of the fracture surface indicated that there was not a unique direction of crack propagation. In addition, the existence of 100-plane cleavage on alloy 2024 fracture surfaces was inferred by comparison of secondary cleavage crack intersection geometry on the 2024 surfaces with the geometry of secondary cleavage crack intersections on the test alloys.

Two combinatorial optimization problems for SNP discovery using base-specific cleavage and mass spectrometry.

PubMed

Chen, Xin; Wu, Qiong; Sun, Ruimin; Zhang, Louxin

2012-01-01

The discovery of single-nucleotide polymorphisms (SNPs) has important implications in a variety of genetic studies on human diseases and biological functions. One valuable approach proposed for SNP discovery is based on base-specific cleavage and mass spectrometry. However, it is still very challenging to achieve the full potential of this SNP discovery approach. In this study, we formulate two new combinatorial optimization problems. While both problems are aimed at reconstructing the sample sequence that would attain the minimum number of SNPs, they search over different candidate sequence spaces. The first problem, denoted as SNP - MSP, limits its search to sequences whose in silico predicted mass spectra have all their signals contained in the measured mass spectra. In contrast, the second problem, denoted as SNP - MSQ, limits its search to sequences whose in silico predicted mass spectra instead contain all the signals of the measured mass spectra. We present an exact dynamic programming algorithm for solving the SNP - MSP problem and also show that the SNP - MSQ problem is NP-hard by a reduction from a restricted variation of the 3-partition problem. We believe that an efficient solution to either problem above could offer a seamless integration of information in four complementary base-specific cleavage reactions, thereby improving the capability of the underlying biotechnology for sensitive and accurate SNP discovery.

Improving the prospects of cleavage-based nanopore sequencing engines

NASA Astrophysics Data System (ADS)

Brady, Kyle T.; Reiner, Joseph E.

2015-08-01

Recently proposed methods for DNA sequencing involve the use of cleavage-based enzymes attached to the opening of a nanopore. The idea is that DNA interacting with either an exonuclease or polymerase protein will lead to a small molecule being cleaved near the mouth of the nanopore, and subsequent entry into the pore will yield information about the DNA sequence. The prospects for this approach seem promising, but it has been shown that diffusion related effects impose a limit on the capture probability of molecules by the pore, which limits the efficacy of the technique. Here, we revisit the problem with the goal of optimizing the capture probability via a step decrease in the nucleotide diffusion coefficient between the pore and bulk solutions. It is shown through random walk simulations and a simplified analytical model that decreasing the molecule's diffusion coefficient in the bulk relative to its value in the pore increases the nucleotide capture probability. Specifically, we show that at sufficiently high applied transmembrane potentials (≥100 mV), increasing the potential by a factor f is equivalent to decreasing the diffusion coefficient ratio Dbulk/Dpore by the same factor f. This suggests a promising route toward implementation of cleavage-based sequencing protocols. We also discuss the feasibility of forming a step function in the diffusion coefficient across the pore-bulk interface.

Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage

PubMed Central

Sheng, Gang; Zhao, Hongtu; Wang, Jiuyu; Rao, Yu; Tian, Wenwen; Swarts, Daan C.; van der Oost, John; Patel, Dinshaw J.; Wang, Yanli

2014-01-01

We report on crystal structures of ternary Thermus thermophilus Argonaute (TtAgo) complexes with 5′-phosphorylated guide DNA and a series of DNA targets. These ternary complex structures of cleavage-incompatible, cleavage-compatible, and postcleavage states solved at improved resolution up to 2.2 Å have provided molecular insights into the orchestrated positioning of catalytic residues, a pair of Mg2+ cations, and the putative water nucleophile positioned for in-line attack on the cleavable phosphate for TtAgo-mediated target cleavage by a RNase H-type mechanism. In addition, these ternary complex structures have provided insights into protein and DNA conformational changes that facilitate transition between cleavage-incompatible and cleavage-compatible states, including the role of a Glu finger in generating a cleavage-competent catalytic Asp-Glu-Asp-Asp tetrad. Following cleavage, the seed segment forms a stable duplex with the complementary segment of the target strand. PMID:24374628

Characteristics of eyes with inner retinal cleavage.

PubMed

Hwang, Young Hoon; Kim, Yong Yeon; Kim, Hwang Ki; Sohn, Yong Ho

2015-02-01

Inner retinal cleavage can be misdiagnosed as a glaucomatous retinal nerve fiber layer (RNFL) defect. This study was performed to characterize eyes with inner retinal cleavage. Inner retinal cleavage is defined as the appearance of a dark spindle-shaped space between the nerve fibers. Patients who presented at our institution with inner retinal cleavage were enrolled in the study. All participants were evaluated by fundus examination, visual field testing with standard automated perimetry, and optical coherence tomography (OCT) imaging. A total of 15 eyes of 11 subjects with inner retinal cleavage were included in the study. The median age of the subjects was 57 years (age range, 30-67 years). In each case, inner retinal cleavage was located adjacent to retinal blood vessels. Tissue bridging the cleavage area was observed in ten eyes. Six eyes had epiretinal membranes (ERMs), two eyes had glaucoma, and one eye had ERM in addition to glaucoma. Six eyes with inner retinal cleavage without combined ocular abnormalities had highly myopic refractive error (-6.50 to -8.50 diopters). Cross-sectional OCT images of the areas of inner retinal cleavage demonstrated defects with irregular margins and empty spaces in the inner layers of the retina. During the follow-up period, no eye showed changes in inner retinal layer cleavage or visual field sensitivity. Inner retinal cleavage was found in eyes with high myopia or ERMs. Inner retinal cleavage was associated with structural changes distinct from those associated with glaucomatous RNFL defects.

Thermodynamic analysis of energy density in pressure retarded osmosis: The impact of solution volumes and costs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reimund, Kevin K.; McCutcheon, Jeffrey R.; Wilson, Aaron D.

A general method was developed for estimating the volumetric energy efficiency of pressure retarded osmosis via pressure-volume analysis of a membrane process. The resulting model requires only the osmotic pressure, π, and mass fraction, w, of water in the concentrated and dilute feed solutions to estimate the maximum achievable specific energy density, uu, as a function of operating pressure. The model is independent of any membrane or module properties. This method utilizes equilibrium analysis to specify the volumetric mixing fraction of concentrated and dilute solution as a function of operating pressure, and provides results for the total volumetric energy densitymore » of similar order to more complex models for the mixing of seawater and riverwater. Within the framework of this analysis, the total volumetric energy density is maximized, for an idealized case, when the operating pressure is π/(1+√w⁻¹), which is lower than the maximum power density operating pressure, Δπ/2, derived elsewhere, and is a function of the solute osmotic pressure at a given mass fraction. It was also found that a minimum 1.45 kmol of ideal solute is required to produce 1 kWh of energy while a system operating at “maximum power density operating pressure” requires at least 2.9 kmol. Utilizing this methodology, it is possible to examine the effects of volumetric solution cost, operation of a module at various pressure, and operation of a constant pressure module with various feed.« less

A serendipitous discovery that in situ proteolysis is essential for the crystallization of yeast CPSF-100 (Ydh1p)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mandel, Corey R.; Gebauer, Damara; Zhang, Hailong

2006-10-01

Proteolysis in situ by a protease secreted by a contaminating fungus is essential for the crystallization of yeast CPSF-100. The cleavage and polyadenylation specificity factor (CPSF) complex is required for the cleavage and polyadenylation of the 3′-end of messenger RNA precursors in eukaryotes. During structural studies of the 100 kDa subunit (CPSF-100, Ydh1p) of the yeast CPSF complex, it was serendipitously discovered that a solution that is infected by a fungus (subsequently identified as Penicillium) is crucial for the crystallization of this protein. Further analyses suggest that the protein has undergone partial proteolysis during crystallization, resulting in the deletion ofmore » an internal segment of about 200 highly charged and hydrophilic residues, very likely catalyzed by a protease secreted by the fungus. With the removal of this segment, yeast CPSF-100 (Ydh1p) has greatly reduced solubility and can be crystallized in the presence of a minute amount of precipitant.« less

Chemical degradation of trimethyl phosphate as surrogate for organo-phosporus pesticides on nanostructured metal oxides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Štengl, Václav, E-mail: stengl@iic.cas.cz; Henych, Jiří; Grygar, Tomáš

Nanostructured TiO{sub 2} and mixed oxides of Ti and Fe, Hf, In, Mn or Zr -were prepared by homogeneous hydrolysis of aqueous solution of metal sulphates with urea. The oxides were characterised by X-ray powder diffraction (XRD), scanning electron microscopy, particle size distribution, surface area and porosity. The oxide materials consists of a few nanometre primary crystals (mainly anatase) arranged in a few micrometre regular spherical agglomerates with specific surface area 133–511 m{sup 2} g{sup −1}. The FTIR diffuse spectroscopy was used for monitoring chemical degradation of trimethylphosphate (TMP) as a surrogate for organo-phosphorus pesticides under ambient and higher temperatures.more » Undoped TiO{sub 2} and Ti,Mn-mixed oxide were most active in cleavage (hydrolysis) of CH{sub 3}O from TMP at room temperature and 100 °C. Cleavage of CH{sub 3}O in the other studied mixed oxides was not complete until temperature exceeds the boiling point of TMP.« less

Pretest analysis of the NESC-1 spinning cylinder experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sattari-Far, I.

This report presents defect assessment results from a final pre-test analysis of the NESC-1 spinning cylinder based on the NDE defect definitions and the determined loading conditions. The analysis covers fracture assessments of a subclad and surface breaking crack. Three-dimensional elastic-plastic finite element calculations, considering the crack-tip constraint, are employed in the assessments. Also performed are sensitivity studies to demonstrate how different affecting parameters, especially the cladding residual stresses, impact the crack driving force. It is found for both the surface and the subclad crack that the situations in the cladding and at the deepest point of the crack frontmore » are far from critical for cleavage fracture. The results of the analysis indicate that a limited amount of ductile crack growth can occur along the crack front in the HAZ and adjacent base material. Cleavage fracture events can be expected in the HAZ. The results also show substantial loss of crack-tip constraint in the HAZ compared with the SSY solutions.« less

Modulation of the Pyrococcus abyssi NucS Endonuclease Activity by Replication Clamp at Functional and Structural Levels*

PubMed Central

Creze, Christophe; Ligabue, Alessio; Laurent, Sébastien; Lestini, Roxane; Laptenok, Sergey P.; Khun, Joelle; Vos, Marten H.; Czjzek, Mirjam; Myllykallio, Hannu; Flament, Didier

2012-01-01

Pyrococcus abyssi NucS is the founding member of a new family of structure-specific DNA endonucleases that interact with the replication clamp proliferating cell nuclear antigen (PCNA). Using a combination of small angle x-ray scattering and surface plasmon resonance analyses, we demonstrate the formation of a stable complex in solution, in which one molecule of the PabNucS homodimer binds to the outside surface of the PabPCNA homotrimer. Using fluorescent labels, PCNA is shown to increase the binding affinity of NucS toward single-strand/double-strand junctions on 5′ and 3′ flaps, as well as to modulate the cleavage specificity on the branched DNA structures. Our results indicate that the presence of a single major contact between the PabNucS and PabPCNA proteins, together with the complex-induced DNA bending, facilitate conformational flexibility required for specific cleavage at the single-strand/double-strand DNA junction. PMID:22431731

Modulation of the Pyrococcus abyssi NucS endonuclease activity by replication clamp at functional and structural levels.

PubMed

Creze, Christophe; Ligabue, Alessio; Laurent, Sébastien; Lestini, Roxane; Laptenok, Sergey P; Khun, Joelle; Vos, Marten H; Czjzek, Mirjam; Myllykallio, Hannu; Flament, Didier

2012-05-04

Pyrococcus abyssi NucS is the founding member of a new family of structure-specific DNA endonucleases that interact with the replication clamp proliferating cell nuclear antigen (PCNA). Using a combination of small angle x-ray scattering and surface plasmon resonance analyses, we demonstrate the formation of a stable complex in solution, in which one molecule of the PabNucS homodimer binds to the outside surface of the PabPCNA homotrimer. Using fluorescent labels, PCNA is shown to increase the binding affinity of NucS toward single-strand/double-strand junctions on 5' and 3' flaps, as well as to modulate the cleavage specificity on the branched DNA structures. Our results indicate that the presence of a single major contact between the PabNucS and PabPCNA proteins, together with the complex-induced DNA bending, facilitate conformational flexibility required for specific cleavage at the single-strand/double-strand DNA junction.

Effect of heat/pressure on cyanidin-3-glucoside ethanol model solutions

NASA Astrophysics Data System (ADS)

Corrales, M.; Lindauer, R.; Butz, P.; Tauscher, B.

2008-07-01

The stability of cyanidin-3-glucoside (Cy3gl) in 50% ethanol model solutions under heat/pressure treatments was investigated. Cy3gl was rapidly degraded when solutions were subjected to a heat/pressure treatment. The higher the pressure and the temperature used, the higher the degradation. Moreover, the degradation was increased according to increasing holding times. Parallel to the degradation of Cy3gl several hydrolytic products were formed and identified by LC-DAD/ESI-MS. The degradation of Cy3gl was well fitted to a first order reaction (R=0.99). This study pointed out the rate of susceptibility of Cy3gl in model solutions to degrade when exposed to a heat/pressure treatment and the trigger effect of high hydrostatic pressure to hydrolyse Cy3gl. By contrast, the degradation of anthocyanins in a food matrix (red grape extract solutions) was negligible after a heat/pressure process at 600MPa, 70°C during 1h (P >0.05).

Sequences downstream of AAUAAA signals affect pre-mRNA cleavage and polyadenylation in vitro both directly and indirectly.

PubMed Central

Ryner, L C; Takagaki, Y; Manley, J L

1989-01-01

To investigate the role of sequences lying downstream of the conserved AAUAAA hexanucleotide in pre-mRNA cleavage and polyadenylation, deletions or substitutions were constructed in polyadenylation signals from simian virus 40 and adenovirus, and their effects were assayed in both crude and fractionated HeLa cell nuclear extracts. As expected, these sequences influenced the efficiency of both cleavage and polyadenylation as well as the accuracy of the cleavage reaction. Sequences near or upstream of the actual site of poly(A) addition appeared to specify a unique cleavage site, since their deletion resulted, in some cases, in heterogeneous cleavage. Furthermore, the sequences that allowed the simian virus 40 late pre-RNA to be cleaved preferentially by partially purified cleavage activity were also those at the cleavage site itself. Interestingly, sequences downstream of the cleavage site interacted with factors not directly involved in catalyzing cleavage and polyadenylation, since the effects of deletions were substantially diminished when partially purified components were used in assays. In addition, these sequences contained elements that could affect 3'-end formation both positively and negatively. Images PMID:2566911

Partition Coefficients of Organics between Water and Carbon Dioxide Revisited: Correlation with Solute Molecular Descriptors and Solvent Cohesive Properties.

PubMed

Roth, Michal

2016-12-06

High-pressure phase behavior of systems containing water, carbon dioxide and organics has been important in several environment- and energy-related fields including carbon capture and storage, CO 2 sequestration and CO 2 -assisted enhanced oil recovery. Here, partition coefficients (K-factors) of organic solutes between water and supercritical carbon dioxide have been correlated with extended linear solvation energy relationships (LSERs). In addition to the Abraham molecular descriptors of the solutes, the explanatory variables also include the logarithm of solute vapor pressure, the solubility parameters of carbon dioxide and water, and the internal pressure of water. This is the first attempt to include also the properties of water as explanatory variables in LSER correlations of K-factor data in CO 2 -water-organic systems. Increasing values of the solute hydrogen bond acidity, the solute hydrogen bond basicity, the solute dipolarity/polarizability, the internal pressure of water and the solubility parameter of water all tend to reduce the K-factor, that is, to favor the solute partitioning to the water-rich phase. On the contrary, increasing values of the solute characteristic volume, the solute vapor pressure and the solubility parameter of CO 2 tend to raise the K-factor, that is, to favor the solute partitioning to the CO 2 -rich phase.

γ-Secretase Modulators and APH1 Isoforms Modulate γ-Secretase Cleavage but Not Position of ε-Cleavage of the Amyloid Precursor Protein (APP).

PubMed

Lessard, Christian B; Cottrell, Barbara A; Maruyama, Hiroko; Suresh, Suraj; Golde, Todd E; Koo, Edward H

2015-01-01

The relative increase in Aβ42 peptides from familial Alzheimer disease (FAD) linked APP and PSEN mutations can be related to changes in both ε-cleavage site utilization and subsequent step-wise cleavage. Cleavage at the ε-site releases the amyloid precursor protein (APP) intracellular domain (AICD), and perturbations in the position of ε-cleavage are closely associated with changes in the profile of amyloid β-protein (Aβ) species that are produced and secreted. The mechanisms by which γ-secretase modulators (GSMs) or FAD mutations affect the various γ-secretase cleavages to alter the generation of Aβ peptides have not been fully elucidated. Recent studies suggested that GSMs do not modulate ε-cleavage of APP, but the data were derived principally from recombinant truncated epitope tagged APP substrate. Here, using full length APP from transfected cells, we investigated whether GSMs modify the ε-cleavage of APP under more native conditions. Our results confirmed the previous findings that ε-cleavage is insensitive to GSMs. In addition, fenofibrate, an inverse GSM (iGSM), did not alter the position or kinetics of ε-cleavage position in vitro. APH1A and APH1B, a subunit of the γ-secretase complex, also modulated Aβ42/Aβ40 ratio without any alterations in ε-cleavage, a result in contrast to what has been observed with PS1 and APP FAD mutations. Consequently, GSMs and APH1 appear to modulate γ-secretase activity and Aβ42 generation by altering processivity but not ε-cleavage site utilization.

Photochemical organic oxidations and dechlorinations with a mu-oxo bridged heme/non-heme diiron complex.

PubMed

Wasser, Ian M; Fry, H Christopher; Hoertz, Paul G; Meyer, Gerald J; Karlin, Kenneth D

2004-12-27

Steady state and laser flash photolysis studies of the heme/non-heme mu-oxo diiron complex [((6)L)Fe(III)-O-Fe(III)-Cl](+) (1) have been undertaken. The anaerobic photolysis of benzene solutions of 1 did not result in the buildup of any photoproduct. However, the addition of excess triphenylphosphine resulted in the quantitative photoreduction of 1 to [((6)L)Fe(II)...Fe(II)-Cl](+) (2), with concomitant production by oxo-transfer of 1 equiv of triphenylphosphine oxide. Under aerobic conditions and excess triphenylphosphine, the reaction produces multiple turnovers (approximately 28) before the diiron complex is degraded. The anaerobic photolysis of tetrahydrofuran (THF) or toluene solutions of 1 likewise results in the buildup of 2. The oxidation products from these reactions included gamma-butyrolactone (approximately 15%) for the reaction in THF and benzaldehyde (approximately 23%) from the reaction in toluene. In either case, the O-atom which is incorporated into the carbonyl product is derived from dioxygen present under workup or under aerobic photolysis conditions. Transient absorption measurements of low-temperature THF solutions of 1 revealed the presence of an (P)Fe(II)-like [P = tetraaryl porphyrinate dianion] species suggesting that the reactive species is a formal (heme)Fe(II)/Fe(IV)=O(non-heme) pair. The non-heme Fe(IV)=O is thus most likely responsible for C-H bond cleavage and subsequent radical chemistry. The photolysis of 1 in chlorobenzene or 1,2-dichlorobenzene resulted in C-Cl cleavage reactions and the formation of [[((6)L)Fe(III)-Cl...Fe(III)-Cl](2)O](2+) (3), with chloride ligands that are derived from solvent dehalogenation chemistry. The resulting organic products are biphenyl trichlorides or biphenyl monochlorides, derived from dichlorobenzene and chlorobenzene, respectively. Similarly, product 3 is obtained by the photolysis of benzene-benzyl chloride solutions of 1; the organic product is benzaldehyde (approximately 70%). A brief discussion of the dehalogenation chemistry, along with relevant environmental perspectives, is included.

On the anomaly of velocity-pressure decoupling in collocated mesh solutions

NASA Technical Reports Server (NTRS)

Kim, Sang-Wook; Vanoverbeke, Thomas

1991-01-01

The use of various pressure correction algorithms originally developed for fully staggered meshes can yield a velocity-pressure decoupled solution for collocated meshes. The mechanism that causes velocity-pressure decoupling is identified. It is shown that the use of a partial differential equation for the incremental pressure eliminates such a mechanism and yields a velocity-pressure coupled solution. Example flows considered are a three dimensional lid-driven cavity flow and a laminar flow through a 90 deg bend square duct. Numerical results obtained using the collocated mesh are in good agreement with the measured data and other numerical results.

Influenza virus site recognized by a murine helper T cell specific for H1 strains. Localization to a nine amino acid sequence in the hemagglutinin molecule.

PubMed

Hackett, C J; Dietzschold, B; Gerhard, W; Ghrist, B; Knorr, R; Gillessen, D; Melchers, F

1983-08-01

The functional helper T cell line Vir-2, derived from a PR8 (H1N1) influenza virus-immunized BALB/c mouse, proliferates in response to syngeneic antigen-presenting cells and naturally occurring strains of subtype H1 human influenza virus from 1934-1957 and 1977-1980 isolates. A conserved region of the hemagglutinin molecule around amino acid position 115 in the heavy chain (HA1) was implicated as being important in this recognition by the lack of stimulatory activity associated with a glutamic acid to lysine substitution at position 115 in the laboratory mutant RV6, derived from wild-type PR8. Characterization of the stimulatory determinant on the wild-type hemagglutinin molecule was then undertaken using cleavage products and synthetic peptides. Vir-2 cells recognized the reduced and alkylated purified HA1 of PR8 virus, and this reactivity was retained after cleavage at methionine and tryptophan residues. High-pressure liquid chromatography separation of cleavage fragments indicated that a short sequence of the HA1 containing residue 115 was being recognized. This recognition was localized to a nine amino acid segment (positions 111-119) by assaying stimulation with synthetic peptide homologues of different lengths from that region. As with native hemagglutinin, Vir-2 cells responded to active peptides when presented by H-2d but not H-2k antigen-presenting cells.

Thermophoresis of dissolved molecules and polymers: Consideration of the temperature-induced macroscopic pressure gradient

NASA Astrophysics Data System (ADS)

Semenov, Semen; Schimpf, Martin

2004-01-01

The movement of molecules and homopolymer chains dissolved in a nonelectrolyte solvent in response to a temperature gradient is considered a consequence of temperature-induced pressure gradients in the solvent layer surrounding the solute molecules. Local pressure gradients are produced by nonuniform London van der Waals interactions, established by gradients in the concentration (density) of solvent molecules. The density gradient is produced by variations in solvent thermal expansion within the nonuniform temperature field. The resulting expression for the velocity of the solute contains the Hamaker constants for solute-solvent and solute-solute interactions, the radius of the solute molecule, and the viscosity and cubic coefficient of thermal expansion of the solvent. In this paper we consider an additional force that arises from directional asymmetry in the interaction between solvent molecules. In a closed cell, the resulting macroscopic pressure gradient gives rise to a volume force that affects the motion of dissolved solutes. An expression for this macroscopic pressure gradient is derived and the resulting force is incorporated into the expression for the solute velocity. The expression is used to calculate thermodiffusion coefficients for polystyrene in several organic solvents. When these values are compared to those measured in the laboratory, the consistency is better than that found in previous reports, which did not consider the macroscopic pressure gradient that arises in a closed thermodiffusion cell. The model also allows for the movement of solute in either direction, depending on the relative values of the solvent and solute Hamaker constants.

Ecto-diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A)-hydrolase is expressed as an ectoenzyme in a variety of mammalian and human cells and adds new aspects to the turnover of Ap4A.

PubMed

von Drygalski, A; Ogilvie, A

2000-01-01

Ap4A and other dinucleotides participate in the regulation of hemostasis and blood pressure control. With the exception of two previously reported surface anchored ectoAp4A-hydrolases on bovine aortic endothelial and chromaffine cells, all Ap4A-hydrolases reported are intracellular or freely soluble. We demonstrated that ectoAp4A-hydrolases are present on a broad variety of cell types of different species: rat mesangial, bovine corneal epithelial, human Hep-G2 and peridontal cells. Ectoenzyme properties were evaluated on rat mesangium cells. Chromatography of purified plasma membranes on Sephacel 300 resulted in enrichment of ectoAp4A-hydrolase and in separation from ectoATPase. In contrast to ATPase, Ap4A-hydrolase was stable at room temperature. EctoAp4A-hydrolase also recognized ATP as substrate, and therefore is not highly specific. The molecular weight was 180 kD. Unlike ectoAMPase ectoAp4A-hydrolase was not attached via a glycosyl-phosphatidylinositol (GPI)-moiety. Concentrations of PI-PLC 10-100-fold higher than effective for ectoAMPase cleavage (10-100 mU/ml) plus extensively extended incubation times up to eight hours did not result in cleavage of ectoAp4A-hydrolase. The enzyme ectoAp4A-hydrolase might presage a direction for pharmaceutical manipulation in the control of blood pressure and hemostasis.

Hydrogen production by aqueous phase reforming of light oxygenated hydrocarbons

NASA Astrophysics Data System (ADS)

Shabaker, John William

Aqueous phase reforming (APR) of renewable oxygenated hydrocarbons (e.g., methanol, ethylene glycol, glycerol, sorbitol, glucose) is a promising new technology for the catalytic production of high-purity hydrogen for fuel cells and chemical processing. Supported Pt catalysts are effective catalysts for stable and rapid H2 production at temperatures near 500 K (H 2 turnover frequencies near 10 min-1). Inexpensive Raney Ni-based catalysts have been developed using a combination of fundamental and high-throughput studies that have similar catalytic properties as Pt-based materials. Promotion of Raney Ni with Sn by controlled surface reaction of organometallic tin compounds is necessary to control formation of thermodynamically-favorable alkane byproducts. Detailed characterization by Mossbauer spectroscopy, electron microscopy, adsorption studies, and x-ray photoelectron spectroscopy (XPS/ESCA) has shown that NiSn alloys are formed during heat treatment, and may be responsible for enhanced stability and selectivity for hydrogen production. Detailed kinetic studies led to the development of a kinetic mechanism for the APR reaction on Pt and NiSn catalysts, in which the oxygenate decomposes through C--H and O--H cleavage, followed by C--C cleavage and water gas shift of the CO intermediate. The rate limiting step on Pt surfaces is the initial dehydrogenation, while C--C cleavage appears rate limiting over NiSn catalysts. Tin promotion of Raney Ni catalysts suppresses C--O bond scission reactions that lead to alkane formation without inhibiting fast C--C and C--H cleavage steps that are necessary for high rates of reforming. A window of operating temperature, pressure, and reactor residence time has been identified for use of the inexpensive NiSn catalysts as a Pt substitute. Concentrated feed stocks and aggressive pretreatments have been found to counteract catalyst deactivation by sintering in the hydrothermal APR environment and allow stable, long-term production of H2 over Raney-NiSn materials.

ZnCl 2 induced catalytic conversion of softwood lignin to aromatics and hydrocarbons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Hongliang; Zhang, Libing; Deng, Tiansheng

2016-01-01

Selective cleavage of C-O-C bonds in lignin without disrupting C-C linkages can result in releasing aromatic monomers and dimers that can be subsequently converted into chemicals and fuels. Results showed that both biomass-derived lignin and lignin model compounds were depolymerized in a highly concentrated ZnCl2 solution. Zn2+ ions in highly concentrated ZnCl2 solutions appeared to selectively coordinate with C-O-C bonds to cause key linkages of lignin much easier to cleave. In 63 wt.% ZnCl2 solution at 200 °C for 6 h, nearly half of the softwood technical lignin was converted to liquid products, of which the majority was alkylphenols. Resultsmore » indicated that most β-O-4 and Cmethyl-OAr bonds of model compounds were cleaved undersame conditions, providing a foundation towards understanding lignin depolymerization in a concentrated ZnCl2 solution. The phenolic products were further converted into cyclic hydrocarbons via hydrodeoxygenation and coupling reactions by co-catalyst Ru/C.« less

Method for solvent extraction with near-equal density solutions

DOEpatents

Birdwell, Joseph F.; Randolph, John D.; Singh, S. Paul

2001-01-01

Disclosed is a modified centrifugal contactor for separating solutions of near equal density. The modified contactor has a pressure differential establishing means that allows the application of a pressure differential across fluid in the rotor of the contactor. The pressure differential is such that it causes the boundary between solutions of near-equal density to shift, thereby facilitating separation of the phases. Also disclosed is a method of separating solutions of near-equal density.

GRAIN BOUNDARY STRENGTHENING PROPERTIES OF TUNGSTEN ALLOYS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Setyawan, Wahyu; Kurtz, Richard J.

2012-10-10

Density functional theory was employed to investigate grain boundary (GB) properties of W alloys. A range of substitutional solutes across the Periodic Table was investigated to understand the behavior of different electronic orbitals in changing the GB cleavage energy in the Σ27a[110]{525} GB. A number of transition metals were predicted to enhance the GB cohesion. This includes Ru, Re, Os, Ir, V, Cr, Mn, Fe, Co, Ti, Hf, Ta and Nb. While lanthanides, s and p elements were tended to cause GB embrittlement.

Accurate and rapid modeling of iron-bleomycin-induced DNA damage using tethered duplex oligonucleotides and electrospray ionization ion trap mass spectrometric analysis.

PubMed

Harsch, A; Marzilli, L A; Bunt, R C; Stubbe, J; Vouros, P

2000-05-01

Bleomycin B(2)(BLM) in the presence of iron [Fe(II)] and O(2)catalyzes single-stranded (ss) and double-stranded (ds) cleavage of DNA. Electrospray ionization ion trap mass spectrometry was used to monitor these cleavage processes. Two duplex oligonucleotides containing an ethylene oxide tether between both strands were used in this investigation, allowing facile monitoring of all ss and ds cleavage events. A sequence for site-specific binding and cleavage by Fe-BLM was incorporated into each analyte. One of these core sequences, GTAC, is a known hot-spot for ds cleavage, while the other sequence, GGCC, is a hot-spot for ss cleavage. Incubation of each oligo-nucleotide under anaerobic conditions with Fe(II)-BLM allowed detection of the non-covalent ternary Fe-BLM/oligonucleotide complex in the gas phase. Cleavage studies were then performed utilizing O(2)-activated Fe(II)-BLM. No work-up or separation steps were required and direct MS and MS/MS analyses of the crude reaction mixtures confirmed sequence-specific Fe-BLM-induced cleavage. Comparison of the cleavage patterns for both oligonucleotides revealed sequence-dependent preferences for ss and ds cleavages in accordance with previously established gel electrophoresis analysis of hairpin oligonucleotides. This novel methodology allowed direct, rapid and accurate determination of cleavage profiles of model duplex oligonucleotides after exposure to activated Fe-BLM.

Electrochemical reduction of hexahydro-1,3,5-trinitro-1,3,5-triazine in aqueous solutions.

PubMed

Bonin, Pascale M L; Bejan, Dorin; Schutt, Leah; Hawari, Jalal; Bunce, Nigel J

2004-03-01

Electrochemical reduction of RDX, hexahydro-1,3,5-trinitro-1,3,5-triazine, a commercial and military explosive, was examined as a possible remediation technology for treating RDX-contaminated groundwater. A cascade of divided flow-through cells was used, with reticulated vitreous carbon cathodes and IrO2/Ti dimensionally stable anodes, initially using acetonitrile/water solutions to increase the solubility of RDX. The major degradation pathway involved reduction of RDX to the corresponding mononitroso compound, followed by ring cleavage to yield formaldehyde and methylenedinitramine. The reaction intermediates underwent further reduction and/or hydrolysis, the net result being the complete transformation of RDX to small molecules. The rate of degradation increased with current density, but the current efficiency was highest at low current densities. The technique was extended successfully both to 100% aqueous solutions of RDX and to an undivided electrochemical cell.

Gold nanoparticles-based protease assay

PubMed Central

Guarise, Cristian; Pasquato, Lucia; De Filippis, Vincenzo; Scrimin, Paolo

2006-01-01

We describe here a simple assay that allows the visual detection of a protease. The method takes advantage of the high molar absorptivity of the plasmon band of gold colloids and is based on the color change of their solution when treated with dithiols. We used C- and N-terminal cysteinyl derivatives of a peptide substrate exploiting its selective recognition and cleavage by a specific protease. Contrary to the native ones, cleaved peptides are unable to induce nanoparticles aggregation; hence, the color of the solution does not change. The detection of two proteases is reported: thrombin (involved in blood coagulation and thrombosis) and lethal factor (an enzyme component of the toxin produced by Bacillus anthracis). The sensitivity of this nanoparticle-based assay is in the low nanomolar range. PMID:16537471

Photodegradation of lambda-cyhalothrin and cypermethrin in aqueous solution as affected by humic acid and/or copper: intermediates and degradation pathways.

PubMed

Xie, Jimin; Wang, Pingli; Liu, Jun; Lv, Xiaomeng; Jiang, Deli; Sun, Cheng

2011-11-01

The influence of coexisting humic acids (HA) or Cu²⁺ on the photodegradation of pesticides lambda-cyhalothrin (λ-CHT) and cypermethrin (CPM) in aqueous solution was studied under xenon lamp irradiation. The removal efficiency of pesticides λ-CHT and CPM were enhanced in the presence of either Cu²⁺ or HA but restrained in the presence of both Cu²⁺ and HA. The photodegradation of λ-CHT and CPM followed first-order reaction kinetics. The photodegradation intermediates of λ-CHT and CPM were determined using gas chromatography/mass spectrometry. Possible photodegradation pathways included decarboxylation, ester bond cleavage, dechlorination, and phenyl group removal. Copyright © 2011 SETAC.

Gold nanoparticles-based protease assay.

PubMed

Guarise, Cristian; Pasquato, Lucia; De Filippis, Vincenzo; Scrimin, Paolo

2006-03-14

We describe here a simple assay that allows the visual detection of a protease. The method takes advantage of the high molar absorptivity of the plasmon band of gold colloids and is based on the color change of their solution when treated with dithiols. We used C- and N-terminal cysteinyl derivatives of a peptide substrate exploiting its selective recognition and cleavage by a specific protease. Contrary to the native ones, cleaved peptides are unable to induce nanoparticles aggregation; hence, the color of the solution does not change. The detection of two proteases is reported: thrombin (involved in blood coagulation and thrombosis) and lethal factor (an enzyme component of the toxin produced by Bacillus anthracis). The sensitivity of this nanoparticle-based assay is in the low nanomolar range.

Formation of tryptophan radicals in irradiated aqueous solutions of hexachloroplatinate(IV): a flash photolysis study.

PubMed

Zang, L; Rodgers, M A

1999-10-01

The oxidation of tryptophan photosensitized by PtCl6(2-) has been investigated in aqueous solutions at different pH using nanosecond laser flash photolysis. Cationic and neutral radicals of tryptophan were detected at pH 2.8 and 8.5, respectively. The generation of the radical was attributed to oxidation by Cl2- that was formed from the homolytic bond cleavage in the excited state of PtCl6(2-). The bimolecular rate constant derived from the kinetics analysis, 2.8 +/- 0.2 x 10(9) M-1 s-1, is in good agreement with the value obtained in earlier pulse radiolysis studies. Both the cationic and neutral radicals decayed by second-order kinetics, consistent with the dimerization process.

Osmotically-assisted desalination method and system

DOEpatents

Achilli, Andrea; Childress, Amy E.; Cath, Tzahi Y.

2014-08-12

Systems and methods for osmotically assisted desalination include using a pressurized concentrate from a pressure desalination process to pressurize a feed to the desalination process. The depressurized concentrate thereby produced is used as a draw solution for a pressure-retarded osmosis process. The pressure-retarded osmosis unit produces a pressurized draw solution stream that is used to pressurize another feed to the desalination process. In one example, the feed to the pressure-retarded osmosis process is impaired water.

The 4D evolution of porosity during ongoing pressure-solution processes in NaCl using x-ray microtomography

NASA Astrophysics Data System (ADS)

Macente, Alice; Fusseis, Florian; Butler, Ian; Tudisco, Erika; Hall, Stephen; Andò, Edward

2016-04-01

Pressure-solution creep is a common deformation mechanism in the upper crust. It represents a mass transfer via dissolution-reprecipitation that critically affects the hydraulic properties of rocks. Successful management of safe radioactive storage sites in rock-salt deposits critically depends on an accurate knowledge of the hydro-mechanical behaviour of salt deposits. Despite numerous lab experiments that have been conducted, many aspects of pressure-solution are still poorly understood. There is little knowledge about the spatio-temporal evolution of porosity and permeability during pressure-solution creep. While rates of pressure-solution creep in silicates and carbonates are slow, which makes laboratory investigations of these materials impractical, compaction experiments have demonstrated that NaCl samples deform sufficiently fast to study pressure-solution creep in a lab environment at room temperature and modest loads. We present results from novel experiments that quantify the 4-dimensional (three spatial dimensions plus time) evolution of pressure-solution processes using in-situ x-ray microtomography. Our experiments are performed in custom made x-ray transparent presses. 5 mm diameter NaCl powder samples with a grain size of 250-300 μm are loaded dry into the press and pre-compacted to produce a starting aggregated material. The sample is then flooded with saturated NaCl solution and loaded uniaxially by means of a pneumatic actuator to a constant uniaxial stress. Different sample mixtures were tested, as well as different uniaxial loads. The resulting deformation of the samples is documented in 3-dimensional microtomographic datasets, acquired at regular time intervals. Image analysis allowed characterization of the microstructural evolution of the NaCl grains and the spatio-temporal distribution of porosity during ongoing mechanical and chemical compaction. The microtomography data have also been analysed with 3D Digital Image Correlation (3D-DIC or DVC) to quantify the fields of displacements in each direction, as well as volumetric and maximum shear strain fields. Following the approach described above, we have been able to quantify and characterize in 4D the evolution of pressure-solution creep and porosity distribution in relation to different sample materials and increasing uniaxial load. The presence of phyllosilicates (biotite) and more competent materials (glass beads) allowed pressure-solution to develop in a much shorter time compared to pure halite sample. The same trend is observed in samples experiencing bigger uniaxial loads (6.6 MPa v 1.6 MPa). We also found that, in the presence of phyllosilicates (biotite), pore size distribution clearly reflects the localisation of pressure-solution processes, as for natural stylolites. In the presence of glass beads, pressure-solution has a greater effect on the pore orientations rather than pore sizes. Our results extend the current understanding of the effect of pressure-solution creep on the mechanical and hydraulic properties of rocks, with implications for natural rock-salt, salt-based repository systems (nuclear and chemical waste storage) and salt mining.

Experimental shock metamorphism of maximum microcline

NASA Technical Reports Server (NTRS)

Robertson, P. B.

1975-01-01

A series of recovery experiments are conducted to study the behavior of single-crystal perthitic maximum microcline shock-loaded to a peak pressure of 417 kbar. Microcline is found to deform in a manner similar to quartz and other alkali feldspars. It is observed that shock-induced cleavages occur initially at or slightly below the Hugoniot elastic limit (60-85 kbar), that shock-induced rather than thermal disordering begins above the Hugoniot elastic limit, and that all types of planar elements form parallel to crystallographic planes of low Miller indices. When increasing pressure, it is found that bulk density, refractive indices, and birefringence of the recovered material decrease and approach diaplectic glass values, whereas disappearance and weakening of reflections in Debye-Sherrer patterns are due to disordering of the feldspar lattice.

The solubility of quartz in aqueous sodium chloride solution at 350°C and 180 to 500 bars

USGS Publications Warehouse

Fournier, Robert O.; Rosenbauer, Robert J.; Bischoff, James L.

1982-01-01

The solubility of quartz in 2, 3, and 4 molal NaCl was measured at 350°C and pressures ranging from 180 to 500 bars. The molal solubility in each of the salt solutions is greater than that in pure water throughout the measured pressure range, with the ratio of solubility in NaCl solution to solubility in pure water decreasing as pressure is increased. The measured solubilities are significantly higher than solubilities calculated using a simple model in which the water activity in NaCl solutions decreases either in proportion to decreasing vapor pressure of the solution as salinity is increased or in proportion to decreasing mole fraction of water in the solvent.

Effect of solute nature on the polyamorphic transition in glassy polyol aqueous solutions.

PubMed

Suzuki, Yoshiharu

2017-08-14

I examined the polyamorphic behavior of glassy dilute aqueous solutions of polyols (ethylene glycol, glycerol, meso-erythritol, xylitol, and D-sorbitol) under pressure at low temperatures. Although the volume change of the glassy aqueous solution varied continuously against pressure, the rate of the volume change appeared to vary discontinuously at the onset pressure of the gradual polyamorphic transition. It is thought that low-density liquid-like solvent water and high-density liquid-like solvent water coexist during the transition. Moreover, the existence of a solute induces the shift of polyamorphic transition to the lower-pressure side. The effect of a solute on the polyamorphic transition becomes larger in the order ethylene glycol, glycerol, meso-erythritol, xylitol, and D-sorbitol. Therefore, the solute can become a variable controlling the polyamorphic state of liquid water. This experimental result suggests that the metastable-equilibrium phase boundary between the low-density and the high-density amorphs for pure water is likely to be located at 0.22-0.23 GPa at about 150 K, which is slightly larger than the previously estimated pressure. Moreover, the solute-nature dependence on the polyamorphic transition seems to connect to that on the homogeneous nucleation temperature of polyol aqueous solution at ambient pressure. The region in which a low-density liquid appears coincides with the region in which the nucleus of ice Ih appears, suggesting that the formation of a low-density liquid is a precursory phenomenon of the nucleation of ice Ih.

Effect of solute nature on the polyamorphic transition in glassy polyol aqueous solutions

NASA Astrophysics Data System (ADS)

Suzuki, Yoshiharu

2017-08-01

I examined the polyamorphic behavior of glassy dilute aqueous solutions of polyols (ethylene glycol, glycerol, meso-erythritol, xylitol, and D-sorbitol) under pressure at low temperatures. Although the volume change of the glassy aqueous solution varied continuously against pressure, the rate of the volume change appeared to vary discontinuously at the onset pressure of the gradual polyamorphic transition. It is thought that low-density liquid-like solvent water and high-density liquid-like solvent water coexist during the transition. Moreover, the existence of a solute induces the shift of polyamorphic transition to the lower-pressure side. The effect of a solute on the polyamorphic transition becomes larger in the order ethylene glycol, glycerol, meso-erythritol, xylitol, and D-sorbitol. Therefore, the solute can become a variable controlling the polyamorphic state of liquid water. This experimental result suggests that the metastable-equilibrium phase boundary between the low-density and the high-density amorphs for pure water is likely to be located at 0.22-0.23 GPa at about 150 K, which is slightly larger than the previously estimated pressure. Moreover, the solute-nature dependence on the polyamorphic transition seems to connect to that on the homogeneous nucleation temperature of polyol aqueous solution at ambient pressure. The region in which a low-density liquid appears coincides with the region in which the nucleus of ice Ih appears, suggesting that the formation of a low-density liquid is a precursory phenomenon of the nucleation of ice Ih.

The RNA-induced silencing complex is a Mg2+-dependent endonuclease.

PubMed

Schwarz, Dianne S; Tomari, Yukihide; Zamore, Phillip D

2004-05-04

In the Drosophila and mammalian RNA interference (RNAi) pathways, target RNA destruction is catalyzed by the siRNA-guided, RNA-induced silencing complex (RISC). RISC has been proposed to be an siRNA-directed endonuclease, catalyzing cleavage of a single phosphodiester bond on the RNA target. Although 5' cleavage products are readily detected for RNAi in vitro, only 3' cleavage products have been observed in vivo. Proof that RISC acts as an endonuclease requires detection of both 5' and 3' cleavage products in a single experimental system. Here, we show that siRNA-programmed RISC generates both 5' and 3' cleavage products in vitro; cleavage requires Mg(2+), but not Ca(2+), and the cleavage product termini suggest a role for Mg(2+) in catalysis. Moreover, a single phosphorothioate in place of the scissile phosphate blocks cleavage; the phosphorothioate effect can be rescued by the thiophilic cation Mn(2+), but not by Ca(2+) or Mg(2+). We propose that during catalysis, a Mg(2+) ion is bound to the RNA substrate through a nonbridging oxygen of the scissile phosphate. The mechanism of endonucleolytic cleavage is not consistent with the mechanisms of the previously identified RISC nuclease, Tudor-SN. Thus, the RISC-component that mediates endonucleolytic cleavage of the target RNA remains to be identified.

Vitrification of polymer solutions as a function of solvent quality, analyzed via vapor pressures

NASA Astrophysics Data System (ADS)

Bercea, Maria; Wolf, Bernhard A.

2006-05-01

Vapor pressures (headspace sampling in combination with gas chromatography) and glass transition temperatures [differential scanning calorimetry (DSC)] have been measured for solutions of polystyrene (PS) in either toluene (TL) (10-70°C) or cyclohexane (CH) (32-60°C) from moderately concentrated solutions up to the pure polymer. As long as the mixtures are liquid, the vapor pressure of TL (good solvent) is considerably lower than that of CH (theta solvent) under other identical conditions. These differences vanish upon the vitrification of the solutions. For TL the isothermal liquid-solid transition induced by an increase of polymer concentration takes place within a finite composition interval at constant vapor pressure; with CH this phenomenon is either absent or too insignificant to be detected. For PS solutions in TL the DSC traces look as usual, whereas these curves may become bimodal for solutions in CH. The implications of the vitrification of the polymer solutions for the determination of Flory-Huggins interaction parameters from vapor pressure data are discussed. A comparison of the results for TL/PS with recently published data on the same system demonstrates that the experimental method employed for the determination of vapor pressures plays an important role at high polymer concentrations and low temperatures.

Design principles for high-pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures.

PubMed

Hölzl, Christoph; Kibies, Patrick; Imoto, Sho; Frach, Roland; Suladze, Saba; Winter, Roland; Marx, Dominik; Horinek, Dominik; Kast, Stefan M

2016-04-14

Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures--while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute's response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.

Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. A comparison of fragmentation patterns of linear dextran obtained by in-source decay, post-source decay and collision-induced dissociation and the stability of linear and cyclic glucans studied by in-source decay.

PubMed

Bashir, Sajid; Giannakopulos, Anastassios E; Derrick, Peter J; Critchley, Peter; Bottrill, Andrew; Padley, Henry J

2004-01-01

In the first part of this study fragmentation patterns from a range of dextran oligomers (containing 4-20 anhydroglucose units) were compared in three different methods of analysis coupled with matrix-assisted laser desorption/ionisation (MALDI) mass spectrometry. Collision-induced-dissociation (CID), prompt in-source decay (ISD) and post-source decay (PSD) all caused cleavage of the glycosidic bonds. Both CID and to a lesser extent ISD caused further cleavage of pyranose rings of the individual sugar residues. There was very little cleavage of pyranose rings detected in the PSD spectrum. Derivatisation of the reducing end-groups of the oligodextrans with 1-phenyl-3-methyl-5-pyrazolone (PMP) restricted cleavage in the MALDI mass spectrometer to the non-reducing end, and further it enabled the saccharides to be separated by HPLC so that a single chain length could be examined as a standard. Maltoheptaose was also used as a standard. In the second part of the study prompt ISD-MALDI mass spectrometry was used to compare the fragmentation of three oligoglucans, dextran, maltodextrin and gamma cyclodextrin, that have different linkages and different secondary structure. The results showed that the degree of fragmentation correlated with the degree of freedom in the saccharide chains in solution determined by NMR. Dextran the most random conformation was fragmented most whereas there was little evidence of any fragments, not even glycosidic bond breakage from cyclodextrin, even when the laser power was increased considerably. The fragmentation pattern of maltodextrin was intermediate. The patterns of fragmentation produced by MALDI mass spectrometry, particularly where standards are available to calibrate the spectrum and the energy of the laser is controlled, can be used to predict the type of linkage present.

The α-Secretase-derived N-terminal Product of Cellular Prion, N1, Displays Neuroprotective Function in Vitro and in Vivo*

PubMed Central

Guillot-Sestier, Marie-Victoire; Sunyach, Claire; Druon, Charlotte; Scarzello, Sabine; Checler, Frédéric

2009-01-01

Cellular prion protein (PrPc) undergoes a disintegrin-mediated physiological cleavage, generating a soluble amino-terminal fragment (N1), the function of which remained unknown. Recombinant N1 inhibits staurosporine-induced caspase-3 activation by modulating p53 transcription and activity, whereas the PrPc-derived pathological fragment (N2) remains biologically inert. Furthermore, N1 protects retinal ganglion cells from hypoxia-induced apoptosis, reduces the number of terminal deoxynucleotidyltransferase-mediated biotinylated UTP nick end labeling-positive and p53-immunoreactive neurons in a pressure-induced ischemia model of the rat retina and triggers a partial recovery of b-waves but not a-waves of rat electroretinograms. Our work is the first demonstration that the α-secretase-derived PrPc fragment N1, but not N2, displays in vivo and in vitro neuroprotective function by modulating p53 pathway. It further demonstrates that distinct N-terminal cleavage products of PrPc harbor different biological activities underlying the various phenotypes linking PrPc to cell survival. PMID:19850936

The optimal pressure for initial flush with UW solution in heart procurement.

PubMed

Mohara, Jun; Tsutsumi, Hirofumi; Takeyoshi, Izumi; Tokumine, Masahiko; Aizaki, Masahiro; Ishikawa, Susumu; Matsumoto, Koshi; Morishita, Yasuo

2002-03-01

University of Wisconsin (UW) solution is widely used in organ preservation. Some investigators have reported that high pressure during initial flush with UW solution may induce vasoconstriction and endothelial damage, because of its high potassium content and high viscosity. However, using lower pressure during the initial flush may lead to irregular distribution of the solution and incomplete flushing of blood components from coronary vascular beds. This experimental study evaluated the effects of a range of initial flush pressures during heart procurement, followed by orthotopic transplantation of the graft after 12 hours of preservation. Twelve pairs of adult mongrel dogs, weighing 9 to 14 kg, formed the recipient-donor combinations. After determining hemodynamic status by measuring cardiac output, left ventricular pressure (LVP), and maximum positive and negative change in LVP (+/-LVdP/dt), donor hearts were excised. Coronary vascular beds were flushed with 4 degrees C UW solution at a pressure of 60 mm Hg in the low-pressure group (n = 6) and at 120 mm Hg in the high-pressure group (n = 6). After 12 hours of cold preservation, orthotopic transplantation was performed using cardiopulmonary bypass (CPB). The hemodynamics of the transplanted graft were assessed by comparing recovery rates (%) from donor hearts 2 hours after weaning from CPB. Endothelin-1 (ET-1) levels were measured in the blood obtained from the coronary sinus 30 minutes after reperfusion. The transplanted grafts were then harvested for histologic study and measurement of adenosine triphosphate (ATP) content. Cardiac output, LVP, LVdP/dt and myocardial tissue ATP content were significantly better (p < 0.05) in the high-pressure group than in the low-pressure group. We found no significant differences in ET-1 levels between the groups. Transmission electron microscopic findings revealed that degeneration of the mitochondria was less extensive in the high-pressure group than in the low-pressure group. We observed no obvious ultrastructural damage to the endothelial cells in either group. When using UW solution in heart procurement, high pressure is better to completely wash out the blood components and distribute the solution.

Microstructural observations of reconsolidated granular salt to 250°C

NASA Astrophysics Data System (ADS)

Mills, M. M.; Hansen, F.; Bauer, S. J.; Stormont, J.

2014-12-01

Very low permeability is a principal reason salt formations are considered viable hosts for disposal of nuclear waste and spent nuclear fuel. Granular salt is likely to be used as back-fill material and as a seal system component. Granular salt is expected to reconsolidate to a low permeability condition because of external pressure from the surrounding salt formation. Understanding the consolidation processes--known to depend on the stress state, moisture availability and temperature--is important for predicting achievement of sealing functions and long-term repository performance. As granular salt consolidates, initial void reduction is accomplished by brittle processes of grain rearrangement and cataclastic flow. At porosities of less than 10%, grain boundary processes and crystal-plastic mechanisms govern further porosity reduction. We investigate the micro-mechanisms operative in granular salt that has been consolidated under high temperatures to relatively low porosity. These conditions would occur proximal to heat-generating canisters. Mine-run salt from the Waste Isolation Pilot Plant was used to create cylindrical samples which were consolidated at 250°C and stresses to 20 MPa. From samples consolidated to fractional densities of 86% and 97% polished thin sections, etched cleavage chips, and fragments were fabricated. Microstructural techniques included scanning electron and optical microscopy. Microstructure of undeformed mine-run salt was compared to the deformed granular salt. Observed deformation mechanisms include glide, cross slip, climb, fluid-assisted creep, pressure-solution redeposition, and annealing. Documentation of operative deformation mechanisms within the consolidating granular salt, particularly at grain boundaries, is essential to establish effects of moisture, stress, and temperature. Future work will include characterization of pore structures. Information gleaned in these studies supports evaluation of a constitutive model for reconsolidating granular salt, which will be used to predict the thermal-mechanical-hydrologic response of salt repository seal structures and backfilled rooms.

A hazard of the Intraflo continuous flush system.

PubMed

Schwartz, A J; Stoner, B B; Jobes, D R

1977-01-01

Patency of pressure sensing systems can be provided by the Intraflow Continuous Flush System (Sorenson Research Company, Salt Lake City, UT 84115). This device allows continuous flow of flush solution through a regulatory valve while preventing transmission of the high pressure of the flush solution. The case presented describes the recognition of a false elevation of a monitored pressure secondary to the malfunction of the Intraflo regulatory valve. Elimination of the flush solution high pressure during monitoring prevents inappropriate data collection.

DNA cleavage site selection by Type III restriction enzymes provides evidence for head-on protein collisions following 1D bidirectional motion

PubMed Central

Schwarz, Friedrich W.; van Aelst, Kara; Tóth, Júlia; Seidel, Ralf; Szczelkun, Mark D.

2011-01-01

DNA cleavage by the Type III Restriction–Modification enzymes requires communication in 1D between two distant indirectly-repeated recognitions sites, yet results in non-specific dsDNA cleavage close to only one of the two sites. To test a recently proposed ATP-triggered DNA sliding model, we addressed why one site is selected over another during cleavage. We examined the relative cleavage of a pair of identical sites on DNA substrates with different distances to a free or protein blocked end, and on a DNA substrate using different relative concentrations of protein. Under these conditions a bias can be induced in the cleavage of one site over the other. Monte-Carlo simulations based on the sliding model reproduce the experimentally observed behaviour. This suggests that cleavage site selection simply reflects the dynamics of the preceding stochastic enzyme events that are consistent with bidirectional motion in 1D and DNA cleavage following head-on protein collision. PMID:21724613

Propagation of solutes and pressure into aquifers following river stage rise

NASA Astrophysics Data System (ADS)

Welch, Chani; Cook, Peter G.; Harrington, Glenn A.; Robinson, Neville I.

2013-09-01

Water level rises associated with river flow events induce both pressure and solute movement into adjacent aquifers at vastly different rates. We present a simple analytical solution that relates the travel time and travel distance of solutes into an aquifer following river stage rise to aquifer properties. Combination with an existing solution for pressure propagation indicates that the ratio of solute to pressure travel times is proportional to the ratio of the volume of water stored in the aquifer before the river stage rise and the volume added by the stage rise and is independent of hydraulic conductivity. Two-dimensional numerical simulations of an aquifer slice perpendicular to a river demonstrate that the solutions are broadly applicable to variably saturated aquifers and partially penetrating rivers. The solutions remain applicable where river stage rise and fall occur, provided that regional hydraulic gradients are low and the duration of the river stage rise is less than pressure and solute travel times to the observation point in the aquifer. Consequently, the solutions provide new insight into the relationships between aquifer properties and distance and time of solute propagation and, in some cases, may be used to estimate system characteristics. Travel time metrics obtained for a flood event in the Cockburn River in eastern Australia using electrical conductivity measurements enabled estimates of aquifer properties and a lateral extent of river-aquifer mixing of 25 m. A detailed time series of any soluble tracer with distinctly different concentrations in river water and groundwater may be used.

GPS-CCD: A Novel Computational Program for the Prediction of Calpain Cleavage Sites

PubMed Central

Gao, Xinjiao; Ma, Qian; Ren, Jian; Xue, Yu

2011-01-01

As one of the most essential post-translational modifications (PTMs) of proteins, proteolysis, especially calpain-mediated cleavage, plays an important role in many biological processes, including cell death/apoptosis, cytoskeletal remodeling, and the cell cycle. Experimental identification of calpain targets with bona fide cleavage sites is fundamental for dissecting the molecular mechanisms and biological roles of calpain cleavage. In contrast to time-consuming and labor-intensive experimental approaches, computational prediction of calpain cleavage sites might more cheaply and readily provide useful information for further experimental investigation. In this work, we constructed a novel software package of GPS-CCD (Calpain Cleavage Detector) for the prediction of calpain cleavage sites, with an accuracy of 89.98%, sensitivity of 60.87% and specificity of 90.07%. With this software, we annotated potential calpain cleavage sites for hundreds of calpain substrates, for which the exact cleavage sites had not been previously determined. In this regard, GPS-CCD 1.0 is considered to be a useful tool for experimentalists. The online service and local packages of GPS-CCD 1.0 were implemented in JAVA and are freely available at: http://ccd.biocuckoo.org/. PMID:21533053

Does the Hertz solution estimate pressures correctly in diamond indentor experiments?

NASA Astrophysics Data System (ADS)

Bruno, M. S.; Dunn, K. J.

1986-05-01

The Hertz solution has been widely used to estimate pressures in a spherical indentor against flat matrix type high pressure experiments. It is usually assumed that the pressure generated when compressing a sample between the indentor and substrate is the same as that generated when compressing an indentor against a flat surface with no sample present. A non-linear finite element analysis of this problem has shown that the situation is far more complex. The actual peak pressure in the sample is highly dependent on plastic deformation and the change in material properties due to hydrostatic pressure. An analysis with two material models is presented and compared with the Hertz solution.

Purification of Restriction Endonuclease EcoRII and its Co-Crystallization

NASA Technical Reports Server (NTRS)

Karpova, E. A.; Chen, L.; Meehan, E.; Pusey, M.; Rose, M. Franklin (Technical Monitor)

2000-01-01

Restriction endonuclease EcoRII (EcoRII) is a homodimeric DNA-binding protein. It belongs to the type II family of restriction-modification enzymes (subclass IIe). EcoRII recognizes the nucleotide sequence 5'-CCWGG (W=A or T) and cleaves the phosphodiester bond preceding the first cytosine. Methylation at C5 of the second cytosine inhibits cleavage. The enzyme has a unique ability to search for the presence of two substrate sites before cleavage. To the best of our knowledge no other subclass IIe restriction endonuclease has been crystallized yet, without or with a DNA-substrate. We have recently grown and characterized the crystals of this enzyme (1) Here we report on the result of co-crystallization experiments of EcoRII with an 11 b.p. oligonucleotide substrate. The dissociation constant (Kd) EcoRII: 11 b.p. was determined earlier (unpublished results). The needle-like crystals of oligonucleotide-EcoRII protein complex were obtained with this substrate by the technique of vapor diffusion hanging drops. The crystals obtained were washed and dissolved in an aliquot of 10 mM Tris-HCl buffer, pH=7.5. Running a portion of this solution on the SDS-get indicated the presence of endonuclease in the solution. A UV-spectrophotometric test of a second portion confirmed the presence of DNA. We are now working on improvement of the DNA-EcoRII protein crystals. Results obtained from these and ongoing efforts will be reported.

Time-of-flight mass spectrometry assessment of fluconazole and climbazole UV and UV/H2O2 degradability: Kinetics study and transformation products elucidation.

PubMed

Castro, Gabriela; Casado, Jorge; Rodríguez, Isaac; Ramil, María; Ferradás, Aida; Cela, Rafael

2016-01-01

The efficiency of UV irradiation for the removal of the antimycotic drugs fluconazole (FCZ) and climbazole (CBZ) from water samples is evaluated. Degradation experiments, at laboratory scale, were carried out with spiked aliquots of ultrapure water solutions and treated wastewater samples using low-pressure mercury lamps emitting at 254 nm. Time course of precursor pollutants and identification of arising transformation products (TPs) was performed by injection of different reaction time aliquots in a liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) system. Chemical structures of identified TPs were proposed from their full-product ion spectra, acquired using different collision energies. During UV irradiation experiments, the half-lives (t1/2) of FCZ and CBZ were similar in ultrapure water solutions and wastewater samples; however, the first species was more recalcitrant than the second one. Four TPs were identified in case of FCZ resulting from substitution of fluorine atoms by hydroxyl moieties and intramolecular cyclization with fluorine removal. CBZ interacted with UV radiation through reductive dechlorination, hydroxylation and cleavage of the ether bond; moreover, five additional primary TPs, with the same empirical formula as CBZ, were also noticed. Given the relatively long t1/2 of FCZ under direct photolysis (ca. 42 min), UV irradiation was combined with H2O2 addition to promote formation of reactive hydroxyl radicals. Under such conditions, the degradation rate of FCZ was enhanced significantly and no TPs were detected. These latter conditions allowed also the effective removal of CBZ TPs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Increased cleavage and blastocyst rate in ewes treated with bovine somatotropin 5 days before the end of progestin-based estrous synchronization.

PubMed

Montero-Pardo, A; Hernández-Cerón, J; Rojas-Maya, S; Valencia, J; Rodríguez-Cortez, A; Gutiérrez, C G

2011-05-01

Treatment with bovine somatotropin (bST) during estrous synchronization increased fertility and prolificacy in sheep. In the present study, a single dose of bST 5 days before the end of progestin treatment improved cleavage and embryo development. Stage of estrous cycle was synchronized in ewes (n=32) with progestin and superovulation was induced by use of FSH. Five days before the end of progestin treatment, ewes were randomly assigned to two groups: bST group (n=16) received a depot injection of 125 mg of bST sc (Lactotropina, Elanco, México) and the control group (n=16) received saline solution. Estrous was detected with rams fitted with an apron every 2 h and estrous sheep were mated every 8 h whilst in estrous. Embryos were recovered on Day 7 post mating, assessed microscopically and fixed in 4% paraformaldehyde. Cell number in blastocysts was counted after Hoechst 33342 staining. Plasma concentrations of IGF-I, insulin and progesterone were determined in eight sheep per group from the day of bST treatment to the day of embryo recovery. Cleavage rate, percentage of transferable embryos (transferable embryos/cleaved) and percentage of embryos reaching the blastocyst stage (blastocyst/cleaved) were compared between groups by logistic regression. IGF-I, insulin and progesterone plasma concentrations were analyzed by ANOVA for repeated measurements and cell number by ANOVA. Cleavage rate was greater (P<0.01) in bST treatment group (86%) than in the control group (62%). Similarly, the proportion of embryos reaching the blastocyst stage (bST=68.7 vs control=42.5) and the number of cells per blastocyst (bST group 91.8±5.5 compared to control group 75±6) were greater (P<0.01) in the bST-treated sheep. Plasma concentrations of IGF-I and insulin were greater (P<0.01) in the bST-treated group. No changes were observed in progesterone concentrations (P=0.5). It is concluded that bST injection 5 days before progestin removal increases cleavage rate and the proportion of embryos that reach the blastocyst stage. These effects are associated with an increase in IGF-I and insulin concentrations. Copyright © 2011 Elsevier B.V. All rights reserved.

Charged Analogues of Henning Knutsen Type Solutions in General Relativity

NASA Astrophysics Data System (ADS)

Gupta, Y. K.; Kumar, Sachin; Pratibha

2011-11-01

In the present article, we have found charged analogues of Henning Knutsen's interior solutions which join smoothly to the Reissner-Nordstrom metric at the pressure free interface. The solutions are singularity free and analyzed numerically with respect to pressure, energy-density and charge-density in details. The solutions so obtained also present the generalization of A.L. Mehra's solutions.

Method of making supercritical fluid molecular spray films, powder and fibers

DOEpatents

Smith, Richard D.

1988-01-01

Solid films are deposited, or fine powders formed, by dissolving a solid material into a supercritical fluid solution at an elevated pressure and then rapidly expanding the solution through a heated nozzle having a short orifice into a region of relatively low pressure. This produces a molecular spray which is directed against a substrate to deposit a solid thin film thereon, or discharged into a collection chamber to collect a fine powder. In another embodiment, the temperature of the solution and nozzle is elevated above the melting point of the solute, which is preferably a polymer, and the solution is maintained at a pressure such that, during expansion, the solute precipitates out of solution within the nozzle in a liquid state. Alternatively, a secondary solvent mutually soluble with the solute and primary solvent and having a higher critical temperature than that of primary solvent is used in a low concentration (<20%) to maintain the solute in a transient liquid state. The solute is discharged in the form of long, thin fibers. The fibers are collected at sufficient distance from the orifice to allow them to solidify in the low pressure/temperature region.

Further investigations of the effect of pressure on retention in ultra-high-pressure liquid chromatography.

PubMed

Fallas, Morgane M; Neue, Uwe D; Hadley, Mark R; McCalley, David V

2010-01-15

In this study, we investigated further the large increases in retention with pressure that we observed previously in RP-LC especially for ionised solutes. These findings were initially confirmed on a conventional silica C(18) column, which gave extremely similar results to the hybrid C(18) phase originally used. Large increases in retention factor of approximately 50% for a pressure increase of 500 bar were also shown for high MW polar but neutral solutes. However, experiments with the same bases in ionised and non-ionised forms suggest that somewhat greater pressure-induced retention increases are found for ionised solutes. Retention increases with pressure were found to be considerably smaller for a C(1) column compared with a C(18) column; decreases in retention with increasing pressure were noted for ionised bases when using a bare silica column in the hydrophilic interaction chromatography (HILIC) mode. These observations are consistent with the partial loss of the solvation layer in RP-LC as the solute is forced into the hydrophobic environment of the stationary phase, and consequent reduction in the solute molar volume, while the water layer on the surface of a HILIC packing increases the hydration of a basic analyte. Finally, retention changes with pressure in RP-LC can also be observed at a mobile phase pH close to the solute pK(a), due to changes in pK(a) with pressure. However, this effect has no influence on the results of most of our studies. 2009 Elsevier B.V. All rights reserved.

Raising the Bar: Increased Hydraulic Pressure Allows Unprecedented High Power Densities in Pressure-Retarded Osmosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Straub, AP; Yip, NY; Elimelech, M

2014-01-01

Pressure-retarded osmosis (PRO) has the potential to generate sustainable energy from salinity gradients. PRO is typically considered for operation with river water and seawater, but a far greater energy of mixing can be harnessed from hypersaline solutions. This study investigates the power density that can be obtained in PRO from such concentrated solutions. Thin-film composite membranes with an embedded woven mesh were supported by tricot fabric feed spacers in a specially designed crossflow cell to maximize the operating pressure of the system, reaching a stable applied hydraulic pressure of 48 bar (700 psi) for more than 10 h. Operation atmore » this increased hydraulic pressure allowed unprecedented power densities, up to 60 W/m(2) with a 3 M (180 g/L) NaCl draw solution. Experimental power densities demonstrate reasonable agreement with power densities modeled using measured membrane properties, indicating high-pressure operation does not drastically alter membrane performance. Our findings exhibit the promise of the generation of power from high-pressure PRO with concentrated solutions.« less

An analytical solution for transient flow of Bingham viscoplastic materials in rock fractures

USGS Publications Warehouse

Amadei, B.; Savage, W.Z.

2001-01-01

We present below an analytical solution to model the one-dimensional transient flow of a Bingham viscoplastic material in a fracture with parallel walls (smooth or rough) that is subjected to an applied pressure gradient. The solution models the acceleration and the deceleration of the material as the pressure gradient changes with time. Two cases are considered: A pressure gradient applied over a finite time interval and an applied pressure gradient that is constant over time. The solution is expressed in dimensionless form and can therefore be used for a wide range of Bingham viscoplastic materials. The solution is also capable of capturing the transition that takes place in a fracture between viscoplastic flow and rigid plug flow. Also, it shows the development of a rigid central layer in fractures, the extent of which depends on the fluid properties (viscosity and yield stress), the magnitude of the pressure gradient, and the fracture aperture and surface roughness. Finally, it is shown that when a pressure gradient is applied and kept constant, the solution for the fracture flow rate converges over time to a steady-state solution that can be defined as a modified cubic law. In this case, the fracture transmissivity is found to be a non-linear function of the head gradient. This solution provides a tool for a better understanding of the flow of Bingham materials in rock fractures, interfaces, and cracks. ?? 2001 Elsevier Science Ltd. All rights reserved.

Shock compression of [001] single crystal silicon

DOE PAGES

Zhao, S.; Remington, B.; Hahn, E. N.; ...

2016-03-14

Silicon is ubiquitous in our advanced technological society, yet our current understanding of change to its mechanical response at extreme pressures and strain-rates is far from complete. This is due to its brittleness, making recovery experiments difficult. High-power, short-duration, laser-driven, shock compression and recovery experiments on [001] silicon (using impedance-matched momentum traps) unveiled remarkable structural changes observed by transmission electron microscopy. As laser energy increases, corresponding to an increase in peak shock pressure, the following plastic responses are are observed: surface cleavage along {111} planes, dislocations and stacking faults; bands of amorphized material initially forming on crystallographic orientations consistent withmore » dislocation slip; and coarse regions of amorphized material. Molecular dynamics simulations approach equivalent length and time scales to laser experiments and reveal the evolution of shock-induced partial dislocations and their crucial role in the preliminary stages of amorphization. Furthermore, application of coupled hydrostatic and shear stresses produce amorphization below the hydrostatically determined critical melting pressure under dynamic shock compression.« less

Shock compression of [001] single crystal silicon

NASA Astrophysics Data System (ADS)

Zhao, S.; Hahn, E. N.; Kad, B.; Remington, B. A.; Bringa, E. M.; Meyers, M. A.

2016-05-01

Silicon is ubiquitous in our advanced technological society, yet our current understanding of change to its mechanical response at extreme pressures and strain-rates is far from complete. This is due to its brittleness, making recovery experiments difficult. High-power, short-duration, laser-driven, shock compression and recovery experiments on [001] silicon (using impedance-matched momentum traps) unveiled remarkable structural changes observed by transmission electron microscopy. As laser energy increases, corresponding to an increase in peak shock pressure, the following plastic responses are are observed: surface cleavage along {111} planes, dislocations and stacking faults; bands of amorphized material initially forming on crystallographic orientations consistent with dislocation slip; and coarse regions of amorphized material. Molecular dynamics simulations approach equivalent length and time scales to laser experiments and reveal the evolution of shock-induced partial dislocations and their crucial role in the preliminary stages of amorphization. Application of coupled hydrostatic and shear stresses produce amorphization below the hydrostatically determined critical melting pressure under dynamic shock compression.

An Apparatus for Pressure Injection of Solutions into Trees

Treesearch

Thomas W. Jones; Garold F. Gregory; Garold F. Gregory

1971-01-01

The construction and use of an apparatus for injecting solutions under pressure into trees is described. A unique and important feature of the apparatus is that it permits injection of solutions into the outermost sapwood. It has been used to inject dye solutions and solubilized benomyl into elm, oak, and maple.

Kinetics of hairpin ribozyme cleavage in yeast.

PubMed Central

Donahue, C P; Fedor, M J

1997-01-01

Hairpin ribozymes catalyze a self-cleavage reaction that provides a simple model for quantitative analyses of intracellular mechanisms of RNA catalysis. Decay rates of chimeric mRNAs containing self-cleaving ribozymes give a direct measure of intracellular cleavage kinetics in yeast. Intracellular ribozyme-mediated cleavage occurs at similar rates and shows similar inhibition by ribozyme mutations as ribozyme-mediated reactions in vitro, but only when ribozymes are located in a favorable mRNA sequence context. The impact of cleavage on mRNA abundance is shown to depend directly on intrinsic mRNA stability. Surprisingly, cleavage products are no more labile than uncleaved mRNAs despite the loss of terminal cap structures or poly (A). PMID:9292496

Ethers on Si(001): A Prime Example for the Common Ground between Surface Science and Molecular Organic Chemistry.

PubMed

Pecher, Lisa; Laref, Slimane; Raupach, Marc; Tonner, Ralf

2017-11-20

By using computational chemistry it has been shown that the adsorption of ether molecules on Si(001) under ultrahigh vacuum conditions can be understood with classical concepts of organic chemistry. Detailed analysis of the two-step reaction mechanism-1) formation of a dative bond between the ether oxygen atom and a Lewis acidic surface atom and 2) nucleophilic attack of a nearby Lewis basic surface atom-shows that it mirrors acid-catalyzed ether cleavage in solution. The O-Si dative bond is the strongest of its kind, and the reactivity in step 2 defies the Bell-Evans-Polanyi principle. Electron rearrangement during C-O bond cleavage has been visualized with a newly developed method for analyzing bonding, which shows that the mechanism of nucleophilic substitutions on semiconductor surfaces is identical to molecular S N 2 reactions. Our findings illustrate how surface science and molecular chemistry can mutually benefit from each other and unexpected insight can be gained. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Impact of steam explosion on the wheat straw lignin structure studied by solution-state nuclear magnetic resonance and density functional methods.

PubMed

Heikkinen, Harri; Elder, Thomas; Maaheimo, Hannu; Rovio, Stella; Rahikainen, Jenni; Kruus, Kristiina; Tamminen, Tarja

2014-10-29

Chemical changes of lignin induced by the steam explosion (SE) process were elucidated. Wheat straw was studied as the raw material, and lignins were isolated by the enzymatic mild acidolysis lignin (EMAL) procedure before and after the SE treatment for analyses mainly by two-dimensional (2D) [heteronuclear single-quantum coherence (HSQC) and heteronuclear multiple-bond correlation (HMBC)] and (31)P nuclear magnetic resonance (NMR). The β-O-4 structures were found to be homolytically cleaved, followed by recoupling to β-5 linkages. The homolytic cleavage/recoupling reactions were also studied by computational methods, which verified their thermodynamic feasibility. The presence of the tricin bound to wheat straw lignin was confirmed, and it was shown to participate in lignin reactions during the SE treatment. The preferred homolytic β-O-4 cleavage reaction was calculated to follow bond dissociation energies: G-O-G (guaiacyl) (69.7 kcal/mol) > G-O-S (syringyl) (68.4 kcal/mol) > G-O-T (tricin) (67.0 kcal/mol).

Cleaving Off Uranyl Oxygens through Chelation: A Mechanistic Study in the Gas Phase

DOE PAGES

Abergel, Rebecca J.; de Jong, Wibe A.; Deblonde, Gauthier J. -P.; ...

2017-10-11

Recent efforts to activate the strong uranium-oxygen bonds in the dioxo uranyl cation have been limited to single oxo-group activation through either uranyl reduction and functionalization in solution, or by collision induced dissociation (CID) in the gas-phase, using mass spectrometry (MS). Here, we report and investigate the surprising double activation of uranyl by an organic ligand, 3,4,3-LI(CAM), leading to the formation of a formal U 6+ chelate in the gas-phase. The cleavage of both uranyl oxo bonds was experimentally evidence d by CID, using deuterium and 18O isotopic substitutions, and by infrared multiple photon dissociation (IRMPD) spectroscopy. Density functional theorymore » (DFT) computations predict that the overall reaction requires only 132 kJ/mol, with the first oxygen activation entailing about 107 kJ/mol. Here, combined with analysis of similar, but unreactive ligands, these results shed light on the chelation-driven mechanism of uranyl oxo bond cleavage, demonstrating its dependence on the presence of ligand hydroxyl protons available for direct interactions with the uranyl oxygens.« less

Aspects on gametogenesis, fertilization and embryogenesis of two deep-sea polychaetes from Eastern Atlantic cold seeps

NASA Astrophysics Data System (ADS)

Gaudron, S. M.; Hourdez, S.; Olu, K.

2017-11-01

We investigated two gonochoristic species of annelid polychaetes (one siboglinid and one polynoid) from cold seeps that ranged from 525 m to 3300 m in depth (Guiness, Worm Hole and Regab pockmarks) on the Gabon and Congo continental margins (Gulf of Guinea). Different aspects of gametogenesis (oocyte diameter, presence of ovisac, spermatozoa shape, and fecundity), fertilization (in vitro fertilization experiments: IVF) and embryogenesis (cleavage rate) were studied. The sampled siboglinid was a new species of Lamellibrachia and the second population of this genus in the Eastern Atlantic. Mean oocyte diameter was about 100 μm and fully-grown primary oocytes were stored in an ovisac, as in other studied siboglinids. The presence of a single spermatozoon was noted within an oviduct, indicating a possible internal fertilization. The rate of cell division at 6 °C was one cleavage every 20 h. Embryos developed normally to the blastula stage after 5-d post-fertilization at atmospheric pressure suggesting some pressure tolerance. The second polychaete was the scale-worm Branchipolynoe cf. seepensis that lives in commensalism in the mantle cavity of Bathymodiolus aff. boomerang. Anatomical reproductive features were similar to those described in B. seepensis from hydrothermal vents on Mid-Atlantic Ridge, with lecithotrophic larval development and continuous gametogenesis. We performed the first IVF carried out on gametes for any deep-sea polynoid species. Fertilization and development occurred but a number of abnormalities were observed demonstrating a limitation to embryogenesis at atmospheric pressure. The rate of cell division was three times faster at 8 °C than at 4 °C with a maximum stage of 8-cells reached after 72 h post-fertilization. We surprisingly observed some oocytes from the negative seawater control during IVF experiments cleaved to the 2-cell stage, demonstrating the possible occurrence of internal fertilization prior to IVF experiment or the accidental release of sperm from the female's spermatheca.

Multiple nucleotide preferences determine cleavage-site recognition by the HIV-1 and M-MuLV RNases H.

PubMed

Schultz, Sharon J; Zhang, Miaohua; Champoux, James J

2010-03-19

The RNase H activity of reverse transcriptase is required during retroviral replication and represents a potential target in antiviral drug therapies. Sequence features flanking a cleavage site influence the three types of retroviral RNase H activity: internal, DNA 3'-end-directed, and RNA 5'-end-directed. Using the reverse transcriptases of HIV-1 (human immunodeficiency virus type 1) and Moloney murine leukemia virus (M-MuLV), we evaluated how individual base preferences at a cleavage site direct retroviral RNase H specificity. Strong test cleavage sites (designated as between nucleotide positions -1 and +1) for the HIV-1 and M-MuLV enzymes were introduced into model hybrid substrates designed to assay internal or DNA 3'-end-directed cleavage, and base substitutions were tested at specific nucleotide positions. For internal cleavage, positions +1, -2, -4, -5, -10, and -14 for HIV-1 and positions +1, -2, -6, and -7 for M-MuLV significantly affected RNase H cleavage efficiency, while positions -7 and -12 for HIV-1 and positions -4, -9, and -11 for M-MuLV had more modest effects. DNA 3'-end-directed cleavage was influenced substantially by positions +1, -2, -4, and -5 for HIV-1 and positions +1, -2, -6, and -7 for M-MuLV. Cleavage-site distance from the recessed end did not affect sequence preferences for M-MuLV reverse transcriptase. Based on the identified sequence preferences, a cleavage site recognized by both HIV-1 and M-MuLV enzymes was introduced into a sequence that was otherwise resistant to RNase H. The isolated RNase H domain of M-MuLV reverse transcriptase retained sequence preferences at positions +1 and -2 despite prolific cleavage in the absence of the polymerase domain. The sequence preferences of retroviral RNase H likely reflect structural features in the substrate that favor cleavage and represent a novel specificity determinant to consider in drug design. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Efficient Cleavage of Ribosome-Associated Poly(A)-Binding Protein by Enterovirus 3C Protease

PubMed Central

Kuyumcu-Martinez, N. Muge; Joachims, Michelle; Lloyd, Richard E.

2002-01-01

Poliovirus (PV) causes a rapid and drastic inhibition of host cell cap-dependent protein synthesis during infection while preferentially allowing cap-independent translation of its own genomic RNA via an internal ribosome entry site element. Inhibition of cap-dependent translation is partly mediated by cleavage of an essential translation initiation factor, eIF4GI, during PV infection. In addition to cleavage of eIF4GI, cleavage of eIF4GII and poly(A)-binding protein (PABP) has been recently proposed to contribute to complete host translation shutoff; however, the relative importance of eIF4GII and PABP cleavage has not been determined. At times when cap-dependent translation is first blocked during infection, only 25 to 35% of the total cellular PABP is cleaved; therefore, we hypothesized that the pool of PABP associated with polysomes may be preferentially targeted by viral proteases. We have investigated what cleavage products of PABP are produced in vivo and the substrate determinants for cleavage of PABP by 2A protease (2Apro) or 3C protease (3Cpro). Our results show that PABP in ribosome-enriched fractions is preferentially cleaved in vitro and in vivo compared to PABP in other fractions. Furthermore, we have identified four N-terminal PABP cleavage products produced during PV infection and have shown that viral 3C protease generates three of the four cleavage products. Also, 3Cpro is more efficient in cleaving PABP in ribosome-enriched fractions than 2Apro in vitro. In addition, binding of PABP to poly(A) RNA stimulates 3Cpro-mediated cleavage and inhibits 2Apro-mediated cleavage. These results suggest that 3Cpro plays a major role in processing PABP during virus infection and that the interaction of PABP with translation initiation factors, ribosomes, or poly(A) RNA may promote its cleavage by viral 2A and 3C proteases. PMID:11836384

Electrodynamic pressure modulation of protein stability in cosolvents.

PubMed

Damodaran, Srinivasan

2013-11-19

Cosolvents affect structural stability of proteins in aqueous solutions. A clear understanding of the mechanism by which cosolvents impact protein stability is critical to understanding protein folding in a biological milieu. In this study, we investigated the Lifshitz-van der Waals dispersion interaction of seven different solutes with nine globular proteins and report that in an aqueous medium the structure-stabilizing solutes exert a positive electrodynamic pressure, whereas the structure-destabilizing solutes exert a negative electrodynamic pressure on the proteins. The net increase in the thermal denaturation temperature (ΔTd) of a protein in 1 M solution of various solutes was linearly related to the electrodynamic pressure (PvdW) between the solutes and the protein. The slope of the PvdW versus ΔTd plots was protein-dependent. However, we find a positive linear relationship (r(2) = 0.79) between the slope (i.e., d(ΔTd)/dPvdW) and the adiabatic compressibility (βs) of the proteins. Together, these results clearly indicate that the Lifshitz's dispersion forces are inextricably involved in solute-induced stabilization/destabilization of globular proteins. The positive and/or negative electrodynamic pressure generated by the solute-protein interaction across the water medium seems to be the fundamental mechanism by which solutes affect protein stability. This is at variance with the existing preferential hydration concept. The implication of these results is significant in the sense that, in addition to the hydrophobic effect that drives protein folding, the electrodynamic forces between the proteins and solutes in the biological milieu also might play a role in the folding process as well as in the stability of the folded state.

Crystal faces of anhydrite (CaSO 4) and their preferential dissolution in aqueous solutions studied with AFM

NASA Astrophysics Data System (ADS)

Shindo, H.; Kaise, M.; Kondoh, H.; Nishihara, C.; Nozoye, H.

Structures of cleaved surfaces of anhydrite were studied with atomic force microscopy (AFM) before and after partial dissolution in aqueous solutions of NH 4Cl and NaHSO 4. Two crystal faces showed atom-resolved images just after cleavage, (100) and (010), of which the former was roughened by the dissolution, while step structures were developed on the latter. After dissolution, steplines ran along the a- and c-axes on the (010) face, while they ran in directions inclined to these axes before. It was revealed that the arrangement of dipoles is a key factor in determining stabilities of step structures on crystal faces. On the terraces, the arrangement of oxygen atoms of the sulfate groups and calcium ions were clearly observed.

Method transfer from high-pressure liquid chromatography to ultra-high-pressure liquid chromatography. II. Temperature and pressure effects.

PubMed

Åsberg, Dennis; Samuelsson, Jörgen; Leśko, Marek; Cavazzini, Alberto; Kaczmarski, Krzysztof; Fornstedt, Torgny

2015-07-03

The importance of the generated temperature and pressure gradients in ultra-high-pressure liquid chromatography (UHPLC) are investigated and compared to high-pressure liquid chromatography (HPLC). The drug Omeprazole, together with three other model compounds (with different chemical characteristics, namely uncharged, positively and negatively charged) were used. Calculations of the complete temperature profile in the column at UHPLC conditions showed, in our experiments, a temperature difference between the inlet and outlet of 16 °C and a difference of 2 °C between the column center and the wall. Through van't Hoff plots, this information was used to single out the decrease in retention factor (k) solely due to the temperature gradient. The uncharged solute was least affected by temperature with a decrease in k of about 5% while for charged solutes the effect was more pronounced, with k decreases up to 14%. A pressure increase of 500 bar gave roughly 5% increase in k for the uncharged solute, while omeprazole and the other two charged solutes gave about 25, 20 and 15% increases in k, respectively. The stochastic model of chromatography was applied to estimate the dependence of the average number of adsorption/desorption events (n) and the average time spent by a molecule in the stationary phase (τs) on temperature and pressure on peak shape for the tailing, basic solute. Increasing the temperature yielded an increase in n and decrease in τs which resulted in less skew at high temperatures. With increasing pressure, the stochastic modeling gave interesting results for the basic solute showing that the skew of the peak increased with pressure. The conclusion is that pressure effects are more pronounced for both retention and peak shape than the temperature effects for the polar or charged compounds in our study. Copyright © 2015 Elsevier B.V. All rights reserved.

A mechanistic study and computational prediction of iron, cobalt and manganese cyclopentadienone complexes for hydrogenation of carbon dioxide.

PubMed

Ge, Hongyu; Chen, Xiangyang; Yang, Xinzheng

2016-10-13

A series of cobalt and manganese cyclopentadienone complexes are proposed and examined computationally as promising catalysts for hydrogenation of CO 2 to formic acid with total free energies as low as 20.0 kcal mol -1 in aqueous solution. Density functional theory study of the newly designed cobalt and manganese complexes and experimentally reported iron cyclopentadienone complexes reveals a stepwise hydride transfer mechanism with a water or a methanol molecule assisted proton transfer for the cleavage of H 2 as the rate-determining step.

Rendering Protein-Based Particles Transiently Insoluble for Therapeutic Applications

PubMed Central

Xu, Jing; Wang, Jin; Luft, J. Christopher; Tian, Shaomin; Owens, Gary; Pandya, Ashish A.; Berglund, Peter; Pohlhaus, Patrick; Maynor, Benjamin W.; Napier, Mary E.; DeSimone, Joseph M.

2012-01-01

Herein we report the fabrication of protein (bovine serum albumin, BSA) particles which were rendered transiently insoluble using a novel, reductively labile disulfide-based cross-linker. After being cross-linked, the protein particles retain their integrity in aqueous solution and dissolve preferentially under a reducing environment. Our data demonstrates that cleavage of the cross-linker leaves no chemical residue on the reactive amino group. Delivery of a self-replicating RNA was achieved via the transiently insoluble PRINT protein particles. These protein particles can provide new opportunities for drug and gene delivery. PMID:22568387

Time-Resolved Hydroxyl Radical Footprinting of RNA with X-Rays.

PubMed

Hao, Yumeng; Bohon, Jen; Hulscher, Ryan; Rappé, Mollie C; Gupta, Sayan; Adilakshmi, Tadepalli; Woodson, Sarah A

2018-06-01

RNA footprinting by hydroxyl radical cleavage provides 'snapshots' of RNA tertiary structure or protein interactions that bury the RNA backbone. Generation of hydroxyl radicals with a high-flux synchrotron X-ray beam provides analysis on a short timescale (5-100 msec), which enables the structures of folding intermediates or other transient conformational states to be determined in biochemical solutions or cells. This article provides protocols for using synchrotron beamlines for hydroxyl radical footprinting. © 2018 by John Wiley & Sons, Inc. © 2018 John Wiley & Sons, Inc.

Non-thermal atmospheric pressure plasma activates lactate in Ringer’s solution for anti-tumor effects

NASA Astrophysics Data System (ADS)

Tanaka, Hiromasa; Nakamura, Kae; Mizuno, Masaaki; Ishikawa, Kenji; Takeda, Keigo; Kajiyama, Hiroaki; Utsumi, Fumi; Kikkawa, Fumitaka; Hori, Masaru

2016-11-01

Non-thermal atmospheric pressure plasma is a novel approach for wound healing, blood coagulation, and cancer therapy. A recent discovery in the field of plasma medicine is that non-thermal atmospheric pressure plasma not only directly but also indirectly affects cells via plasma-treated liquids. This discovery has led to the use of non-thermal atmospheric pressure plasma as a novel chemotherapy. We refer to these plasma-treated liquids as plasma-activated liquids. We chose Ringer’s solutions to produce plasma-activated liquids for clinical applications. In vitro and in vivo experiments demonstrated that plasma-activated Ringer’s lactate solution has anti-tumor effects, but of the four components in Ringer’s lactate solution, only lactate exhibited anti-tumor effects through activation by non-thermal plasma. Nuclear magnetic resonance analyses indicate that plasma irradiation generates acetyl and pyruvic acid-like groups in Ringer’s lactate solution. Overall, these results suggest that plasma-activated Ringer’s lactate solution is promising for chemotherapy.

High nitrogen pressure solution growth of GaN

NASA Astrophysics Data System (ADS)

Bockowski, Michal

2014-10-01

Results of GaN growth from gallium solution under high nitrogen pressure are presented. Basic of the high nitrogen pressure solution (HNPS) growth method is described. A new approach of seeded growth, multi-feed seed (MFS) configuration, is demonstrated. The use of two kinds of seeds: free-standing hydride vapor phase epitaxy GaN (HVPE-GaN) obtained from metal organic chemical vapor deposition (MOCVD)-GaN/sapphire templates and free-standing HVPE-GaN obtained from the ammonothermally grown GaN crystals, is shown. Depending on the seeds’ structural quality, the differences in the structural properties of pressure grown material are demonstrated and analyzed. The role and influence of impurities, like oxygen and magnesium, on GaN crystals grown from gallium solution in the MFS configuration is presented. The properties of differently doped GaN crystals are discussed. An application of the pressure grown GaN crystals as substrates for electronic and optoelectronic devices is reported.

Different residues in the SARS-CoV spike protein determine cleavage and activation by the host cell protease TMPRSS2

PubMed Central

Reinke, Lennart Michel; Hartleib, Anika; Nehlmeier, Inga; Gierer, Stefanie; Hoffmann, Markus; Hofmann-Winkler, Heike; Winkler, Michael

2017-01-01

The spike (S) protein of severe acute respiratory syndrome coronavirus (SARS-CoV) mediates viral entry into target cells. Cleavage and activation of SARS S by a host cell protease is essential for infectious viral entry and the responsible enzymes are potential targets for antiviral intervention. The type II transmembrane serine protease TMPRSS2 cleaves and activates SARS S in cell culture and potentially also in the infected host. Here, we investigated which determinants in SARS S control cleavage and activation by TMPRSS2. We found that SARS S residue R667, a previously identified trypsin cleavage site, is also required for S protein cleavage by TMPRSS2. The cleavage fragments produced by trypsin and TMPRSS2 differed in their decoration with N-glycans, suggesting that these proteases cleave different SARS S glycoforms. Although R667 was required for SARS S cleavage by TMPRSS2, this residue was dispensable for TMPRSS2-mediated S protein activation. Conversely, residue R797, previously reported to be required for SARS S activation by trypsin, was dispensable for S protein cleavage but required for S protein activation by TMPRSS2. Collectively, these results show that different residues in SARS S control cleavage and activation by TMPRSS2, suggesting that these processes are more complex than initially appreciated. PMID:28636671

Different residues in the SARS-CoV spike protein determine cleavage and activation by the host cell protease TMPRSS2.

PubMed

Reinke, Lennart Michel; Spiegel, Martin; Plegge, Teresa; Hartleib, Anika; Nehlmeier, Inga; Gierer, Stefanie; Hoffmann, Markus; Hofmann-Winkler, Heike; Winkler, Michael; Pöhlmann, Stefan

2017-01-01

The spike (S) protein of severe acute respiratory syndrome coronavirus (SARS-CoV) mediates viral entry into target cells. Cleavage and activation of SARS S by a host cell protease is essential for infectious viral entry and the responsible enzymes are potential targets for antiviral intervention. The type II transmembrane serine protease TMPRSS2 cleaves and activates SARS S in cell culture and potentially also in the infected host. Here, we investigated which determinants in SARS S control cleavage and activation by TMPRSS2. We found that SARS S residue R667, a previously identified trypsin cleavage site, is also required for S protein cleavage by TMPRSS2. The cleavage fragments produced by trypsin and TMPRSS2 differed in their decoration with N-glycans, suggesting that these proteases cleave different SARS S glycoforms. Although R667 was required for SARS S cleavage by TMPRSS2, this residue was dispensable for TMPRSS2-mediated S protein activation. Conversely, residue R797, previously reported to be required for SARS S activation by trypsin, was dispensable for S protein cleavage but required for S protein activation by TMPRSS2. Collectively, these results show that different residues in SARS S control cleavage and activation by TMPRSS2, suggesting that these processes are more complex than initially appreciated.

SWI/SNF interacts with cleavage and polyadenylation factors and facilitates pre-mRNA 3' end processing.

PubMed

Yu, Simei; Jordán-Pla, Antonio; Gañez-Zapater, Antoni; Jain, Shruti; Rolicka, Anna; Östlund Farrants, Ann-Kristin; Visa, Neus

2018-05-31

SWI/SNF complexes associate with genes and regulate transcription by altering the chromatin at the promoter. It has recently been shown that these complexes play a role in pre-mRNA processing by associating at alternative splice sites. Here, we show that SWI/SNF complexes are involved also in pre-mRNA 3' end maturation by facilitating 3' end cleavage of specific pre-mRNAs. Comparative proteomics show that SWI/SNF ATPases interact physically with subunits of the cleavage and polyadenylation complexes in fly and human cells. In Drosophila melanogaster, the SWI/SNF ATPase Brahma (dBRM) interacts with the CPSF6 subunit of cleavage factor I. We have investigated the function of dBRM in 3' end formation in S2 cells by RNA interference, single-gene analysis and RNA sequencing. Our data show that dBRM facilitates pre-mRNA cleavage in two different ways: by promoting the association of CPSF6 to the cleavage region and by stabilizing positioned nucleosomes downstream of the cleavage site. These findings show that SWI/SNF complexes play a role also in the cleavage of specific pre-mRNAs in animal cells.

Integrated vacuum absorption steam cycle gas separation

DOEpatents

Chen, Shiaguo [Champaign, IL; Lu, Yonggi [Urbana, IL; Rostam-Abadi, Massoud [Champaign, IL

2011-11-22

Methods and systems for separating a targeted gas from a gas stream emitted from a power plant. The gas stream is brought into contact with an absorption solution to preferentially absorb the targeted gas to be separated from the gas stream so that an absorbed gas is present within the absorption solution. This provides a gas-rich solution, which is introduced into a stripper. Low pressure exhaust steam from a low pressure steam turbine of the power plant is injected into the stripper with the gas-rich solution. The absorbed gas from the gas-rich solution is stripped in the stripper using the injected low pressure steam to provide a gas stream containing the targeted gas. The stripper is at or near vacuum. Water vapor in a gas stream from the stripper is condensed in a condenser operating at a pressure lower than the stripper to concentrate the targeted gas. Condensed water is separated from the concentrated targeted gas.

The updated bottom up solution applied to atmospheric pressure photoionization and electrospray ionization mass spectrometry

USDA-ARS?s Scientific Manuscript database

The Updated Bottom Up Solution (UBUS) was recently applied to atmospheric pressure chemical ionization (APCI) mass spectrometry (MS) of triacylglycerols (TAGs). This report demonstrates that the UBUS applies equally well to atmospheric pressure photoionization (APPI) MS and to electrospray ionizatio...

Direct Coupling Method for Time-Accurate Solution of Incompressible Navier-Stokes Equations

NASA Technical Reports Server (NTRS)

Soh, Woo Y.

1992-01-01

A noniterative finite difference numerical method is presented for the solution of the incompressible Navier-Stokes equations with second order accuracy in time and space. Explicit treatment of convection and diffusion terms and implicit treatment of the pressure gradient give a single pressure Poisson equation when the discretized momentum and continuity equations are combined. A pressure boundary condition is not needed on solid boundaries in the staggered mesh system. The solution of the pressure Poisson equation is obtained directly by Gaussian elimination. This method is tested on flow problems in a driven cavity and a curved duct.

Bond cleavage of lignin model compounds into aromatic monomers using supported metal catalysts in supercritical water

PubMed Central

Yamaguchi, Aritomo; Mimura, Naoki; Shirai, Masayuki; Sato, Osamu

2017-01-01

More efficient use of lignin carbon is necessary for carbon-efficient utilization of lignocellulosic biomass. Conversion of lignin into valuable aromatic compounds requires the cleavage of C–O ether bonds and C–C bonds between lignin monomer units. The catalytic cleavage of C–O bonds is still challenging, and cleavage of C–C bonds is even more difficult. Here, we report cleavage of the aromatic C–O bonds in lignin model compounds using supported metal catalysts in supercritical water without adding hydrogen gas and without causing hydrogenation of the aromatic rings. The cleavage of the C–C bond in bibenzyl was also achieved with Rh/C as a catalyst. Use of this technique may greatly facilitate the conversion of lignin into valuable aromatic compounds. PMID:28387304

Multifaceted regulation of V(D)J recombination

NASA Astrophysics Data System (ADS)

Wang, Guannan

V(D)J recombination is responsible for generating an enormous repertoire of immunoglobulins and T cell receptors, therefore it is a centerpiece to the formation of the adaptive immune system. The V(D)J recombination process proceeds through two steps, site-specific cleavage at RSS (Recombination Signal Sequence) site mediated by the RAG recombinase (RAG1/2) and the subsequent imprecise resolution of the DNA ends, which is carried out by the ubiquitous non-homologous end joining pathway (NHEJ). The V(D)J recombination reaction is obliged to be tightly controlled under all circumstances, as it involves generations of DNA double strand breaks, which are considered the most dangerous lesion to a cell. Multifaceted regulatory mechanisms have been evolved to create great diversity of the antigen receptor repertoire while ensuring genome stability. The RAG-mediated cleavage reaction is stringently regulated at both the pre-cleavage stage and the post-cleavage stage. Specifically, RAG1/2 first forms a pre-cleavage complex assembled at the boarder of RSS and coding flank, which ensures the appropriate DNA targeting. Subsequently, this complex initiates site-specific cleavage, generating two types of double stranded DNA breaks, hairpin-ended coding ends (HP-CEs) and blunt signal ends (SEs). After the cleavage, RAG1/2 proteins bind and retain the recombination ends to form post-cleavage complexes (PCC), which collaborates with the NHEJ machinery for appropriate transfer of recombination ends to NHEJ for proper end resolution. However, little is known about the molecular basis of this collaboration, partly attributed to the lack of sensitive assays to reveal the interaction of PCC with HP-CEs. Here, for the first time, by using two complementary fluorescence-based techniques, fluorescence anisotropy and fluorescence resonance energy transfer (FRET), I managed to monitor the RAG1/2-catalyzed cleavage reaction in real time, from the pre-cleavage to the post-cleavage stages. By examining the dynamic fluorescence changes during the RAG-mediated cleavage reactions, and by manipulating the reaction conditions, I was able to characterize some fundamental properties of RAG-DNA interactions before and after cleavage. Firstly, Mg 2+, known as a physiological cofactor at the excision step, also promotes the HP-CEs retention in the RAG complex after cleavage. Secondly, the structure of pre-cleavage complex may affect the subsequent collaborations with NHEJ for end resolution. Thirdly, the non-core region of RAG2 may have differential influences on the PCC retention of HP-CEs and SEs. Furthermore, I also provide the first evidence of RAG1-mediated regulation of RAG2. Our study provides important insights into the multilayered regulatory mechanisms, in modulating recombination events in developing lymphocytes and paves the way for possible development of detection and diagnotic markers for defective recombination events that are often associated immunodeficiency and/or lymphoid malignancy.

Determining Double Bond Position in Lipids Using Online Ozonolysis Coupled to Liquid Chromatography and Ion Mobility-Mass Spectrometry.

PubMed

Harris, Rachel A; May, Jody C; Stinson, Craig A; Xia, Yu; McLean, John A

2018-02-06

The increasing focus on lipid metabolism has revealed a need for analytical techniques capable of structurally characterizing lipids with a high degree of specificity. Lipids can exist as any one of a large number of double bond positional isomers, which are indistinguishable by single-stage mass spectrometry alone. Ozonolysis reactions coupled to mass spectrometry have previously been demonstrated as a means for localizing double bonds in unsaturated lipids. Here we describe an online, solution-phase reactor using ozone produced via a low-pressure mercury lamp, which generates aldehyde products diagnostic of cleavage at a particular double bond position. This flow-cell device is utilized in conjunction with structurally selective ion mobility-mass spectrometry. The lamp-mediated reaction was found to be effective for multiple lipid species in both positive and negative ionization modes, and the conversion efficiency from precursor to product ions was tunable across a wide range (20-95%) by varying the flow rate through the ozonolysis device. Ion mobility separation of the ozonolysis products generated additional structural information and revealed the presence of saturated species in a complex mixture. The method presented here is simple, robust, and readily coupled to existing instrument platforms with minimal modifications necessary. For these reasons, application to standard lipidomic workflows is possible and aids in more comprehensive structural characterization of a myriad of lipid species.

Mineralogical, micromorphological and geochemical transformations in the initial steps of the weathering process of charnockite from the Caparaó Range, southeastern Brazil

NASA Astrophysics Data System (ADS)

Soares, Caroline Cibele Vieira; Varajão, Angélica Fortes Drummond Chicarino; Varajão, César Augusto Chicarino; Boulangé, Bruno

2014-12-01

X-ray diffraction (XRD), X-ray Fluorescence (XRF), optical microscopy, Scanning Electron Microscopy coupled with Energy Dispersive Spectrometry (SEM-EDS) and Electron Probe micro-analyser (EPMA) and Wavelength-Dispersive Spectroscopy (WDS) were conducted on charnockite from the Caparaó Suite and its alteration cortex to determine the mineralogical, micromorphological and geochemical transformations resulting from the weathering process. The hydrolysis of the charnockite occurred in different stages, in accordance with the order of stability of the minerals with respect to weathering: andesine/orthopyroxene, pargasite and alkali feldspar. The rock modifications had begun with the formation of a layer of incipient alteration due to the percolation of weathering solutions first in the pressure relief fractures and then in cleavage and mineral edges. The iron exuded from ferromagnesian minerals precipitated in the intermineral and intramineral discontinuities. The layer of incipient alteration evolves into an inner cortex where the plagioclase changes into gibbsite by direct alitisation, the ferromagnesian minerals initiate the formation of goethitic boxworks with kaolinitic cores, and the alkali feldspar initiates indirect transformation into gibbsite, forming an intermediate phase of illite and kaolinite. In the outer cortex, mostly traces of alkali feldspar remain, and they are surrounded by goethite and gibbsite as alteromorphics, characterising the formation of the isalteritic horizon that occurs along the slope and explains the bauxitization process at the Caparaó Range, SE Brazil.

Micromechanics of pressure-induced grain crushing in porous rocks

NASA Astrophysics Data System (ADS)

Davis, Daniel M.

1990-01-01

The hydrostatic compaction behavior of a suite of porous sandstones was investigated at confining pressures up to 600 MPa and constant pore pressures ranging up to 50 MPa. These five sandstones (Boise, Kayenta, St. Peter, Berea, and Weber) were selected because of their wide range of porosity (5-35%) and grain size (60-460 μm). We tested the law of effective stress for the porosity change as a function of pressure. Except for Weber sandstone (which has the lowest porosity and smallest grain size), the hydrostat of each sandstone shows an inflection point corresponding to a critical effective pressure beyond which an accelerated, irrecoverable compaction occurs. Our microstructural observations show that brittle grain crushing initiates at this critical pressure. We also observed distributed cleavage cracking in calcite and intensive kinking in mica. The critical pressures for grain crushing in our sandstones range from 75 to 380 MPa. In general, a sandstone with higher porosity and larger grain size has a critical pressure which is lower than that of a sandstone with lower porosity and smaller grain size. We formulate a Hertzian fracture model to analyze the micromechanics of grain crushing. Assuming that the solid grains have preexisting microcracks with dimensions which scale with grain size, we derive an expression for the critical pressure which depends on the porosity, grain size, and fracture toughness of the solid matrix. The theoretical prediction is in reasonable agreement with our experimental data as well as other data from soil and rock mechanics studies for which the critical pressures range over 3 orders of magnitude.

The decisive role of free water in determining homogenous ice nucleation behavior of aqueous solutions

PubMed Central

Wang, Qiang; Zhao, Lishan; Li, Chenxi; Cao, Zexian

2016-01-01

It is a challenging issue to quantitatively characterize how the solute and pressure affect the homogeneous ice nucleation in a supercooled solution. By measuring the glass transition behavior of solutions, a universal feature of water-content dependence of glass transition temperature is recognized, which can be used to quantify hydration water in solutions. The amount of free water can then be determined for water-rich solutions, whose mass fraction, Xf, is found to serve as a universal relevant parameter for characterizing the homogeneous ice nucleation temperature, the meting temperature of primary ice, and even the water activity of solutions of electrolytes and smaller organic molecules. Moreover, the effects of hydrated solute and pressure on ice nucleation is comparable, and the pressure, when properly scaled, can be incorporated into the universal parameter Xf. These results help establish the decisive role of free water in determining ice nucleation and other relevant properties of aqueous solutions. PMID:27225427

Does Cleavage Work at Work? Men, but Not Women, Falsely Believe Cleavage Sells a Weak Product

ERIC Educational Resources Information Center

Glick, Peter; Chrislock, Karyna; Petersik, Korinne; Vijay, Madhuri; Turek, Aleksandra

2008-01-01

We examined whether men, but not women, would be distracted by a female sales representative's exposed cleavage, leading to greater perceived efficacy for a weak, but not for a strong product. A community sample of 88 men and 97 women viewed a video of a female pharmaceutical sales representative who (a) had exposed cleavage or dressed modestly…

Mechanisms for ribotoxin-induced ribosomal RNA cleavage

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Kaiyu; Center for Integrative Toxicology, Michigan State University, East Lansing, MI 48824; Zhou, Hui-Ren

The Type B trichothecene deoxynivalenol (DON), a ribotoxic mycotoxin known to contaminate cereal-based foods, induces ribosomal RNA (rRNA) cleavage in the macrophage via p38-directed activation of caspases. Here we employed the RAW 264.7 murine macrophage model to test the hypothesis that this rRNA cleavage pathway is similarly induced by other ribotoxins. Capillary electrophoresis confirmed that the antibiotic anisomycin (≥ 25 ng/ml), the macrocylic trichothecene satratoxin G (SG) (≥ 10 ng/ml) and ribosome-inactivating protein ricin (≥ 300 ng/ml) induced 18s and 28s rRNA fragmentation patterns identical to that observed for DON. Also, as found for DON, inhibition of p38, double-stranded RNA-activatedmore » kinase (PKR) and hematopoietic cell kinase (Hck) suppressed MAPK anisomycin-induced rRNA cleavage, while, in contrast, their inhibition did not affect SG- and ricin-induced rRNA fragmentation. The p53 inhibitor pifithrin-μ and pan caspase inhibitor Z-VAD-FMK suppressed rRNA cleavage induced by anisomycin, SG and ricin, indicating that these ribotoxins shared with DON a conserved downstream pathway. Activation of caspases 8, 9 and 3 concurrently with apoptosis further suggested that rRNA cleavage occurred in parallel with both extrinsic and intrinsic pathways of programmed cell death. When specific inhibitors of cathepsins L and B (lysosomal cysteine cathepsins active at cytosolic neutral pH) were tested, only the former impaired anisomycin-, SG-, ricin- and DON-induced rRNA cleavage. Taken together, the data suggest that (1) all four ribotoxins induced p53-dependent rRNA cleavage via activation of cathepsin L and caspase 3, and (2) activation of p53 by DON and anisomycin involved p38 whereas SG and ricin activated p53 by an alternative mechanism. Highlights: ► Deoxynivalenol (DON) anisomycin, satratoxin G (SG) and ricin are ribotoxins. ► Ribotoxins induce 18s and 28s rRNA cleavage in the RAW 264.7 macrophage model. ► Ribotoxins induce rRNA cleavage via activation of p53, caspases and cathepsins. ► DON- and anisomycin-triggered rRNA cleavage is p38-dependent. ► SG- and ricin-induced rRNA cleavage is p38-independent.« less

Energetics and dynamics of the fragmentation reactions of protonated peptides containing methionine sulfoxide or aspartic acid via energy- and time-resolved surface induced dissociation.

PubMed

Lioe, Hadi; Laskin, Julia; Reid, Gavin E; O'Hair, Richard A J

2007-10-25

The surface-induced dissociation (SID) of six model peptides containing either methionine sulfoxide or aspartic acid (GAILM(O)GAILR, GAILM(O)GAILK, GAILM(O)GAILA, GAILDGAILR, GAILDGAILK, and GAILDGAILA) have been studied using a specially configured Fourier transform ion-cyclotron resonance mass spectrometer (FT-ICR MS). In particular, we have investigated the energetics and dynamics associated with (i) preferential cleavage of the methionine sulfoxide side chain via the loss of CH3SOH (64 Da), and (ii) preferential cleavage of the amide bond C-terminal to aspartic acid. The role of proton mobility in these selective bond cleavage reactions was examined by changing the C-terminal residue of the peptide from arginine (nonmobile proton conditions) to lysine (partially mobile proton conditions) to alanine (mobile proton conditions). Time- and energy-resolved fragmentation efficiency curves (TFECs) reveal that selective cleavages due to the methionine sulfoxide and aspartic acid residues are characterized by slow fragmentation kinetics. RRKM modeling of the experimental data suggests that the slow kinetics is associated with large negative entropy effects and these may be due to the presence of rearrangements prior to fragmentation. It was found that the Arrhenius pre-exponential factor (A) for peptide fragmentations occurring via selective bond cleavages are 1-2 orders of magnitude lower than nonselective peptide fragmentation reactions, while the dissociation threshold (E0) is relatively invariant. This means that selective bond cleavage is kinetically disfavored compared to nonselective amide bond cleavage. It was also found that the energetics and dynamics for the preferential loss of CH3SOH from peptide ions containing methionine sulfoxide are very similar to selective C-terminal amide bond cleavage at the aspartic acid residue. These results suggest that while preferential cleavage can compete with amide bond cleavage energetically, dynamically, these processes are much slower compared to amide bond cleavage, explaining why these selective bond cleavages are not observed if fragmentation is performed under mobile proton conditions. This study further affirms that fragmentation of peptide ions in the gas phase are predominantly governed by entropic effects.

Thermal Decomposition of the Solid Phase of Nitromethane: Ab Initio Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Chang, Jing; Lian, Peng; Wei, Dong-Qing; Chen, Xiang-Rong; Zhang, Qing-Ming; Gong, Zi-Zheng

2010-10-01

The Car-Parrinello molecular dynamics simulations were employed to investigate thermal decomposition of the solid nitromethane. It is found that it undergoes chemical decomposition at about 2200 K under ambient pressure. The initiation of reactions involves both proton transfer and commonly known C-N bond cleavage. About 75 species and 100 elementary reactions were observed with the final products being H2O, CO2, N2, and CNCNC. It represents the first complete simulation of solid-phase explosive reactions reported to date, which is of far-reaching implication for design and development of new energetic materials.

PrP(C) homodimerization stimulates the production of PrPC cleaved fragments PrPN1 and PrPC1.

PubMed

Béland, Maxime; Motard, Julie; Barbarin, Alice; Roucou, Xavier

2012-09-19

An endoproteolytic cleavage termed α-cleavage between residues 111/112 is a characteristic feature of the cellular prion protein (PrP(C)). This cleavage generates a soluble N-terminal fragment (PrPN1) and a glycosylphosphatidylinositol-anchored C-terminal fragment (PrPC1). Independent studies demonstrate that modulating PrP(C) α-cleavage represents a potential therapeutic strategy in prion diseases. The regulation of PrP(C) α-cleavage is unclear. The only known domain that is essential for the α-cleavage to occur is a hydrophobic domain (HD). Importantly, the HD is also essential for the formation of PrP(C) homodimers. To explore the role of PrP(C) homodimerization on the α-cleavage, we used a well described inducible dimerization strategy whereby a chimeric PrP(C) composed of a modified FK506-binding protein (Fv) fused with PrP(C) and termed Fv-PrP is incubated in the presence of a dimerizer AP20187 ligand. We show that homodimerization leads to a considerable increase of PrP(C) α-cleavage in cultured cells and release of PrPN1 and PrPC1. Interestingly, enforced homodimerization increased PrP(C) levels at the plasma membrane, and preventing PrP(C) trafficking to the cell surface inhibited dimerization-induced α-cleavage. These observations were confirmed in primary hippocampal neurons from transgenic mice expressing Fv-PrP. The proteases responsible for the α-cleavage are still elusive, and in contrast to initial studies we confirm more recent investigations that neither ADAM10 nor ADAM17 are involved. Importantly, PrPN1 produced after PrP(C) homodimerization protects against toxic amyloid-β (Aβ) oligomers. Thus, our results show that PrP(C) homodimerization is an important regulator of PrP(C) α-cleavage and may represent a potential therapeutic avenue against Aβ toxicity in Alzheimer's disease.

Recent Advances in Characterization of Lignin Polymer by Solution-State Nuclear Magnetic Resonance (NMR) Methodology

PubMed Central

Wen, Jia-Long; Sun, Shao-Long; Xue, Bai-Liang; Sun, Run-Cang

2013-01-01

The demand for efficient utilization of biomass induces a detailed analysis of the fundamental chemical structures of biomass, especially the complex structures of lignin polymers, which have long been recognized for their negative impact on biorefinery. Traditionally, it has been attempted to reveal the complicated and heterogeneous structure of lignin by a series of chemical analyses, such as thioacidolysis (TA), nitrobenzene oxidation (NBO), and derivatization followed by reductive cleavage (DFRC). Recent advances in nuclear magnetic resonance (NMR) technology undoubtedly have made solution-state NMR become the most widely used technique in structural characterization of lignin due to its versatility in illustrating structural features and structural transformations of lignin polymers. As one of the most promising diagnostic tools, NMR provides unambiguous evidence for specific structures as well as quantitative structural information. The recent advances in two-dimensional solution-state NMR techniques for structural analysis of lignin in isolated and whole cell wall states (in situ), as well as their applications are reviewed. PMID:28809313

Assessment of the breakdown products of solar/UV induced photolytic degradation of food dye tartrazine.

PubMed

dos Santos, Tuane Cristina; Zocolo, Guilherme Julião; Morales, Daniel Alexandre; Umbuzeiro, Gisela de Aragão; Zanoni, Maria Valnice Boldrin

2014-06-01

The food dye tartrazine (CI 19140) was exposed to UV irradiation from an artificial source, a mercury vapor lamp, and a natural one, sunlight. It was observed that conditions such as energy dose, irradiation time, pH and initial dye concentration affected its discoloration. There was 100% of color removal, after 30min of irradiation, when a dye solution 1×10(-5)molL(-1) was submitted to an energy dose of 37.8Jcm(-2). Liquid Chromatography coupled to Diode Array Detection and Mass Spectrometry confirmed the cleavage of the chromophore group and the formation of five by-products at low concentration. Although by-products were formed, the Salmonella/microsome mutagenicity assay performed for both, the dye solution at a dose of 5.34mg/plate and the solutions obtained after exposure to UV irradiation, did not present mutagenic activity for TA98 and TA100 with and without S9. Copyright © 2014 Elsevier Ltd. All rights reserved.

How can macromolecular crowding inhibit biological reactions? The enhanced formation of DNA nanoparticles

PubMed Central

Hou, Sen; Trochimczyk, Piotr; Sun, Lili; Wisniewska, Agnieszka; Kalwarczyk, Tomasz; Zhang, Xuzhu; Wielgus-Kutrowska, Beata; Bzowska, Agnieszka; Holyst, Robert

2016-01-01

In contrast to the already known effect that macromolecular crowding usually promotes biological reactions, solutions of PEG 6k at high concentrations stop the cleavage of DNA by HindIII enzyme, due to the formation of DNA nanoparticles. We characterized the DNA nanoparticles and probed the prerequisites for their formation using multiple techniques such as fluorescence correlation spectroscopy, dynamic light scattering, fluorescence analytical ultracentrifugation etc. In >25% PEG 6k solution, macromolecular crowding promotes the formation of DNA nanoparticles with dimensions of several hundreds of nanometers. The formation of DNA nanoparticles is a fast and reversible process. Both plasmid DNA (2686 bp) and double-stranded/single-stranded DNA fragment (66bp/nt) can form nanoparticles. We attribute the enhanced nanoparticle formation to the depletion effect of macromolecular crowding. This study presents our idea to enhance the formation of DNA nanoparticles by macromolecular crowding, providing the first step towards a final solution to efficient gene therapy. PMID:26903405

How can macromolecular crowding inhibit biological reactions? The enhanced formation of DNA nanoparticles.

PubMed

Hou, Sen; Trochimczyk, Piotr; Sun, Lili; Wisniewska, Agnieszka; Kalwarczyk, Tomasz; Zhang, Xuzhu; Wielgus-Kutrowska, Beata; Bzowska, Agnieszka; Holyst, Robert

2016-02-23

In contrast to the already known effect that macromolecular crowding usually promotes biological reactions, solutions of PEG 6k at high concentrations stop the cleavage of DNA by HindIII enzyme, due to the formation of DNA nanoparticles. We characterized the DNA nanoparticles and probed the prerequisites for their formation using multiple techniques such as fluorescence correlation spectroscopy, dynamic light scattering, fluorescence analytical ultracentrifugation etc. In >25% PEG 6k solution, macromolecular crowding promotes the formation of DNA nanoparticles with dimensions of several hundreds of nanometers. The formation of DNA nanoparticles is a fast and reversible process. Both plasmid DNA (2686 bp) and double-stranded/single-stranded DNA fragment (66 bp/nt) can form nanoparticles. We attribute the enhanced nanoparticle formation to the depletion effect of macromolecular crowding. This study presents our idea to enhance the formation of DNA nanoparticles by macromolecular crowding, providing the first step towards a final solution to efficient gene therapy.

Functional analysis of coordinated cleavage in V(D)J recombination.

PubMed

Kim, D R; Oettinger, M A

1998-08-01

V(D)J recombination in vivo requires a pair of signals with distinct spacer elements of 12 and 23 bp that separate conserved heptamer and nonamer motifs. Cleavage in vitro by the RAG1 and RAG2 proteins can occur at individual signals when the reaction buffer contains Mn2+, but cleavage is restricted to substrates containing two signals when Mg2+ is the divalent cation. By using a novel V(D)J cleavage substrate, we show that while the RAG proteins alone establish a moderate preference for a 12/23 pair versus a 12/12 pair, a much stricter dependence of cleavage on the 12/23 signal pair is produced by the inclusion of HMG1 and competitor double-stranded DNA. The competitor DNA serves to inhibit the cleavage of substrates carrying a 12/12 or 23/23 pair, as well as the cutting at individual signals in 12/23 substrates. We show that a 23/33 pair is more efficiently recombined than a 12/33 pair, suggesting that the 12/23 rule can be generalized to a requirement for spacers that differ from each other by a single helical turn. Furthermore, we suggest that a fixed spatial orientation of signals is required for cleavage. In general, the same signal variants that can be cleaved singly can function under conditions in which a signal pair is required. However, a chemically modified substrate with one noncleavable signal enables us to show that formation of a functional cleavage complex is mechanistically separable from the cleavage reaction itself and that although cleavage requires a pair of signals, cutting does not have to occur simultaneously at both. The implications of these results are discussed with respect to the mechanism of V(D)J recombination and the generation of chromosomal translocations.

The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure

PubMed Central

Tobé, Sylvia; Heams, Thomas; Vergne, Jacques; Hervé, Guy; Maurel, Marie-Christine

2005-01-01

The discovery of ribozymes strengthened the RNA world hypothesis, which assumes that these precursors of modern life both stored information and acted as catalysts. For the first time among extensive studies on ribozymes, we have investigated the influence of hydrostatic pressure on the hairpin ribozyme catalytic activity. High pressures are of interest when studying life under extreme conditions and may help to understand the behavior of macromolecules at the origins of life. Kinetic studies of the hairpin ribozyme self-cleavage were performed under high hydrostatic pressure. The activation volume of the reaction (34 ± 5 ml/mol) calculated from these experiments is of the same order of magnitude as those of common protein enzymes, and reflects an important compaction of the RNA molecule during catalysis, associated to a water release. Kinetic studies were also carried out under osmotic pressure and confirmed this interpretation and the involvement of water movements (78 ± 4 water molecules per RNA molecule). Taken together, these results are consistent with structural studies indicating that loops A and B of the ribozyme come into close contact during the formation of the transition state. While validating baro-biochemistry as an efficient tool for investigating dynamics at work during RNA catalysis, these results provide a complementary view of ribozyme catalytic mechanisms. PMID:15870387

Cystic fibrosis airway secretions exhibit mucin hyperconcentration and increased osmotic pressure

PubMed Central

Henderson, Ashley G.; Ehre, Camille; Button, Brian; Abdullah, Lubna H.; Cai, Li-Heng; Leigh, Margaret W.; DeMaria, Genevieve C.; Matsui, Hiro; Donaldson, Scott H.; Davis, C. William; Sheehan, John K.; Boucher, Richard C.; Kesimer, Mehmet

2014-01-01

The pathogenesis of mucoinfective lung disease in cystic fibrosis (CF) patients likely involves poor mucus clearance. A recent model of mucus clearance predicts that mucus flow depends on the relative mucin concentration of the mucus layer compared with that of the periciliary layer; however, mucin concentrations have been difficult to measure in CF secretions. Here, we have shown that the concentration of mucin in CF sputum is low when measured by immunologically based techniques, and mass spectrometric analyses of CF mucins revealed mucin cleavage at antibody recognition sites. Using physical size exclusion chromatography/differential refractometry (SEC/dRI) techniques, we determined that mucin concentrations in CF secretions were higher than those in normal secretions. Measurements of partial osmotic pressures revealed that the partial osmotic pressure of CF sputum and the retained mucus in excised CF lungs were substantially greater than the partial osmotic pressure of normal secretions. Our data reveal that mucin concentration cannot be accurately measured immunologically in proteolytically active CF secretions; mucins are hyperconcentrated in CF secretions; and CF secretion osmotic pressures predict mucus layer–dependent osmotic compression of the periciliary liquid layer in CF lungs. Consequently, mucin hypersecretion likely produces mucus stasis, which contributes to key infectious and inflammatory components of CF lung disease. PMID:24892808

Design principles for high–pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hölzl, Christoph; Horinek, Dominik, E-mail: dominik.horinek@ur.de; Kibies, Patrick

Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures – while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatmentmore » of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute’s response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.« less

Hairpin ribozyme cleavage catalyzed by aminoglycoside antibiotics and the polyamine spermine in the absence of metal ions.

PubMed Central

Earnshaw, D J; Gait, M J

1998-01-01

The hairpin ribozyme is a small catalytic RNA that achieves an active configuration by docking of its two helical domains in an antiparallel fashion. Both docking and subsequent cleavage are dependent on the presence of divalent metal ions, such as magnesium, but there is no evidence to date for direct participation of such ions in the chemical cleavage step. We show that aminoglycoside antibiotics inhibit cleavage of the hairpin ribozyme in the presence of metal ions with the most effective being 5-epi-sisomicin and neomycin B. In contrast, in the absence of metal ions, a number of aminoglycoside antibiotics at 10 mM concentration promote hairpin cleavage with rates only 13-20-fold lower than the magnesium-dependent reaction. We show that neomycin B competes with metal ions by ion replacement with the postively charged amino groups of the antibiotic. In addition, we show that the polyamine spermine at 10 mM promotes efficient hairpin cleavage with rates similar to the magnesium-dependent reaction. Low concentrations of either spermine or the shorter polyamine spermidine synergize with 5 mM magnesium ions to boost cleavage rates considerably. In contrast, at 500 microM magnesium ions, 4 mM spermine, but not spermidine, boosts the cleavage rate. The results have significance both in understanding the role of ions in hairpin ribozyme cleavage and in potential therapeutic applications in mammalian cells. PMID:9837982

Constitutive α- and β-secretase cleavages of the amyloid precursor protein are partially coupled in neurons, but not in frequently used cell lines.

PubMed

Colombo, Alessio; Wang, Huanhuan; Kuhn, Peer-Hendrik; Page, Richard; Kremmer, Elisabeth; Dempsey, Peter J; Crawford, Howard C; Lichtenthaler, Stefan F

2013-01-01

Proteolytic cleavage of the amyloid precursor protein (APP) by the two proteases α- and β-secretases controls the generation of the amyloid β peptide (Aβ), a key player in Alzheimer's disease pathogenesis. The α-secretase ADAM10 and the β-secretase BACE1 have opposite effects on Aβ generation and are assumed to compete for APP as a substrate, such that their cleavages are inversely coupled. This concept was mainly demonstrated in studies using activation or overexpression of α- and β-secretases. Here, we report that this inverse coupling is not seen to the same extent upon inhibition of the endogenous proteases. Genetic and pharmacological inhibition of ADAM10 and BACE1 revealed that the endogenous, constitutive α-secretase cleavage of APP is largely uncoupled from β-secretase cleavage and Aβ generation in neuroglioma H4 cells and in neuronally differentiated SH-SY5Y cells. In contrast, inverse coupling was observed in primary cortical neurons. However, this coupling was not bidirectional. Inhibition of BACE1 increased ADAM10 cleavage of APP, but a reduction of ADAM10 activity did not increase the BACE1 cleavage of APP in the neurons. Our analysis shows that the inverse coupling of the endogenous α- and β-secretase cleavages depends on the cellular model and suggests that a reduction of ADAM10 activity is unlikely to increase the AD risk through increased β-secretase cleavage. Copyright © 2012 Elsevier Inc. All rights reserved.

Intermolecular cleavage by UmuD-like mutagenesis proteins

PubMed Central

McDonald, John P.; Frank, Ekaterina G.; Levine, Arthur S.; Woodgate, Roger

1998-01-01

The activity of a number of proteins is regulated by self-processing reactions. Elegant examples are the cleavage of the prokaryotic LexA and λCI transcriptional repressors and the UmuD-like mutagenesis proteins. Various studies support the hypothesis that LexA and λCI cleavage reactions are predominantly intramolecular in nature. The recently described crystal structure of the Escherichia coli UmuD′ protein (the posttranslational cleavage product of the UmuD protein) suggests, however, that the region of the protein corresponding to the cleavage site is at least 50 Å away from the catalytic active site. We considered the possibility, therefore, that the UmuD-like proteins might undergo self-processing that, in contrast to LexA and λCI, occurs via an intermolecular rather than intramolecular reaction. To test this hypothesis, we introduced into E. coli compatible plasmids with mutations at either the cleavage or the catalytic site of three UmuD-like proteins. Cleavage of these proteins only occurs in the presence of both plasmids, indicating that the reaction is indeed intermolecular in nature. Furthermore, this intermolecular reaction is completely dependent upon the multifunctional RecA protein and leads to the restoration of cellular mutagenesis in nonmutable E. coli strains. Intermolecular cleavage of a biotinylated UmuD active site mutant was also observed in vitro in the presence of the wild-type UmuD′ protein, indicating that in addition to the intact UmuD protein, the normal cleavage product (UmuD′) can also act as a classical enzyme. PMID:9465040

Pressure Distribution in a Squeeze Film Spherical Bearing with Rough Surfaces Lubricated by an Ellis Fluid

NASA Astrophysics Data System (ADS)

Jurczak, P.; Falicki, J.

2016-08-01

In this paper, the solution to a problem of pressure distribution in a curvilinear squeeze film spherical bearing is considered. The equations of motion of an Ellis pseudo-plastic fluid are presented. Using Christensen's stochastic model of rough surfaces, different forms of Reynolds equation for various types of surface roughness pattern are obtained. The analytical solutions of these equations for the cases of externally pressurized bearing and squeeze film bearing are presented. Analytical solutions for the film pressure are found for the longitudinal and circumferential roughness patterns. As a result the formulae expressing pressure distribution in the clearance of bearing lubricated by an Ellis fluid was obtained. The numerical considerations for a spherical bearing are given in detail.

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

PubMed Central

Sripathi, Kamali N.; Tay, Wendy W.; Banáš, Pavel; Otyepka, Michal; Šponer, Jiří; Walter, Nils G.

2014-01-01

The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2′-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape. PMID:24854621

Reaction kinetics and oxidation products formation in the degradation of ciprofloxacin and ibuprofen by ferrate(VI).

PubMed

Zhou, Zhengwei; Jiang, Jia-Qian

2015-01-01

The treatment of ciprofloxacin (CIP) and ibuprofen (IBU) in test solutions by ferrate(VI) was investigated in this study. A series of jar test was performed in bench-scale at pH 6-9 and ferrate(VI) dose of 1-5 mg L(-1). Results demonstrated that ferrate(VI) removed CIP from test solutions efficiently, with above 70% of reduction under study conditions. In contrary, the removal rates of IBU were very low, less than 25% in all conditions. Raising ferrate(VI) dose improved the treatment performance, while the influence of solution pH was not significant at pH 6-9 compared with that of ferrate(VI) dose. In addition, kinetic studies of ferrate(VI) with both compounds were carried out at pH 8 and pH 9 (20 °C). Ferrate(VI) had a much higher reactivity with CIP than IBU at pH 8 and pH 9, with CIP's apparent second-order rate constants of 113.7±6.3 M(-1) s(-1) and 64.1±1.0 M(-1) s(-1), respectively. The rate constants of ferrate(VI) with IBU were less than 0.2 M(-1) s(-1) at pH 8 and pH 9. Furthermore, seven oxidation products (OPs) were formed during CIP degradation by ferrate(VI). The attack on the piperazinyl ring of the CIP by ferrate(VI) appeared to lead to the cleavage or hydroxylation of the rings, and the attack on the quinolone moiety by ferrate(VI) might lead to the cleavage of the double bond at the six-member heterocyclic ring. No OPs of IBU were detected during ferrate(VI) oxidation due to very small part of IBU was degraded by ferrate(VI). Copyright © 2014 Elsevier Ltd. All rights reserved.

Application of Newton's method to the postbuckling of rings under pressure loadings

NASA Technical Reports Server (NTRS)

Thurston, Gaylen A.

1989-01-01

The postbuckling response of circular rings (or long cylinders) is examined. The rings are subjected to four types of external pressure loadings; each type of pressure is defined by its magnitude and direction at points on the buckled ring. Newton's method is applied to the nonlinear differential equations of the exact inextensional theory for the ring problem. A zeroth approximation for the solution of the nonlinear equations, based on the mode shape corresponding to the first buckling pressure, is derived in closed form for each of the four types of pressure. The zeroth approximation is used to start the iteration cycle in Newton's method to compute numerical solutions of the nonlinear equations. The zeroth approximations for the postbuckling pressure-deflection curves are compared with the converged solutions from Newton's method and with similar results reported in the literature.

Pretest fracture evaluation of the NESC-1 spinning-cylinder experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keeney, J.A.; Bass, B.R.; Williams, P.T.

This paper describes a pretest fracture analysis of the cylinder specimen being used in the Network for Evaluating Steel Components (NESC) large-scale spinning-cylinder project (NESC-1). Organized as an international forum to exchange information on procedures for structural integrity assessment, to collaborate on specific projects, and to promote the harmonization of international standards, the NESC is currently focusing on a research project funded by United Kingdom Health and Safety Executive (HSE) to study the total process of structural integrity assessments of aged reactor pressure vessels (RPVs) containing subclad cracks. The intent is to have the problem studied by a wide rangemore » of organizations involved in RPV safety assessment. In this project, important safety assessment issues are being investigated by inspection and analysis of a spinning cylinder test which was performed at the AEA Technology facility at Risley, UK. Thermoelastic-plastic analyses were carried out for a clad cylinder model with a 74-mm-deep through-clad inner-surface crack. For this loading, the analytical results indicate that cleavage initiation may be achieved. The intervention of warm prestressing and loss of constraint may make cleavage initiation difficult to achieve in the heat-affected zone (HAZ) and near-HAZ regions.« less

In situ and theoretical studies for the dissociation of water on an active Ni/CeO2 catalyst: importance of strong metal-support interactions for the cleavage of O-H bonds.

PubMed

Carrasco, Javier; López-Durán, David; Liu, Zongyuan; Duchoň, Tomáš; Evans, Jaime; Senanayake, Sanjaya D; Crumlin, Ethan J; Matolín, Vladimir; Rodríguez, José A; Ganduglia-Pirovano, M Verónica

2015-03-23

Water dissociation is crucial in many catalytic reactions on oxide-supported transition-metal catalysts. Supported by experimental and density-functional theory results, the effect of the support on OH bond cleavage activity is elucidated for nickel/ceria systems. Ambient-pressure O 1s photoemission spectra at low Ni loadings on CeO2 (111) reveal a substantially larger amount of OH groups as compared to the bare support. Computed activation energy barriers for water dissociation show an enhanced reactivity of Ni adatoms on CeO2 (111) compared with pyramidal Ni4 particles with one Ni atom not in contact with the support, and extended Ni(111) surfaces. At the origin of this support effect is the ability of ceria to stabilize oxidized Ni(2+) species by accommodating electrons in localized f-states. The fast dissociation of water on Ni/CeO2 has a dramatic effect on the activity and stability of this system as a catalyst for the water-gas shift and ethanol steam reforming reactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

In-situ and theoretical studies for the dissociation of water on an active Ni/CeO₂ catalyst: Importance of strong metal-support interactions for the cleavage of O-H bonds

DOE PAGES

Carrasco, Javier; Rodriguez, Jose A.; Lopez-Duran, David; ...

2015-03-23

Water dissociation is crucial in many catalytic reactions on oxide-supported transition-metal catalysts. Here, supported by experimental and density-functional theory results, we elucidate the effect of the support on O-H bond cleavage activity for nickel/ceria systems. Ambient-pressure O1s photoemission spectra at low Ni loadings on CeO₂(111) reveal a substantially larger amount of OH groups as compared to the bare support. Our computed activation energy barriers for water dissociation show an enhanced reactivity of Ni adatoms on CeO₂(111) compared with pyramidal Ni₄ particles with one Ni atom not in contact with the support, and extended Ni(111) surfaces. At the origin of thismore » support effect is the ability of ceria to stabilize oxidized Ni²⁺ species by accommodating electrons in localized f-states. The fast dissociation of water on Ni/CeO₂ has a dramatic effect on the activity and stability of this system as a catalyst for the water-gas shift and ethanol steam reforming reactions.« less

Superacid Catalyzed Coal Conversion Chemistry. 1st and 2nd Quarterly Technical Progress Reports, September 1, 1983-March 30, 1984.

DOE R&D Accomplishments Database

Olah, G. A.

1984-01-01

In our laboratories we have previously developed a mild coal conversion process. This involves the use of a superacid system consisting of HF and BF{sub 3} in presence of hydrogen and/or a hydrogen donor solvent. In order to understand the chemistry involved in the process of depolymerization of coal by the HF:BF{sub 3}:H{sub 2} system we are carrying out a systematic study of a number of coal model compounds. The model compounds selected for present study have two benzene rings connected with various bridging units such as alkylidene, ether, sulfide etc. From studies so far carried out it appears that high pyridine extractibilities achieved by treating coal at temperature below 100 degrees C results from the cleavage of bridges such as present in bibenzyl, diphenyl methane, dibenzyl ether, dibenzyl sulfide etc. On the other hand the increased cyclohexane extractibility and distillability observed at relatively higher temperatures and hydrogen pressures reflects the hydrogenation and cleavage of the aromatic backbone in coal structure similar to what is seen in the conversion of model compounds such as biphenyl, diphenyl ether, diphenyl sulfide, anthracene, etc.

The Role of the Pressure in the Partial Regularity Theory for Weak Solutions of the Navier-Stokes Equations

NASA Astrophysics Data System (ADS)

Chamorro, Diego; Lemarié-Rieusset, Pierre-Gilles; Mayoufi, Kawther

2018-04-01

We study the role of the pressure in the partial regularity theory for weak solutions of the Navier-Stokes equations. By introducing the notion of dissipative solutions, due to D uchon and R obert (Nonlinearity 13:249-255, 2000), we will provide a generalization of the Caffarelli, Kohn and Nirenberg theory. Our approach sheels new light on the role of the pressure in this theory in connection to Serrin's local regularity criterion.

Fluid Lavage of Open Wounds (FLOW): A Multicenter, Blinded, Factorial Trial Comparing Alternative Irrigating Solutions and Pressures in Patients with Open Fractures

DTIC Science & Technology

2013-10-01

Multicenter, Blinded, Factorial Trial Comparing Alternative Irrigating Solutions and Pressures in Patients with Open Fractures PRINCIPAL...Solutions and Pressures in Patients with Open Fractures 5b. GRANT NUMBER W81XWH-12-1-0530 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Kyle J. Jeray...important initial step in preventing infection in open fractures . However, there is little clinical evidence as to the best irrigation methods and additives

Specific Cleavage of the Nucleoprotein of Fish Rhabdovirus.

PubMed

Zhou, G-Z; Yi, Y-J; Chen, Z-Y; Zhang, Q-Y

2015-11-01

Siniperca chuatsi rhabdovirus (SCRV) is one of myriad rhabdoviruses recorded in fish. Preliminary data show that inhibition of the SCRV nucleoprotein (N) could significantly reduce the progeny virus titers in infected Epithelioma papulosum cyprinid (EPC) cells. Here, the authors propose that cleavage of the viral 47-kDa N protein is caspase-mediated based on caspase inhibition experiments, transient expression in EPC transfection, and analysis of cleavage sites. Cleavage of the SCRV N protein in culture was prevented by a pan-caspase inhibitor, z-VAD-FMK (z-Val-Ala-DL-Asp-fluoromethyl ketone). Subsequently, N was transiently expressed in EPC cells, the results of which indicated that the specific cleavage of N also occurred in the cells transfected with N-GFP plasmid. Several truncated fragments of the N gene were constructed and transiently transfected into EPC cells. Immunoblotting results indicated that D324 and D374 are the cleavage sites of N by caspases. The authors also found that z-VAD-FMK could inhibit the cytopathic effect in SCRV-infected EPC cells but not affect the production of infectious progeny, suggesting that the caspase-mediated cleavage of N protein is not required for in vitro SCRV replication. To the authors' knowledge, this is the first report on the cleavage of rhabdovirus proteins. © The Author(s) 2015.

Analysis of RNA Processing Reactions Using Cell Free Systems: 3' End Cleavage of Pre-mRNA Substrates in vitro

PubMed Central

Jablonski, Joseph; Clementz, Mark; Ryan, Kevin; Valente, Susana T.

2014-01-01

The 3’ end of mammalian mRNAs is not formed by abrupt termination of transcription by RNA polymerase II (RNPII). Instead, RNPII synthesizes precursor mRNA beyond the end of mature RNAs, and an active process of endonuclease activity is required at a specific site. Cleavage of the precursor RNA normally occurs 10-30 nt downstream from the consensus polyA site (AAUAAA) after the CA dinucleotides. Proteins from the cleavage complex, a multifactorial protein complex of approximately 800 kDa, accomplish this specific nuclease activity. Specific RNA sequences upstream and downstream of the polyA site control the recruitment of the cleavage complex. Immediately after cleavage, pre-mRNAs are polyadenylated by the polyA polymerase (PAP) to produce mature stable RNA messages. Processing of the 3’ end of an RNA transcript may be studied using cellular nuclear extracts with specific radiolabeled RNA substrates. In sum, a long 32P-labeled uncleaved precursor RNA is incubated with nuclear extracts in vitro, and cleavage is assessed by gel electrophoresis and autoradiography. When proper cleavage occurs, a shorter 5’ cleaved product is detected and quantified. Here, we describe the cleavage assay in detail using, as an example, the 3’ end processing of HIV-1 mRNAs. PMID:24835792

Characterization of Bleomycin-Mediated Cleavage of a Hairpin DNA Library

PubMed Central

Segerman, Zachary J.; Roy, Basab; Hecht, Sidney M.

2013-01-01

A study of BLM A5 was conducted using a previously isolated library of hairpin DNAs found to bind strongly to metal free BLM. The ability of Fe(II)•BLM to effect cleavage on both the 3' and 5'-arms of the hairpin DNAs was characterized. The strongly bound DNAs were found to be efficient substrates for Fe•BLM A5-mediated hairpin DNA cleavage. Surprisingly, the most prevalent site of BLM-mediated cleavage was found to be the 5′-AT-3′ dinucleotide sequence. This dinucleotide sequence, and other sequences generally not cleaved well by BLM when examined using arbitrarily chosen DNA substrates, were apparent when examining the library of ten hairpin DNAs. In total, 132 sites of DNA cleavage were produced by exposure of the hairpin DNA library to Fe•BLM A5. The existence of multiple sites of cleavage on both the 3′- and 5′-arms of the hairpin DNAs suggested that some of these might be double-strand cleavage events. Accordingly, an assay was developed with which to test the propensity of the hairpin DNAs to undergo double-strand DNA damage. One hairpin DNA was characterized using this method, and gave results consistent with earlier reports of double-strand DNA cleavage, but with a sequence selectivity different from those reported previously. PMID:23834496

Quantification of DNA cleavage specificity in Hi-C experiments.

PubMed

Meluzzi, Dario; Arya, Gaurav

2016-01-08

Hi-C experiments produce large numbers of DNA sequence read pairs that are typically analyzed to deduce genomewide interactions between arbitrary loci. A key step in these experiments is the cleavage of cross-linked chromatin with a restriction endonuclease. Although this cleavage should happen specifically at the enzyme's recognition sequence, an unknown proportion of cleavage events may involve other sequences, owing to the enzyme's star activity or to random DNA breakage. A quantitative estimation of these non-specific cleavages may enable simulating realistic Hi-C read pairs for validation of downstream analyses, monitoring the reproducibility of experimental conditions and investigating biophysical properties that correlate with DNA cleavage patterns. Here we describe a computational method for analyzing Hi-C read pairs to estimate the fractions of cleavages at different possible targets. The method relies on expressing an observed local target distribution downstream of aligned reads as a linear combination of known conditional local target distributions. We validated this method using Hi-C read pairs obtained by computer simulation. Application of the method to experimental Hi-C datasets from murine cells revealed interesting similarities and differences in patterns of cleavage across the various experiments considered. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Mechanisms of selective cleavage of C–O bonds in di-aryl ethers in aqueous phase

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Jiayue; Zhao, Chen; Mei, Donghai

2014-01-01

A novel route for cleaving the C-O aryl ether bonds of p-substituted H-, CH 3-, and OH- diphenyl ethers has been explored over Ni/SiO 2 catalysts at very mild conditions. The C-O bond of diphenyl ether is cleaved by parallel hydrogenolysis and hydrolysis (hydrogenolysis combined with HO* addition) on Ni. The rates as a function of H 2 pressure from 0 to 10 MPa indicate that the rate-determining step is the C-O bond cleavage on Ni. H* atoms compete with the organic reactant for adsorption leading to a maximum in the rate with increasing H 2 pressure. In contrast tomore » diphenyl ether, hydrogenolysis is the exclusive route for cleaving an ether C-O bond of di-p-tolyl ether to form p-cresol and toluene. 4,4'-dihydroxydiphenyl ether undergoes sequential surface hydrogenolysis, first to phenol and HOC 6H 4O* (adsorbed), which is then cleaved to phenol (C 6H 5O* with added H*) and H 2O (O* with two added H*) in a second step. Density function theory supports the operation of this pathway. Notably, addition of H* to HOC 6H 4O* is less favorable than a further hydrogenolytic C-O bond cleavage. The TOFs of three aryl ethers with Ni/SiO 2 in water followed the order 4,4'-dihydroxydiphenyl ether (69 h -1) > diphenyl ether (26 h -1) > di-p-tolyl ether (1.3 h -1), in line with the increasing apparent activation energies, ranging from 93 kJ∙mol -1 (4,4'-dihydroxydiphenyl ether) < diphenyl ether (98 kJ∙mol -1) to di-p-tolyl ether (105 kJ∙mol -1). D.M. thanks the support from the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and by the National Energy Research Scientific Computing Center (NERSC). EMSL is a national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and sponsored by DOE’s Office of Biological and Environmental Research.« less

Sequence specificity of the hammerhead ribozyme revisited; the NHH rule.

PubMed Central

Kore, A R; Vaish, N K; Kutzke, U; Eckstein, F

1998-01-01

The sequence specificity of hammerhead ribozyme cleavage has been re-evaluated with respect to the NUH rule. Contrary to previous reports it was found that substrates with GAC triplets were also cleaved. This was established in three different sequence contexts. The rate of cleavage under single turnover conditions was between 3 and 7% that of cleavage 3' of GUC. Specificity of cleavage of substrates containing a central A in the cleavable triplet can be described as NAH, where N can be any nucleotide and H any nucleotide but G. As cleavage 3' of NCH triplets has recently been described, the NUH rule can be reformulated to NHH. PMID:9722629

Effect of pressure fluctuations on Richtmyer-Meshkov coherent structures

NASA Astrophysics Data System (ADS)

Bhowmick, Aklant K.; Abarzhi, Snezhana

2016-11-01

We investigate the formation and evolution of Richtmyer Meshkov bubbles after the passage of a shock wave across a two fluid interface in the presence of pressure fluctuations. The fluids are ideal and incompressible and the pressure fluctuations are scale invariant in space and time, and are modeled by a power law time dependent acceleration field with exponent -2. Solutions indicate sensitivity to pressure fluctuations. In the linear regime, the growth of curvature and bubble velocity is linear. The growth rate is dominated by the initial velocity for weak pressure fluctuations, and by the acceleration term for strong pressure fluctuations. In the non-linear regime, the bubble curvature is constant and the solutions form a one parameter family (parametrized by the bubble curvature). The solutions are shown to be convergent and asymptotically stable. The physical solution (stable fastest growing) is a flat bubble for small pressure fluctuations and a curved bubble for large pressure fluctuations. The velocity field (in the frame of references accounting for the background motion) involves intense motion of the fluids in a vicinity of the interface, effectively no motion of the fluids away from the interfaces, and formation of vortical structures at the interface. The work is supported by the US National Science Foundation.

Effect of pressure fluctuations on Richtmyer-Meshkov coherent structures

NASA Astrophysics Data System (ADS)

Bhowmick, Aklant K.; Abarzhi, Snezhana

2016-10-01

We investigate the formation and evolution of Richtmyer Meshkov bubbles after the passage of a shock wave across a two fluid interface in the presence of pressure fluctuations. The fluids are ideal and incompressible and the pressure fluctuations are scale invariant in space and time, and are modeled by a power law time dependent acceleration field with exponent -2. Solutions indicate sensitivity to pressure fluctuations. In the linear regime, the growth of curvature and bubble velocity is linear. The growth rate is dominated by the initial velocity for weak pressure fluctuations, and by the acceleration term for strong pressure fluctuations. In the non-linear regime, the bubble curvature is constant and the solutions form a one parameter family (parametrized by the bubble curvature). The solutions are shown to be convergent and asymptotically stable. The physical solution (stable fastest growing) is a flat bubble for small pressure fluctuations and a curved bubble for large pressure fluctuations. The velocity field (in the frame of references accounting for the background motion) involves intense motion of the fluids in a vicinity of the interface, effectively no motion of the fluids away from the interfaces, and formation of vortical structures at the interface. The work is supported by the US National Science Foundation.

An Inexpensive High Pressure Optical Absorption Cell for IR-VIS-UV Studies.

ERIC Educational Resources Information Center

Rodgers, V. E.; Angell, C. A.

1983-01-01

Describes an optical cell, suitable for high-pressure studies between at least -130 and +150 degrees Celsius, which may be assembled for about $50. Discusses experimental demonstration of principles involved when using the apparatus, including effects of pressure on coordination of ions in solution and on reaction rates in solution. (JN)

Development of Quenching-qPCR (Q-Q) assay for measuring absolute intracellular cleavage efficiency of ribozyme.

PubMed

Kim, Min Woo; Sun, Gwanggyu; Lee, Jung Hyuk; Kim, Byung-Gee

2018-06-01

Ribozyme (Rz) is a very attractive RNA molecule in metabolic engineering and synthetic biology fields where RNA processing is required as a control unit or ON/OFF signal for its cleavage reaction. In order to use Rz for such RNA processing, Rz must have highly active and specific catalytic activity. However, current methods for assessing the intracellular activity of Rz have limitations such as difficulty in handling and inaccuracies in the evaluation of correct cleavage activity. In this paper, we proposed a simple method to accurately measure the "intracellular cleavage efficiency" of Rz. This method deactivates unwanted activity of Rz which may consistently occur after cell lysis using DNA quenching method, and calculates the cleavage efficiency by analyzing the cleaved fraction of mRNA by Rz from the total amount of mRNA containing Rz via quantitative real-time PCR (qPCR). The proposed method was applied to measure "intracellular cleavage efficiency" of sTRSV, a representative Rz, and its mutant, and their intracellular cleavage efficiencies were calculated as 89% and 93%, respectively. Copyright © 2018 Elsevier Inc. All rights reserved.

Resolution of model Holliday junctions by yeast endonuclease: effect of DNA structure and sequence.

PubMed Central

Parsons, C A; Murchie, A I; Lilley, D M; West, S C

1989-01-01

The resolution of Holliday junctions in DNA involves specific cleavage at or close to the site of the junction. A nuclease from Saccharomyces cerevisiae cleaves model Holliday junctions in vitro by the introduction of nicks in regions of duplex DNA adjacent to the crossover point. In previous studies [Parsons and West (1988) Cell, 52, 621-629] it was shown that cleavage occurred within homologous arm sequences with precise symmetry across the junction. In contrast, junctions with heterologous arm sequences were cleaved asymmetrically. In this work, we have studied the effect of sequence changes and base modification upon the site of cleavage. It is shown that the specificity of cleavage is unchanged providing that perfect homology is maintained between opposing arm sequences. However, in the absence of homology, cleavage depends upon sequence context and is affected by minor changes such as base modification. These data support the proposed mechanism for cleavage of a Holliday junction, which requires homologous alignment of arm sequences in an enzyme--DNA complex as a prerequisite for symmetrical cleavage by the yeast endonuclease. Images PMID:2653810

Mesotrypsin Has Evolved Four Unique Residues to Cleave Trypsin Inhibitors as Substrates.

PubMed

Alloy, Alexandre P; Kayode, Olumide; Wang, Ruiying; Hockla, Alexandra; Soares, Alexei S; Radisky, Evette S

2015-08-28

Human mesotrypsin is highly homologous to other mammalian trypsins, and yet it is functionally unique in possessing resistance to inhibition by canonical serine protease inhibitors and in cleaving these inhibitors as preferred substrates. Arg-193 and Ser-39 have been identified as contributors to the inhibitor resistance and cleavage capability of mesotrypsin, but it is not known whether these residues fully account for the unusual properties of mesotrypsin. Here, we use human cationic trypsin as a template for engineering a gain of catalytic function, assessing mutants containing mesotrypsin-like mutations for resistance to inhibition by bovine pancreatic trypsin inhibitor (BPTI) and amyloid precursor protein Kunitz protease inhibitor (APPI), and for the ability to hydrolyze these inhibitors as substrates. We find that Arg-193 and Ser-39 are sufficient to confer mesotrypsin-like resistance to inhibition; however, compared with mesotrypsin, the trypsin-Y39S/G193R double mutant remains 10-fold slower at hydrolyzing BPTI and 2.5-fold slower at hydrolyzing APPI. We identify two additional residues in mesotrypsin, Lys-74 and Asp-97, which in concert with Arg-193 and Ser-39 confer the full catalytic capability of mesotrypsin for proteolysis of BPTI and APPI. Novel crystal structures of trypsin mutants in complex with BPTI suggest that these four residues function cooperatively to favor conformational dynamics that assist in dissociation of cleaved inhibitors. Our results reveal that efficient inhibitor cleavage is a complex capability to which at least four spatially separated residues of mesotrypsin contribute. These findings suggest that inhibitor cleavage represents a functional adaptation of mesotrypsin that may have evolved in response to positive selection pressure. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Mesotrypsin has evolved four unique residues to cleave trypsin inhibitors as substrates [Mesotrypsin has evolved to cleave trypsin inhibitors as substrates using four unique residues

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alloy, Alexandre P.; Kayode, Olumide; Wang, Ruiying

Human mesotrypsin is highly homologous to other mammalian trypsins, and yet it is functionally unique in possessing resistance to inhibition by canonical serine protease inhibitors and in cleaving these inhibitors as preferred substrates. Arg-193 and Ser-39 have been identified as contributors to the inhibitor resistance and cleavage capability of mesotrypsin, but it is not known whether these residues fully account for the unusual properties of mesotrypsin. Here, we use human cationic trypsin as a template for engineering a gain of catalytic function, assessing mutants containing mesotrypsin-like mutations for resistance to inhibition by bovine pancreatic trypsin inhibitor (BPTI) and amyloid precursormore » protein Kunitz protease inhibitor (APPI), and for the ability to hydrolyze these inhibitors as substrates. We find that Arg-193 and Ser-39 are sufficient to confer mesotrypsin-like resistance to inhibition; however, compared with mesotrypsin, the trypsin-Y39S/G193R double mutant remains 10-fold slower at hydrolyzing BPTI and 2.5-fold slower at hydrolyzing APPI. We identify two additional residues in mesotrypsin, Lys-74 and Asp-97, which in concert with Arg-193 and Ser-39 confer the full catalytic capability of mesotrypsin for proteolysis of BPTI and APPI. Novel crystal structures of trypsin mutants in complex with BPTI suggest that these four residues function cooperatively to favor conformational dynamics that assist in dissociation of cleaved inhibitors. Our results reveal that efficient inhibitor cleavage is a complex capability to which at least four spatially separated residues of mesotrypsin contribute. As a result, these findings suggest that inhibitor cleavage represents a functional adaptation of mesotrypsin that may have evolved in response to positive selection pressure.« less

An Angiotensin I-Converting Enzyme Mutation (Y465D) Causes a Dramatic Increase in Blood ACE via Accelerated ACE Shedding

PubMed Central

Gordon, Kerry; Nesterovitch, Andrew B.; Lünsdorf, Heinrich; Chen, Zhenlong; Castellon, Maricela; Popova, Isolda A.; Kalinin, Sergey; Mendonca, Emma; Petukhov, Pavel A.; Schwartz, David E.

2011-01-01

Background Angiotensin I-converting enzyme (ACE) metabolizes a range of peptidic substrates and plays a key role in blood pressure regulation and vascular remodeling. Thus, elevated ACE levels may be associated with an increased risk for different cardiovascular or respiratory diseases. Previously, a striking familial elevation in blood ACE was explained by mutations in the ACE juxtamembrane region that enhanced the cleavage-secretion process. Recently, we found a family whose affected members had a 6-fold increase in blood ACE and a Tyr465Asp (Y465D) substitution, distal to the stalk region, in the N domain of ACE. Methodology/Principal Findings HEK and CHO cells expressing mutant (Tyr465Asp) ACE demonstrate a 3- and 8-fold increase, respectively, in the rate of ACE shedding compared to wild-type ACE. Conformational fingerprinting of mutant ACE demonstrated dramatic changes in ACE conformation in several different epitopes of ACE. Cell ELISA carried out on CHO-ACE cells also demonstrated significant changes in local ACE conformation, particularly proximal to the stalk region. However, the cleavage site of the mutant ACE - between Arg1203 and Ser1204 - was the same as that of WT ACE. The Y465D substitution is localized in the interface of the N-domain dimer (from the crystal structure) and abolishes a hydrogen bond between Tyr465 in one monomer and Asp462 in another. Conclusions/Significance The Y465D substitution results in dramatic increase in the rate of ACE shedding and is associated with significant local conformational changes in ACE. These changes could result in increased ACE dimerization and accessibility of the stalk region or the entire sACE, thus increasing the rate of cleavage by the putative ACE secretase (sheddase). PMID:21998728

Mesotrypsin has evolved four unique residues to cleave trypsin inhibitors as substrates [Mesotrypsin has evolved to cleave trypsin inhibitors as substrates using four unique residues

DOE PAGES

Alloy, Alexandre P.; Kayode, Olumide; Wang, Ruiying; ...

2015-07-14

Human mesotrypsin is highly homologous to other mammalian trypsins, and yet it is functionally unique in possessing resistance to inhibition by canonical serine protease inhibitors and in cleaving these inhibitors as preferred substrates. Arg-193 and Ser-39 have been identified as contributors to the inhibitor resistance and cleavage capability of mesotrypsin, but it is not known whether these residues fully account for the unusual properties of mesotrypsin. Here, we use human cationic trypsin as a template for engineering a gain of catalytic function, assessing mutants containing mesotrypsin-like mutations for resistance to inhibition by bovine pancreatic trypsin inhibitor (BPTI) and amyloid precursormore » protein Kunitz protease inhibitor (APPI), and for the ability to hydrolyze these inhibitors as substrates. We find that Arg-193 and Ser-39 are sufficient to confer mesotrypsin-like resistance to inhibition; however, compared with mesotrypsin, the trypsin-Y39S/G193R double mutant remains 10-fold slower at hydrolyzing BPTI and 2.5-fold slower at hydrolyzing APPI. We identify two additional residues in mesotrypsin, Lys-74 and Asp-97, which in concert with Arg-193 and Ser-39 confer the full catalytic capability of mesotrypsin for proteolysis of BPTI and APPI. Novel crystal structures of trypsin mutants in complex with BPTI suggest that these four residues function cooperatively to favor conformational dynamics that assist in dissociation of cleaved inhibitors. Our results reveal that efficient inhibitor cleavage is a complex capability to which at least four spatially separated residues of mesotrypsin contribute. As a result, these findings suggest that inhibitor cleavage represents a functional adaptation of mesotrypsin that may have evolved in response to positive selection pressure.« less

Degradation of chloramphenicol by potassium ferrate (VI) oxidation: kinetics and products.

PubMed

Zhou, Jia-Heng; Chen, Kai-Bo; Hong, Qian-Kun; Zeng, Fan-Cheng; Wang, Hong-Yu

2017-04-01

The oxidation of chloramphenicol (CAP) by potassium ferrate (VI) in test solution was studied in this paper. A series of jar tests were performed at bench scale with pH of 5-9 and molar ratio [VI/CAP] of 16.3:1-81.6:1. Results showed that raising VI dose could improve the treatment performance and the influence of solution pH was significant. VI is more reactive in neutral conditions, presenting the highest removal efficiency of CAP. The rate law for the oxidation of CAP by VI was first order with respect to each reactant, yielding an overall second-order reaction. Furthermore, five oxidation products were observed during CAP oxidation by VI. Results revealed that VI attacked the amide group of CAP, leading to the cleavage of the group, while benzene ring remained intact.

Pressure solution and microfracturing in primary oil migration, Upper Cretaceous Austin Chalk, Texas Gulf Coast

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chanchani, J.; Berg, R.R.; Lee, C.I.

1996-09-01

The Upper Cretaceous Austin Chalk is a well known source rock and fractured reservoir in the Gulf Coast. Production is mainly from tectonic fractures, and the mechanism by which oil migrated from the matrix into the fractures is poorly understood. Microfracturing due to oil generation offers a possible explanation for the mechanism of the primary migration of oil in the Austin Chalk. Petrographic study shows that the major components of the primary migration system are the solution seams and the associated microfractures. Pressure solution is manifest as centimeter to millimeter-scale solution seams and smaller microseams. The solution seams are compositesmore » formed by the superposition of the smaller microseams. A significant amount of organic matter was concentrated in the seams along with other insoluble residue. Swarms of horizontal microfractures, many of them filled with calcite and other residue, are associated with the seams. Vertical, tectonic fractures that constitute the reservoir porosity, intersect the solution seams. Pressure solution concentrated organic matter within the solution seams and oil was generated there. It is postulated that the accompanying increase in fluid volume raised the pore pressures and fractured the rock. The newly created microfractures were avenues for migration of fluids from the seams, perhaps by microfracture propagation.« less

Identification of Proteolytic Cleavage Sites of EphA2 by Membrane Type 1 Matrix Metalloproteinase on the Surface of Cancer Cells.

PubMed

Kikuchi, Keiji; Kozuka-Hata, Hiroko; Oyama, Masaaki; Seiki, Motoharu; Koshikawa, Naohiko

2018-01-01

Proteolytic cleavage of membrane proteins can alter their functions depending on the cleavage sites. We recently demonstrated that membrane type 1 matrix metalloproteinase (MT1-MMP ) converts the tumor suppressor EphA2 into an oncogenic signal transducer through EphA2 cleavage. The cleaved EphA2 fragment that remains at the cell surface may be a better target for cancer therapy than intact EphA2. To analyze the cleavage site(s) of EphA2, we purified the fragments from tumor cells expressing MT1-MMP and Myc- and 6× His-tagged EphA2 by two-step affinity purification . The purified fragment was digested with trypsin to generate proteolytic peptides , and the amino acid sequences of these peptides were determined by nano-LC-mass spectrometry to identify the MT1-MMP-mediated cleavage site(s) of EphA2.

Effect of Initiation Time of Hydrostatic Pressure Shock on Chromosome Set Doubling of Tetraploidization in Turbot Scophthalmus maximus.

PubMed

Zhu, Xiangping; Lin, Zhengmei; Wu, Zhihao; Li, Jiandong; You, Feng

2017-10-01

The objective of the study was to clarify the effects of initiation time on chromosome set doubling induced by hydrostatic pressure shock through nuclear phase fluorescent microscopy in turbot Scophthalmus maximus. The ratio of developmentally delayed embryo and chromosome counting was used to assess induction efficiency. For the embryos subjected to a pressure of 67.5 MPa for 6 min at prometaphase (A group), chromosomes recovered to the pre-treatment condition after 11-min recovering. The first nuclear division and cytokinesis proceeded normally. During the second cell cycle, chromosomes did not enter into metaphase after prometaphase, but spread around for about 13 min, then assembled together and formed a large nucleus without anaphase separation; the second nuclear division and cytokinesis was inhibited. The ratio of developmentally delayed embryo showed that the second mitosis of 78% A group embryo was inhibited. The result of chromosome counting showed that the tetraploidization rate of A group was 72%. For the embryos subjected to a pressure of 67.5 MPa for 6 min at anaphase (B group), chromosomes recovered to the pre-treatment condition after about 31-min recovering. Afterwards, one telophase nucleus formed without anaphase separation; the first nuclear division was inhibited. The time of the first cleavage furrow occurrence of B group embryos delayed 27 min compared with that of A group embryos. With the first cytokinesis proceeding normally, 81.3% B group embryos were at two-cell stage around the middle of the second cell cycle after treatment. Those embryos were one of the two blastomeres containing DNA and the other without DNA. The first nuclear division of those embryos was inhibited. During the third cell cycle after treatment, 65.2% of those abovementioned embryos were at four-cell stage, cytokinesis occurred in both blastomeres, and nuclear division only occurred in the blastomere containing DNA. Of those abovementioned embryos, 14.0% were at three-cell stage and cytokinesis only occurred in the blastomere containing DNA. The result of chromosome counting showed that the tetraploidization rate of B group was only 7%. To summarize what had been mentioned above, mechanisms on chromosome set doubling of tetraploid induction would be different with different initiation time of hydrostatic pressure treatment. Chromosome set doubling was mainly due to inhibition of the second mitosis when hydrostatic pressure treatment was performed at prometaphase. Otherwise, chromosome set doubling was mainly due to inhibition of the first nuclear division when hydrostatic pressure treatment was performed at anaphase. Induction efficiency of tetraploidization resulted from inhibition of the second cleavage was higher than which resulted from inhibition of the first nuclear division. This study was the first to reveal biological mechanisms on the two viewpoints of chromosome set doubling through effect of initiation time of hydrostatic pressure treatment on chromosome set doubling in tetraploid induction.

A thin-walled pressurized sphere exposed to external general corrosion and nonuniform heating

NASA Astrophysics Data System (ADS)

Sedova, Olga S.; Pronina, Yulia G.; Kuchin, Nikolai L.

2018-05-01

A thin-walled spherical shell subjected to simultaneous action of internal and external pressure, nonuniform heating and outside mechanochemical corrosion is considered. It is assumed that the shell is homogeneous, isotropic and linearly elastic. The rate of corrosion is linearly dependent on the equivalent stress, which is the sum of mechanical and temperature stress components. Paper presents a new analytical solution, which takes into account the effect of the internal and external pressure values themselves, not only their difference. At the same time, the new solution has a rather simple form as compared to the results based on the solution to the Lame problem for a thick-walled sphere under pressure. The solution obtained can serve as a benchmark for numerical analysis and for a qualitative forecast of durability of the vessel.

Generation of energy

DOEpatents

Kalina, Alexander I.

1984-01-01

A method of generating energy which comprises utilizing relatively lower temperature available heat to effect partial distillation of at least portion of a multicomponent working fluid stream at an intermediate pressure to generate working fluid fractions of differing compositions. The fractions are used to produce at least one main rich solution which is relatively enriched with respect to the lower boiling component, and to produce at least one lean solution which is relatively improverished with respect to the lower boiling component. The pressure of the main rich solution is increased whereafter it is evaporated to produce a charged gaseous main working fluid. The main working fluid is expanded to a low pressure level to release energy. The spent low pressure level working fluid is condensed in a main absorption stage by dissolving with cooling in the lean solution to regenerate an initial working fluid for reuse.

The action of the bacterial toxin microcin B17. Insight into the cleavage-religation reaction of DNA gyrase.

PubMed

Pierrat, Olivier A; Maxwell, Anthony

2003-09-12

We have examined the effects of the bacterial toxin microcin B17 (MccB17) on the reactions of Escherichia coli DNA gyrase. MccB17 slows down but does not completely inhibit the DNA supercoiling and relaxation reactions of gyrase. A kinetic analysis of the cleavage-religation equilibrium of gyrase was performed to determine the effect of the toxin on the forward (cleavage) and reverse (religation) reactions. A simple mechanism of two consecutive reversible reactions with a nicked DNA intermediate was used to simulate the kinetics of cleavage and religation. The action of MccB17 on the kinetics of cleavage and religation was compared with that of the quinolones ciprofloxacin and oxolinic acid. With relaxed DNA as substrate, only a small amount of gyrase cleavage complex is observed with MccB17 in the absence of ATP, whereas the presence of the nucleotide significantly enhances the effect of the toxin on both the cleavage and religation reactions. In contrast, ciprofloxacin, oxolinic acid, and Ca2+ show lesser dependence on ATP to stabilize the cleavage complex. MccB17 enhances the overall rate of DNA cleavage by increasing the forward rate constant (k2) of the second equilibrium. In contrast, ciprofloxacin increases the amount of cleaved DNA by a combined effect on the forward and reverse rate constants of both equilibria. Based on these results and on the observations that MccB17 only slowly inhibits the supercoiling and relaxation reactions, we suggest a model of the interaction of MccB17 with gyrase.

Single crystal growth, crystalline structure investigation and high-pressure behavior of impurity-free siderite (FeCO3)

NASA Astrophysics Data System (ADS)

Liang, Wen; Yin, Yuan; Li, Zeming; Li, Rui; Li, Lin; He, Yu; Dong, Haini; Li, Zengsheng; Yan, Shuai; Zhai, Shuangmeng; Li, Heping

2018-03-01

Single crystals of impurity-free siderite were grown successfully using high-temperature-pressure annealing. The size of crystals ranged up to 100 µm, and they exhibited a rhomboid shape upon cleavage along the (101) plane. The composition of Fe0.9988±0.0011CO3 was quantified using electron probe analysis. Accurate crystalline structural data were investigated by means of single crystal X-ray diffraction (XRD) and the unit cell dimensions obtained in the rhombohedral symmetry of the R\\bar {3}c space group were a = 4.6861(3) and c = 15.362(2), and the final R = 0.0499. Using in situ synchrotron XRD, the high-pressure behavior of impurity-free siderite was investigated up to 20 GPa at ambient temperature. The pressure-volume (P-V) EoS was fitted by a third-order Birch-Murnaghan equation, and the isothermal bulk modulus was K 0 = 97.5(11) GPa for K 0' = 4. High-pressure Raman spectroscopy was performed at up to 30 GPa at ambient temperature, and the Raman bands shifted as the increase of pressure ({{d/ν _i}}{{{d}P}} ) was determined. In combination with the high-pressure Raman results and the bulk modulus K 0, the mode Grüneisen parameters of each vibration were calculated. Meanwhile, high-temperature Raman spectroscopy was carried out at up to 300 °C and the Raman band shift ({{d/ν _i}}{{{d}t}} ) was also quantified.

Computational Investigation of the Performance and Back-Pressure Limits of a Hypersonic Inlet

NASA Technical Reports Server (NTRS)

Smart, Michael K.; White, Jeffery A.

2002-01-01

A computational analysis of Mach 6.2 operation of a hypersonic inlet with rectangular-to-elliptical shape transition has been performed. The results of the computations are compared with experimental data for cases with and without a manually imposed back-pressure. While the no-back-pressure numerical solutions match the general trends of the data, certain features observed in the experiments did not appear in the computational solutions. The reasons for these discrepancies are discussed and possible remedies are suggested. Most importantly, however, the computational analysis increased the understanding of the consequences of certain aspects of the inlet design. This will enable the performance of future inlets of this class to be improved. Computational solutions with back-pressure under-estimated the back-pressure limit observed in the experiments, but did supply significant insight into the character of highly back-pressured inlet flows.

Pressure in isochoric systems containing aqueous solutions at subzero Centigrade temperatures.

PubMed

Ukpai, Gideon; Năstase, Gabriel; Șerban, Alexandru; Rubinsky, Boris

2017-01-01

Preservation of biological materials at subzero Centigrade temperatures, cryopreservation, is important for the field of tissue engineering and organ transplantation. Our group is studying the use of isochoric (constant volume) systems of aqueous solution for cryopreservation. Previous studies measured the pressure-temperature relations in aqueous isochoric systems in the temperature range from 0°C to - 20°C. The goal of this study is to expand the pressure-temperature measurement beyond the range reported in previous publications. To expand the pressure-temperature measurements beyond the previous range, we have developed a new isochoric device capable of withstanding liquid nitrogen temperatures and pressures of up to 413 MPa. The device is instrumented with a pressure transducer than can monitor and record the pressures in the isochoric chamber in real time. Measurements were made in a temperature range from - 5°C to liquid nitrogen temperatures for various solutions of pure water and Me2SO (a chemical additive used for protection of biological materials in a frozen state and for vitrification (glass formation) of biological matter). Undissolved gaseous are is carefully removed from the system. Temperature-pressure data from - 5°C to liquid nitrogen temperature for pure water and other solutions are presented in this study. Following are examples of some, temperature-pressure values, that were measured in an isochoric system containing pure water: (- 20°C, 187 MPa); (-25°C, 216 MPa); (- 30°C, 242.3 MPa); (-180°C, 124 MPa). The data is consistent with the literature, which reports that the pressure and temperature at the triple point, between ice I, ice III and water is, - 21.993°C and 209.9 MPa, respectively. It was surprising to find that the pressure in the isochoric system increases at temperatures below the triple point and remains high to liquid nitrogen temperatures. Measurements of pressure-temperature relations in solutions of pure water and Me2SO in different concentrations show that, for concentrations in which vitrification is predicted, no increase in pressure was measured during rapid cooling to liquid nitrogen temperatures. However, ice formation either during cooling or warming to and from liquid nitrogen temperatures produced an increase in pressure. The data obtained in this study can be used to aid in the design of isochoric cryopreservation protocols. The results suggest that the pressure measurement is important in the design of "constant volume" systems and can provide a simple means to gain information on the occurrence of vitrification and devitrification during cryopreservation processes of aqueous solutions in an isochoric system.

CO dissociation and CO hydrogenation on smooth and ion-bombarded Pd(1 1 1): SFG and XPS spectroscopy at mbar pressures

NASA Astrophysics Data System (ADS)

Rupprechter, G.; Kaichev, V. V.; Unterhalt, H.; Morkel, M.; Bukhtiyarov, V. I.

2004-07-01

The CO dissociation probability on transition metals is often invoked to explain the product distribution (selectivity) of catalytic CO hydrogenation. Along these lines, we have investigated CO adsorption and dissociation on smooth and ion-bombarded Pd(1 1 1) at pressures up to 1 mbar using vibrational sum frequency generation (SFG) and X-ray photoelectron spectroscopy (XPS). Under high pressure, CO adsorbate structures were observed that were identical to high-coverage structures in UHV. On ion-bombarded surfaces an additional species was detected which was attributed to CO bridge bonded to defect (low-coordinated) sites. On both surfaces, no indications of CO dissociation were found even after hours of 0.1 mbar CO exposure. However, exposing CO/H 2 mixtures to ion-bombarded Pd(1 1 1) produced carbonaceous deposits suggesting CH xO species as precursors for CO bond cleavage and that the formation of CH xO is facilitated by surface defects. The relevance of the observations for CO hydrogenation on Pd catalysts is discussed.

Genetic Ablation of Fgf23 or Klotho Does not Modulate Experimental Heart Hypertrophy Induced by Pressure Overload.

PubMed

Slavic, Svetlana; Ford, Kristopher; Modert, Magalie; Becirovic, Amarela; Handschuh, Stephan; Baierl, Andreas; Katica, Nejla; Zeitz, Ute; Erben, Reinhold G; Andrukhova, Olena

2017-09-12

Left ventricular hypertrophy (LVH) ultimately leads to heart failure in conditions of increased cardiac pre- or afterload. The bone-derived phosphaturic and sodium-conserving hormone fibroblast growth factor-23 (FGF23) and its co-receptor Klotho have been implicated in the development of uremic LVH. Using transverse aortic constriction (TAC) in gene-targeted mouse models, we examine the role of Fgf23 and Klotho in cardiac hypertrophy and dysfunction induced by pressure overload. TAC profoundly increases serum intact Fgf23 due to increased cardiac and bony Fgf23 transcription and downregulation of Fgf23 cleavage. Aldosterone receptor blocker spironolactone normalizes serum intact Fgf23 levels after TAC by reducing bony Fgf23 transcription. Notably, genetic Fgf23 or Klotho deficiency does not influence TAC-induced hypertrophic remodelling, LV functional impairment, or LV fibrosis. Despite the profound, aldosterone-mediated increase in circulating intact Fgf23 after TAC, our data do not support an essential role of Fgf23 or Klotho in the pathophysiology of pressure overload-induced cardiac hypertrophy.

The Speed of Axial Propagation of a Cylindrical Bubble Through a Cylindrical Vortex

NASA Technical Reports Server (NTRS)

Shariff, Karim; Mansour, Nagi N. (Technical Monitor)

2002-01-01

Inspired by the rapid elongation of air columns injected into vortices by dolphins, we present an exact inviscid solution for the axial speed (assumed steady) of propagation of the tip of a semi-infinite cylindrical bubble along the axis of a cylindrical vortex. The bubble is assumed to be held at constant pressure by being connected to a reservoir, the lungs of the dolphin, say. For a given bubble pressure, there is a modest critical rotation rate above which steadily propagating bubbles exist. For a bubble at ambient pressure, the propagation speed of the bubble (relative to axial velocity within the vortex) varies between 0.5 and 0.6 of the maximum rotational speed of the vortex. Surprisingly, the bubble tip can propagate (almost as rapidly) even when the pressure minimum in the vortex core is greater than the bubble pressure; in this case, solutions exhibit a dimple on the nose of the bubble. A situation important for incipient vortex cavitation, and one which dolphins also demonstrate, is elongation of a free bubble, i.e., one whose internal pressure may vary. Under the assumption that the acceleration term is small (checked a posteriori), the steady solution is applied at each instant during the elongation. Three types of behavior are then possible depending on physical parameters and initial conditions: (A) Unabated elongation with slowly increasing bubble pressure, and nearly constant volume. Volume begins to decrease in the late stages. (B1) Elongation with decreasing bubble pressure. A limit point of the steady solution is encountered at a finite bubble length. (B2) Unabated elongation with decreasing bubble pressure and indefinite creation of volume. This is made possible by the existence of propagating solutions at bubble pressures below the minimum vortex pressure. As the bubble stretches, its radius initially decreases but then becomes constant; this is also observed in experiments on incipient vortex cavitation.

The genome-wide DNA sequence specificity of the anti-tumour drug bleomycin in human cells.

PubMed

Murray, Vincent; Chen, Jon K; Tanaka, Mark M

2016-07-01

The cancer chemotherapeutic agent, bleomycin, cleaves DNA at specific sites. For the first time, the genome-wide DNA sequence specificity of bleomycin breakage was determined in human cells. Utilising Illumina next-generation DNA sequencing techniques, over 200 million bleomycin cleavage sites were examined to elucidate the bleomycin genome-wide DNA selectivity. The genome-wide bleomycin cleavage data were analysed by four different methods to determine the cellular DNA sequence specificity of bleomycin strand breakage. For the most highly cleaved DNA sequences, the preferred site of bleomycin breakage was at 5'-GT* dinucleotide sequences (where the asterisk indicates the bleomycin cleavage site), with lesser cleavage at 5'-GC* dinucleotides. This investigation also determined longer bleomycin cleavage sequences, with preferred cleavage at 5'-GT*A and 5'- TGT* trinucleotide sequences, and 5'-TGT*A tetranucleotides. For cellular DNA, the hexanucleotide DNA sequence 5'-RTGT*AY (where R is a purine and Y is a pyrimidine) was the most highly cleaved DNA sequence. It was striking that alternating purine-pyrimidine sequences were highly cleaved by bleomycin. The highest intensity cleavage sites in cellular and purified DNA were very similar although there were some minor differences. Statistical nucleotide frequency analysis indicated a G nucleotide was present at the -3 position (relative to the cleavage site) in cellular DNA but was absent in purified DNA.

Enhancing Interleukin-6 and Interleukin-11 receptor cleavage.

PubMed

Lokau, Juliane; Wandel, Marieke; Garbers, Christoph

2017-04-01

Proteolytic cleavage of the membrane-bound Interleukin-6 receptor (IL-6R) by the metalloprotease ADAM17 releases an agonistic soluble form of the IL-6R (sIL-6R), which is responsible for the pro-inflammatory trans-signaling branch of the cytokine's activities. This proteolytic step, which is also called ectodomain shedding, is critically regulated by the cleavage site within the IL-6R stalk, because mutations or small deletions within this region are known to render the IL-6R irresponsive towards proteolysis. In the present study, we employed cleavage site profiling data of ADAM17 to generate an IL-6R with increased cleavage susceptibility. Using site-directed mutagenesis, we showed that the non-prime sites P3 and P2 and the prime site P1' were critical for this increase in proteolysis, whereas other positions within the cleavage site were of minor importance. Insertion of this optimized cleavage site into the stalk of the Interleukin-11 receptor (IL-11R) was not sufficient to enable ADAM17-mediated proteolysis, but transfer of different parts of the IL-6R stalk enabled shedding by ADAM17. These findings shed light on the cleavage site specificities of ADAM17 using a native substrate and reveal further differences in the proteolysis of IL-6R and IL-11R. Copyright © 2017 Elsevier Ltd. All rights reserved.

The large terminase DNA packaging motor grips DNA with its ATPase domain for cleavage by the flexible nuclease domain

PubMed Central

Hilbert, Brendan J.; Hayes, Janelle A.; Stone, Nicholas P.; Xu, Rui-Gang

2017-01-01

Abstract Many viruses use a powerful terminase motor to pump their genome inside an empty procapsid shell during virus maturation. The large terminase (TerL) protein contains both enzymatic activities necessary for packaging in such viruses: the adenosine triphosphatase (ATPase) that powers DNA translocation and an endonuclease that cleaves the concatemeric genome at both initiation and completion of genome packaging. However, how TerL binds DNA during translocation and cleavage remains mysterious. Here we investigate DNA binding and cleavage using TerL from the thermophilic phage P74-26. We report the structure of the P74-26 TerL nuclease domain, which allows us to model DNA binding in the nuclease active site. We screened a large panel of TerL variants for defects in binding and DNA cleavage, revealing that the ATPase domain is the primary site for DNA binding, and is required for nuclease activity. The nuclease domain is dispensable for DNA binding but residues lining the active site guide DNA for cleavage. Kinetic analysis of DNA cleavage suggests flexible tethering of the nuclease domains during DNA cleavage. We propose that interactions with the procapsid during DNA translocation conformationally restrict the nuclease domain, inhibiting cleavage; TerL release from the capsid upon completion of packaging unlocks the nuclease domains to cleave DNA. PMID:28082398

Site-specific Phosphorylation Protects Glycogen Synthase Kinase-3β from Calpain-mediated Truncation of Its N and C Termini*

PubMed Central

Ma, Shanshan; Liu, Shaojun; Huang, Qiaoying; Xie, Bo; Lai, Bingquan; Wang, Chong; Song, Bin; Li, Mingtao

2012-01-01

Glycogen synthase kinase-3β (GSK-3β), a key regulator of neuronal apoptosis, is inhibited by the phosphorylation of Ser-9/Ser-389 and was recently shown to be cleaved by calpain at the N terminus, leading to its subsequent activation. In this study calpain was found to cleave GSK-3β not only at the N terminus but also at the C terminus, and cleavage sites were identified at residues Thr-38–Thr-39 and Ile-384–Gln-385. Furthermore, the cleavage of GSK-3β occurred in tandem with Ser-9 dephosphorylation during cerebellar granule neuron apoptosis. Increasing Ser-9 phosphorylation of GSK-3β by inhibiting phosphatase 1/2A or pretreating with purified active Akt inhibited calpain-mediated cleavage of GSK-3β at both N and C termini, whereas non-phosphorylatable mutant GSK-3β S9A facilitated its cleavage. In contrast, Ser-389 phosphorylation selectively inhibited the cleavage of GSK-3β at the C terminus but not the N terminus. Calpain-mediated cleavage resulted in three truncated products, all of which contained an intact kinase domain: ΔN-GSK-3β (amino acids 39–420), ΔC-GSK-3β (amino acids 1–384), and ΔN/ΔC-GSK-3β (amino acids 39–384). All three truncated products showed increased kinase and pro-apoptotic activity, with ΔN/ΔC-GSK-3β being the most active form. This observation suggests that the GSK-3β C terminus acts as an autoinhibitory domain similar to the N terminus. Taken together, these findings demonstrate that calpain-mediated cleavage activates GSK-3β by removing its N- and C-terminal autoinhibitory domains and that Ser-9 phosphorylation inhibits the cleavage of GSK-3β at both termini. In contrast, Ser-389 phosphorylation inhibits only C-terminal cleavage but not N-terminal cleavage. These findings also identify a mechanism by which site-specific phosphorylation and calpain-mediated cleavage operate in concert to regulate GSK-3β activity. PMID:22496446

Site-specific phosphorylation protects glycogen synthase kinase-3β from calpain-mediated truncation of its N and C termini.

PubMed

Ma, Shanshan; Liu, Shaojun; Huang, Qiaoying; Xie, Bo; Lai, Bingquan; Wang, Chong; Song, Bin; Li, Mingtao

2012-06-29

Glycogen synthase kinase-3β (GSK-3β), a key regulator of neuronal apoptosis, is inhibited by the phosphorylation of Ser-9/Ser-389 and was recently shown to be cleaved by calpain at the N terminus, leading to its subsequent activation. In this study calpain was found to cleave GSK-3β not only at the N terminus but also at the C terminus, and cleavage sites were identified at residues Thr-38-Thr-39 and Ile-384-Gln-385. Furthermore, the cleavage of GSK-3β occurred in tandem with Ser-9 dephosphorylation during cerebellar granule neuron apoptosis. Increasing Ser-9 phosphorylation of GSK-3β by inhibiting phosphatase 1/2A or pretreating with purified active Akt inhibited calpain-mediated cleavage of GSK-3β at both N and C termini, whereas non-phosphorylatable mutant GSK-3β S9A facilitated its cleavage. In contrast, Ser-389 phosphorylation selectively inhibited the cleavage of GSK-3β at the C terminus but not the N terminus. Calpain-mediated cleavage resulted in three truncated products, all of which contained an intact kinase domain: ΔN-GSK-3β (amino acids 39-420), ΔC-GSK-3β (amino acids 1-384), and ΔN/ΔC-GSK-3β (amino acids 39-384). All three truncated products showed increased kinase and pro-apoptotic activity, with ΔN/ΔC-GSK-3β being the most active form. This observation suggests that the GSK-3β C terminus acts as an autoinhibitory domain similar to the N terminus. Taken together, these findings demonstrate that calpain-mediated cleavage activates GSK-3β by removing its N- and C-terminal autoinhibitory domains and that Ser-9 phosphorylation inhibits the cleavage of GSK-3β at both termini. In contrast, Ser-389 phosphorylation inhibits only C-terminal cleavage but not N-terminal cleavage. These findings also identify a mechanism by which site-specific phosphorylation and calpain-mediated cleavage operate in concert to regulate GSK-3β activity.

New analytical solutions to the two-phase water faucet problem

DOE PAGES

Zou, Ling; Zhao, Haihua; Zhang, Hongbin

2016-06-17

Here, the one-dimensional water faucet problem is one of the classical benchmark problems originally proposed by Ransom to study the two-fluid two-phase flow model. With certain simplifications, such as massless gas phase and no wall and interfacial frictions, analytical solutions had been previously obtained for the transient liquid velocity and void fraction distribution. The water faucet problem and its analytical solutions have been widely used for the purposes of code assessment, benchmark and numerical verifications. In our previous study, the Ransom’s solutions were used for the mesh convergence study of a high-resolution spatial discretization scheme. It was found that, atmore » the steady state, an anticipated second-order spatial accuracy could not be achieved, when compared to the existing Ransom’s analytical solutions. A further investigation showed that the existing analytical solutions do not actually satisfy the commonly used two-fluid single-pressure two-phase flow equations. In this work, we present a new set of analytical solutions of the water faucet problem at the steady state, considering the gas phase density’s effect on pressure distribution. This new set of analytical solutions are used for mesh convergence studies, from which anticipated second-order of accuracy is achieved for the 2nd order spatial discretization scheme. In addition, extended Ransom’s transient solutions for the gas phase velocity and pressure are derived, with the assumption of decoupled liquid and gas pressures. Numerical verifications on the extended Ransom’s solutions are also presented.« less

Free-Field Ground Shock Pressures from Buried Detonations in Saturated and Unsaturated Soils

DTIC Science & Technology

1983-05-01

pressures are, therefore, which is shown in Figure 4 and compared to the higher at various standoff distances, unsaturated soil solution and test data on...IK-82 an4 ?g-84 bombs. As can be seen, the hydrodynamic Instead of using a soil solution , the propaga- solution works much better and predicts much

Spectroscopic and thermodynamic properties of molecular hydrogen dissolved in water at pressures up to 200 MPa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Borysow, Jacek, E-mail: jborysow@mtu.edu; Rosso, Leonardo del; Celli, Milva

2014-04-28

We have measured the Raman Q-branch of hydrogen in a solution with water at a temperature of about 280 K and at pressures from 20 to 200 MPa. From a least-mean-square fitting analysis of the broad Raman Q-branch, we isolated the contributions from the four lowest individual roto-vibrational lines. The vibrational lines were narrower than the pure rotational Raman lines of hydrogen dissolved in water measured previously, but significantly larger than in the gas. The separations between these lines were found to be significantly smaller than in gaseous hydrogen and their widths were slightly increasing with pressure. The lines weremore » narrowing with increasing rotational quantum number. The Raman frequencies of all roto-vibrational lines were approaching the values of gas phase hydrogen with increasing pressure. Additionally, from the comparison of the integrated intensity signal of Q-branch of hydrogen to the integrated Raman signal of the water bending mode, we have obtained the concentration of hydrogen in a solution with water along the 280 K isotherm. Hydrogen solubility increases slowly with pressure, and no deviation from a smooth behaviour was observed, even reaching thermodynamic conditions very close to the transition to the stable hydrogen hydrate. The analysis of the relative hydrogen concentration in solution on the basis of a simple thermodynamic model has allowed us to obtain the molar volume for the hydrogen gas/water solution. Interestingly, the volume relative to one hydrogen molecule in solution does not decrease with pressure and, at high pressure, is larger than the volume pertinent to one molecule of water. This is in favour of the theory of hydrophobic solvation, for which a larger and more stable structure of the water molecules is expected around a solute molecule.« less

Spectroscopic and thermodynamic properties of molecular hydrogen dissolved in water at pressures up to 200 MPa.

PubMed

Borysow, Jacek; del Rosso, Leonardo; Celli, Milva; Moraldi, Massimo; Ulivi, Lorenzo

2014-04-28

We have measured the Raman Q-branch of hydrogen in a solution with water at a temperature of about 280 K and at pressures from 20 to 200 MPa. From a least-mean-square fitting analysis of the broad Raman Q-branch, we isolated the contributions from the four lowest individual roto-vibrational lines. The vibrational lines were narrower than the pure rotational Raman lines of hydrogen dissolved in water measured previously, but significantly larger than in the gas. The separations between these lines were found to be significantly smaller than in gaseous hydrogen and their widths were slightly increasing with pressure. The lines were narrowing with increasing rotational quantum number. The Raman frequencies of all roto-vibrational lines were approaching the values of gas phase hydrogen with increasing pressure. Additionally, from the comparison of the integrated intensity signal of Q-branch of hydrogen to the integrated Raman signal of the water bending mode, we have obtained the concentration of hydrogen in a solution with water along the 280 K isotherm. Hydrogen solubility increases slowly with pressure, and no deviation from a smooth behaviour was observed, even reaching thermodynamic conditions very close to the transition to the stable hydrogen hydrate. The analysis of the relative hydrogen concentration in solution on the basis of a simple thermodynamic model has allowed us to obtain the molar volume for the hydrogen gas/water solution. Interestingly, the volume relative to one hydrogen molecule in solution does not decrease with pressure and, at high pressure, is larger than the volume pertinent to one molecule of water. This is in favour of the theory of hydrophobic solvation, for which a larger and more stable structure of the water molecules is expected around a solute molecule.

Spectroscopic and thermodynamic properties of molecular hydrogen dissolved in water at pressures up to 200 MPa

NASA Astrophysics Data System (ADS)

Borysow, Jacek; del Rosso, Leonardo; Celli, Milva; Moraldi, Massimo; Ulivi, Lorenzo

2014-04-01

We have measured the Raman Q-branch of hydrogen in a solution with water at a temperature of about 280 K and at pressures from 20 to 200 MPa. From a least-mean-square fitting analysis of the broad Raman Q-branch, we isolated the contributions from the four lowest individual roto-vibrational lines. The vibrational lines were narrower than the pure rotational Raman lines of hydrogen dissolved in water measured previously, but significantly larger than in the gas. The separations between these lines were found to be significantly smaller than in gaseous hydrogen and their widths were slightly increasing with pressure. The lines were narrowing with increasing rotational quantum number. The Raman frequencies of all roto-vibrational lines were approaching the values of gas phase hydrogen with increasing pressure. Additionally, from the comparison of the integrated intensity signal of Q-branch of hydrogen to the integrated Raman signal of the water bending mode, we have obtained the concentration of hydrogen in a solution with water along the 280 K isotherm. Hydrogen solubility increases slowly with pressure, and no deviation from a smooth behaviour was observed, even reaching thermodynamic conditions very close to the transition to the stable hydrogen hydrate. The analysis of the relative hydrogen concentration in solution on the basis of a simple thermodynamic model has allowed us to obtain the molar volume for the hydrogen gas/water solution. Interestingly, the volume relative to one hydrogen molecule in solution does not decrease with pressure and, at high pressure, is larger than the volume pertinent to one molecule of water. This is in favour of the theory of hydrophobic solvation, for which a larger and more stable structure of the water molecules is expected around a solute molecule.

Superoxide Dismutase and Transcription Factor sox9 as Mediators of Tumor Suppression by mac25 (IGFBP-rp1) in Prostate Cancer Cells

DTIC Science & Technology

2006-10-01

6 SSC, 5 Denhardt’s solution, 0.1M NaPO4 (pH 7.2), 10mM sodium pyrophosphate, and 50mg/ml sonicated herring sperm DNA (Ulrich et al., 1984). 32P... retention of SOX9 expression. Apoptosis assay Apoptosis was assessed by demonstrating cleavage of PARP by Western blotting (Drivdahl et al., 2001...is the second leading cause of cancer deaths in men and the seventh cause of all cancer deaths (30,000 per year) [1]. From a treatment perspective

Directed hydroxyl radical probing of the rRNA neighborhood of ribosomal protein S13 using tethered Fe(II).

PubMed Central

Heilek, G M; Noller, H F

1996-01-01

Directed hydroxyl radical probing was used to probe the rRNA neighborhood around protein S13 in the 30S ribosomal subunit. The unique cysteine at position 84 of S13 served as a tethering site for attachment of Fe(II)-1-(p-bromoacetamidobenzyl)-EDTA. Derivatized S13 (Fe-C84-S13) was then assembled into 30S ribosomal subunits by in vitro reconstitution with 16S rRNA and a mixture of the remaining 30S subunit proteins. Hydroxyl radicals generated from the tethered Fe(II) resulted in cleavage of the RNA backbone in two localized regions of the 3' major domain of 16S rRNA. One region spans nt 1308-1333 and is close to a site previously crosslinked to S13. A second set of cleavages is found in the 950/1230 helix. Both regions have been implicated in binding of S13 by previous chemical footprinting studies using base-specific chemical probes and solution-based hydroxyl radical probing. These results place both regions of 16S rRNA in proximity to position C84 of S13 in the three-dimensional structure of the 30S ribosomal subunit. PMID:8718688

Highly Efficient Release of Glycopeptides from Hydrazide Beads by Hydroxylamine Assisted PNGase F Deglycosylation for N-Glycoproteome Analysis.

PubMed

Huang, Junfeng; Wan, Hao; Yao, Yating; Li, Jinan; Cheng, Kai; Mao, Jiawei; Chen, Jin; Wang, Yan; Qin, Hongqiang; Zhang, Weibing; Ye, Mingliang; Zou, Hanfa

2015-10-20

Selective enrichment of glycopeptides from complex sample followed by cleavage of N-glycans by PNGase F to expose an easily detectable mark on the former glycosylation sites has become the popular protocol for comprehensive glycoproteome analysis. On account of the high enrichment specificity, hydrazide chemistry based solid-phase extraction of N-linked glycopeptides technique has sparked numerous interests. However, the enzymatic release of glycopeptides captured by hydrazide beads through direct incubation of the beads with PNGase F is not efficient due to the inherent steric hindrance effect. In this study, we developed a hydroxylamine assisted PNGase F deglycosylation (HAPD) method using the hydroxylamine to release glycopeptides captured on the hydrazide beads through the cleavage of hydrazone bonds by transamination followed with the PNGase F deglycosylation of the released glycopeptides in the free solution. Because of the homogeneous condition for the deglycosylation, the recovery of deglycosylated peptides (deglycopeptides) was improved significantly. It was found that 27% more N-glycosylation sites were identified by the HAPD strategy compared with the conventional method. Moreover, the ratio of identified N-terminal glycosylated peptides was improved over 5-fold.

Catalysis and co-catalysis of bond cleavages in coal and coal analogs. Final report, August 1, 1990--January 31, 1994

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, B.

1994-05-01

In work prior to the inception of this project, the authors observed that mixtures of phenolic materials and polyalkoxyaromatic molecules were appreciably more effective in catalyzing the decompositions of di-2-naphthyl ether and of di-1-naphthyl sulfide in tetralin solutions at 450{degrees}C than were the phenols by themselves, even though the polyalkoxyaromatic molecules, in the absence of phenolic co- catalysts, show essentially no catalytic activity. This was of appreciable interest in coal research because dinapthyl ether and dinapthyl sulfide have been employed as model compounds for coals in studies aimed at cleaving ether and sulfide bonds similar to those in coals. Themore » authors proposed (R. K. Sharma, K. P. Raman, and B. Miller) that the mixed catalysts used in these studies catalyze cleavages of ether and sulfide bonds by means of a mechanism involving electron transfer from the polyalkoxyaromatics to the substrates, which are activated as electron acceptors by hydrogen bonding to phenols. Since phenols themselves are electron donors, they also proposed that the well known effects of phenols in catalyzing the conversion of coals are due to similar electron transfer mechanisms.« less

Poly(ethyl glyoxylate)-Poly(ethylene oxide) Nanoparticles: Stimuli-Responsive Drug Release via End-to-End Polyglyoxylate Depolymerization.

PubMed

Fan, Bo; Gillies, Elizabeth R

2017-08-07

The ability to disrupt polymer assemblies in response to specific stimuli provides the potential to release drugs selectively at certain sites or conditions in vivo. However, most stimuli-responsive delivery systems require many stimuli-initiated events to release drugs. "Self-immolative polymers" offer the potential to provide amplified responses to stimuli as they undergo complete end-to-end depolymerization following the cleavage of a single end-cap. Herein, linker end-caps were developed to conjugate self-immolative poly(ethyl glyoxylate) (PEtG) with poly(ethylene oxide) (PEO) to form amphiphilic block copolymers. These copolymers were self-assembled to form nanoparticles in aqueous solution. Cleavage of the linker end-caps were triggered by a thiol reducing agent, UV light, H 2 O 2 , and combinations of these stimuli, resulting in nanoparticle disintegration. Low stimuli concentrations were effective in rapidly disrupting the nanoparticles. Nile red, doxorubin, and curcumin were encapsulated into the nanoparticles and were selectively released upon application of the appropriate stimulus. The ability to tune the stimuli-responsiveness simply by changing the linker end-cap makes this new platform highly attractive for applications in drug delivery.

Dry-spraying of ascorbic acid or acetaminophen solutions with supercritical carbon dioxide

NASA Astrophysics Data System (ADS)

Wubbolts, F. E.; Bruinsma, O. S. L.; van Rosmalen, G. M.

1999-03-01

Carbon dioxide is a very poor solvent for many organic compounds, which makes it a good anti-solvent. When a solution is sprayed into carbon dioxide vapour the anti-solvent reduces the solubility within several tens of milliseconds and the solute precipitates. Two distinct regions can be identified, below and above the mixture critical pressure. Below this critical pressure the yield remains relatively low and the process is not well controlled. Above the critical pressure small crystals are obtained of about 2 μm with a yield of 90%.

New Insight into the Cleavage Reaction of Nostoc sp. Strain PCC 7120 Carotenoid Cleavage Dioxygenase in Natural and Nonnatural Carotenoids

PubMed Central

Heo, Jinsol; Kim, Se Hyeuk

2013-01-01

Carotenoid cleavage dioxygenases (CCDs) are enzymes that catalyze the oxidative cleavage of carotenoids at a specific double bond to generate apocarotenoids. In this study, we investigated the activity and substrate preferences of NSC3, a CCD of Nostoc sp. strain PCC 7120, in vivo and in vitro using natural and nonnatural carotenoid structures. NSC3 cleaved β-apo-8′-carotenal at 3 positions, C-13C-14, C-15C-15′, and C-13′C-14′, revealing a unique cleavage pattern. NSC3 cleaves the natural structure of carotenoids 4,4′-diaponeurosporene, 4,4′-diaponeurosporen-4′-al, 4,4′-diaponeurosporen-4′-oic acid, 4,4′-diapotorulene, and 4,4′-diapotorulen-4′-al to generate novel cleavage products (apo-14′-diaponeurosporenal, apo-13′-diaponeurosporenal, apo-10′-diaponeurosporenal, apo-14′-diapotorulenal, and apo-10′-diapotorulenal, respectively). The study of carotenoids with natural or nonnatural structures produced by using synthetic modules could provide information valuable for understanding the cleavage reactions or substrate preferences of other CCDs in vivo and in vitro. PMID:23524669

Identification of N-glycosylation in prolyl endoprotease from Aspergillus niger and evaluation of the enzyme for its possible application in proteomics.

PubMed

Sebela, Marek; Rehulka, Pavel; Kábrt, Jaromír; Rehulková, Helena; Ozdian, Tomás; Raus, Martin; Franc, Vojtech; Chmelík, Josef

2009-11-01

An acidic prolyl endoprotease from Aspergillus niger was isolated from the commercial product Brewers Clarex to evaluate its possible application in proteomics. The chromatographic purification yielded a single protein band in sodium dodecyl sulfate polyacrylamide gel electrophoresis providing an apparent molecular mass of 63 kDa and a broad peak (m/z 58,061) in linear matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) indicating the glycoprotein nature of the enzyme. Indeed, a colorimetric assessment with phenol and sulfuric acid showed the presence of neutral sugars (9% of weight). The subsequent treatment with N-glycosidase F released a variety of high-mannose type N-glycans, which were successfully detected using MALDI-TOF MS. MALDI-TOF/TOF tandem MS analysis of glycopeptides from a tryptic digest of prolyl endoprotease unraveled the identity of the N-glycosylation site in the primary structure. The data obtained also show that the enzyme is present in its processed form, i.e. without putative signal and propeptide parts. Spectrophotometric measurements demonstrated optimal activity at pH 4.0-4.5 and also high thermostability for the cleavage at the C-terminal part of proline residues. In-solution digestion of standard proteins (12-200 kDa) allowed to evaluate the cleavage specificity. The enzyme acts upon proline and alanine residues, but there is an additional minor cleavage at some other residues like Gly, Leu, Arg, Ser and Tyr. The digestion of a honeybee peptide comprising six proline residues (apidaecin 1A) led to the detection of specific peptides terminated by proline as it was confirmed by MALDI postsource decay analysis. Copyright 2009 John Wiley & Sons, Ltd.

Analytical methods to determine the comparative DNA binding studies of curcumin-Cu(II) complexes

NASA Astrophysics Data System (ADS)

Rajesh, Jegathalaprathaban; Rajasekaran, Marichamy; Rajagopal, Gurusamy; Athappan, Periakaruppan

2012-11-01

DNA interaction studies of two mononuclear [1:1(1); 1:2(2)] copper(II) complexes of curcumin have been studied. The interaction of these complexes with CT-DNA has been explored by physical methods to propose modes of DNA binding of the complexes. Absorption spectral titrations of complex 1 with CT-DNA shows a red-shift of 3 nm with the DNA binding affinity of Kb, 5.21 × 104 M-1 that are higher than that obtained for 2 (red-shift, 2 nm; Kb, 1.73 × 104 M-1) reveal that the binding occurs in grooves as a result of the interaction is via exterior phosphates. The CD spectra of these Cu(II) complexes show a red shift of 3-10 nm in the positive band with increase in intensities. This spectral change of induced CD due to the hydrophobic interaction of copper complexes with DNA is the characteristic of B to A conformational change. The EB displacement assay also reveals the same trend as observed in UV-Vis spectral titration. The addition of complexes 1 and 2 to the DNA bound ethidium bromide (EB) solutions causes an obvious reduction in emission intensities indicating that these complexes competitively bind to DNA with EB. The positive shift of both the Epc and E0' accompanied by reduction of peak currents in differential pulse voltammogram (DPV), upon adding different concentrations of DNA to the metal complexes, are obviously in favor of strong binding to DNA. The super coiled plasmid pUC18 DNA cleavage ability of Cu(II) complexes in the presence of reducing agent reveals the single strand DNA cleavage (ssDNA) is observed. The hydroxyl radical (HOrad ) and the singlet oxygen are believed to be the reactive species responsible for the cleavage.

Determining osmotic pressure of drug solutions by air humidity in equilibrium method.

PubMed

Zhan, Xiancheng; Li, Hui; Yu, Lan; Wei, Guocui; Li, Chengrong

2014-06-01

To establish a new osmotic pressure measuring method with a wide measuring range. The osmotic pressure of drug solutions is determined by measuring the relative air humidity in equilibrium with the solution. The freezing point osmometry is used as a control. The data obtained by the proposed method are comparable to those by the control method, and the measuring range of the proposed method is significantly wider than that of the control method. The proposed method is performed in an isothermal and equilibrium state, so it overcomes the defects of the freezing point and dew point osmometries which result from the heterothermal process in the measurement, and therefore is not limited to diluted solutions.

Theory for solubility in static systems

NASA Astrophysics Data System (ADS)

Gusev, Andrei A.; Suter, Ulrich W.

1991-06-01

A theory for the solubility of small particles in static structures has been developed. The distribution function of the solute in a frozen solid has been derived in analytical form for the quantum and the quasiclassical cases. The solubility at infinitesimal gas pressure (Henry's constant) as well as the pressure dependence of the solute concentration at elevated pressures has been found from the statistical equilibrium between the solute in the static matrix and the ideal-gas phase. The distribution function of a solute containing different particles has been evaluated in closed form. An application of the theory to the sorption of methane in the computed structures of glassy polycarbonate has resulted in a satisfactory agreement with experimental data.

Orion Service Module Reaction Control System Plume Impingement Analysis Using PLIMP/RAMP2

NASA Technical Reports Server (NTRS)

Wang, Xiao-Yen J.; Gati, Frank; Yuko, James R.; Motil, Brian J.; Lumpkin, Forrest E.

2009-01-01

The Orion Crew Exploration Vehicle Service Module Reaction Control System engine plume impingement was computed using the plume impingement program (PLIMP). PLIMP uses the plume solution from RAMP2, which is the refined version of the reacting and multiphase program (RAMP) code. The heating rate and pressure (force and moment) on surfaces or components of the Service Module were computed. The RAMP2 solution of the flow field inside the engine and the plume was compared with those computed using GASP, a computational fluid dynamics code, showing reasonable agreement. The computed heating rate and pressure using PLIMP were compared with the Reaction Control System plume model (RPM) solution and the plume impingement dynamics (PIDYN) solution. RPM uses the GASP-based plume solution, whereas PIDYN uses the SCARF plume solution. Three sets of the heating rate and pressure solutions agree well. Further thermal analysis on the avionic ring of the Service Module showed that thermal protection is necessary because of significant heating from the plume.

Dark energy fingerprints in the nonminimal Wu-Yang wormhole structure

NASA Astrophysics Data System (ADS)

Balakin, Alexander B.; Zayats, Alexei E.

2014-08-01

We discuss new exact solutions to nonminimally extended Einstein-Yang-Mills equations describing spherically symmetric static wormholes supported by the gauge field of the Wu-Yang type in a dark energy environment. We focus on the analysis of three types of exact solutions to the gravitational field equations. Solutions of the first type relate to the model, in which the dark energy is anisotropic; i.e., the radial and tangential pressures do not coincide. Solutions of the second type correspond to the isotropic pressure tensor; in particular, we discuss the exact solution, for which the dark energy is characterized by the equation of state for a string gas. Solutions of the third type describe the dark energy model with constant pressure and energy density. For the solutions of the third type, we consider in detail the problem of horizons and find constraints for the parameters of nonminimal coupling and for the constitutive parameters of the dark energy equation of state, which guarantee that the nonminimal wormholes are traversable.

Cleavage of nucleic acids

DOEpatents

Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor L.; Brow, Mary Ann D.; Dahlberg, James E.

2007-12-11

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Invasive cleavage of nucleic acids

DOEpatents

Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

1999-01-01

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Invasive cleavage of nucleic acids

DOEpatents

Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

2002-01-01

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Cleavage of nucleic acids

DOEpatents

Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow; Mary Ann D.; Dahlberg, James E.

2010-11-09

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Cleavage of nucleic acids

DOEpatents

Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

2000-01-01

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Solubility of crude oil in methane as a function of pressure and temperature

USGS Publications Warehouse

Price, L.C.; Wenger, L.M.; Ging, T.; Blount, C.W.

1983-01-01

The solubility of a 44?? API (0.806 sp. gr.) whole crude oil has been measured in methane with water present at temperatures of 50 to 250??C and pressures of 740 to 14,852 psi, as have the solubilities of two high molecular weight petroleum distillation fractions at temperatures of 50 to 250??C and pressures of 4482 to 25,266 psi. Both increases in pressure and temperature increase the solubility of crude oil and petroleum distillation fractions in methane, the effect of pressure being greater than that of temperature. Unexpectedly high solubility levels (0.5-1.5 grams of oil per liter of methane-at laboratory temperature and pressure) were measured at moderate conditions (50-200??C and 5076-14504 psi). Similar results were found for the petroleum distillation fractions, one of which was the highest molecular weight material of petroleum (material boiling above 266??C at 6 microns pressure). Unexpectedly mild conditions (100??C and 15,200 psi; 200??C and 7513 psi) resulted in cosolubility of crude oil and methane. Under these conditions, samples of the gas-rich phase gave solubility values of 4 to 5 g/l, or greater. Qualitative analyses of the crude-oil solute samples showed that at low pressure and temperature equilibration conditions, the solute condensate would be enriched in C5-C15 range hydrocarbons and in saturated hydrocarbons in the C15+ fraction. With increases in temperature and especially pressure, these tendencies were reversed, and the solute condensate became identical to the starting crude oil. The data of this study, compared to that of previous studies, shows that methane, with water present, has a much greater carrying capacity for crude oil than in dry systems. The presence of water also drastically lowers the temperature and pressure conditions required for cosolubility. The data of this and/or previous studies demonstrate that the addition of carbon dioxide, ethane, propane, or butane to methane also has a strong positive effect on crude oil solubility, as does the presence of fine grained rocks. The n-paraffin distributions (as well as the overall composition) of the solute condensates are controlled by the temperature and pressure of solution and exsolution, as well as by the composition of the original starting material. It appears quite possible that primary migration by gaseous solution could 'strip' a source rock of crude-oil like components leaving behind a bitumen totally unlike the migrated crude oil. The data of this study demonstrate previous criticisms of primary petroleum migration by gas solution are invalid; that primary migration by gaseous solution cannot occur because methane cannot dissolve sufficient volumes of crude oil or cannot dissolve the highest molecular weight components of petroleum (tars and asphaltenes). ?? 1983.

Leaching under Oxygen Pressure with Carbonate Solution Reduction by Hydrogen; LIXIVIATION OXYDANTE DES PECHBLENDES ET PRECIPITATION DE L'URANIUM PAR L'HYDROGENE. APPLICATION AUX MINERAIS PAUVRES FRANCAIS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balaceanu, J.C.; Coussemant, F.; Mouret, P.

1959-10-31

A study was made of the basic characteristics of the leaching with carbonate solution under oxygen pressure and of the catalytic hydrogen reduction of low-grade French ores. Pure U/sub 3/O/sub 8/ was used in the investigations on leaching. The effects of oxygen pressure, temperature, initial surface of the oxide, surfuce during the course of the reaction, and concentration of the carbonate solution were determined. It was shown that the heterogeneous reactions involve a constant surface and two steps. A pilot plant experiment was made on a number of low-grade French ores. With ores the leaching is not sensitive to oxygenmore » pressure. Dilute solutions of sodium uranyl carbonate are obtained from the leaching. The uranium can be precipitated as an oxide of a lower valent state by catalytic reduction with hydrogen. The study of this step was made on pure solutions of sodium uranyl carbonate in the presence of nickel and platinum catalysts. The reaction is strongly modified by the presence of even low concentrations of sodium bicarbonate. The reaction velocity increases with hydrogen pressure up to 5 atm, but then becomes independent of the pressure. The precipitation is accelerated by an increase in temperature. (J.S.R.)« less

The Efficiency of Dentin Sialoprotein-Phosphophoryn Processing Is Affected by Mutations Both Flanking and Distant from the Cleavage Site*

PubMed Central

Yang, Robert T.; Lim, Glendale L.; Dong, Zhihong; Lee, Arthur M.; Yee, Colin T.; Fuller, Robert S.; Ritchie, Helena H.

2013-01-01

Normal dentin mineralization requires two highly acidic proteins, dentin sialoprotein (DSP) and phosphophoryn (PP). DSP and PP are synthesized as part of a single secreted precursor, DSP-PP, which is conserved in marsupial and placental mammals. Using a baculovirus expression system, we previously found that DSP-PP is accurately cleaved into DSP and PP after secretion into medium by an endogenous, secreted, zinc-dependent Sf9 cell activity. Here we report that mutation of conserved residues near and distant from the G447↓D448 cleavage site in DSP-PP240 had dramatic effects on cleavage efficiency by the endogenous Sf9 cell processing enzyme. We found that: 1) mutation of residues flanking the cleavage site from P4 to P4′ blocked, impaired, or enhanced DSP-PP240 cleavage; 2) certain conserved amino acids distant from the cleavage site were important for precursor cleavage; 3) modification of the C terminus by appending a C-terminal tag altered the pattern of processing; and 4) mutations in DSP-PP240 had similar effects on cleavage by recombinant human BMP1, a candidate physiological processing enzyme, as was seen with the endogenous Sf9 cell activity. An analysis of a partial TLR1 cDNA from Sf9 cells indicates that residues that line the substrate-binding cleft of Sf9 TLR1 and human BMP1 are nearly perfectly conserved, offering an explanation of why Sf9 cells so accurately process mammalian DSP-PP. The fact that several mutations in DSP-PP240 significantly modified the amount of PP240 product generated from DSP-PP240 precursor protein cleavage suggests that such mutation may affect the mineralization process. PMID:23297400

The efficiency of dentin sialoprotein-phosphophoryn processing is affected by mutations both flanking and distant from the cleavage site.

PubMed

Yang, Robert T; Lim, Glendale L; Dong, Zhihong; Lee, Arthur M; Yee, Colin T; Fuller, Robert S; Ritchie, Helena H

2013-02-22

Normal dentin mineralization requires two highly acidic proteins, dentin sialoprotein (DSP) and phosphophoryn (PP). DSP and PP are synthesized as part of a single secreted precursor, DSP-PP, which is conserved in marsupial and placental mammals. Using a baculovirus expression system, we previously found that DSP-PP is accurately cleaved into DSP and PP after secretion into medium by an endogenous, secreted, zinc-dependent Sf9 cell activity. Here we report that mutation of conserved residues near and distant from the G(447)↓D(448) cleavage site in DSP-PP(240) had dramatic effects on cleavage efficiency by the endogenous Sf9 cell processing enzyme. We found that: 1) mutation of residues flanking the cleavage site from P(4) to P(4)' blocked, impaired, or enhanced DSP-PP(240) cleavage; 2) certain conserved amino acids distant from the cleavage site were important for precursor cleavage; 3) modification of the C terminus by appending a C-terminal tag altered the pattern of processing; and 4) mutations in DSP-PP(240) had similar effects on cleavage by recombinant human BMP1, a candidate physiological processing enzyme, as was seen with the endogenous Sf9 cell activity. An analysis of a partial TLR1 cDNA from Sf9 cells indicates that residues that line the substrate-binding cleft of Sf9 TLR1 and human BMP1 are nearly perfectly conserved, offering an explanation of why Sf9 cells so accurately process mammalian DSP-PP. The fact that several mutations in DSP-PP(240) significantly modified the amount of PP(240) product generated from DSP-PP(240) precursor protein cleavage suggests that such mutation may affect the mineralization process.

Crack stability and branching at interfaces

NASA Astrophysics Data System (ADS)

Thomson, Robb

1995-11-01

The various events that occur at a crack on an interface are explored, and described in terms of a simple graphical construction called the crack stability diagram. For simple Griffith cleavage in a homogeneous material, the stability diagram is a sector of a circle in the space of stress intensity factors, KI/KII. The Griffith circle is limited in both positive and negative KII directions by nonblunting dislocation emission on the cleavage plane. For a branching plane inclined at an angle to the original cleavage plane, both cleavage and emission (which blunts the crack) can be described as a balance between an elastic driving force and a lattice resistance for the event. We use an analytic expression obtained by Cotterell and Rice for cleavage, and show that it is an excellent approximation, but show that the lattice resistance includes a cornering resistance, in addition to the standard surface energy in the final cleavage criterion. Our discussion of the lattaice resistance is derived from simulations in two-dimensional hexagonal lattices with UBER force laws with a variety of shapes. Both branching cleavage and blunting emission can be described in terms of a stability diagram in the space of the remote stress intensity factors, and the competition between events on the initial cleavage plane and those on the branching plane can be described by overlays of the two appropriate stability diagrams. The popular criterion that kII=0 on the branching plane is explored for lattices and found to fail significantly, because the lattice stabilizes cleavage by the anisotropy of the surface energy. Also, in the lattice, dislocation emission must must always be considered as an alternative competing event to branching.

Effects of Single Amino Acid Substitution on the Collision-Induced Dissociation of Intact Protein Ions: Turkey Ovomucoid Third Domain

PubMed Central

Newton, Kelly A.; Pitteri, Sharon J.; Laskowski, Michael; McLuckey, Scott A.

2005-01-01

Expanded understanding of the factors that direct polypeptide ion fragmentation can lead to improved specificity in the use of tandem mass spectrometry for the identification and characterization of proteins. Like the fragmentation of peptide cations, the dissociation of whole protein cations shows several preferred cleavages, the likelihood for which is parent ion charge dependent. While such cleavages are often observed, they are far from universally observed, despite the presence of the residues known to promote them. Furthermore, cleavages at residues not noted to be common in a variety of proteins can be dominant for a particular protein or protein ion charge state. Motivated by the ability to study a small protein, turkey ovomucoid third domain, for which a variety of single amino acid variants are available, the effects of changing the identity of one amino acid in the protein sequence on its dissociation behavior were examined. In particular, changes in amino acids associated with C-terminal aspartic acid cleavage and N-terminal proline cleavage were emphasized. Consistent with previous studies, the product ion spectra were found to be dependent upon the parent ion charge state. Furthermore, the fraction of possible C-terminal aspartic acid cleavages observed to occur for this protein was significantly larger than the fraction of possible N-terminal proline cleavages. In fact, very little N-terminal proline cleavage was noted for the wild-type protein despite the presence of three proline residues in the protein. The addition/removal of proline and aspartic acids was studied along with changes in selected residues adjacent to proline residues. Evidence for inhibition of proline cleavage by the presence of nearby basic residues was noted, particularly if the basic residue was likely to be protonated. PMID:15473693

Specific detection of the cleavage activity of mycobacterial enzymes using a quantum dot based DNA nanosensor

NASA Astrophysics Data System (ADS)

Jepsen, Morten Leth; Harmsen, Charlotte; Godbole, Adwait Anand; Nagaraja, Valakunja; Knudsen, Birgitta R.; Ho, Yi-Ping

2015-12-01

We present a quantum dot based DNA nanosensor specifically targeting the cleavage step in the reaction cycle of the essential DNA-modifying enzyme, mycobacterial topoisomerase I. The design takes advantages of the unique photophysical properties of quantum dots to generate visible fluorescence recovery upon specific cleavage by mycobacterial topoisomerase I. This report, for the first time, demonstrates the possibility to quantify the cleavage activity of the mycobacterial enzyme without the pre-processing sample purification or post-processing signal amplification. The cleavage induced signal response has also proven reliable in biological matrices, such as whole cell extracts prepared from Escherichia coli and human Caco-2 cells. It is expected that the assay may contribute to the clinical diagnostics of bacterial diseases, as well as the evaluation of treatment outcomes.We present a quantum dot based DNA nanosensor specifically targeting the cleavage step in the reaction cycle of the essential DNA-modifying enzyme, mycobacterial topoisomerase I. The design takes advantages of the unique photophysical properties of quantum dots to generate visible fluorescence recovery upon specific cleavage by mycobacterial topoisomerase I. This report, for the first time, demonstrates the possibility to quantify the cleavage activity of the mycobacterial enzyme without the pre-processing sample purification or post-processing signal amplification. The cleavage induced signal response has also proven reliable in biological matrices, such as whole cell extracts prepared from Escherichia coli and human Caco-2 cells. It is expected that the assay may contribute to the clinical diagnostics of bacterial diseases, as well as the evaluation of treatment outcomes. Electronic supplementary information (ESI) available: Characterization of the QD-based DNA Nanosensor. See DOI: 10.1039/c5nr06326d

Effects of flexibility of the α2 chain of type I collagen on collagenase cleavage.

PubMed

Mekkat, Arya; Poppleton, Erik; An, Bo; Visse, Robert; Nagase, Hideaki; Kaplan, David L; Brodsky, Barbara; Lin, Yu-Shan

2018-05-12

Cleavage of collagen by collagenases such as matrix metalloproteinase 1 (MMP-1) is a key step in development, tissue remodeling, and tumor proliferation. The abundant heterotrimeric type I collagen composed of two α1(I) chains and one α2(I) chain is efficiently cleaved by MMP-1 at a unique site in the triple helix, a process which may be initiated by local unfolding within the peptide chains. Atypical homotrimers of the α1(I) chain, found in embryonic and cancer tissues, are very resistant to MMP cleavage. To investigate MMP-1 cleavage, recombinant homotrimers were constructed with sequences from the MMP cleavage regions of human collagen chains inserted into a host bacterial collagen protein system. All triple-helical constructs were cleaved by MMP-1, with α2(I) homotrimers cleaved efficiently at a rate similar to that seen for α1(II) and α1(III) homotrimers, while α1(I) homotrimers were cleaved at a much slower rate. The introduction of destabilizing Gly to Ser mutations within the human collagenase susceptible region of the α2(I) chain did not interfere with MMP-1 cleavage. Molecular dynamics simulations indicated a greater degree of transient hydrogen bond breaking in α2(I) homotrimers compared with α1(I) homotrimers at the MMP-1 cleavage site, and showed an extensive disruption of hydrogen bonding in the presence of a Gly to Ser mutation, consistent with chymotrypsin digestion results. This study indicates that α2(I) homotrimers are susceptible to MMP-1, proves that the presence of an α1(I) chain is not a requirement for α2(I) cleavage, and supports the importance of local unfolding of α2(I) in collagenase cleavage. Copyright © 2018. Published by Elsevier Inc.

A peptide-based approach to evaluate the adaptability of influenza A virus to humans based on its hemagglutinin proteolytic cleavage site

PubMed Central

Straus, Marco R.; Whittaker, Gary R.

2017-01-01

Cleavage activation of the hemagglutinin (HA) protein by host proteases is a crucial step in the infection process of influenza A viruses (IAV). However, IAV exists in eighteen different HA subtypes in nature and their cleavage sites vary considerably. There is uncertainty regarding which specific proteases activate a given HA in the human respiratory tract. Understanding the relationship between different HA subtypes and human-specific proteases will be valuable in assessing the pandemic potential of circulating viruses. Here we utilized fluorogenic peptides mimicking the HA cleavage motif of representative IAV strains causing disease in humans or of zoonotic/pandemic potential and tested them with a range of proteases known to be present in the human respiratory tract. Our results show that peptides from the H1, H2 and H3 subtypes are cleaved efficiently by a wide range of proteases including trypsin, matriptase, human airway tryptase (HAT), kallikrein-related peptidases 5 (KLK5) and 12 (KLK12) and plasmin. Regarding IAVs currently of concern for human adaptation, cleavage site peptides from H10 viruses showed very limited cleavage by respiratory tract proteases. Peptide mimics from H6 viruses showed broader cleavage by respiratory tract proteases, while H5, H7 and H9 subtypes showed variable cleavage; particularly matriptase appeared to be a key protease capable of activating IAVs. We also tested HA substrate specificity of Factor Xa, a protease required for HA cleavage in chicken embryos and relevant for influenza virus production in eggs. Overall our data provide novel tool allowing the assessment of human adaptation of IAV HA subtypes. PMID:28358853

Osmotic effects of polyethylene glycol.

PubMed

Schiller, L R; Emmett, M; Santa Ana, C A; Fordtran, J S

1988-04-01

Polyethylene glycol (PEG) has been used to increase the osmotic pressure of fluids used to cleanse the gastrointestinal tract. However, little is known about its osmotic activity. To investigate this activity systematically, solutions of PEG of differing molecular weights were made and subjected to measurement of osmolality by both freezing point depression and vapor pressure osmometry. Measured osmolality was increasingly greater than predicted from average molecular weight as PEG concentration increased. Measurement of sodium activity in NaCl/PEG solutions by means of an ion-selective electrode suggested that the higher than expected osmolality could be due in part to interactions that, in effect, sequestered water from the solution. Osmolality was consistently greater by freezing point osmometry than by vapor pressure osmometry. To determine which osmometry method reflected biologically relevant osmolality, normal subjects underwent steady-state total gut perfusion with an electrolyte solution containing 105 g/L of PEG 3350. This produced rectal effluent that was hypertonic by freezing point osmometry but isotonic by vapor pressure osmometry. Assuming that luminal fluid reaches osmotic equilibrium with plasma during total gut perfusion, this result suggests that the vapor pressure osmometer accurately reflects the biologically relevant osmolality of intestinal contents. We conclude that PEG exerts more of an osmotic effect than would be predicted from its molecular weight. This phenomenon may reflect interactions between PEG and water molecules that alter the physical chemistry of the solution and sequester water from the solution.

Site-Specific Pyrolysis Induced Cleavage at Aspartic Acid Residue in Peptides and Proteins

PubMed Central

Zhang, Shaofeng; Basile, Franco

2011-01-01

A simple and site-specific non-enzymatic method based on pyrolysis has been developed to cleave peptides and proteins. Pyrolytic cleavage was found to be specific and rapid as it induced a cleavage at the C-terminal side of aspartic acid in the temperature range of 220–250 °C in 10 seconds. Electrospray Ionization (ESI) mass spectrometry (MS) and tandem-MS (MS/MS) were used to characterize and identify pyrolysis cleavage products, confirming that sequence information is conserved after the pyrolysis process in both peptides and protein tested. This suggests that pyrolysis-induced cleavage at aspartyl residues can be used as a rapid protein digestion procedure for the generation of sequence specific protein biomarkers. PMID:17388620

Assessment of the accuracy of pharmacy students' compounded solutions using vapor pressure osmometry.

PubMed

Kolling, William M; McPherson, Timothy B

2013-04-12

OBJECTIVE. To assess the effectiveness of using a vapor pressure osmometer to measure the accuracy of pharmacy students' compounding skills. DESIGN. Students calculated the theoretical osmotic pressure (mmol/kg) of a solution as a pre-laboratory exercise, compared their calculations with actual values, and then attempted to determine the cause of any errors found. ASSESSMENT. After the introduction of the vapor pressure osmometer, the first-time pass rate for solution compounding has varied from 85% to 100%. Approximately 85% of students surveyed reported that the instrument was valuable as a teaching tool because it objectively assessed their work and provided immediate formative assessment. CONCLUSIONS. This simple technique of measuring compounding accuracy using a vapor pressure osmometer allowed students to see the importance of quality control and assessment in practice for both pharmacists and technicians.

Assessment of the Accuracy of Pharmacy Students’ Compounded Solutions Using Vapor Pressure Osmometry

PubMed Central

McPherson, Timothy B.

2013-01-01

Objective. To assess the effectiveness of using a vapor pressure osmometer to measure the accuracy of pharmacy students’ compounding skills. Design. Students calculated the theoretical osmotic pressure (mmol/kg) of a solution as a pre-laboratory exercise, compared their calculations with actual values, and then attempted to determine the cause of any errors found. Assessment. After the introduction of the vapor pressure osmometer, the first-time pass rate for solution compounding has varied from 85% to 100%. Approximately 85% of students surveyed reported that the instrument was valuable as a teaching tool because it objectively assessed their work and provided immediate formative assessment. Conclusions. This simple technique of measuring compounding accuracy using a vapor pressure osmometer allowed students to see the importance of quality control and assessment in practice for both pharmacists and technicians. PMID:23610476

Binding and cleavage of nucleic acids by the "hairpin" ribozyme.

PubMed

Chowrira, B M; Burke, J M

1991-09-03

The "hairpin" ribozyme derived from the minus strand of tobacco ringspot virus satellite RNA [(-)sTRSV] efficiently catalyzes sequence-specific RNA hydrolysis in trans (Feldstein et al., 1989; Hampel & Triz, 1989; Haseloff & Gerlach, 1989). The ribozyme does not cleave DNA. An RNA substrate analogue containing a single deoxyribonucleotide residue 5' to the cleavage site (A-1) binds to the ribozyme efficiently but cannot be cleaved. A DNA substrate analogue with a ribonucleotide at A-1 is cleaved; thus A-1 provides the only 2'-OH required for cleavage. These results support cleavage via a transphosphorylation mechanism initiated by attack of the 2'-OH of A-1 on the scissile phosphodiester. The ribozyme discriminates between DNA and RNA in both binding and cleavage. Results indicate that the 2'-OH of A-1 functions in complex stabilization as well as cleavage. The ribozyme efficiently cleaves a phosphorothioate diester linkage, suggesting that the pro-Rp oxygen at the scissile phosphodiester does not coordinate Mg2+.

Autotransporter structure reveals intra-barrel cleavage followed by conformational changes.

PubMed

Barnard, Travis J; Dautin, Nathalie; Lukacik, Petra; Bernstein, Harris D; Buchanan, Susan K

2007-12-01

Autotransporters are virulence factors produced by Gram-negative bacteria. They consist of two domains, an N-terminal 'passenger' domain and a C-terminal beta-domain. beta-domains form beta-barrel structures in the outer membrane while passenger domains are translocated into the extracellular space. In some autotransporters, the two domains are separated by proteolytic cleavage. Using X-ray crystallography, we solved the 2.7-A structure of the post-cleavage state of the beta-domain of EspP, an autotransporter produced by Escherichia coli strain O157:H7. The structure consists of a 12-stranded beta-barrel with the passenger domain-beta-domain cleavage junction located inside the barrel pore, approximately midway between the extracellular and periplasmic surfaces of the outer membrane. The structure reveals an unprecedented intra-barrel cleavage mechanism and suggests that two conformational changes occur in the beta-domain after cleavage, one conferring increased stability on the beta-domain and another restricting access to the barrel pore.

Timing of porosity destruction related to pressure-solution in limestones

NASA Astrophysics Data System (ADS)

Beaudoin, Nicolas; Koehn, Daniel; Aharonov, Einat; Boyce, Adrian; Billi, Andrea; Hamilton, Andrea

2017-04-01

Among effects that affect sedimentary rocks during diagenesis, pressure-solution has a very strong impact on the physical properties of rocks such as porosity and permeability. Intergranular pressure-solution results in rough or wavy surfaces called stylolites, which are very common in sedimentary basins, especially in limestone. According to the opening of the system, dissolved material can precipitate locally, leading to the destruction of the porosity around the stylolite. That can namely occur during the development of sedimentary stylolites, when no fracture of fault can allow dissolved material to flow away before precipitating again. This contribution aims at unravelling the depth at which the material dissolved during compaction precipitated in the open porosity, adding new data to discuss when pressure-solution starts to be an efficient mechanism of deformation in limestone during strata burial in sedimentary basins. We report the results of the study of cements that fill the fractures developed at the tips of stylolites in a sample of dolostone from the Jurassic Calcare Massiccio formation, coming from the Umbria-Marche area (Italy). The fractures developed from stylolite-induced stress, and the filling cements' oxygen and carbon isotopic values range between 10.6‰ to -6.1‰ PDB and -8.2‰ to -0.6‰ PDB, respectively. Considering a closed system, we use fractionation equations to convert δ18O values into temperature, which shows that the material put in solution during pressure-solution precipitated at a temperature ranging from 18°C to 39°C. Temperature range and geothermal gradient estimates suggest that the mechanism of pressure-solution actually was primarily active at depth as low as 1 km. In the studied sample, up to 18% of the original volume has been dissolved on stylolites, and that volume loss would have occurred in the first 2 km of the burial history. This natural example feeds the growing body of evidence that stylolites can start developing at a very low depth level. Our results suggest that the porosity in sedimentary rocks can be destroyed very early during burial, both by dissolution and by precipitation, which make the pressure-solution mechanism's impact on fluid flow in basin likely to be underestimated.

The Dimer Interfaces of Protease and Extra-Protease Domains Influence the Activation of Protease and the Specificity of GagPol Cleavage

PubMed Central

Pettit, Steven C.; Gulnik, Sergei; Everitt, Lori; Kaplan, Andrew H.

2003-01-01

Activation of the human immunodeficiency virus type 1 (HIV-1) protease is an essential step in viral replication. As is the case for all retroviral proteases, enzyme activation requires the formation of protease homodimers. However, little is known about the mechanisms by which retroviral proteases become active within their precursors. Using an in vitro expression system, we have examined the determinants of activation efficiency and the order of cleavage site processing for the protease of HIV-1 within the full-length GagPol precursor. Following activation, initial cleavage occurs between the viral p2 and nucleocapsid proteins. This is followed by cleavage of a novel site located in the transframe domain. Mutational analysis of the dimer interface of the protease produced differential effects on activation and specificity. A subset of mutations produced enhanced cleavage at the amino terminus of the protease, suggesting that, in the wild-type precursor, cleavages that liberate the protease are a relatively late event. Replacement of the proline residue at position 1 of the protease dimer interface resulted in altered cleavage of distal sites and suggests that this residue functions as a cis-directed specificity determinant. In summary, our studies indicate that interactions within the protease dimer interface help determine the order of precursor cleavage and contribute to the formation of extended-protease intermediates. Assembly domains within GagPol outside the protease domain also influence enzyme activation. PMID:12477841

The dimer interfaces of protease and extra-protease domains influence the activation of protease and the specificity of GagPol cleavage.

PubMed

Pettit, Steven C; Gulnik, Sergei; Everitt, Lori; Kaplan, Andrew H

2003-01-01

Activation of the human immunodeficiency virus type 1 (HIV-1) protease is an essential step in viral replication. As is the case for all retroviral proteases, enzyme activation requires the formation of protease homodimers. However, little is known about the mechanisms by which retroviral proteases become active within their precursors. Using an in vitro expression system, we have examined the determinants of activation efficiency and the order of cleavage site processing for the protease of HIV-1 within the full-length GagPol precursor. Following activation, initial cleavage occurs between the viral p2 and nucleocapsid proteins. This is followed by cleavage of a novel site located in the transframe domain. Mutational analysis of the dimer interface of the protease produced differential effects on activation and specificity. A subset of mutations produced enhanced cleavage at the amino terminus of the protease, suggesting that, in the wild-type precursor, cleavages that liberate the protease are a relatively late event. Replacement of the proline residue at position 1 of the protease dimer interface resulted in altered cleavage of distal sites and suggests that this residue functions as a cis-directed specificity determinant. In summary, our studies indicate that interactions within the protease dimer interface help determine the order of precursor cleavage and contribute to the formation of extended-protease intermediates. Assembly domains within GagPol outside the protease domain also influence enzyme activation.

A role for exosomes in the constitutive and stimulus-induced ectodomain cleavage of L1 and CD44.

PubMed

Stoeck, Alexander; Keller, Sascha; Riedle, Svenja; Sanderson, Michael P; Runz, Steffen; Le Naour, Francois; Gutwein, Paul; Ludwig, Andreas; Rubinstein, Eric; Altevogt, Peter

2006-02-01

Ectodomain shedding is a proteolytic mechanism by which transmembrane molecules are converted into a soluble form. Cleavage is mediated by metalloproteases and proceeds in a constitutive or inducible fashion. Although believed to be a cell-surface event, there is increasing evidence that cleavage can take place in intracellular compartments. However, it is unknown how cleaved soluble molecules get access to the extracellular space. By analysing L1 (CD171) and CD44 in ovarian carcinoma cells, we show in the present paper that the cleavage induced by ionomycin, APMA (4-aminophenylmercuric acetate) or MCD (methyl-beta-cyclodextrin) is initiated in an endosomal compartment that is subsequently released in the form of exosomes. Calcium influx augmented the release of exosomes containing functionally active forms of ADAM10 (a disintegrin and metalloprotease 10) and ADAM17 [TACE (tumour necrosis factor a-converting enzyme)] as well as CD44 and L1 cytoplasmic cleavage fragments. Cleavage could also proceed in released exosomes, but only depletion of ADAM10 by small interfering RNA blocked cleavage under constitutive and induced conditions. In contrast, cleavage of L1 in response to PMA occurred at the cell surface and was mediated by ADAM17. We conclude that different ADAMs are involved in distinct cellular compartments and that ADAM10 is responsible for shedding in vesicles. Our findings open up the possibility that exosomes serve as a platform for ectodomain shedding and as a vehicle for the cellular export of soluble molecules.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zou, Ling; Zhao, Haihua; Zhang, Hongbin

Here, the one-dimensional water faucet problem is one of the classical benchmark problems originally proposed by Ransom to study the two-fluid two-phase flow model. With certain simplifications, such as massless gas phase and no wall and interfacial frictions, analytical solutions had been previously obtained for the transient liquid velocity and void fraction distribution. The water faucet problem and its analytical solutions have been widely used for the purposes of code assessment, benchmark and numerical verifications. In our previous study, the Ransom’s solutions were used for the mesh convergence study of a high-resolution spatial discretization scheme. It was found that, atmore » the steady state, an anticipated second-order spatial accuracy could not be achieved, when compared to the existing Ransom’s analytical solutions. A further investigation showed that the existing analytical solutions do not actually satisfy the commonly used two-fluid single-pressure two-phase flow equations. In this work, we present a new set of analytical solutions of the water faucet problem at the steady state, considering the gas phase density’s effect on pressure distribution. This new set of analytical solutions are used for mesh convergence studies, from which anticipated second-order of accuracy is achieved for the 2nd order spatial discretization scheme. In addition, extended Ransom’s transient solutions for the gas phase velocity and pressure are derived, with the assumption of decoupled liquid and gas pressures. Numerical verifications on the extended Ransom’s solutions are also presented.« less

Thermal decomposition of the solid phase of nitromethane: ab initio molecular dynamics simulations.

PubMed

Chang, Jing; Lian, Peng; Wei, Dong-Qing; Chen, Xiang-Rong; Zhang, Qing-Ming; Gong, Zi-Zheng

2010-10-29

The Car-Parrinello molecular dynamics simulations were employed to investigate thermal decomposition of the solid nitromethane. It is found that it undergoes chemical decomposition at about 2200 K under ambient pressure. The initiation of reactions involves both proton transfer and commonly known C-N bond cleavage. About 75 species and 100 elementary reactions were observed with the final products being H2O, CO2, N2, and CNCNC. It represents the first complete simulation of solid-phase explosive reactions reported to date, which is of far-reaching implication for design and development of new energetic materials.

Uncatalyzed, Regioselective Oxidation of Saturated Hydrocarbons in an Ambient Corona Discharge.

PubMed

Ayrton, Stephen T; Jones, Rhys; Douce, David S; Morris, Mike R; Cooks, R Graham

2018-01-15

Atmospheric pressure chemical ionization (APCI) in air or in nitrogen with just traces of oxygen is shown to yield regioselective oxidation, dehydrogenation, and fragmentation of alkanes. Ozone is produced from ambient oxygen in situ and is responsible for the observed ion chemistry, which includes partial oxidation to ketones and C-C cleavage to give aldehydes. The mechanism of oxidation is explored and relationships between ionic species produced from individual alkanes are established. Unusually, dehydrogenation occurs by water loss. Competitive incorporation into the hydrocarbon chain of nitrogen versus oxygen as a mode of ionization is also demonstrated. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Environment-dependent interfacial strength using first principles thermodynamics: The example of the Pt-HfO2 interface

NASA Astrophysics Data System (ADS)

Cardona Quintero, Y.; Ramanath, Ganpati; Ramprasad, R.

2013-10-01

A parameter-free, quantitative, first-principles methodology to determine the environment-dependent interfacial strength of metal-metal oxide interfaces is presented. This approach uses the notion of the weakest link to identify the most likely cleavage plane, and first principles thermodynamics to calculate the average work of separation as a function of the environment (in this case, temperature and oxygen pressure). The method is applied to the case of the Pt-HfO2 interface, and it is shown that the computed environment-dependent work of separation is in quantitative agreement with available experimental data.

Influence of pressure on acoustic and rheologic parameters in water solutions of laury sodium sulfate

NASA Astrophysics Data System (ADS)

Khamidov, B. T.; Lezhnev, N. B.

1995-10-01

Ultrasonic velocity and density in water solutions of lauril sodium sulphate at frequency 36 MHz, within the range of pressures from 0.1 to 105 MPa at temperature T equals 293 K were measured. According to data of ultrasonic velocity and density under high pressures there was calculated adiabatic compressibility in objects studied from pressure. It was found out that the region of critical concentration of micelle formation has been shifted to the zone of much more low concentrations.

Transient isomers in the photodissociation of bromoiodomethane

NASA Astrophysics Data System (ADS)

Marcellini, Moreno; Nasedkin, Alexandr; Zietz, Burkhard; Petersson, Jonas; Vincent, Jonathan; Palazzetti, Federico; Malmerberg, Erik; Kong, Qingyu; Wulff, Michael; van der Spoel, David; Neutze, Richard; Davidsson, Jan

2018-04-01

The photochemistry of halomethanes is fascinating for the complex cascade reactions toward either the parent or newly synthesized molecules. Here, we address the structural rearrangement of photodissociated CH2IBr in methanol and cyclohexane, probed by time-resolved X-ray scattering in liquid solution. Upon selective laser cleavage of the C-I bond, we follow the reaction cascade of the two geminate geometrical isomers, CH2I-Br and CH2Br-I. Both meta-stable isomers decay on different time scales, mediated by solvent interaction, toward the original parent molecule. We observe the internal rearrangement of CH2Br-I to CH2I-Br in cyclohexane by extending the time window up to 3 μs. We track the photoproduct kinetics of CH2Br-I in methanol solution where only one isomer is observed. The effect of the polarity of solvent on the geminate recombination pathways is discussed.

On the anomalous adsorption of [Pd(edta)]2- at the water/Goethite interface: spectroscopic evidence for two types of surface complexes.

PubMed

Kaplun, Marina; Nordin, Agneta; Persson, Per

2008-01-15

The structure of palladium(II) ethylenediaminetetraacetate (edta) in aqueous solutions and its adsorption on the surface of goethite (alpha-FeOOH) were studied using extended X-ray absorption fine structure spectroscopy and attenuated total reflection Fourier transform infrared spectroscopy. The obtained results show that in aqueous solutions, Pd-edta exists as a 1:1 complex, [Pd(edta)]2-, with edta acting as a quadridentate ligand. On the surface of goethite, [Pd(edta)]2- forms two different types of complexes over a pH range of 3.40-8.12. At pH < 5, [Pd(edta)]2- adsorbs as an outer-sphere species with possible hydrogen bonding. At higher pH values, the formation of inner-sphere complexes of the cation-type sets in after a cleavage of one glycinate ring and the formation of an (edta)Pd-O-Fe linkage.

Novel fluorogenic probe for fluoride ion based on the fluoride-induced cleavage of tert-butyldimethylsilyl ether

NASA Astrophysics Data System (ADS)

Yang, Xiao-Feng

2007-06-01

A highly sensitive and selective fluorogenic probe for fluoride ion, 4-methylumbelliferyl tert-butyldimethylsilyl ether (4-MUTBS), was designed and synthesized. 4-MUTBS was a weakly fluorescent compound and was synthesized via the one-step reaction of 4-MU with tert-butyldimethylsilyl chloride. Upon incubation with fluoride ion in acetone-water solution (7:3, v/v), the Si-O bond of 4-MUTBS was cleaved and highly fluorescent 4-methylumbelliferone (4-MU) was released, hence leading to the fluorescence increase of the reaction solution. The fluorescence increase is linearly with fluoride concentration in the range 50-8000 nmol l -1 with a detection limit of 19 nmol l -1 (3 σ). Because of the high affinity of silicon toward fluoride ion, the proposed probe shows excellent selectivity toward fluoride ion over other anions. The method has been successfully applied to the fluoride determination in toothpaste and tap water samples.

Effect of hydrogen on fatigue crack propagation in vanadium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chung, D.W.; Stoloff, N.S.

The influence of hydrogen on fatigue crack propagation in unalloyed vanadium and several hydrogen-charged vanadium alloys has been investigated. The Paris--Erdogan equation, da/dN = C(..delta..K)/sup m/, was approximately obeyed for all alloys. Crack growth rates were lowest in vanadium and dilute vanadium-hydrogen alloys, and were not very sensitive to volume fraction of hydrides in more concentrated alloys. The crack growth exponent, m, is inversely proportional to the cyclic strain hardening rate, n', and the rate constant C is inversely proportional to the square of the ultimate tensile stress, sigma/sub UTS/: metallographic examination showed hydride reorientation and growth in the originallymore » hydrided alloys. No stress-induced hydrides were observed in V-H solid-solution alloys. Fractures in hydrided materials exhibited cleavage-like features, while striations were noted in unalloyed vanadium and dilute solid-solution alloys.« less

Effect of hydrogen on fatigue crack propagation in vanadium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chung, D.W.; Stoloff, N.S.

The influence of hydrogen on fatigue crack propagation in unalloyed vanadium and several hydrogen-charged vanadium alloys has been investigated. The Paris--Erdogan equation, da/dN = C(..delta..K)/sup m/, was approximately obeyed for all alloys. Crack growth rates were lowest in vanadium and dilute vanadium--hydrogen alloys, and were not very sensitive to volume fraction of hydrides in more concentrated alloys. The crack growth exponent, m, is inversely proportional to the cyclic strain hardening rate, n', and the rate constant C is inversely proportional to the square of the ultimate tensile stress, sigma/sub UTS/: metallographic examination showed hydride reorientation and growth in the originallymore » hydrided alloys. No stress-induced hydrides were observed in V--H solid-solution alloys. Fractures in hydrided materials exhibited cleavage-like features, while striations were noted in unalloyed vanadium and dilute solid-solution alloys.« less

Degradation chemistry of gemcitabine hydrochloride, a new antitumor agent.

PubMed

Anliker, S L; McClure, M S; Britton, T C; Stephan, E A; Maple, S R; Cooke, G G

1994-05-01

The anti-tumor agent gemcitabine hydrochloride, a beta-difluoronucleoside, is remarkably stable in the solid state. In 0.1 N HCI solution at 40 degrees C, deamination of gemcitabine occurs, yielding its uridine analogue. Approximately 86% of the initial gemcitabine remains after 4 weeks under these conditions. Cleavage of the N-glycosidic bond of gemcitabine or conversion to its alpha-anomer in 0.1 N HCI solution is not observed over a 4-week period. However, this work has shown that gemcitabine hydrochloride anomerizes in 0.1 N NaOH at 40 degrees C. Approximately 72% of the initial gemcitabine remains after 4 weeks under the basic conditions used. Uridine hydrolysis products are also formed under these conditions. The anormerization reaction, which is unusual under basic conditions, has been confirmed by characterization of the chromatographically isolated alpha-anomer by NMR and mass spectrometry. A mechanism involving an acyclic intermediate is proposed.

Second-wave hydrodissection for aspiration of cortical remains after femtosecond laser-assisted cataract surgery.

PubMed

Lake, Jonathan C; Boianovsky, Celso; de Faria Pacini, Thiago; Crema, Armando

2018-06-14

We describe the technique of second-wave hydrodissection (the first wave being the initial cortical cleaving hydrodissection) performed after the removal of the cataract nucleus in femtosecond laser-assisted cataract surgery. After femtosecond laser application, the cortex is typically found adhered to the anterior capsule. Under high magnification, a steady stream of a balanced salt solution is directed toward the anterior capsule using a hydrodissection cannula. Full cleavage of the remaining cortex is observed by noting the appearance of a dark inner circle by the capsulotomy edge once the balanced salt solution wave has separated the cortex from the capsule. Irrigation/aspiration (I/A) of the cortical remains after the second wave is faster than I/A without this step in femtosecond laser-assisted cataract surgery. Copyright © 2018 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

Tissue-specific expression of transgenic secreted ACE in vasculature can restore normal kidney functions, but not blood pressure, of Ace-/- mice.

PubMed

Chattopadhyay, Saurabh; Kessler, Sean P; Colucci, Juliana Almada; Yamashita, Michifumi; Senanayake, Preenie deS; Sen, Ganes C

2014-01-01

Angiotensin-converting enzyme (ACE) regulates normal blood pressure and fluid homeostasis through its action in the renin-angiotensin-system (RAS). Ace-/- mice are smaller in size, have low blood pressure and defective kidney structure and functions. All of these defects are cured by transgenic expression of somatic ACE (sACE) in vascular endothelial cells of Ace-/- mice. sACE is expressed on the surface of vascular endothelial cells and undergoes a natural cleavage secretion process to generate a soluble form in the body fluids. Both the tissue-bound and the soluble forms of ACE are enzymatically active, and generate the vasoactive octapeptide Angiotensin II (Ang II) with equal efficiency. To assess the relative physiological roles of the secreted and the cell-bound forms of ACE, we expressed, in the vascular endothelial cells of Ace-/- mice, the ectodomain of sACE, which corresponded to only the secreted form of ACE. Our results demonstrated that the secreted form of ACE could normalize kidney functions and RAS integrity, growth and development of Ace-/- mice, but not their blood pressure. This study clearly demonstrates that the secreted form of ACE cannot replace the tissue-bound ACE for maintaining normal blood pressure; a suitable balance between the tissue-bound and the soluble forms of ACE is essential for maintaining all physiological functions of ACE.

Tissue-Specific Expression of Transgenic Secreted ACE in Vasculature Can Restore Normal Kidney Functions, but Not Blood Pressure, of Ace-/- Mice

PubMed Central

Chattopadhyay, Saurabh; Kessler, Sean P.; Colucci, Juliana Almada; Yamashita, Michifumi; Senanayake, Preenie deS; Sen, Ganes C.

2014-01-01

Angiotensin-converting enzyme (ACE) regulates normal blood pressure and fluid homeostasis through its action in the renin-angiotensin-system (RAS). Ace-/- mice are smaller in size, have low blood pressure and defective kidney structure and functions. All of these defects are cured by transgenic expression of somatic ACE (sACE) in vascular endothelial cells of Ace-/- mice. sACE is expressed on the surface of vascular endothelial cells and undergoes a natural cleavage secretion process to generate a soluble form in the body fluids. Both the tissue-bound and the soluble forms of ACE are enzymatically active, and generate the vasoactive octapeptide Angiotensin II (Ang II) with equal efficiency. To assess the relative physiological roles of the secreted and the cell-bound forms of ACE, we expressed, in the vascular endothelial cells of Ace-/- mice, the ectodomain of sACE, which corresponded to only the secreted form of ACE. Our results demonstrated that the secreted form of ACE could normalize kidney functions and RAS integrity, growth and development of Ace-/- mice, but not their blood pressure. This study clearly demonstrates that the secreted form of ACE cannot replace the tissue-bound ACE for maintaining normal blood pressure; a suitable balance between the tissue-bound and the soluble forms of ACE is essential for maintaining all physiological functions of ACE. PMID:24475296

Pressure (Or No Royal Road)

ERIC Educational Resources Information Center

Bradley, J.

1973-01-01

Discusses how difficult the various problems of pressure, partial pressure, gas laws, and vapor pressure are for students. Outlines the evolution of the concept of pressure, the gas equation for a perfect gas, partial pressures, saturated vapor pressure, Avogadro's hypothesis, Raoult's law, and the vapor pressure of ideal solutions. (JR)

Formation of Pmel17 Amyloid Is Regulated by Juxtamembrane Metalloproteinase Cleavage, and the Resulting C-terminal Fragment Is a Substrate for γ-Secretase*

PubMed Central

Kummer, Markus P.; Maruyama, Hiroko; Huelsmann, Claudia; Baches, Sandra; Weggen, Sascha; Koo, Edward H.

2009-01-01

The formation of insoluble cross β-sheet amyloid is pathologically associated with disorders such as Alzheimer, Parkinson, and Huntington diseases. One exception is the nonpathological amyloid derived from the protein Pmel17 within melanosomes to generate melanin pigment. Here we show that the formation of insoluble MαC intracellular fragments of Pmel17, which are the direct precursors to Pmel17 amyloid, depends on a novel juxtamembrane cleavage at amino acid position 583 between the furin-like proprotein convertase cleavage site and the transmembrane domain. The resulting Pmel17 C-terminal fragment is then processed by the γ-secretase complex to release a short-lived intracellular domain fragment. Thus, by analogy to the Notch receptor, we designate this cleavage the S2 cleavage site, whereas γ-secretase mediates proteolysis at the intramembrane S3 site. Substitutions or deletions at this S2 cleavage site, the use of the metalloproteinase inhibitor TAPI-2, as well as small interfering RNA-mediated knock-down of the metalloproteinases ADAM10 and 17 reduced the formation of insoluble Pmel17 fragments. These results demonstrate that the release of the Pmel17 ectodomain, which is critical for melanin amyloidogenesis, is initiated by S2 cleavage at a juxtamembrane position. PMID:19047044

Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA.

PubMed

Dayeh, Daniel M; Cantara, William A; Kitzrow, Jonathan P; Musier-Forsyth, Karin; Nakanishi, Kotaro

2018-06-12

The recent identification and development of RNA-guided enzymes for programmable cleavage of target nucleic acids offers exciting possibilities for both therapeutic and biotechnological applications. However, critical challenges such as expensive guide RNAs and inability to predict the efficiency of target recognition, especially for highly-structured RNAs, remain to be addressed. Here, we introduce a programmable RNA restriction enzyme, based on a budding yeast Argonaute (AGO), programmed with cost-effective 23-nucleotide (nt) single-stranded DNAs as guides. DNA guides offer the advantage that diverse sequences can be easily designed and purchased, enabling high-throughput screening to identify optimal recognition sites in the target RNA. Using this DNA-induced slicing complex (DISC) programmed with 11 different guide DNAs designed to span the sequence, sites of cleavage were identified in the 352-nt human immunodeficiency virus type 1 5'-untranslated region. This assay, coupled with primer extension and capillary electrophoresis, allows detection and relative quantification of all DISC-cleavage sites simultaneously in a single reaction. Comparison between DISC cleavage and RNase H cleavage reveals that DISC not only cleaves solvent-exposed sites, but also sites that become more accessible upon DISC binding. This study demonstrates the advantages of the DISC system for programmable cleavage of highly-structured, functional RNAs.

Association of a peptoid ligand with the apical loop of pri-miR-21 inhibits cleavage by Drosha

PubMed Central

Diaz, Jason P.; Chirayil, Rachel; Chirayil, Sara; Tom, Martin; Head, Katie J.; Luebke, Kevin J.

2014-01-01

We have found a small molecule that specifically inhibits cleavage of a precursor to the oncogenic miRNA, miR-21, by the microprocessor complex of Drosha and DGCR8. We identified novel ligands for the apical loop of this precursor from a screen of 14,024 N-substituted oligoglycines (peptoids) in a microarray format. Eight distinct compounds with specific affinity were obtained, three having affinities for the targeted loop in the low micromolar range and greater than 15-fold discrimination against a closely related hairpin. One of these compounds completely inhibits microprocessor cleavage of a miR-21 primary transcript at concentrations at which cleavage of another miRNA primary transcript, pri-miR-16, is little affected. The apical loop of pri-miR-21, placed in the context of pri-miR-16, is sufficient for inhibition of microprocessor cleavage by the peptoid. This compound also inhibits cleavage of pri-miR-21 containing the pri-miR-16 apical loop, suggesting an additional site of association within pri-miR-21. The reported peptoid is the first example of a small molecule that inhibits microprocessor cleavage by binding to the apical loop of a pri-miRNA. PMID:24497550

Nicked-site substrates for a serine recombinase reveal enzyme-DNA communications and an essential tethering role of covalent enzyme-DNA linkages.

PubMed

Olorunniji, Femi J; McPherson, Arlene L; Pavlou, Hania J; McIlwraith, Michael J; Brazier, John A; Cosstick, Richard; Stark, W Marshall

2015-07-13

To analyse the mechanism and kinetics of DNA strand cleavages catalysed by the serine recombinase Tn3 resolvase, we made modified recombination sites with a single-strand nick in one of the two DNA strands. Resolvase acting on these sites cleaves the intact strand very rapidly, giving an abnormal half-site product which accumulates. We propose that these reactions mimic second-strand cleavage of an unmodified site. Cleavage occurs in a synapse of two sites, held together by a resolvase tetramer; cleavage at one site stimulates cleavage at the partner site. After cleavage of a nicked-site substrate, the half-site that is not covalently linked to a resolvase subunit dissociates rapidly from the synapse, destabilizing the entire complex. The covalent resolvase-DNA linkages in the natural reaction intermediate thus perform an essential DNA-tethering function. Chemical modifications of a nicked-site substrate at the positions of the scissile phosphodiesters result in abolition or inhibition of resolvase-mediated cleavage and effects on resolvase binding and synapsis, providing insight into the serine recombinase catalytic mechanism and how resolvase interacts with the substrate DNA. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Index of refraction, density, and solubility of ammonium iodide solutions at high pressure.

PubMed

Lamelas, F J

2013-03-07

An asymmetric moissanite anvil cell is used to study aqueous solutions of ammonium iodide at pressures up to 10 kbar. The index of refraction is measured using the rotating Fabry-Perot technique, with an accuracy of approximately 1%. The mass density and molar volume of the solutions are estimated using the measured index values, and the molar volume is used to predict the pressure dependence of the solubility. The solubility derived from the index of refraction measurements is shown to agree with that which is determined by direct observation of the onset of crystallization.

Pressure-driven laminar flow switching for rapid exchange of solution environment around surface adhered biological particles

PubMed Central

Allen, Peter B.; Milne, Graham; Doepker, Byron R.; Chiu, Daniel T.

2010-01-01

This paper describes a technique for rapidly exchanging the solution environment near a surface by displacing laminar flow fluid streams using sudden changes in applied pressure. The method employs off-chip solenoid valves to induce pressure changes, which is important in keeping the microfluidic design simple and the operation of the system robust. The performance of this technique is characterized using simulation and validated with experiments. This technique adds to the microfluidic tool box that is currently available for manipulating the solution environment around biological particles and molecules. PMID:20221560

Pressure in isochoric systems containing aqueous solutions at subzero Centigrade temperatures

PubMed Central

Șerban, Alexandru; Rubinsky, Boris

2017-01-01

Objective Preservation of biological materials at subzero Centigrade temperatures, cryopreservation, is important for the field of tissue engineering and organ transplantation. Our group is studying the use of isochoric (constant volume) systems of aqueous solution for cryopreservation. Previous studies measured the pressure-temperature relations in aqueous isochoric systems in the temperature range from 0°C to – 20°C. The goal of this study is to expand the pressure-temperature measurement beyond the range reported in previous publications. Materials and methods To expand the pressure-temperature measurements beyond the previous range, we have developed a new isochoric device capable of withstanding liquid nitrogen temperatures and pressures of up to 413 MPa. The device is instrumented with a pressure transducer than can monitor and record the pressures in the isochoric chamber in real time. Measurements were made in a temperature range from – 5°C to liquid nitrogen temperatures for various solutions of pure water and Me2SO (a chemical additive used for protection of biological materials in a frozen state and for vitrification (glass formation) of biological matter). Undissolved gaseous are is carefully removed from the system. Results Temperature-pressure data from – 5°C to liquid nitrogen temperature for pure water and other solutions are presented in this study. Following are examples of some, temperature-pressure values, that were measured in an isochoric system containing pure water: (- 20°C, 187 MPa); (-25°C, 216 MPa); (- 30°C, 242.3 MPa); (-180°C, 124 MPa). The data is consistent with the literature, which reports that the pressure and temperature at the triple point, between ice I, ice III and water is, - 21.993°C and 209.9 MPa, respectively. It was surprising to find that the pressure in the isochoric system increases at temperatures below the triple point and remains high to liquid nitrogen temperatures. Measurements of pressure-temperature relations in solutions of pure water and Me2SO in different concentrations show that, for concentrations in which vitrification is predicted, no increase in pressure was measured during rapid cooling to liquid nitrogen temperatures. However, ice formation either during cooling or warming to and from liquid nitrogen temperatures produced an increase in pressure. Conclusions The data obtained in this study can be used to aid in the design of isochoric cryopreservation protocols. The results suggest that the pressure measurement is important in the design of “constant volume” systems and can provide a simple means to gain information on the occurrence of vitrification and devitrification during cryopreservation processes of aqueous solutions in an isochoric system. PMID:28817681

Linkage of iron elution and dissolved oxygen consumption with removal of organic pollutants by nanoscale zero-valent iron: Effects of pH on iron dissolution and formation of iron oxide/hydroxide layer.

PubMed

Fujioka, Nanae; Suzuki, Moe; Kurosu, Shunji; Kawase, Yoshinori

2016-02-01

The iron elution and dissolved oxygen (DO) consumption in organic pollutant removal by nanoscale zero-valent iron (nZVI) was examined in the range of solution pH from 3.0 to 9.0. Their behaviors were linked with the removal of organic pollutant through the dissolution of iron and the formation of iron oxide/hydroxide layer affected strongly by solution pH and DO. As an example of organic pollutants, azo-dye Orange II was chosen in this study. The chemical composition analyses before and after reaction confirmed the corrosion of nZVI into ions, the formation of iron oxide/hydroxide layer on nZVI surface and the adsorption of the pollutant and its intermediates. The complete decolorization of Orange II with nZVI was accomplished very quickly. On the other hand, the total organic carbon (TOC) removal was considerably slow and the maximum TOC removal was around 40% obtained at pH 9.0. The reductive cleavage of azo-bond by emitted electrons more readily took place as compared with the cleavage of aromatic rings of Orange II leading to the degradation to smaller molecules and subsequently the mineralization. A reaction kinetic model based on the Langmuir-Hinshelwood/Eley-Rideal approach was developed to elucidate mechanisms for organic pollutant removal controlled by the formation of iron oxide/hydroxide layer, the progress of which could be characterized by considering the dynamic concentration changes in Fe(2+) and DO. The dynamic profiles of Orange II removal linked with Fe(2+) and DO could be reasonably simulated in the range of pH from 3.0 to 9.0. Copyright © 2015 Elsevier Ltd. All rights reserved.

Chemical evolution of RNA under hydrothermal conditions and the role of thermal copolymers of amino acids for the prebiotic degradation and formation of RNA

NASA Technical Reports Server (NTRS)

Kawamura, K.; Nagahama, M.; Kuranoue, K.

2005-01-01

The roles of thermal copolymers of amino acids (TCAA) were studied for the prebiotic degradation of RNA. A weak catalytic ability of TCAA consisted of Glu, L-Ala, L-Val, L-Glu, L-Asp, and optionally L-His was detected for the cleavage of the ribose phosphodiester bond of a tetranucleotide (5'-dCrCdGdG) in aqueous solution at 80 degees C. The rate constants of the disappearance of 5'-dCrCdGdG were determined in aqueous solutions using different pH buffer and TCAA. The degradation rates were enhanced 1.3-3.0 times in the presence of TCAA at pH 7.5 and 8.0 at 80 degrees C, while the hydrolysis of oligoguanylate (oligo(G)) was accelerated about 1.6 times at pH 8.0. A weak inhibitory activity for the cleavage of oligo(G) was detected in the presence of 0.055 M TCAA-Std. On the other hand, our recent study on the influences of TCAA for the template-directed reaction of oligo(G) on a polycytidylic acid template showed that TCAA has an acceleration activity for the degradation of the activated nucleotide monomer and an acceleration activity for the formation of G5' ppG capped oligo(G). This series of studies suggest that efficient and selective catalytic or inhibitory activities for either the degradation or formation of RNA under hydrothermal conditions could have hardly emerged from the simple thermal condensation products of amino acids. A scenario is going to be deduced on the chemical evolution of enzymatic activities and RNA molecules concerning hydrothermal earth conditions. c2005 COSPAR. Published by Elsevier Ltd. All rights reserved.

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.

PubMed

Sripathi, Kamali N; Tay, Wendy W; Banáš, Pavel; Otyepka, Michal; Šponer, Jiří; Walter, Nils G

2014-07-01

The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2'-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape. © 2014 Sripathi et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Chemical stability of insulin. 1. Hydrolytic degradation during storage of pharmaceutical preparations.

PubMed

Brange, J; Langkjaer, L; Havelund, S; Vølund, A

1992-06-01

Hydrolysis of insulin has been studied during storage of various preparations at different temperatures. Insulin deteriorates rapidly in acid solutions due to extensive deamidation at residue AsnA21. In neutral formulations deamidation takes place at residue AsnB3 at a substantially reduced rate under formation of a mixture of isoAsp and Asp derivatives. The rate of hydrolysis at B3 is independent of the strength of the preparation, and in most cases the species of insulin, but varies with storage temperature and formulation. Total transformation at B3 is considerably reduced when insulin is in the crystalline as compared to the amorphous or soluble state, indicating that formation of the rate-limiting cyclic imide decreases when the flexibility of the tertiary structure is reduced. Neutral solutions containing phenol showed reduced deamidation probably because of a stabilizing effect of phenol on the tertiary structure (alpha-helix formation) around the deamidating residue, resulting in a reduced probability for formation of the intermediate imide. The ratio of isoAsp/Asp derivative was independent of time and temperature, suggesting a pathway involving only intermediate imide formation, without any direct side-chain hydrolysis. However, increasing formation of Asp relative to isoAsp derivative was observed with decreasing flexibility of the insulin three-dimensional structure in the formulation. In certain crystalline suspensions a cleavage of the peptide bond A8-A9 was observed. Formation of this split product is species dependent: bovine greater than porcine greater than human insulin. The hydrolytic cleavage of the peptide backbone takes place only in preparations containing rhombohedral crystals in addition to free zinc ions.

All solution-processed micro-structured flexible electrodes for low-cost light-emitting pressure sensors fabrication.

PubMed

Shimotsu, Rie; Takumi, Takahiro; Vohra, Varun

2017-07-31

Recent studies have demonstrated the advantage of developing pressure-sensitive devices with light-emitting properties for direct visualization of pressure distribution, potential application to next generation touch panels and human-machine interfaces. To ensure that this technology is available to everyone, its production cost should be kept as low as possible. Here, simple device concepts, namely, pressure sensitive flexible hybrid electrodes and OLED architecture, are used to produce low-cost resistive or light-emitting pressure sensors. Additionally, integrating solution-processed self-assembled micro-structures into the flexible hybrid electrodes composed of an elastomer and conductive materials results in enhanced device performances either in terms of pressure or spatial distribution sensitivity. For instance, based on the pressure applied, the measured values for the resistances of pressure sensors range from a few MΩ down to 500 Ω. On the other hand, unlike their evaporated equivalents, the combination of solution-processed flexible electrodes with an inverted OLED architectures display bright green emission when a pressure over 200 kPa is applied. At a bias of 3 V, their luminance can be tuned by applying a higher pressure of 500 kPa. Consequently, features such as fingernails and fingertips can be clearly distinguished from one another in these long-lasting low-cost devices.

Growth inhibition, turgor maintenance, and changes in yield threshold after cessation of solute import in pea epicotyls

NASA Technical Reports Server (NTRS)

Schmalstig, J. G.; Cosgrove, D. J.

1988-01-01

The dependence of stem elongation on solute import was investigated in etiolated pea seedlings (Pisum sativum L. var Alaska) by excising the cotyledons. Stem elongation was inhibited by 60% within 5 hours of excision. Dry weight accumulation into the growing region stopped and osmotic pressure of the cell sap declined by 0.14 megapascal over 5 hours. Attempts to assay phloem transport via ethylenediaminetetraacetate-enhanced exudation from cut stems revealed no effect of cotyledon excision, indicating that the technique measured artifactual leakage from cells. Despite the drop in cell osmotic pressure, turgor pressure (measured directly via a pressure probe) did not decline. Turgor maintenance is postulated to occur via uptake of solutes from the free space, thereby maintaining the osmotic pressure difference across the cell membrane. Cell wall properties were measured by the pressure-block stress relaxation technique. Results indicate that growth inhibition after cotyledon excision was mediated primarily via an increase in the wall yield threshold.

Effect of solvent on absorption spectra of all-trans-{beta}-carotene under high pressure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, W. L.; Zheng, Z. R.; Liu, Z. G.

The absorption spectra of all-trans-{beta}-carotene in n-hexane and carbon disulfide (CS{sub 2}) solutions are measured under high pressure at ambient temperature. The common redshift and broadening in the spectra are observed. Simulation of the absorption spectra was performed by using the time-domain formula of the stochastic model. The pressure dependence of the 0-0 band wavenumber is in agreement with the Bayliss theory at pressure higher than 0.2 GPa. The deviation of the linearity at lower pressure is ascribed to the reorientation of the solvent molecules. Both the redshift and broadening are stronger in CS{sub 2} than that in n-hexane becausemore » of the more sensitive pressure dependence of dispersive interactions in CS{sub 2} solution. The effect of pressure on the transition moment is explained with the aid of a simple model involving the relative dimension, location, and orientation of the solute and solvent molecules. The implication of these results for light-harvesting functions of carotenoids in photosynthesis is also discussed.« less

Modification of Encapsulation Pressure of Reverse Micelles in Liquid Ethane

PubMed Central

Peterson, Ronald W.; Nucci, Nathaniel V.; Wand, A. Joshua

2011-01-01

Encapsulation of within reverse micelles dissolved in low viscosity fluids offers a potential solution to the slow tumbling problem presented by large soluble macromolecules to solution NMR spectroscopy. The reduction in effective macromolecular tumbling is directly dependent upon the viscosity of the solvent. Liquid ethane is of sufficiently low viscosity at pressures below 5,000 p.s.i. to offer a significant advantage. Unfortunately, the viscosity of liquid ethane shows appreciable pressure dependence. Reverse micelle encapsulation in liquid ethane often requires significantly higher pressures, which obviates the potential advantages offered by liquid ethane over liquid propane. Addition of co-surfactants or co-solvents can be used to manipulate the minimum pressure required to obtain stable, well-behaved solutions of reverse micelles prepared in liquid ethane. A library of potential additives is examined and several candidates suitable for use with encapsulated proteins are described. PMID:21764613

Modification of encapsulation pressure of reverse micelles in liquid ethane.

PubMed

Peterson, Ronald W; Nucci, Nathaniel V; Wand, A Joshua

2011-09-01

Encapsulation within reverse micelles dissolved in low viscosity fluids offers a potential solution to the slow tumbling problem presented by large soluble macromolecules to solution NMR spectroscopy. The reduction in effective macromolecular tumbling is directly dependent upon the viscosity of the solvent. Liquid ethane is of sufficiently low viscosity at pressures below 5000 psi to offer a significant advantage. Unfortunately, the viscosity of liquid ethane shows appreciable pressure dependence. Reverse micelle encapsulation in liquid ethane often requires significantly higher pressures, which obviates the potential advantages offered by liquid ethane over liquid propane. Addition of co-surfactants or co-solvents can be used to manipulate the minimum pressure required to obtain stable, well-behaved solutions of reverse micelles prepared in liquid ethane. A library of potential additives is examined and several candidates suitable for use with encapsulated proteins are described. Copyright © 2011 Elsevier Inc. All rights reserved.

Silicon nitride-aluminum oxide solid solution (SiAION) formation and densification by pressure sintering

NASA Technical Reports Server (NTRS)

Yeh, H. C.; Sanders, W. A.; Fiyalko, J. L.

1975-01-01

Stirred-ball-mill-blended Si3N4 and Al2O3 powders were pressure sintered in order to investigate the mechanism of solid solution formation and densification in the Si3N4-Al2O3 system. Powder blends with Si3N4:Al2O3 mole ratios of 4:1, 3:2, and 2:3 were pressure sintered at 27.6-MN/sq m pressure at temperatures to 17000 C (3090 F). The compaction behavior of the powder blends during pressure sintering was determined by observing the density of the powder compact as a function of temperature and time starting from room temperature. This information, combined with the results of X-ray diffraction and metallographic analyses regarding solutioning and phase transformation phenomena in the Si3N4-Al2O3 system, was used to describe the densification behavior.

Mechanism of Intramembrane Cleavage of Alcadeins by γ-Secretase

PubMed Central

Piao, Yi; Kimura, Ayano; Urano, Satomi; Saito, Yuhki; Taru, Hidenori; Yamamoto, Tohru; Hata, Saori; Suzuki, Toshiharu

2013-01-01

Background Alcadein proteins (Alcs; Alcα, Alcβand Alcγ) are predominantly expressed in neurons, as is Alzheimer's β-amyloid (Aβ) precursor protein (APP). Both Alcs and APP are cleaved by primary α- or β-secretase to generate membrane-associated C-terminal fragments (CTFs). Alc CTFs are further cleaved by γ-secretase to secrete p3-Alc peptide along with the release of intracellular domain fragment (Alc ICD) from the membrane. In the case of APP, APP CTFβ is initially cleaved at the ε-site to release the intracellular domain fragment (AICD) and consequently the γ-site is determined, by which Aβ generates. The initial ε-site is thought to define the final γ-site position, which determines whether Aβ40/43 or Aβ42 is generated. However, initial intracellular ε-cleavage sites of Alc CTF to generate Alc ICD and the molecular mechanism that final γ-site position is determined remains unclear in Alcs. Methodology Using HEK293 cells expressing Alcs plus presenilin 1 (PS1, a catalytic unit of γ-secretase) and the membrane fractions of these cells, the generation of p3-Alc possessing C-terminal γ-cleavage site and Alc ICD possessing N-terminal ε-cleavage site were analysed with MALDI-TOF/MS. We determined the initial ε-site position of all Alcα, Alcβ and Alcγ, and analyzed the relationship between the initially determined ε-site position and the final γ-cleavage position. Conclusions The initial ε-site position does not always determine the final γ-cleavage position in Alcs, which differed from APP. No additional γ-cleavage sites are generated from artificial/non-physiological positions of ε-cleavage for Alcs, while the artificial ε-cleavage positions can influence in selection of physiological γ-site positions. Because alteration of γ-secretase activity is thought to be a pathogenesis of sporadic Alzheimer's disease, Alcs are useful and sensitive substrate to detect the altered cleavage of substrates by γ-secretase, which may be induced by malfunction of γ-secretase itself or changes of membrane environment for enzymatic reaction. PMID:23658629

Thrombin specificity. Requirement for apolar amino acids adjacent to the thrombin cleavage site of polypeptide substrate.

PubMed

Chang, J Y

1985-09-02

alpha-Thrombin cleavage of 30 polypeptide hormones and their derivatives were analysed by quantitative amino-terminal analysis. The polypeptides included secretin, vasoactive intestinal polypeptide, cholecystokinin fragment, dynorphin A, somatostatins, gastrin-releasing peptide, calcitonins and human parathyroid hormone fragment. Most of them were selected mainly on the ground that they contain sequence structures homologous to the well known tripeptide substrates of alpha-thrombin. All selected polypeptides have one single major cleavage site and both Arg-Xaa and Lys-Xaa bonds were found to be selectively cleaved by alpha-thrombin. Under fixed conditions (1 nmol polypeptide/0.5 NIH unit alpha-thrombin in 20 microliters of 50 mM ammonium bicarbonate at 25 degrees C), the time required for 50% cleavage ranges from less than 1 min to longer than 24 h. Heparin invariably enhanced thrombin cleavage on all polypeptide analysed. The optimum cleavage site for alpha-thrombin has the structures of (a) P4-P3-Pro-Arg-P1'-P2', where P3 and P4 are hydrophobic amino acid and P1', P2' are nonacidic amino acids and (b) P2-Arg-P1', where P2 or P1' are Gly. The requirement for hydrophobic P3 and P4 was further demonstrated by the drastic decrease of thrombin cleavage rates in both gastrin-releasing peptide and calcitonins after chemical removal of hydrophobic P3 and P4 residues. The requirement for nonacidic P1' and P2' residues was demonstrated by the drastic increase of thrombin cleavage rates in both calcitonin and parathyroid hormone fragments, after specific chemical modification of acidic P1' and P2' residues. These findings confirm the importance of hydrophobic P2-P4 residues for thrombin specificity and provide new evidence to indicate that apolar P1' and P2' residues are also crucial for thrombin specificity. It is concluded that specific cleavage of polypeptides by alpha-thrombin can be reasonably predicted and that chemical modification can be a useful tool in enhancing thrombin cleavage.

Removal of Manganese from Solution using Polyamide Membrane

NASA Astrophysics Data System (ADS)

Mathaba, M.; Sithole, N.; Mashifana, T.

2018-03-01

The work demonstrates the performance of polyamide membrane in the removal of manganese ions from single salt aqueous solution simulating real acid mine drainage. The membrane was tested using a dead-end filtration cell with manganese sulphate was used to prepare a feed solution. The membrane flux and metal rejection was evaluated. Effect of operating parameters such as pH, initial feed concentration and pressure on membrane performance was investigated. The pressure was varied between 10 and 15 bar and it was observed that increasing the pressure increases the membrane flux. Acidic pH conditions contributed to the removal of the contaminate as Mn2+ ions are freely at low pH. The percentage rejection was found to be 63.5 to 77.6 % as concentration is increased from 290 ppm to 321 ppm for a feed solution. The membrane showed satisfactory results in removing metal ions from solution.

Fire safety arrangement of inhabited pressurized compartments of manned spacecraft

NASA Astrophysics Data System (ADS)

Bolodian, Ivan; Melikhov, Anatoliy; Tanklevskiy, Leonid

2017-06-01

The article deals with innovative technical solutions that provide fire safety in inhabited pressurized compartments of manned spacecraft by means of a fireproof device of inhabited pressurized compartments via application of engineering means of fire prevention and fire spreading prevention by lowering fire load in an inhabited pressurized module up to the point when the maximum possible levels of fire factors in an inhabited pressurized compartment of a manned spacecraft are prevented. Represented technical solutions are used at the present time according to stated recommendations during provision of fire safety of equipment created by a number of Russian organizations for equipage of inhabited pressurized compartments of spacecraft of the Russian segment of International space station.

RNase P cleaves transient structures in some riboswitches.

PubMed

Altman, Sidney; Wesolowski, Donna; Guerrier-Takada, Cecilia; Li, Yong

2005-08-09

RNase P from Escherichia coli cleaves the coenzyme B12 riboswitch from E. coli and a similar one from Bacillus subtilis. The cleavage sites do not occur in any recognizable structure, as judged from theoretical schemes that have been drawn for these 5' UTRs. However, it is possible to draw a scheme that is a good representation of the E. coli cleavage site for RNase P and for the cleavage site in B. subtilis. These data indicate that transient structures are important in RNase P cleavage and in riboswitch function. Coenzyme B12 has a small inhibitory effect on E. coli RNase P cleavage of the E. coli riboswitch. Both E. coli RNase P and a partially purified RNase P from Aspergillus nidulans mycelia succeeded in cleaving a putative arginine riboswitch from A. nidulans. The cleavage site may be a representative of another model substrate for eukaryotic RNase P. This 5' UTR controls splicing of the arginase mRNA in A. nidulans. Four other riboswitches in E. coli were not cleaved by RNase P under the conditions tested.

RNase P cleaves transient structures in some riboswitches

PubMed Central

Altman, Sidney; Wesolowski, Donna; Guerrier-Takada, Cecilia; Li, Yong

2005-01-01

RNase P from Escherichia coli cleaves the coenzyme B12 riboswitch from E. coli and a similar one from Bacillus subtilis. The cleavage sites do not occur in any recognizable structure, as judged from theoretical schemes that have been drawn for these 5′ UTRs. However, it is possible to draw a scheme that is a good representation of the E. coli cleavage site for RNase P and for the cleavage site in B. subtilis. These data indicate that transient structures are important in RNase P cleavage and in riboswitch function. Coenzyme B12 has a small inhibitory effect on E. coli RNase P cleavage of the E. coli riboswitch. Both E. coli RNase P and a partially purified RNase P from Aspergillus nidulans mycelia succeeded in cleaving a putative arginine riboswitch from A. nidulans. The cleavage site may be a representative of another model substrate for eukaryotic RNase P. This 5′ UTR controls splicing of the arginase mRNA in A. nidulans. Four other riboswitches in E. coli were not cleaved by RNase P under the conditions tested. PMID:16061811

Classical Swine Fever Virus Glycoprotein Erns Is an Endoribonuclease with an Unusual Base Specificity

PubMed Central

Hausmann, Yvonne; Roman-Sosa, Gleyder; Thiel, Heinz-Jürgen; Rümenapf, Till

2004-01-01

The glycoprotein Erns of pestiviruses is a virion-associated and -secreted RNase that is involved in virulence. The requirements at the cleavage site in heteropolymeric RNA substrates were studied for Erns. Limited digestion of heteropolymeric RNA substrates indicated a cleavage 5′ of uridine residues irrespective of the preceding nucleotide (Np/U). To further study specificity radiolabeled RNA, molecules of 45 to 56 nucleotides in length were synthesized that contained no or a single Np/U cleavage site. Cleavage was only observed in substrates containing an ApU, CpU, GpU, or UpU dinucleotide and occurred in two steps, an initial NpU-specific and a consecutive unspecific degradation. The NpU-specific cleavage was resistant to 7 M urea while the second-order cleavage was sensitive to denaturation. Kinetic analyses revealed that Erns is a highly active endoribonuclease (kcat/Km = 2 × 106 to 10 × 106 M−1 s−1) with a strong affinity to NpU containing single-stranded RNA substrates (Km = 85 to 260 nM). PMID:15113930

AID-induced decrease in topoisomerase 1 induces DNA structural alteration and DNA cleavage for class switch recombination.

PubMed

Kobayashi, Maki; Aida, Masatoshi; Nagaoka, Hitoshi; Begum, Nasim A; Kitawaki, Yoko; Nakata, Mikiyo; Stanlie, Andre; Doi, Tomomitsu; Kato, Lucia; Okazaki, Il-mi; Shinkura, Reiko; Muramatsu, Masamichi; Kinoshita, Kazuo; Honjo, Tasuku

2009-12-29

To initiate class switch recombination (CSR) activation-induced cytidine deaminase (AID) induces staggered nick cleavage in the S region, which lies 5' to each Ig constant region gene and is rich in palindromic sequences. Topoisomerase 1 (Top1) controls the supercoiling of DNA by nicking, rotating, and religating one strand of DNA. Curiously, Top1 reduction or AID overexpression causes the genomic instability. Here, we report that the inactivation of Top1 by its specific inhibitor camptothecin drastically blocked both the S region cleavage and CSR, indicating that Top1 is responsible for the S region cleavage in CSR. Surprisingly, AID expression suppressed Top1 mRNA translation and reduced its protein level. In addition, the decrease in the Top1 protein by RNA-mediated knockdown augmented the AID-dependent S region cleavage, as well as CSR. Furthermore, Top1 reduction altered DNA structure of the Smu region. Taken together, AID-induced Top1 reduction alters S region DNA structure probably to non-B form, on which Top1 can introduce nicks but cannot religate, resulting in S region cleavage.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamilton, Brian S.; Sun, Xiangjie; Chung, Changik

A critical feature of highly pathogenic avian influenza viruses (H5N1 and H7N7) is the efficient intracellular cleavage of the hemagglutinin (HA) protein. H7N7 viruses also exist in equine species, and a unique feature of the equine H7N7 HA is the presence of an eleven amino acid insertion directly N-terminal to a tetrabasic cleavage site. Here, we show that three histidine residues within the unique insertion of the equine H7N7 HA are essential for intracellular cleavage. An asparagine residue within the insertion-derived glycosylation site was also found to be essential for intracellular cleavage. The presence of the histidine residues also appearmore » to be involved in triggering fusion, since mutation of the histidine residues resulted in a destabilizing effect. Importantly, the addition of a tetrabasic site and the eleven amino acid insertion conferred efficient intracellular cleavage to the HA of an H7N3 low pathogenicity avian influenza virus. Our studies show that acquisition of the eleven amino acid insertion offers an alternative mechanism for intracellular cleavage of influenza HA.« less

Cleavage Entropy as Quantitative Measure of Protease Specificity

PubMed Central

Fuchs, Julian E.; von Grafenstein, Susanne; Huber, Roland G.; Margreiter, Michael A.; Spitzer, Gudrun M.; Wallnoefer, Hannes G.; Liedl, Klaus R.

2013-01-01

A purely information theory-guided approach to quantitatively characterize protease specificity is established. We calculate an entropy value for each protease subpocket based on sequences of cleaved substrates extracted from the MEROPS database. We compare our results with known subpocket specificity profiles for individual proteases and protease groups (e.g. serine proteases, metallo proteases) and reflect them quantitatively. Summation of subpocket-wise cleavage entropy contributions yields a measure for overall protease substrate specificity. This total cleavage entropy allows ranking of different proteases with respect to their specificity, separating unspecific digestive enzymes showing high total cleavage entropy from specific proteases involved in signaling cascades. The development of a quantitative cleavage entropy score allows an unbiased comparison of subpocket-wise and overall protease specificity. Thus, it enables assessment of relative importance of physicochemical and structural descriptors in protease recognition. We present an exemplary application of cleavage entropy in tracing substrate specificity in protease evolution. This highlights the wide range of substrate promiscuity within homologue proteases and hence the heavy impact of a limited number of mutations on individual substrate specificity. PMID:23637583

LaSota fusion (F) cleavage motif-mediated fusion activity is affected by other regions of the F protein from different genotype Newcastle disease virus in a chimeric virus: implication for virulence attenuation.

PubMed

Kim, Shin-Hee; Xiao, Sa; Collins, Peter L; Samal, Siba K

2016-06-01

The cleavage site sequence of the fusion (F) protein contributes to a wide range of virulence of Newcastle disease virus (NDV). In this study, we identified other important amino acid sequences of the F protein that affect cleavage and modulation of fusion. We generated chimeric Beaudette C (BC) viruses containing the cleavage site sequence of avirulent strain LaSota (Las-Fc) together with various regions of the F protein of another virulent strain AKO. We found that the F1 subunit is important for cleavage inhibition. Further dissection of the F1 subunit showed that replacement of four amino acids in the BC/Las-Fc protein with their AKO counterparts (T341S, M384I, T385A and I386L) resulted in an increase in fusion and replication in vitro. In contrast, the mutation N403D greatly reduced cleavage and viral replication, and affected protein conformation. These findings will be useful in developing improved live NDV vaccines and vaccine vectors.

Real-time single cell analysis of Bid cleavage and translocation in cisplatin-induced apoptosis

NASA Astrophysics Data System (ADS)

Liu, Lei; Xing, Da; Pei, Yihui; Chen, Wei R.

2007-02-01

Cancer cell apoptosis can be induced by cisplatin, an efficient anticancer agent. However, its mechanism is not fully understood. Bcl-2 homology domain (BH) 3-only proteins couple stress signals to mitochondrial apoptotic pathways. Calpain-mediated cleavage of the BH3-only protein Bid into a 14 kD truncated protein (tBid) has been implicated in cisplatin-induced apoptotic pathway. We utilized a recombinant fluorescence resonance energy transfer (FRET) Bid probe to determine the kinetics of Bid cleavage during cisplatin-induced apoptosis in ASTC-a-1 cells. The cells were also co-transfected with Bid-CFP and DsRed-Mit to dynamically detect tBid translocation. Cells showed a cleavage of the Bid-FRET probe occurring at about 4-5 h after treated with 20 µM cisplatin. Cleavage of the Bid-FRET probe coincided with a translocation of tBid from the cytosolic to the mitochondria, and the translocation lasted about 1.5 h. Using real-time single-cell analysis, we first observed the kinetics of Bid cleavage and translocation to mitochondria in living cells during cisplatin-induced apoptosis.

Orion Service Module Reaction Control System Plume Impingement Analysis Using PLIMP/RAMP2

NASA Technical Reports Server (NTRS)

Wang, Xiao-Yen; Lumpkin, Forrest E., III; Gati, Frank; Yuko, James R.; Motil, Brian J.

2009-01-01

The Orion Crew Exploration Vehicle Service Module Reaction Control System engine plume impingement was computed using the plume impingement program (PLIMP). PLIMP uses the plume solution from RAMP2, which is the refined version of the reacting and multiphase program (RAMP) code. The heating rate and pressure (force and moment) on surfaces or components of the Service Module were computed. The RAMP2 solution of the flow field inside the engine and the plume was compared with those computed using GASP, a computational fluid dynamics code, showing reasonable agreement. The computed heating rate and pressure using PLIMP were compared with the Reaction Control System plume model (RPM) solution and the plume impingement dynamics (PIDYN) solution. RPM uses the GASP-based plume solution, whereas PIDYN uses the SCARF plume solution. Three sets of the heating rate and pressure solutions agree well. Further thermal analysis on the avionic ring of the Service Module was performed using MSC Patran/Pthermal. The obtained temperature results showed that thermal protection is necessary because of significant heating from the plume.

Lower critical solution temperature (LCST) phase separation of glycol ethers for forward osmotic control.

PubMed

Nakayama, Daichi; Mok, Yeongbong; Noh, Minwoo; Park, Jeongseon; Kang, Sunyoung; Lee, Yan

2014-03-21

Lower critical solution temperature (LCST) phase transition of glycol ether (GE)-water mixtures induces an abrupt change in osmotic pressure driven by a mild temperature change. The temperature-controlled osmotic change was applied for the forward osmosis (FO) desalination. Among three GEs evaluated, di(ethylene glycol) n-hexyl ether (DEH) was selected as a potential FO draw solute. A DEH-water mixture with a high osmotic pressure could draw fresh water from a high-salt feed solution such as seawater through a semipermeable membrane at around 10 °C. The water-drawn DEH-water mixture was phase-separated into a water-rich phase and a DEH-rich phase at around 30 °C. The water-rich phase with a much reduced osmotic pressure released water into a low-salt solution, and the DEH-rich phase was recovered into the initial DEH-water mixture. The phase separation behaviour, the residual GE concentration in the water-rich phase, the osmotic pressure of the DEH-water mixture, and the osmotic flux between the DEH-water mixture and salt solutions were carefully analysed for FO desalination. The liquid-liquid phase separation of the GE-water mixture driven by the mild temperature change between 10 °C and 30 °C is very attractive for the development of an ideal draw solute for future practical FO desalination.

In situ observation of sol-gel transition of agarose aqueous solution by fluorescence measurement.

PubMed

Wang, Zheng; Yang, Kun; Li, Haining; Yuan, Chaosheng; Zhu, Xiang; Huang, Haijun; Wang, Yongqiang; Su, Lei; Fang, Yapeng

2018-06-01

Sol-gel transition behavior of agarose aqueous solution was investigated by using rheology and fluorescence measurement. On heating, the storage modulus G' decreased gradually, then deviated abruptly at the temperature of about 65°C, and finally decreased slowly again. For fluorescence measurement, the phase transition point kept almost at the temperature of 65°C, which was consistent with that in rheology measurement. Upon compression, it was indicated that the fluorescence lifetime for the probe in the agarose aqueous solution showed a dramatic change in the vicinity of the phase transition point. T vs. P phase diagram of agarose aqueous solution was constructed, which showed that the melting point was an increasing function of pressure. Based on the phase diagram, the agarose gels were prepared by cooling under atmospheric pressure and the pressure of 300MPa, respectively. From the result of the recovered samples studied by optical rheometry, it was found that agarose gel prepared under high pressure had a higher elasticity and lower viscosity index, compared with that under atmospheric pressure. It could be speculated that such kinds of properties might be attributed to the smaller pore size during gelation under high pressure. Copyright © 2018. Published by Elsevier B.V.

Identification of Caspase Cleavage Sites in KSHV Latency-Associated Nuclear Antigen and Their Effects on Caspase-Related Host Defense Responses.

PubMed

Davis, David A; Naiman, Nicole E; Wang, Victoria; Shrestha, Prabha; Haque, Muzammel; Hu, Duosha; Anagho, Holda A; Carey, Robert F; Davidoff, Katharine S; Yarchoan, Robert

2015-07-01

Kaposi's sarcoma-associated herpesvirus (KSHV), also known as human herpesvirus-8, is the causative agent of three hyperproliferative disorders: Kaposi's sarcoma, primary effusion lymphoma (PEL) and multicentric Castleman's disease. During viral latency a small subset of viral genes are produced, including KSHV latency-associated nuclear antigen (LANA), which help the virus thwart cellular defense responses. We found that exposure of KSHV-infected cells to oxidative stress, or other inducers of apoptosis and caspase activation, led to processing of LANA and that this processing could be inhibited with the pan-caspase inhibitor Z-VAD-FMK. Using sequence, peptide, and mutational analysis, two caspase cleavage sites within LANA were identified: a site for caspase-3 type caspases at the N-terminus and a site for caspase-1 and-3 type caspases at the C-terminus. Using LANA expression plasmids, we demonstrated that mutation of these cleavage sites prevents caspase-1 and caspase-3 processing of LANA. This indicates that these are the principal sites that are susceptible to caspase cleavage. Using peptides spanning the identified LANA cleavage sites, we show that caspase activity can be inhibited in vitro and that a cell-permeable peptide spanning the C-terminal cleavage site could inhibit cleavage of poly (ADP-ribose) polymerase and increase viability in cells undergoing etoposide-induced apoptosis. The C-terminal peptide of LANA also inhibited interleukin-1 beta (IL-1β) production from lipopolysaccharide-treated THP-1 cells by more than 50%. Furthermore, mutation of the two cleavage sites in LANA led to a significant increase in IL-1β production in transfected THP-1 cells; this provides evidence that these sites function to blunt the inflammasome, which is known to be activated in latently infected PEL cells. These results suggest that specific caspase cleavage sites in KSHV LANA function to blunt apoptosis as well as interfere with the caspase-1-mediated inflammasome, thus thwarting key cellular defense mechanisms.

Role of cleavage at the core-E1 junction of hepatitis C virus polyprotein in viral morphogenesis.

PubMed

Pène, Véronique; Lemasson, Matthieu; Harper, Francis; Pierron, Gérard; Rosenberg, Arielle R

2017-01-01

In hepatitis C virus (HCV) polyprotein sequence, core protein terminates with E1 envelope signal peptide. Cleavage by signal peptidase (SP) separates E1 from the complete form of core protein, anchored in the endoplasmic reticulum (ER) membrane by the signal peptide. Subsequent cleavage of the signal peptide by signal-peptide peptidase (SPP) releases the mature form of core protein, which preferentially relocates to lipid droplets. Both of these cleavages are required for the HCV infectious cycle, supporting the idea that HCV assembly begins at the surface of lipid droplets, yet SPP-catalyzed cleavage is dispensable for initiation of budding in the ER. Here we have addressed at what step(s) of the HCV infectious cycle SP-catalyzed cleavage at the core-E1 junction is required. Taking advantage of the sole system that has allowed visualization of HCV budding events in the ER lumen of mammalian cells, we showed that, unexpectedly, mutations abolishing this cleavage did not prevent but instead tended to promote the initiation of viral budding. Moreover, even though no viral particles were released from Huh-7 cells transfected with a full-length HCV genome bearing these mutations, intracellular viral particles containing core protein protected by a membrane envelope were formed. These were visualized by electron microscopy as capsid-containing particles with a diameter of about 70 nm and 40 nm before and after delipidation, respectively, comparable to intracellular wild-type particle precursors except that they were non-infectious. Thus, our results show that SP-catalyzed cleavage is dispensable for HCV budding per se, but is required for the viral particles to acquire their infectivity and secretion. These data support the idea that HCV assembly occurs in concert with budding at the ER membrane. Furthermore, capsid-containing particles did not accumulate in the absence of SP-catalyzed cleavage, suggesting the quality of newly formed viral particles is controlled before secretion.

RNase L targets distinct sites in influenza A virus RNAs.

PubMed

Cooper, Daphne A; Banerjee, Shuvojit; Chakrabarti, Arindam; García-Sastre, Adolfo; Hesselberth, Jay R; Silverman, Robert H; Barton, David J

2015-03-01

Influenza A virus (IAV) infections are influenced by type 1 interferon-mediated antiviral defenses and by viral countermeasures to these defenses. When IAV NS1 protein is disabled, RNase L restricts virus replication; however, the RNAs targeted for cleavage by RNase L under these conditions have not been defined. In this study, we used deep-sequencing methods to identify RNase L cleavage sites within host and viral RNAs from IAV PR8ΔNS1-infected A549 cells. Short hairpin RNA knockdown of RNase L allowed us to distinguish between RNase L-dependent and RNase L-independent cleavage sites. RNase L-dependent cleavage sites were evident at discrete locations in IAV RNA segments (both positive and negative strands). Cleavage in PB2, PB1, and PA genomic RNAs suggests that viral RNPs are susceptible to cleavage by RNase L. Prominent amounts of cleavage mapped to specific regions within IAV RNAs, including some areas of increased synonymous-site conservation. Among cellular RNAs, RNase L-dependent cleavage was most frequent at precise locations in rRNAs. Our data show that RNase L targets specific sites in both host and viral RNAs to restrict influenza virus replication when NS1 protein is disabled. RNase L is a critical component of interferon-regulated and double-stranded-RNA-activated antiviral host responses. We sought to determine how RNase L exerts its antiviral activity during influenza virus infection. We enhanced the antiviral activity of RNase L by disabling a viral protein, NS1, that inhibits the activation of RNase L. Then, using deep-sequencing methods, we identified the host and viral RNAs targeted by RNase L. We found that RNase L cleaved viral RNAs and rRNAs at very precise locations. The direct cleavage of IAV RNAs by RNase L highlights an intimate battle between viral RNAs and an antiviral endonuclease. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Degradation of neurotensin by rat brain synaptic membranes: involvement of a thermolysin-like metalloendopeptidase (enkephalinase), angiotensin-converting enzyme, and other unidentified peptidases.

PubMed

Checler, F; Vincent, J P; Kitabgi, P

1983-08-01

Neurotensin was inactivated by membrane-bound and soluble degrading activities present in purified preparations of rat brain synaptic membranes. Degradation products were identified by HPLC and amino acid analysis. The major points of cleavage of neurotensin were the Arg8-Arg9, Pro10-Tyr11, and Tyr11-Ile12 peptide bonds with the membrane-bound activity and the Arg8-Arg9 and Pro10-Tyr11 bonds with the soluble activity. Several lines of evidence indicated that the cleavage of the Arg8-Arg9 bond by the membrane-bound activity resulted mainly from the conversion of neurotensin1-10 to neurotensin1-8 by a dipeptidyl carboxypeptidase. In particular, captopril inhibited this cleavage with an IC50 (5.7 nM) close to its K1 (7 nM) for angiotensin-converting enzyme. Thiorphan inhibited the cleavage at the Tyr11-Ile12 bond by the membrane-bound activity with an IC50 (17 nM) similar to its K1 (4.7 nM) for enkephalinase. Both cleavages were inhibited by 1,10-phenanthroline. These and other data suggested that angiotensin-converting enzyme and a thermolysin-like metalloendopeptidase (enkephalinase) were the membrane-bound peptidases responsible for cleavages at the Arg8-Arg9 and Tyr11-Ile12 bonds, respectively. In contrast, captopril had no effect on the cleavage at the Arg8-Arg9 bond by the soluble activity, indicating that the enzyme responsible for this cleavage was different from angiotensin-converting enzyme. The cleavage at the Pro10-Tyr11 bond by both the membrane-bound and the soluble activities appeared to be catalyzed by an endopeptidase different from known brain proline endopeptidases. The possibility is discussed that the enzymes described here participate in physiological mechanisms of neurotensin inactivation at the synaptic level.

Role of cleavage at the core-E1 junction of hepatitis C virus polyprotein in viral morphogenesis

PubMed Central

Pène, Véronique; Lemasson, Matthieu; Harper, Francis; Pierron, Gérard; Rosenberg, Arielle R.

2017-01-01

In hepatitis C virus (HCV) polyprotein sequence, core protein terminates with E1 envelope signal peptide. Cleavage by signal peptidase (SP) separates E1 from the complete form of core protein, anchored in the endoplasmic reticulum (ER) membrane by the signal peptide. Subsequent cleavage of the signal peptide by signal-peptide peptidase (SPP) releases the mature form of core protein, which preferentially relocates to lipid droplets. Both of these cleavages are required for the HCV infectious cycle, supporting the idea that HCV assembly begins at the surface of lipid droplets, yet SPP-catalyzed cleavage is dispensable for initiation of budding in the ER. Here we have addressed at what step(s) of the HCV infectious cycle SP-catalyzed cleavage at the core-E1 junction is required. Taking advantage of the sole system that has allowed visualization of HCV budding events in the ER lumen of mammalian cells, we showed that, unexpectedly, mutations abolishing this cleavage did not prevent but instead tended to promote the initiation of viral budding. Moreover, even though no viral particles were released from Huh-7 cells transfected with a full-length HCV genome bearing these mutations, intracellular viral particles containing core protein protected by a membrane envelope were formed. These were visualized by electron microscopy as capsid-containing particles with a diameter of about 70 nm and 40 nm before and after delipidation, respectively, comparable to intracellular wild-type particle precursors except that they were non-infectious. Thus, our results show that SP-catalyzed cleavage is dispensable for HCV budding per se, but is required for the viral particles to acquire their infectivity and secretion. These data support the idea that HCV assembly occurs in concert with budding at the ER membrane. Furthermore, capsid-containing particles did not accumulate in the absence of SP-catalyzed cleavage, suggesting the quality of newly formed viral particles is controlled before secretion. PMID:28437468

Method of digesting an explosive nitro compound

DOEpatents

Shah, Manish M.

2000-01-01

The present invention is a process wherein bleaching oxidants are used to digest explosive nitro compounds. The process has an excellent reaction rate for digesting explosives and operates under multivariate conditions. Reaction solutions may be aqueous, non-aqueous or a combination thereof, and can also be any pH, but preferably have a pH between 2 and 9. The temperature may be ambient as well as any temperature above which freezing of the solution would occur and below which any degradation of the bleaching oxidant would occur or below which any explosive reaction would be initiated. The pressure may be any pressure, but is preferably ambient or atmospheric, or a pressure above a vapor pressure of the aqueous solution to avoid boiling of the solution. Because the bleaching oxidant molecules are small, much smaller than an enzyme molecule for example, they can penetrate the microstructure of plastic explosives faster. The bleaching oxidants generate reactive hydroxyl radicals, which can destroy other organic contaminants, if necessary, along with digesting the explosive nitro compound.

Identification of critical process variables affecting particle size following precipitation using a supercritical fluid.

PubMed

Sacha, Gregory A; Schmitt, William J; Nail, Steven L

2006-01-01

The critical processing parameters affecting average particle size, particle size distribution, yield, and level of residual carrier solvent using the supercritical anti-solvent method (SAS) were identified. Carbon dioxide was used as the supercritical fluid. Methylprednisolone acetate was used as the model solute in tetrahydrofuran. Parameters examined included pressure of the supercritical fluid, agitation rate, feed solution flow rate, impeller diameter, and nozzle design. Pressure was identified as the most important process parameter affecting average particle size, either through the effect of pressure on dispersion of the feed solution into the precipitation vessel or through the effect of pressure on solubility of drug in the CO2/organic solvent mixture. Agitation rate, impeller diameter, feed solution flow rate, and nozzle design had significant effects on particle size, which suggests that dispersion of the feed solution is important. Crimped HPLC tubing was the most effective method of introducing feed solution into the precipitation vessel, largely because it resulted in the least amount of clogging during the precipitation. Yields of 82% or greater were consistently produced and were not affected by the processing variables. Similarly, the level of residual solvent was independent of the processing variables and was present at 0.0002% wt/wt THF or less.

cis-Apa: a practical linker for the microwave-assisted preparation of cyclic pseudopeptides via RCM cyclative cleavage.

PubMed

Baron, Alice; Verdié, Pascal; Martinez, Jean; Lamaty, Frédéric

2011-02-04

A new linker cis-5-aminopent-3-enoic acid (cis-Apa) was prepared for the synthesis of cyclic pseudopeptides by cyclization-cleavage by using ring-closing methatesis (RCM). We developed a new synthetic pathway for the preparation of the cis-Apa linker that was tested in the cyclization-cleavage process of different RGD peptide sequences. Different macrocyclic peptidomimetics were prepared by using this integrated microwave-assisted method, showing that the readily available cis-Apa amino acid is well adapted as a linker in the cyclization-cleavage process.

Experiments on schistosity and slaty cleavage

USGS Publications Warehouse

Becker, George Ferdinand

1904-01-01

Schistosity as a structure is important, and it is a part of the business of geologists to explain its origin. Slaty cleavage has further and greater importance as a possible tectonic feature. Scarcely a great mountain range exists, or has existed, along the course of which belts of slaty rock are not found, the dip of the cleavage usually approaching verticality. Are these slate belts equivalent to minutely distributed step faults of great total throw, or do they indicate compression perpendicular to the cleavage without attendant relative dislocation? Evidently the answer to this question is of first importance in the interpretation of orogenic phenomena.

Antibodies to H2a and H2b histones from the sera of HIV-infected patients catalyze site-specific degradation of these histones.

PubMed

Baranova, Svetlana V; Dmitrienok, Pavel S; Ivanisenko, Nikita V; Buneva, Valentina N; Nevinsky, Georgy A

2017-06-01

Histones and their post-translational modifications have key roles in chromatin remodeling and gene transcription. Besides intranuclear functions, histones act as damage-associated molecules when they are released into the extracellular space. Administration of histones to animals leads to systemic inflammatory and toxic responses. Autoantibodies with enzymatic activities (abzymes) are distinctive features of some autoimmune and viral diseases. Electrophoretically homogeneous IgGs containing no canonical enzymes were isolated from the sera of HIV-infected patients by chromatography on several affinity sorbents including anti-histone Sepharose. In contrast to canonical proteases (trypsin, chymotrypsin, proteinase K), IgGs from HIV-infected patients specifically hydrolyzed only histones but not many other tested globular proteins. Using MALDI mass spectrometry the sites of H2a and H2b histone cleavage by anti-histone IgGs were determined for the first time. One cluster of H2a hydrolysis contains two major (↕) and four moderate (↓) cleavage sites: 31-H↓R↓L↓L↓R↕K G↕N-38. One major and two moderate sites of cleavage were revealed in the second cluster: 14-A↕KSRS↓SRA↓G-22. The third cluster corresponding to the H2a C-terminal part contains only five minor (†) sites of cleavage: 82-H†LQLAIRNDEELN†KLLG†RV†T†I-102. It was shown that two major and four moderate sites of cleavage were present in the main cluster of H2b hydrolysis: 46-K↕QvhpD↓TgiS↓SkA↓M↕GiM↓N-63. Two moderate sites of cleavage correspond to a relatively short 6-mer cluster: 12-K↓GskK↓A-17. The third relatively long 9-mer cluster contains one major and two minor sites of H2b cleavage: 80-L↕AHYN†KRS†T-88. In the nucleosome core particle, most of the major and moderate cleavage sites are located at the H2a/H2b interaction interface. Minor cleavage sites of H2a are involved in binding with H3 in the nucleosome core. Two moderate cleavage sites of H2b and one major cleavage site of H2a are located in the disordered N-terminal region interacting with DNA. According to the crystal structure of the nucleosome core particle, all identified cleavage sites are expected to affect H2a and H2b folding, nucleosome assembly, and binding of H2a and H2b with DNA. The existence of H2a and H2b hydrolyzing abzymes may be very important for the further understanding of unknown possibilities of immune systems and biological functions of antibodies.

Single-Chain Soluble BG505.SOSIP gp140 Trimers as Structural and Antigenic Mimics of Mature Closed HIV-1 Env.

PubMed

Georgiev, Ivelin S; Joyce, M Gordon; Yang, Yongping; Sastry, Mallika; Zhang, Baoshan; Baxa, Ulrich; Chen, Rita E; Druz, Aliaksandr; Lees, Christopher R; Narpala, Sandeep; Schön, Arne; Van Galen, Joseph; Chuang, Gwo-Yu; Gorman, Jason; Harned, Adam; Pancera, Marie; Stewart-Jones, Guillaume B E; Cheng, Cheng; Freire, Ernesto; McDermott, Adrian B; Mascola, John R; Kwong, Peter D

2015-05-01

Similar to other type I fusion machines, the HIV-1 envelope glycoprotein (Env) requires proteolytic activation; specifically, cleavage of a gp160 precursor into gp120 and gp41 subunits creates an N-terminal gp41 fusion peptide and permits folding from an immature uncleaved state to a mature closed state. While the atomic-level consequences of cleavage for HIV-1 Env are still being determined, the uncleaved state is antigenically distinct from the mature closed state, and cleavage has been reported to be essential for mimicry of the mature viral spike by soluble versions of Env. Here we report the redesign of a current state-of-the-art soluble Env mimic, BG505.SOSIP, to make it cleavage independent. Specifically, we replaced the furin cleavage site between gp120 and gp41 with Gly-Ser linkers of various lengths. The resultant linked gp120-gp41 constructs, termed single-chain gp140 (sc-gp140), exhibited different levels of structural and antigenic mimicry of the parent cleaved BG505.SOSIP. When constructs were subjected to negative selection to remove subspecies recognized by poorly neutralizing antibodies, trimers of high antigenic mimicry of BG505.SOSIP could be obtained; negative-stain electron microscopy indicated these to resemble the mature closed state. Higher proportions of BG505.SOSIP-trimer mimicry were observed in sc-gp140s with linkers of 6 or more residues, with a linker length of 15 residues exhibiting especially promising traits. Overall, flexible linkages between gp120 and gp41 in BG505.SOSIP can thus substitute for cleavage, and sc-gp140s that closely mimicked the vaccine-preferred mature closed state of Env could be obtained. The trimeric HIV-1 envelope glycoprotein (Env) is the sole target of virus-directed neutralizing antibody responses and a primary focus of vaccine design. Soluble mimics of Env have proven challenging to obtain and have been thought to require proteolytic cleavage into two-component subunits, gp120 and gp41, to achieve structural and antigenic mimicry of mature Env spikes on virions. Here we show that replacement of the cleavage site between gp120 and gp41 in a lead soluble gp140 construct, BG505.SOSIP, with flexible linkers can result in molecules that do not require cleavage to fold efficiently into the mature closed state. Our results provide insights into the impact of cleavage on HIV-1 Env folding. In some contexts such as genetic immunization, optimized cleavage-independent soluble gp140 constructs may have utility over the parental BG505.SOSIP, as they would not require furin cleavage to achieve mimicry of mature Env spikes on virions. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Factors affecting plant growth in membrane nutrient delivery

NASA Technical Reports Server (NTRS)

Dreschel, T. W.; Wheeler, R. M.; Sager, J. C.; Knott, W. M.

1990-01-01

The development of the tubular membrane plant growth unit for the delivery of water and nutrients to roots in microgravity has recently focused on measuring the effects of changes in physical variables controlling solution availability to the plants. Significant effects of membrane pore size and the negative pressure used to contain the solution were demonstrated. Generally, wheat grew better in units with a larger pore size but equal negative pressure and in units with the same pore size but less negative pressure. Lettuce also exhibited better plant growth at less negative pressure.

The influence of pressure on the activity coefficients of the solutes and on the solubility of minerals in the system Na-Ca-Cl-SO 4-H 2O to 200°C and 1 kbar and to high NaCl concentration

NASA Astrophysics Data System (ADS)

Monnin, Christophe

1990-12-01

A model is presented which is used to calculate the effect of pressure on activity coefficients of aqueous solutes in the system Na-Ca-Cl-SO 4-H 2O to 200°C. Literature data for the density and compressibility of aqueous binary solutions of Na 2SO 4 and CaCl 2 to 200°C are used to calculate the first and second pressure derivatives of Pitzer's ion interaction model parameters, as well as the standard molal compressibility and volume of these two salts. Empirical correlations between the apparent molal volume and compressibility of the aqueous electrolytes are used to guide the choice of the temperature dependent expressions used for the numerical representation of the derivatives of Pitzer's parameters with respect to pressure. For sodium sulfate solutions, such correlations are used to extrapolate compressibilities to 200°C. The change in the thermodynamic properties of the-CaSO 04 ion pair with pressure is taken into account by the variation of its dissociation constant. The volumetric properties (partial molal volumes and compressibilities) of multicomponent solutions in the Na-Ca-Cl-SO 4-H 2O system can be predicted from the information generated here and the volumetric equations of ROGERS and PITZER (1982) for NaCl. This model is then combined with the high temperature model of MOLLER (1988) of the same system in order to calculate activity coefficients at high pressures to 200°C. The resulting model is validated by comparing calculated and measured solubilities of anhydrite and gypsum in pure water and in NaCl solutions up to 6 M. The agreement between the calculated and measured solubilities of the calcium sulfates is typically better than 10% up to 200°C and 1 kbar. The relevance of temperature and pressure corrections to the activity coefficients of aqueous solutes is discussed in regard to the assumed accuracy with which geochemical models are able to calculate mineral solubilities.

Prothrombin activation on the activated platelet surface optimizes expression of procoagulant activity

PubMed Central

Wood, Jeremy P.; Silveira, Jay R.; Maille, Nicole M.; Haynes, Laura M.

2011-01-01

Effective hemostasis relies on the timely formation of α-thrombin via prothrombinase, a Ca2+-dependent complex of factors Va and Xa assembled on the activated platelet surface, which cleaves prothrombin at Arg271 and Arg320. Whereas initial cleavage at Arg271 generates the inactive intermediate prethrombin-2, initial cleavage at Arg320 generates the enzymatically active intermediate meizothrombin. To determine which of these intermediates is formed when prothrombin is processed on the activated platelet surface, the cleavage of prothrombin, and prothrombin mutants lacking either one of the cleavage sites, was monitored on the surface of either thrombin- or collagen-activated platelets. Regardless of the agonist used, prothrombin was initially cleaved at Arg271 generating prethrombin-2, with α-thrombin formation quickly after via cleavage at Arg320. The pathway used was independent of the source of factor Va (plasma- or platelet-derived) and was unaffected by soluble components of the platelet releasate. When both cleavage sites are presented within the same substrate molecule, Arg271 effectively competes against Arg320 (with an apparent IC50 = 0.3μM), such that more than 90% to 95% of the initial cleavage occurs at Arg271. We hypothesize that use of the prethrombin-2 pathway serves to optimize the procoagulant activity expressed by activated platelets, by limiting the anticoagulant functions of the alternate intermediate, meizothrombin. PMID:21131592

Prothrombin activation on the activated platelet surface optimizes expression of procoagulant activity.

PubMed

Wood, Jeremy P; Silveira, Jay R; Maille, Nicole M; Haynes, Laura M; Tracy, Paula B

2011-02-03

Effective hemostasis relies on the timely formation of α-thrombin via prothrombinase, a Ca(2+)-dependent complex of factors Va and Xa assembled on the activated platelet surface, which cleaves prothrombin at Arg271 and Arg320. Whereas initial cleavage at Arg271 generates the inactive intermediate prethrombin-2, initial cleavage at Arg320 generates the enzymatically active intermediate meizothrombin. To determine which of these intermediates is formed when prothrombin is processed on the activated platelet surface, the cleavage of prothrombin, and prothrombin mutants lacking either one of the cleavage sites, was monitored on the surface of either thrombin- or collagen-activated platelets. Regardless of the agonist used, prothrombin was initially cleaved at Arg271 generating prethrombin-2, with α-thrombin formation quickly after via cleavage at Arg320. The pathway used was independent of the source of factor Va (plasma- or platelet-derived) and was unaffected by soluble components of the platelet releasate. When both cleavage sites are presented within the same substrate molecule, Arg271 effectively competes against Arg320 (with an apparent IC(50) = 0.3μM), such that more than 90% to 95% of the initial cleavage occurs at Arg271. We hypothesize that use of the prethrombin-2 pathway serves to optimize the procoagulant activity expressed by activated platelets, by limiting the anticoagulant functions of the alternate intermediate, meizothrombin.

On the temperature independence of statistical model parameters for cleavage fracture in ferritic steels

NASA Astrophysics Data System (ADS)

Qian, Guian; Lei, Wei-Sheng; Niffenegger, M.; González-Albuixech, V. F.

2018-04-01

The work relates to the effect of temperature on the model parameters in local approaches (LAs) to cleavage fracture. According to a recently developed LA model, the physical consensus of plastic deformation being a prerequisite to cleavage fracture enforces any LA model of cleavage fracture to observe initial yielding of a volume element as its threshold stress state to incur cleavage fracture in addition to the conventional practice of confining the fracture process zone within the plastic deformation zone. The physical consistency of the new LA model to the basic LA methodology and the differences between the new LA model and other existing models are interpreted. Then this new LA model is adopted to investigate the temperature dependence of LA model parameters using circumferentially notched round tensile specimens. With the published strength data as input, finite element (FE) calculation is conducted for elastic-perfectly plastic deformation and the realistic elastic-plastic hardening, respectively, to provide stress distributions for model calibration. The calibration results in temperature independent model parameters. This leads to the establishment of a 'master curve' characteristic to synchronise the correlation between the nominal strength and the corresponding cleavage fracture probability at different temperatures. This 'master curve' behaviour is verified by strength data from three different steels, providing a new path to calculate cleavage fracture probability with significantly reduced FE efforts.

SKI2 mediates degradation of RISC 5′-cleavage fragments and prevents secondary siRNA production from miRNA targets in Arabidopsis

PubMed Central

Branscheid, Anja; Marchais, Antonin; Schott, Gregory; Lange, Heike; Gagliardi, Dominique; Andersen, Stig Uggerhøj; Voinnet, Olivier; Brodersen, Peter

2015-01-01

Small regulatory RNAs are fundamental in eukaryotic and prokaryotic gene regulation. In plants, an important element of post-transcriptional control is effected by 20–24 nt microRNAs (miRNAs) and short interfering RNAs (siRNAs) bound to the ARGONAUTE1 (AGO1) protein in an RNA induced silencing complex (RISC). AGO1 may cleave target mRNAs with small RNA complementarity, but the fate of the resulting cleavage fragments remains incompletely understood. Here, we show that SKI2, SKI3 and SKI8, subunits of a cytoplasmic cofactor of the RNA exosome, are required for degradation of RISC 5′, but not 3′-cleavage fragments in Arabidopsis. In the absence of SKI2 activity, many miRNA targets produce siRNAs via the RNA-dependent RNA polymerase 6 (RDR6) pathway. These siRNAs are low-abundant, and map close to the cleavage site. In most cases, siRNAs were produced 5′ to the cleavage site, but several examples of 3′-spreading were also identified. These observations suggest that siRNAs do not simply derive from RDR6 action on stable 5′-cleavage fragments and hence that SKI2 has a direct role in limiting secondary siRNA production in addition to its function in mediating degradation of 5′-cleavage fragments. PMID:26464441

Novel insights into the fungal oxidation of monoaromatic and biarylic environmental pollutants by characterization of two new ring cleavage enzymes.

PubMed

Schlüter, Rabea; Lippmann, Ramona; Hammer, Elke; Gesell Salazar, Manuela; Schauer, Frieder

2013-06-01

The phenol-degrading yeast Trichosporon mucoides can oxidize and detoxify biarylic environmental pollutants such as dibenzofuran, diphenyl ether and biphenyl by ring cleavage. The degradation pathways are well investigated, but the enzymes involved are not. The high similarity of hydroxylated biphenyl derivatives and phenol raised the question if the enzymes of the phenol degradation are involved in ring cleavage or whether specific enzymes are necessary. Purification of enzymes from T. mucoides with catechol cleavage activity demonstrated the existence of three different enzymes: a classical catechol-1,2-dioxygenase (CDO), not able to cleave the aromatic ring system of 3,4-dihydroxybiphenyl, and two novel enzymes with a high affinity towards 3,4-dihydroxybiphenyl. The comparison of the biochemical characteristics and mass spectrometric sequence data of these three enzymes demonstrated that they have different substrate specificities. CDO catalyzes the ortho-cleavage of dihydroxylated monoaromatic compounds, while the two novel enzymes carry out a similar reaction on biphenyl derivatives. The ring fission of 3,4-dihydroxybiphenyl by the purified enzymes results in the formation of (5-oxo-3-phenyl-2,5-dihydrofuran-2-yl)acetic acid. These results suggest that the ring cleavage enzymes catalyzing phenol degradation are not involved in the ring cleavage of biarylic compounds by this yeast, although some intermediates of the phenol metabolism may function as inducers.

Recycling of protein subunits during DNA translocation and cleavage by Type I restriction-modification enzymes

PubMed Central

Simons, Michelle; Szczelkun, Mark D.

2011-01-01

The Type I restriction-modification enzymes comprise three protein subunits; HsdS and HsdM that form a methyltransferase (MTase) and HsdR that associates with the MTase and catalyses Adenosine-5′-triphosphate (ATP)-dependent DNA translocation and cleavage. Here, we examine whether the MTase and HsdR components can ‘turnover’ in vitro, i.e. whether they can catalyse translocation and cleavage events on one DNA molecule, dissociate and then re-bind a second DNA molecule. Translocation termination by both EcoKI and EcoR124I leads to HsdR dissociation from linear DNA but not from circular DNA. Following DNA cleavage, the HsdR subunits appear unable to dissociate even though the DNA is linear, suggesting a tight interaction with the cleaved product. The MTases of EcoKI and EcoAI can dissociate from DNA following either translocation or cleavage and can initiate reactions on new DNA molecules as long as free HsdR molecules are available. In contrast, the MTase of EcoR124I does not turnover and additional cleavage of circular DNA is not observed by inclusion of RecBCD, a helicase–nuclease that degrades the linear DNA product resulting from Type I cleavage. Roles for Type I restriction endonuclease subunit dynamics in restriction alleviation in the cell are discussed. PMID:21712244

Distinct oxidative cleavage and modification of bovine [Cu-Zn]-SOD by an ascorbic acid/Cu(II) system: Identification of novel copper binding site on SOD molecule

PubMed Central

Uehara, Hiroshi; Luo, Shen; Aryal, Baikuntha; Levine, Rodney L.; Rao, V. Ashutosh

2016-01-01

We investigated the combined effect of ascorbate and copper [Asc/Cu(II)] on the integrity of bovine [Cu-Zn]-superoxide dismutase (bSOD1) as a model system to study the metal catalyzed oxidation (MCO) and fragmentation of proteins. We found Asc/Cu(II) mediates specific cleavage of bSOD1 and generates 12.5 and 3.2 kDa fragments in addition to oxidation/carbonylation of the protein. The effect of other tested transition metals, a metal chelator, and hydrogen peroxide on the cleavage and oxidation indicated that binding of copper to a previously unknown site on SOD1 is responsible for the Asc/Cu(II) specific cleavage and oxidation. We utilized tandem mass spectrometry to identify the specific cleavage sites of Asc/Cu(II)-treated bSOD1. Analyses of tryptic- and AspN-peptides have demonstrated the cleavage to occur at Gly31 with peptide bond breakage with Thr30 and Ser32 through diamide and α-amidation pathways, respectively. The three-dimensional structure of bSOD1 reveals the imidazole ring of His19 localized within 5 Angstrom from the α-carbon of Gly31 providing a structural basis that copper ion, most likely coordinated by His19, catalyzes the specific cleavage reaction. PMID:26872685

Distinct oxidative cleavage and modification of bovine [Cu- Zn]-SOD by an ascorbic acid/Cu(II) system: Identification of novel copper binding site on SOD molecule.

PubMed

Uehara, Hiroshi; Luo, Shen; Aryal, Baikuntha; Levine, Rodney L; Rao, V Ashutosh

2016-05-01

We investigated the combined effect of ascorbate and copper [Asc/Cu(II)] on the integrity of bovine [Cu-Zn]-superoxide dismutase (bSOD1) as a model system to study the metal catalyzed oxidation (MCO) and fragmentation of proteins. We found Asc/Cu(II) mediates specific cleavage of bSOD1 and generates 12.5 and 3.2kDa fragments in addition to oxidation/carbonylation of the protein. The effect of other tested transition metals, a metal chelator, and hydrogen peroxide on the cleavage and oxidation indicated that binding of copper to a previously unknown site on SOD1 is responsible for the Asc/Cu(II) specific cleavage and oxidation. We utilized tandem mass spectrometry to identify the specific cleavage sites of Asc/Cu(II)-treated bSOD1. Analyses of tryptic- and AspN-peptides have demonstrated the cleavage to occur at Gly31 with peptide bond breakage with Thr30 and Ser32 through diamide and α-amidation pathways, respectively. The three-dimensional structure of bSOD1 reveals the imidazole ring of His19 localized within 5Å from the α-carbon of Gly31 providing a structural basis that copper ion, most likely coordinated by His19, catalyzes the specific cleavage reaction. Published by Elsevier Inc.

Cleavage fracture in high strength low alloy weld metal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bose, W.W.; Bowen, P.; Strangwood, M.

1996-12-31

The present investigation gives an evaluation of the effect of microstructure on the cleavage fracture process of High Strength Low Alloy (HSLA) multipass weld metals. With additions of alloying elements, such as Ti, Ni, Mo and Cr, the microstructure of C-Mn weld metal changes from the classical composition, i.e., allotriomorphic ferrite with acicular ferrite and Widmanstaetten ferrite, to bainite and low carbon martensite. Although the physical metallurgy of some HSLA weld metals has been studied before, more work is necessary to correlate the effect of the microstructure on the fracture behavior of such weld metals. In this work detailed microstructuralmore » analysis was carried out using optical and electron (SEM and TEM) microscopy. Single edge notched (SEN) bend testpieces were used to assess the cleavage fracture stress, {sigma}{sub F}. Inclusions beneath the notch surface were identified as the crack initiators of unstable cleavage fracture. From the size of such inclusions and the value of tensile stress predicted at the initiation site, the effective surface energy for cleavage was calculated using a modified Griffth energy balance for a penny shape crack. The results suggest that even though inclusions initiate cleavage fracture, the local microstructure may play an important role in the fracture process of these weld metals. The implications of these observations for a quantitative theory of the cleavage fracture of ferritic steels is discussed.« less

Precipitation of anion inclusions and plasticity under hydrostatic pressure in II-VI crystals

NASA Astrophysics Data System (ADS)

Lindberg, G. P.; Weinstein, B. A.

2016-10-01

Precipitation of anion nanocrystals (NCs) in initially stoichiometric II-VI crystals under hydrostatic pressure and light exposure is explored by Raman spectroscopy, and the mechanism for this effect is analyzed by model calculations. ZnSe, ZnTe, and CdSe crystals are studied in bulk and/or epitaxial-film forms. Se and Te NCs in the trigonal (t) phase precipitate in ZnSe and ZnTe, but the effect is absent or minimal in CdSe. The precipitation is induced by pressure and assisted by sub-band-gap light. In ZnSe, t-Se NCs appear for pressure exceeding 4.8 GPa and light flux above 50 -70 W /m m2 . In ZnTe, the precipitation of t-Te NCs requires less pressure to initiate, and there is a clear upper-pressure limit for t-Te nuclei to form. We find also that ZnTe samples with cleavage damage or elevated zinc-vacancy content are more prone to form t-Te NCs at lower pressures (even 1 atm in some cases) and lower flux. The precipitation seen in ZnSe and ZnTe occurs at pressures far below their phase transitions, and cannot be due to those transitions. Rather, we propose that the NCs nucleate on dislocations that arise from hydrostatic-pressure induced plastic flow triggered by noncubic defect sites. Calculations of the kinetic barrier for growth of an optimally shaped nucleus are performed, including hydrostatic pressure in the energy minimization scheme. Using sensible values for the model parameters related to the cohesive energies of Se and Te, the calculations account for our main observations, including the existence of an upper pressure limit for precipitation, and the absence of precipitation in CdSe. We consider the effects of pressure-induced precipitate formation on the I-II phase transitions in a variety of binary semiconductors and make predictions of when this effect should be important.

Observation of Early Cleavage in Animal Development: A Simple Technique for Obtaining the Eggs of Rhabditis (Nematoda)

ERIC Educational Resources Information Center

Hinchliffe, J. R.

1973-01-01

Outlines the advantages of using the readily available eggs of the nematode Rhabditis in studying the early cleavage stages of animal development. Discusses the identification and life history of Rhabditis, how to culture and examine the organism, the cleavage stages and cell lineage, and sources of visual aids. (JR)

Controlling Vapor Pressure In Hanging-Drop Crystallization

NASA Technical Reports Server (NTRS)

Carter, Daniel C.; Smith, Robbie

1988-01-01

Rate of evaporation adjusted to produce larger crystals. Device helps to control vapor pressure of water and other solvents in vicinity of hanging drop of solution containing dissolved enzyme protein. Well of porous frit (sintered glass) holds solution in proximity to drop of solution containing protein or enzyme. Vapor from solution in frit controls evaporation of solvent from drop to control precipitation of protein or enzyme. With device, rate of nucleation limited to decrease number and increase size (and perhaps quality) of crystals - large crystals of higher quality needed for x-ray diffraction studies of macromolecules.

Crystallization of calcium oxalate dihydrate in a buffered calcium-containing glucose solution by irradiation with non-equilibrium atmospheric pressure plasma

NASA Astrophysics Data System (ADS)

Kurake, Naoyuki; Tanaka, Hiromasa; Ishikawa, Kenji; Nakamura, Kae; Kajiyama, Hiroaki; Kikkawa, Fumitaka; Mizuno, Masaaki; Ikehara, Yuzuru; Hori, Masaru

2017-10-01

Oxalate was synthesized in the glucose solution by irradiation with non-equilibrium atmospheric pressure plasma (NEAPP), in which the NEAPP plume contacted the solution surface, via the generation of several intermediate organic products such as gluconic acid. A thermodynamically unstable phase of calcium oxalate dihydrate crystallized rapidly during incubation of a NEAPP-irradiated glucose solution that contained calcium ions and was buffered at neutral pH. Longer irradiation times increased the growth rate and the number of seed crystals.

Investigation of the required length for fully developed pipe flow with drag-reducing polymer solutions

NASA Astrophysics Data System (ADS)

Farsiani, Yasaman; Elbing, Brian

2015-11-01

Adding trace amounts of long chain polymers into a liquid flow is known to reduce skin friction drag by up to 80%. While polymer drag reduction (PDR) has been successfully implemented in internal flows, diffusion and degradation have limited its external flow applications. A weakness in many previous PDR studies is that there was no characterization of the polymer being injected into the turbulent boundary layer, which can be accomplished by testing a sample in a pressure-drop tube. An implicit assumption in polymer characterization is that the flow is fully developed at the differential pressure measurement. While available data in the literature shows that the entry length to achieve fully developed flow increases with polymeric solutions, it is unclear how long is required to achieve fully developed flow for non-Newtonian turbulent flows. In the present study, the pressure-drop is measured across a 1.05 meter length section of a 1.04 cm inner diameter pipe. Differential pressure is measured with a pressure transducer for different entry lengths, flow and polymer solution properties. This presentation will present preliminary data on the required entrance length as well as characterization of polymer solution an estimate of the mean molecular weight.

Yeast ribonuclease III uses a network of multiple hydrogen bonds for RNA binding and cleavage.

PubMed

Lavoie, Mathieu; Abou Elela, Sherif

2008-08-19

Members of the bacterial RNase III family recognize a variety of short structured RNAs with few common features. It is not clear how this group of enzymes supports high cleavage fidelity while maintaining a broad base of substrates. Here we show that the yeast orthologue of RNase III (Rnt1p) uses a network of 2'-OH-dependent interactions to recognize substrates with different structures. We designed a series of bipartite substrates permitting the distinction between binding and cleavage defects. Each substrate was engineered to carry a single or multiple 2'- O-methyl or 2'-fluoro ribonucleotide substitutions to prevent the formation of hydrogen bonds with a specific nucleotide or group of nucleotides. Interestingly, introduction of 2'- O-methyl ribonucleotides near the cleavage site increased the rate of catalysis, indicating that 2'-OH are not required for cleavage. Substitution of nucleotides in known Rnt1p binding site with 2'- O-methyl ribonucleotides inhibited cleavage while single 2'-fluoro ribonucleotide substitutions did not. This indicates that while no single 2'-OH is essential for Rnt1p cleavage, small changes in the substrate structure are not tolerated. Strikingly, several nucleotide substitutions greatly increased the substrate dissociation constant with little or no effect on the Michaelis-Menten constant or rate of catalysis. Together, the results indicate that Rnt1p uses a network of nucleotide interactions to identify its substrate and support two distinct modes of binding. One mode is primarily mediated by the dsRNA binding domain and leads to the formation of stable RNA/protein complex, while the other requires the presence of the nuclease and N-terminal domains and leads to RNA cleavage.

The roles of SSU processome components and surveillance factors in the initial processing of human ribosomal RNA

PubMed Central

Sloan, Katherine E.; Bohnsack, Markus T.; Schneider, Claudia; Watkins, Nicholas J.

2014-01-01

During eukaryotic ribosome biogenesis, three of the mature ribosomal (r)RNAs are released from a single precursor transcript (pre-rRNA) by an ordered series of endonucleolytic cleavages and exonucleolytic processing steps. Production of the 18S rRNA requires the removal of the 5′ external transcribed spacer (5′ETS) by endonucleolytic cleavages at sites A0 and A1/site 1. In metazoans, an additional cleavage in the 5′ETS, at site A′, upstream of A0, has also been reported. Here, we have investigated how A′ processing is coordinated with assembly of the early preribosomal complex. We find that only the tUTP (UTP-A) complex is critical for A′ cleavage, while components of the bUTP (UTP-B) and U3 snoRNP are important, but not essential, for efficient processing at this site. All other factors involved in the early stages of 18S rRNA processing that were tested here function downstream from this processing step. Interestingly, we show that the RNA surveillance factors XRN2 and MTR4 are also involved in A′ cleavage in humans. A′ cleavage is largely bypassed when XRN2 is depleted, and we also discover that A′ cleavage is not always the initial processing event in all cell types. Together, our data suggest that A′ cleavage is not a prerequisite for downstream pre-rRNA processing steps and may, in fact, represent a quality control step for initial pre-rRNA transcripts. Furthermore, we show that components of the RNA surveillance machinery, including the exosome and TRAMP complexes, also play key roles in the recycling of excised spacer fragments and degradation of aberrant pre-rRNAs in human cells. PMID:24550520

Non-T cell activation linker (NTAL) proteolytic cleavage as a terminator of activatory intracellular signals.

PubMed

Arbulo-Echevarria, Mikel M; Muñoz-Miranda, Juan Pedro; Caballero-García, Andrés; Poveda-Díaz, José L; Fernández-Ponce, Cecilia; Durán-Ruiz, M Carmen; Miazek, Arkadiusz; García-Cózar, Francisco; Aguado, Enrique

2016-08-01

Non-T cell activation linker is an adaptor protein that is tyrosine phosphorylated upon cross-linking of immune receptors expressed on B lymphocytes, NK cells, macrophages, basophils, or mast cells, allowing the recruitment of cytosolic mediators for downstream signaling pathways. Fas receptor acts mainly as a death receptor, and when cross-linked with Fas ligand, many proteins are proteolytically cleaved, including several signaling molecules in T and B cells. Fas receptor triggering also interferes with TCR intracellular signals, probably by means of proteolytic cleavage of several adaptor proteins. We have previously found that the adaptor linker for activation of T cells, evolutionarily related to non-T cell activation linker, is cleaved upon proapoptotic stimuli in T lymphocytes and thymocytes, in a tyrosine phosphorylation-dependent fashion. Here, we describe non-T cell activation linker proteolytic cleavage triggered in human B cells and monocytes by Fas cross-linking and staurosporine treatment. Non-T cell activation linker is cleaved, producing an N-terminal fragment of ∼22 kDa, and such cleavage is abrogated in the presence of caspase 8/granzyme B and caspase 3 inhibitors. Moreover, we have identified an aspartic acid residue at which non-T cell activation linker is cleaved, which similar to linker for activation of T cells, this aspartic acid residue is located close to tyrosine and serine residues, suggesting an interdependence of phosphorylation and proteolytic cleavage. Consistently, induction of non-T cell activation linker phosphorylation by pervanadate inhibits its cleavage. Interestingly, the truncated isoform of non-T cell activation linker, generated after cleavage, has a decreased signaling ability when compared with the full-length molecule. Altogether, our results suggest that cleavage of transmembrane adaptors constitutes a general mechanism for signal termination of immune receptors. © Society for Leukocyte Biology.

Control of cleavage spindle orientation in Caenorhabditis elegans: The role of the genes par-2 and par-3

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, N.N.; Kirby, C.M.; Kemphues, K.J.

1995-02-01

Polarized asymmetric divisions play important roles in the development of plants and animals. The first two embryonic cleavages of Caenorhabditis elegans provide an opportunity to study the mechanisms controlling polarized asymmetric divisions. The first cleavage is unequal, producing daughters with different sizes and fates. The daughter blastomeres divide with different orientations at the second cleavage; the anterior blastomere divides equally across the long axis of the egg, whereas the posterior blastomere divides unequally along the long axis. We report here the results of our analysis of the genes par-2 and par-3 with respect to their contribution to the polarity ofmore » these divisions. Strong loss-of-function mutations in both genes lead to an equal first cleavage and an altered second cleavage. Interestingly, the mutations exhibit striking gene-specific differences at the second cleavage. The par-2 mutations lead to transverse spindle orientations in both blastomeres, whereas par-3 mutations lead to longitudinal spindle orientations in both blastomeres. The spindle orientation defects correlate with defects in centrosome movements during both the first and the second cell cycle. Temperature shift experiments with par-2 (it5ts) indicate that the par-2(+) activity is not required after the two-cell stage. Analysis of double mutants shows that par-3 is epistatic to par-2. We propose a model wherein par-2(+) and par-3(+) act in concert during the first cell cycle to affect asymmetric modification of the cytoskeleton. This polar modification leads to different behaviors of centrosomes in the anterior and posterior and leads ultimately to blastomere-specific spindle orientations at the second cleavage. 44 refs., 5 figs., 5 tabs.« less

A mutagenic analysis of the RNase mechanism of the bacterial Kid toxin by mass spectrometry.

PubMed

Diago-Navarro, Elizabeth; Kamphuis, Monique B; Boelens, Rolf; Barendregt, Arjan; Heck, Albert J; van den Heuvel, Robert H; Díaz-Orejas, Ramón

2009-09-01

Kid, the toxin of the parD (kis, kid) maintenance system of plasmid R1, is an endoribonuclease that preferentially cleaves RNA at the 5' of A in the core sequence 5'-UA(A/C)-3'. A model of the Kid toxin interacting with the uncleavable mimetic 5'-AdUACA-3' is available. To evaluate this model, a significant collection of mutants in some of the key residues proposed to be involved in RNA binding (T46, A55, T69 and R85) or RNA cleavage (R73, D75 and H17) were analysed by mass spectrometry in RNA binding and cleavage assays. A pair of substrates, 5'-AUACA-3', and its uncleavable mimetic 5'-AdUACA-3', used to establish the model and structure of the Kid-RNA complex, were used in both the RNA cleavage and binding assays. A second RNA substrate, 5'-UUACU-3' efficiently cleaved by Kid both in vivo and in vitro, was also used in the cleavage assays. Compared with the wild-type protein, mutations in the residues of the catalytic site abolished RNA cleavage without substantially altering RNA binding. Mutations in residues proposed to be involved in RNA binding show reduced binding efficiency and a corresponding decrease in RNA cleavage efficiency. The cleavage profiles of the different mutants were similar with the two substrates used, but RNA cleavage required much lower protein concentrations when the 5'-UUACU-3' substrate was used. Protein synthesis and growth assays are consistent with there being a correlation between the RNase activity of Kid and its inhibitory potential. These results give important support to the available models of Kid RNase and the Kid-RNA complex.

A novel quantitative electrochemical method to monitor DNA double-strand breaks caused by a DNA cleavage agent at a DNA sensor.

PubMed

Banasiak, Anna; Cassidy, John; Colleran, John

2018-06-01

To date, DNA cleavage, caused by cleavage agents, has been monitored mainly by gel and capillary electrophoresis. However, these techniques are time-consuming, non-quantitative and require gel stains. In this work, a novel, simple and, importantly, a quantitative method for monitoring the DNA nuclease activity of potential anti-cancer drugs, at a DNA electrochemical sensor, is presented. The DNA sensors were prepared using thiol-modified oligonucleotides that self-assembled to create a DNA monolayer at gold electrode surfaces. The quantification of DNA double-strand breaks is based on calculating the DNA surface coverage, before and after exposure to a DNA cleavage agent. The nuclease properties of a model DNA cleavage agent, copper bis-phenanthroline ([Cu II (phen) 2 ] 2+ ), that can cleave DNA in a Fenton-type reaction, were quantified electrochemically. The DNA surface coverage decreased on average by 21% after subjecting the DNA sensor to a nuclease assay containing [Cu II (phen) 2 ] 2+ , a reductant and an oxidant. This percentage indicates that 6 base pairs were cleaved in the nuclease assay from the immobilised 30 base pair strands. The DNA cleavage can be also induced electrochemically in the absence of a chemical reductant. [Cu II (phen) 2 ] 2+ intercalates between DNA base pairs and, on application of a suitable potential, can be reduced to [Cu I (phen) 2 ] + , with dissolved oxygen acting as the required oxidant. This reduction process is facilitated through DNA strands via long-range electron transfer, resulting in DNA cleavage of 23%. The control measurements for both chemically and electrochemically induced cleavage revealed that DNA strand breaks did not occur under experimental conditions in the absence of [Cu II (phen) 2 ] 2+ . Copyright © 2018 Elsevier B.V. All rights reserved.

Anti-amyloid precursor protein antibodies inhibit amyloid-β production by steric hindrance

PubMed Central

Thomas, Rhian S.; Liddell, J. Eryl; Kidd, Emma J.

2015-01-01

Summary Cleavage of amyloid precursor protein (APP) by β- and γ-secretases results in the production of amyloid-β (Aβ) in Alzheimer’s disease (AD). We raised two monoclonal antibodies, 2B3 and 2B12, that recognise the β-secretase cleavage site on APP but not Aβ. We hypothesised that these antibodies would reduce Aβ levels via steric hindrance of β-secretase. Both antibodies decreased extracellular Aβ levels from astrocytoma cells, but 2B3 was more potent than 2B12. Levels of soluble sAPPα from the non-amyloidogenic α-secretase pathway and intracellular APP were not affected by either antibody nor were there any effects on cell viability. 2B3 exhibited a higher affinity for APP than 2B12 and its epitope appeared to span the cleavage site while 2B12 bound slightly upstream. Both of these factors probably contribute to its greater effect on Aβ levels. After 60 minutes incubation at pH 4.0, most 2B3 and 2B12 remained bound to their antigen, suggesting that the antibodies will remain bound to APP in the acidic endosomes where β-secretase cleavage probably occurs. Only 2B3 and 2B12, but not control antibodies, inhibited the cleavage of sAPPα by β-secretase in a cell-free assay where effects of antibody internalisation and intracellular degradation were excluded. 2B3 virtually abolished this cleavage. In addition, levels of C-terminal APP fragments, βCTF, generated following β-secretase cleavage, were significantly reduced in cells after incubation with 2B3. These results strongly suggest that anti-cleavage site antibodies can generically reduce Aβ levels via inhibition of β-secretase by steric hindrance and may provide a novel alternative therapy for AD. PMID:21122073

The effect of pressure on the hydration structure around hydrophobic solute: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Sarma, Rahul; Paul, Sandip

2012-03-01

Molecular dynamics simulations are performed to study the effects of pressure on the hydrophobic interactions between neopentane molecules immersed in water. Simulations are carried out for five different pressure values ranging from 1 atm to 8000 atm. From potential of mean force calculations, we find that with enhancement of pressure, there is decrease in the well depth of contact minimum (CM) and the relative stability of solvent separated minimum over CM increases. Lower clustering of neopentane at high pressure is also observed in association constant and cluster-structure analysis. Selected site-site radial distribution functions suggest efficient packing of water molecules around neopentane molecules at elevated pressure. The orientational profile calculations of water molecules show that the orientation of water molecules in the vicinity of solute molecule is anisotropic and this distribution becomes flatter as we move away from the solute. Increasing pressure slightly changes the water distribution. Our hydrogen bond properties and dynamics calculations reveal pressure-induced formation of more and more number of water molecules with five and four hydrogen bond at the expense of breaking of two and three hydrogen bonded water molecules. We also find lowering of water-water continuous hydrogen bond lifetime on application of pressure. Implication of these results for relative dispersion of hydrophobic molecules at high pressure are discussed.

THE PRODUCTION OF HYDROGEN PEROXIDE BY HIGH OXYGEN PRESSURES

PubMed Central

Gilbert, Daniel L.; Gerschman, Rebeca; Ruhm, K. Barclay; Price, William E.

1958-01-01

Hydrogen peroxide is formed in solutions of glutathione exposed to oxygen. This hydrogen peroxide or its precursors will decrease the viscosity of polymers like desoxyribonucleic acid and sodium alginate. Further knowledge of the mechanism of these chemical effects of oxygen might further the understanding of the biological effects of oxygen. This study deals with the rate of solution of oxygen and with the decomposition of hydrogen peroxide in chemical systems exposed to high oxygen pressures. At 6 atmospheres, the absorption coefficient for oxygen into water was about 1 cm./hour and at 143 atmospheres, it was about 2 cm./hour; the difference probably being due to the modus operandi. The addition of cobalt (II), manganese (II), nickel (II), or zinc ions in glutathione (GSH) solutions exposed to high oxygen pressure decreased the net formation of hydrogen peroxide and also the reduced glutathione remaining in the solution. Studies on hydrogen peroxide decomposition indicated that these ions act probably by accelerating the hydrogen perioxide oxidation of glutathione. The chelating agent, ethylenediaminetetraacetic acid disodium salt, inhibited the oxidation of GSH exposed to high oxygen pressure for 14 hours. However, indication that oxidation still occurred, though at a much slower rate, was found in experiments lasting 10 weeks. Thiourea decomposed hydrogen peroxide very rapidly. When GSH solutions were exposed to high oxygen pressure, there was oxidation of the GSH, which became relatively smaller with increasing concentrations of GSH. PMID:13525677

The study of latent heat transport characteristics by solid particles and saccharide solution mixtures

NASA Astrophysics Data System (ADS)

Morita, Shin-ichi; Hayamizu, Yasutaka; Inaba, Hideo

2011-06-01

The purpose of this study is the development of latent heat transport system by using the mixture of the minute latent heat storage materials and the saccharine solution as medium. The experimental studies are carried out by the evaluation of viscosity and pressure loss in a pipe. Polyethylene (P.E.) is selected as the dispersed minute material that has closeness density (920kg/m3) of ice (917kg/m3). D-sorbitol and D-xylose solutions are picked as continuum phase of the test mixture. The concentration of D-sorbitol solution is set 48mass% from measured results of saturation solubility and the melting point. 40mass% solution of D-xylose is selected as the other test continuum phase. The non-ion surfactant, EA157 Dai-ichiseiyaku CO. Ltd, is used in order to prevent of dispersed P.E. powder cohere. The pressure loss of test mixture is measured by the straight circular pipe that has smooth inner surface. The measuring length for pressure loss is 1000 mm, and the inner diameter of pipe is 15mm. The accuracy of experiment apparatus for measuring pressure loss is within ±5%. The pressure loss data is estimated by the relationship between the heat transport ratio and the required pump power. It is clarified that the optimum range of mixing ratio exists over 10mass% of latent heat storage material.

Physics of lithium bromide (LiBr) solution dewatering through vapor venting membranes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Isfahani, RN; Fazeli, A; Bigham, S

2014-01-01

The physics of water desorption from a lithium bromide (LiBr) solution flow through an array of microchannels capped by a porous membrane is studied. The membrane allows the vapor to exit the flow and retains the liquid. Effects of different parameters such as wall temperature, solution and vapor pressures, and solution mass flux on the desorption rate were studied. Two different mechanisms of desorption are analyzed. These mechanisms consisted of: (1) direct diffusion of water molecules out of the solution and their subsequent flow through the membrane and (2) formation of water vapor bubbles within the solution and their ventingmore » through the membrane. Direct diffusion was the dominant desorption mode at low surface temperatures and its magnitude was directly related to the vapor pressure, the solution concentration, and the heated wall temperature. Desorption at the boiling regime was predominantly controlled by the solution flow pressure and mass flux. Microscale visualization studies suggested that at a critical mass flux, some bubbles are carried out of the desorber through the solution microchannels rather than being vented through the membrane. Overall, an order of magnitude higher desorption rate compare to a previous study on a membrane-based desorber was achieved. Published by Elsevier Ltd.« less

The osmotic pressure of the maintenance medium and reproduction of poliovirus.

PubMed

Tolskaya, E A; Agol, V I; Voroshilova, M K; Lipskaya, G Y

1966-08-01

When the osmotic pressure of the maintenance medium is decreased, poliovirus reproduction is inhibited. Poliovirus strains may vary in their sensitivity to the effect of hypotonic solutions. Mutants have been selected (designated as osm mutants) the reproduction of which is characterized by particularly high resistance to media with reduced osmotic pressure. Initial stages of the virus-cell interaction proceed at similar rates in physiologic and hypotonic solutions. Reactions sensitive to hypotonic solutions take place in the second half of the latent period and during the stage of virus maturation. The multiplication of viruses in moderately hypotonic solutions exhibits a marked dependence upon the temperature and the presence of cystine in the medium, even though these factors have relatively small influence upon the reproduction of the viruses in isotonic solutions. Despite complete cessation of the production of infectious virus in certain hypotonic media, there is a considerable synthesis of virus-induced RNA. At least some of the RNA produced under these conditions is infectious. With a further decrease of the osmotic pressure of the medium the synthesis of the viral RNA is inhibited. Some possible explanations of the observed facts are briefly discussed.

XAFS measurements on zinc chloride aqueous solutions from ambient to supercritical conditions using the diamond anvil cell

USGS Publications Warehouse

Mayanovic, Robert A.; Anderson, Alan J.; Bassett, William A.; Chou, I.-Ming

1999-01-01

The structure and bonding properties of metal complexes in subcritical and supercritical fluids are still largely unknown. Conventional high pressure and temperature cell designs impose considerable limitations on the pressure, temperature, and concentration of metal salts required for measurements on solutions under supercritical conditions. In this study, we demonstrate the first application of the diamond anvil cell, specially designed for x-ray absorption studies of first-row transition metal ions in supercritical fluids. Zn K-edge XAFS spectra were measured from aqueous solutions of 1-2m ZnCl2 and up to 6m NaCl, at temperatures ranging from 25-660 ??C and pressures up to 800 MPa. Our results indicate that the ZnCl42- complex is predominant in the 1m ZnCl2/6m NaCl solution, while ZnCl2(H2O)2 is similarly predominant in the 2m ZnCl2 solution, at all temperatures and pressures. The Zn-Cl bond length of both types of chlorozinc(II) complexes was found to decrease at a rate of about 0.01 A??/100 ??C.

Separase is recruited to mitotic chromosomes to dissolve sister chromatid cohesion in a DNA-dependent manner.

PubMed

Sun, Yuxiao; Kucej, Martin; Fan, Heng-Yu; Yu, Hong; Sun, Qing-Yuan; Zou, Hui

2009-04-03

Sister chromatid separation is triggered by the separase-catalyzed cleavage of cohesin. This process is temporally controlled by cell-cycle-dependent factors, but its biochemical mechanism and spatial regulation remain poorly understood. We report that cohesin cleavage by human separase requires DNA in a sequence-nonspecific manner. Separase binds to DNA in vitro, but its proteolytic activity, measured by its autocleavage, is not stimulated by DNA. Instead, biochemical characterizations suggest that DNA mediates cohesin cleavage by bridging the interaction between separase and cohesin. In human cells, a fraction of separase localizes to the mitotic chromosome. The importance of the chromosomal DNA in cohesin cleavage is further demonstrated by the observation that the cleavage of the chromosome-associated cohesins is sensitive to nuclease treatment. Our observations explain why chromosome-associated cohesins are specifically cleaved by separase and the soluble cohesins are left intact in anaphase.

A density functional theory study on peptide bond cleavage at aspartic residues: direct vs cyclic intermediate hydrolysis.

PubMed

Sang-aroon, Wichien; Amornkitbamrung, Vittaya; Ruangpornvisuti, Vithaya

2013-12-01

In this work, peptide bond cleavages at carboxy- and amino-sides of the aspartic residue in a peptide model via direct (concerted and step-wise) and cyclic intermediate hydrolysis reaction pathways were explored computationally. The energetics, thermodynamic properties, rate constants, and equilibrium constants of all hydrolysis reactions, as well as their energy profiles were computed at the B3LYP/6-311++G(d,p) level of theory. The result indicated that peptide bond cleavage of the Asp residue occurred most preferentially via the cyclic intermediate hydrolysis pathway. In all reaction pathways, cleavage of the peptide bond at the amino-side occurred less preferentially than at the carboxy-side. The overall reaction rate constants of peptide bond cleavage of the Asp residue at the carboxy-side for the assisted system were, in increasing order: concerted < step-wise < cyclic intermediate.

Detection of nucleic acids by multiple sequential invasive cleavages

DOEpatents

Hall, Jeff G.; Lyamichev, Victor I.; Mast, Andrea L.; Brow, Mary Ann D.

1999-01-01

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

Detection of nucleic acids by multiple sequential invasive cleavages 02

DOEpatents

Hall, Jeff G.; Lyamichev, Victor I.; Mast, Andrea L.; Brow, Mary Ann D.

2002-01-01

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

Detection of nucleic acids by multiple sequential invasive cleavages

DOEpatents

Hall, Jeff G; Lyamichev, Victor I; Mast, Andrea L; Brow, Mary Ann D

2012-10-16

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

Saturation curve of SiO{sub 2} component in rutile-type GeO{sub 2}: A recoverable high-temperature pressure standard from 3 GPa to 10 GPa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leinenweber, Kurt, E-mail: kurtl@asu.edu; Gullikson, Amber L.; Stoyanov, Emil

2015-09-15

The accuracy and precision of pressure measurements and the pursuit of reliable and readily available pressure scales at simultaneous high temperatures and pressures are still topics in development in high pressure research despite many years of work. In situ pressure scales based on x-ray diffraction are widely used but require x-ray access, which is lacking outside of x-ray beam lines. Other methods such as fixed points require several experiments to bracket a pressure calibration point. In this study, a recoverable high-temperature pressure gauge for pressures ranging from 3 GPa to 10 GPa is presented. The gauge is based on themore » pressure-dependent solubility of an SiO{sub 2} component in the rutile-structured phase of GeO{sub 2} (argutite), and is valid when the argutite solid solution coexists with coesite. The solid solution varies strongly in composition, mainly in pressure but also somewhat in temperature, and the compositional variations are easily detected by x-ray diffraction of the recovered products because of significant changes in the lattice parameters. The solid solution is measured here on two isotherms, one at 1200 °C and the other at 1500 °C, and is developed as a pressure gauge by calibrating it against three fixed points for each temperature and against the lattice parameter of MgO measured in situ at a total of three additional points. A somewhat detailed thermodynamic analysis is then presented that allows the pressure gauge to be used at other temperatures. This provides a way to accurately and reproducibly evaluate the pressure in high pressure experiments and applications in this pressure-temperature range, and could potentially be used as a benchmark to compare various other pressure scales under high temperature conditions. - Graphical abstract: The saturation curve of SiO{sub 2} in TiO{sub 2} shows a strong pressure dependence and a strong dependence of unit cell volume on composition. This provides an opportunity to use this saturation curve as a measurement of pressure during a high-pressure experiment. The curve is a sensitive measure of pressure from 3 GPa to 10 GPa at high temperatures. The pressure is derived from lattice parameter measurements on the recovered solid solution, meaning that in-situ measurements are not necessary to evaluate the pressure of the experiment. - Highlights: • The unit cell of a saturated GeO{sub 2}–SiO{sub 2} solid solution is used as a pressure sensor. • We measure nine bracketed pressure points on the GeO{sub 2}–SiO{sub 2} saturation surface. • We provide a pressure calibrant from 3 GPa to 10 GPa at two temperatures. • Four points are measured at 1200 °C and five points at 1500 °C. • A thermodynamic model is developed for use of the calibrant at other temperatures.« less

Highly stable aerosol generator

DOEpatents

DeFord, H.S.; Clark, M.L.

1981-11-03

An improved compressed air nebulizer has been developed such that a uniform aerosol particle size and concentration may be produced over long time periods. This result is achieved by applying a vacuum pressure to the makeup assembly and by use of a vent tube between the atmosphere and the makeup solution. By applying appropriate vacuum pressures to the makeup solution container and by proper positioning of the vent tube, a constant level of aspirating solution may be maintained within the aspirating assembly with aspirating solution continuously replaced from the makeup solution supply. This device may also be adapted to have a plurality of aerosol generators and only one central makeup assembly. 2 figs.

Highly stable aerosol generator

DOEpatents

DeFord, Henry S.; Clark, Mark L.

1981-01-01

An improved compressed air nebulizer has been developed such that a uniform aerosol particle size and concentration may be produced over long time periods. This result is achieved by applying a vacuum pressure to the makeup assembly and by use of a vent tube between the atmosphere and the makeup solution. By applying appropriate vacuum pressures to the makeup solution container and by proper positioning of the vent tube, a constant level of aspirating solution may be maintained within the aspirating assembly with aspirating solution continuously replaced from the makeup solution supply. This device may also be adapted to have a plurality of aerosol generators and only one central makeup assembly.

Laser-induced breakdown spectroscopy of bulk aqueous solutions at oceanic pressures: evaluation of key measurement parameters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Michel, Anna P. M.; Lawrence-Snyder, Marion; Angel, S. Michael

The development of in situ chemical sensors is critical for present-day expeditionary oceanography and the new mode of ocean observing systems that we are entering. New sensors take a significant amount of time to develop; therefore, validation of techniques in the laboratory for use in the ocean environment is necessary. Laser-induced breakdown spectroscopy (LIBS) is a promising in situ technique for oceanography. Laboratory investigations on the feasibility of using LIBS to detect analytes in bulk liquids at oceanic pressures were carried out. LIBS was successfully used to detect dissolved Na, Mn, Ca, K, and Li at pressures up to 2.76x107more » Pa. The effects of pressure, laser-pulse energy, interpulse delay, gate delay, temperature, and NaCl concentration on the LIBS signal were examined. An optimal range of laser-pulse energies was found to exist for analyte detection in bulk aqueous solutions at both low and high pressures. No pressure effect was seen on the emission intensity for Ca and Na, and an increase in emission intensity with increased pressure was seen for Mn. Using the dual-pulse technique for several analytes, a very short interpulse delay resulted in the greatest emission intensity. The presence of NaCl enhanced the emission intensity for Ca, but had no effect on peak intensity of Mn or K. Overall, increased pressure, the addition of NaCl to a solution, and temperature did not inhibit detection of analytes in solution and sometimes even enhanced the ability to detect the analytes. The results suggest that LIBS is a viable chemical sensing method for in situ analyte detection in high-pressure environments such as the deep ocean.« less

Quasiblack holes with pressure: Relativistic charged spheres as the frozen stars

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lemos, Jose P. S.; Zanchin, Vilson T.; Centro de Ciencias Naturais e Humanas, Universidade Federal do ABC, Rua Santa Adelia 166, 09210-170 Santo Andre, SP, Brazil and Coordenadoria de Astronomia e Astrofisica, Observatorio Nacional-MCT, Rua General Jose Cristino 77, 20921-400 Rio de Janeiro

2010-06-15

In general relativity coupled to Maxwell's electromagnetism and charged matter, when the gravitational potential W{sup 2} and the electric potential field {phi} obey a relation of the form W{sup 2}=a(-{epsilon}{phi}+b){sup 2}+c, where a, b, and c are arbitrary constants, and {epsilon}={+-}1 (the speed of light c and Newton's constant G are put to one), a class of very interesting electrically charged systems with pressure arises. We call the relation above between W and {phi}, the Weyl-Guilfoyle relation, and it generalizes the usual Weyl relation, for which a=1. For both, Weyl and Weyl-Guilfoyle relations, the electrically charged fluid, if present, maymore » have nonzero pressure. Fluids obeying the Weyl-Guilfoyle relation are called Weyl-Guilfoyle fluids. These fluids, under the assumption of spherical symmetry, exhibit solutions which can be matched to the electrovacuum Reissner-Nordstroem spacetime to yield global asymptotically flat cold charged stars. We show that a particular spherically symmetric class of stars found by Guilfoyle has a well-behaved limit which corresponds to an extremal Reissner-Nordstroem quasiblack hole with pressure, i.e., in which the fluid inside the quasihorizon has electric charge and pressure, and the geometry outside the quasihorizon is given by the extremal Reissner-Nordstroem metric. The main physical properties of such charged stars and quasiblack holes with pressure are analyzed. An important development provided by these stars and quasiblack holes is that without pressure the solutions, Majumdar-Papapetrou solutions, are unstable to kinetic perturbations. Solutions with pressure may avoid this instability. If stable, these cold quasiblack holes with pressure, i.e., these compact relativistic charged spheres, are really frozen stars.« less

Development of Personalized Fitting Device With 3-Dimensional Solution for Prevention of NIV Oronasal Mask-Related Pressure Ulcers.

PubMed

Shikama, Maiko; Nakagami, Gojiro; Noguchi, Hiroshi; Mori, Taketoshi; Sanada, Hiromi

2018-05-22

Pressure ulcers related to oronasal masks used with noninvasive ventilation (NIV), along with patient discomfort, occur due to improper fit of the mask. We developed a personalized fitting device using a 3-dimensional (3D) scanning solution to prevent the formation of NIV mask-related pressure ulcers. This study aimed to evaluate the effectiveness of the proposed personalized fitting device. We conducted a randomized crossover experimental study of 20 healthy participants to study the use of this personalized fitting device between the face and an NIV mask designed with 3D solutions. The fitting device was not used under the NIV mask for the control. The outcome measures were the presence of blanchable erythema, standardized redness intensity, discomfort level, and contact pressure. The incidence of blanchable erythema and standardized redness intensity values were significantly lower for subjects who used the fitting device when worn for 30 min ( P < .001). The discomfort levels at the forehead, nasal bridge, and both cheeks, as well as leakage, were significantly reduced as well ( P = .008, P < .001, P = .001, P = .002, P = .001, P = .02, P < .001, P < .001, P < .001). Contact pressure at the nasal bridge, where pressure ulcers most frequently develop, was significantly decreased with the fitting device ( P < .001). Personalized fitting devices that incorporate 3D scanning solutions may contribute to the prevention of NIV mask-related pressure ulcers and the reduction of discomfort. Copyright © 2018 by Daedalus Enterprises.

Electron attachment-induced DNA single-strand breaks at the pyrimidine sites

PubMed Central

Gu, Jiande; Wang, Jing; Leszczynski, Jerzy

2010-01-01

To elucidate the contribution of pyrimidine in DNA strand breaks caused by low-energy electrons (LEEs), theoretical investigations of the LEE attachment-induced C3′–O3′, and C5′–O5′ σ bond as well as N-glycosidic bond breaking of 2′-deoxycytidine-3′,5′-diphosphate and 2′-deoxythymidine-3′,5′-diphosphate were performed using the B3LYP/DZP++ approach. The base-centered radical anions are electronically stable enough to assure that either the C–O or glycosidic bond breaking processes might compete with the electron detachment and yield corresponding radical fragments and anions. In the gas phase, the computed glycosidic bond breaking activation energy (24.1 kcal/mol) excludes the base release pathway. The low-energy barrier for the C3′–O3′ σ bond cleavage process (∼6.0 kcal/mol for both cytidine and thymidine) suggests that this reaction pathway is the most favorable one as compared to other possible pathways. On the other hand, the relatively low activation energy barrier (∼14 kcal/mol) for the C5′–O5′ σ bond cleavage process indicates that this bond breaking pathway could be possible, especially when the incident electrons have relatively high energy (a few electronvolts). The presence of the polarizable medium greatly increases the activation energies of either C–O σ bond cleavage processes or the N-glycosidic bond breaking process. The only possible pathway that dominates the LEE-induced DNA single strands in the presence of the polarizable surroundings (such as in an aqueous solution) is the C3′–O3′ σ bond cleavage (the relatively low activation energy barrier, ∼13.4 kcal/mol, has been predicted through a polarizable continuum model investigation). The qualitative agreement between the ratio for the bond breaks of C5′–O5′, C3′–O3′ and N-glycosidic bonds observed in the experiment of oligonucleotide tetramer CGAT and the theoretical sequence of the bond breaking reaction pathways have been found. This consistency between the theoretical predictions and the experimental observations provides strong supportive evidences for the base-centered radical anion mechanism of the LEE-induced single-strand bond breaking around the pyrimidine sites of the DNA single strands. PMID:20430827

Theoretical Proposal for the Whole Phosphate Diester Hydrolysis Mechanism Promoted by a Catalytic Promiscuous Dinuclear Copper(II) Complex.

PubMed

Esteves, Lucas F; Rey, Nicolás A; Dos Santos, Hélio F; Costa, Luiz Antônio S

2016-03-21

The catalytic mechanism that involves the cleavage of the phosphate diester model BDNPP (bis(2,4-dinitrophenyl) phosphate) catalyzed through a dinuclear copper complex is investigated in the current study. The metal complex was originally designed to catalyze catechol oxidation, and it showed an interesting catalytic promiscuity case in biomimetic systems. The current study investigates two different reaction mechanisms through quantum mechanics calculations in the gas phase, and it also includes the solvent effect through PCM (polarizable continuum model) single-point calculations using water as solvent. Two mechanisms are presented in order to fully describe the phosphate diester hydrolysis. Mechanism 1 is of the S(N)2 type, which involves the direct attack of the μ-OH bridge between the two copper(II) ions toward the phosphorus center, whereas mechanism 2 is the process in which hydrolysis takes place through proton transfer between the oxygen atom in the bridging hydroxo ligand and the other oxygen atom in the phosphate model. Actually, the present theoretical study shows two possible reaction paths in mechanism 1. Its first reaction path (p1) involves a proton transfer that occurs immediately after the hydrolytic cleavage, so that the proton transfer is the rate-determining step, which is followed by the entry of two water molecules. Its second reaction path (p2) consists of the entry of two water molecules right after the hydrolytic cleavage, but with no proton transfer; thus, hydrolytic cleavage is the rate-limiting step. The most likely catalytic path occurs in mechanism 1, following the second reaction path (p2), since it involves the lowest free energy activation barrier (ΔG(⧧) = 23.7 kcal mol(-1), in aqueous solution). A kinetic analysis showed that the experimental k(obs) value of 1.7 × 10(-5) s(-1) agrees with the calculated value k1 = 2.6 × 10(-5) s(-1); the concerted mechanism is kinetically favorable. The KIE (kinetic isotope effect) analysis applied to the second reaction path (p2) in mechanism 1 was also taken into account to assess the changes that take place in TS1-i (transition state of mechanism 1) and to perfectly characterize the mechanism described herein.

Effects of microstructural variation on Charpy impact properties in heavy-section Mn-Mo-Ni low alloy steel for reactor pressure vessel

NASA Astrophysics Data System (ADS)

Hong, Seokmin; Song, Jaemin; Kim, Min-Chul; Choi, Kwon-Jae; Lee, Bong-Sang

2016-03-01

The effects of microstructural changes in heavy-section Mn-Mo-Ni low alloy steel on Charpy impact properties were investigated using a 210 mm thick reactor pressure vessel. Specimens were sampled from 5 different positions at intervals of 1/4 thickness from the inner surface to the outer surface. A detailed microstructural analysis of impact-fractured specimens showed that coarse carbides along the lath boundaries acted as fracture initiation sites, and cleavage cracks deviated at prior-austenite grain boundaries and bainite lath boundaries. Upper shelf energy was higher and energy transition temperature was lower at the surface positon, where fine bainitic microstructure with homogeneously distributed fine carbides were present. Toward the center, coarse upper bainite and precipitation of coarse inter-lath carbides were observed, which deteriorated impact properties. At the 1/4T position, the Charpy impact properties were worse than those at other positions owing to the combination of elongated-coarse inter-lath carbides and large effective grain size.

Fabric changes and their influence on P-wave velocity patterns—examples from a polyphase deformed orthogneiss

NASA Astrophysics Data System (ADS)

Siegesmund, S.; Vollbrecht, A.; Pros, Z.

1993-10-01

The complete P-wave velocity distribution, preferred orientation of rock-forming minerals and microcracks of two differently deformed orthogneisses from the Kutna Hora Crystalline Unit were investigated. The complete symmetry of P-wave velocities were determined as a function of confining pressure on the basis of 132 independent propagation directions up to 400 MPa. The two samples are of almost identical mineralogical composition, but exhibit different fabrics which can be related to different positions within a large-scale fold structure. The symmetry of the Vp-diagrams change from nearly transversely isotropic for the sample from the limb area to orthorhombic for the sample from the hinge zone, which shows an additional crenulation cleavage. This change of symmetry is observed at all pressure levels. Reorientation of the main velocity directions ( Vpmin, Vpmax, Kpint) between hinge and limb is controlled by the microcrack fabric and the texture of the rock-forming minerals. This can cause significant differences in reflectivity related to fabric changes within large-scale folds.

Optical and Transport Properties of Energetic Materials

NASA Astrophysics Data System (ADS)

Choi, Chang Sun

1990-01-01

The densities of Hydroxyl ammonium nitrate (HAN) based fast reacting liquids were measured as a function of pressure (up to 4.83 kbars) at several temperatures and the results of density measurements were fit to the Tait equation. Also the shear viscosities of this liquid were measured as a function of both pressure and temperature. The free volume model was applied to explain behavior of the shear viscosity with the assumption that only the reference temperature (T_0) in the Fulcher (1925), WLF (Williams, Landel, and Ferry) and Angell equations depends on pressure. The general relation to predict viscosity of this liquid at any temperature and pressure was derived and the difference between expected and measured values are about 5%. The phase diagrams of the HAN solution, Triethanol ammonium nitrate (TEAN) solution and LP-1845 were obtained through Differential Scanning Calorimetry (DSC) measurements. The TEAN solution has a eutectic temperature in the vicinity of 260^circK. The measured phase diagrams are in good agreement with the calculated phase diagrams. The TEAN solutions show a large supercooling effect. Some phase separation was observed in the TEAN solutions and this separation was believed to be due to eutectic composition of the TEAN solution. The expected freezing temperature of LP-1845 was almost the same with the calculated T_0 from the viscosity data. Raman spectra from the HAN solution, TEAN solution and LP-1845 were measured. Every peak in the spectra was assigned. These solutions show various interactions, such as ion-ion pairing and ion-water interaction. The strongest peak was a NO_3^- symmetric stretch mode at 1050 cm^{-1}. The time correlation functions were calculated from the Raman spectra of the 1050 cm^{-1} peak. The correlation time, which can be calculated from the linewidth, become shorter with decreasing temperatures and with increasing concentrations. The Kubo's stochastic theory explains the correlation functions very well if the solution is relatively dilute. The pressure dependence of the reaction rate was estimated by using the density data and Raman peak shift data.

A new approximation for pore pressure accumulation in marine sediment due to water waves

NASA Astrophysics Data System (ADS)

Jeng, D.-S.; Seymour, B. R.; Li, J.

2007-01-01

The residual mechanism of wave-induced pore water pressure accumulation in marine sediments is re-examined. An analytical approximation is derived using a linear relation for pore pressure generation in cyclic loading, and mistakes in previous solutions (Int. J. Numer. Anal. Methods Geomech. 2001; 25:885-907; J. Offshore Mech. Arctic Eng. (ASME) 1989; 111(1):1-11) are corrected. A numerical scheme is then employed to solve the case with a non-linear relation for pore pressure generation. Both analytical and numerical solutions are verified with experimental data (Laboratory and field investigation of wave-sediment interaction. Joseph H. Defrees Hydraulics Laboratory, School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 1983), and provide a better prediction of pore pressure accumulation than the previous solution (J. Offshore Mech. Arctic Eng. (ASME) 1989; 111(1):1-11). The parametric study concludes that the pore pressure accumulation and use of full non-linear relation of pore pressure become more important under the following conditions: (1) large wave amplitude, (2) longer wave period, (3) shallow water, (4) shallow soil and (5) softer soils with a low consolidation coefficient. Copyright

Dynamics of a Pipeline under the Action of Internal Shock Pressure

NASA Astrophysics Data System (ADS)

Il'gamov, M. A.

2017-11-01

The static and dynamic bending of a pipeline in the vertical plane under the action of its own weight is considered with regard to the interaction of the internal pressure with the curvature of the axial line and the axisymmetric deformation. The pressure consists of a constant and timevarying parts and is assumed to be uniformly distributed over the entire span between the supports. The pipeline reaction to the stepwise increase in the pressure is analyzed in the case where it is possible to determine the exact solution of the problem. The initial stage of bending determined by the smallness of elastic forces as compared to the inertial forces is introduced into the consideration. At this stage, the solution is sought in the form of power series and the law of pressure variation can be arbitrary. This solution provides initial conditions for determining the further process. The duration of the inertial stage is compared with the times of sharp changes of the pressure and the shock waves in fluids. The structure parameters are determined in the case where the shock pressure is accepted only by the inertial forces in the pipeline.

Role of partial miscibility on pressure buildup due to constant rate injection of CO2 into closed and open brine aquifers

NASA Astrophysics Data System (ADS)

Mathias, Simon A.; Gluyas, Jon G.; GonzáLez MartíNez de Miguel, Gerardo J.; Hosseini, Seyyed A.

2011-12-01

This work extends an existing analytical solution for pressure buildup because of CO2 injection in brine aquifers by incorporating effects associated with partial miscibility. These include evaporation of water into the CO2 rich phase and dissolution of CO2 into brine and salt precipitation. The resulting equations are closed-form, including the locations of the associated leading and trailing shock fronts. Derivation of the analytical solution involves making a number of simplifying assumptions including: vertical pressure equilibrium, negligible capillary pressure, and constant fluid properties. The analytical solution is compared to results from TOUGH2 and found to accurately approximate the extent of the dry-out zone around the well, the resulting permeability enhancement due to residual brine evaporation, the volumetric saturation of precipitated salt, and the vertically averaged pressure distribution in both space and time for the four scenarios studied. While brine evaporation is found to have a considerable effect on pressure, the effect of CO2 dissolution is found to be small. The resulting equations remain simple to evaluate in spreadsheet software and represent a significant improvement on current methods for estimating pressure-limited CO2 storage capacity.

An in vitro evaluation of the pressure generated during programmed intermittent epidural bolus injection at varying infusion delivery speeds.

PubMed

Klumpner, Thomas T; Lange, Elizabeth M S; Ahmed, Heena S; Fitzgerald, Paul C; Wong, Cynthia A; Toledo, Paloma

2016-11-01

Programmed intermittent bolus injection of epidural anesthetic solution results in decreased anesthetic consumption and better patient satisfaction compared with continuous infusion, presumably by better spread of the anesthetic solution in the epidural space. It is not known whether the delivery speed of the bolus injection influences analgesia outcomes. The objective of this in vitro study was to determine the pressure generated by a programmed intermittent bolus pump at 4 infusion delivery speeds through open-ended, single-orifice and closed-end, multiorifice epidural catheters. In vitro observational study. Not applicable. Not applicable. A CADD-Solis Pain Management System v3.0 with Programmed Intermittent Bolus Model 2110 was connected via a 3-way adapter to an epidural catheter and a digital pressure transducer. Pressures generated by delivery speeds of 100, 175, 300, and 400 mL/h of saline solution were tested with 4 epidural catheters (2 single orifice and 2 multiorifice). These runs were replicated on 5 pumps. Analysis of variance was used to compare the mean peak pressures of each delivery speed within each catheter group (single orifice and multiorifice). Thirty runs at each delivery speed were performed with each type of catheter for a total of 240 experimental runs. Peak pressure increased with increasing delivery speeds in both catheter groups (P<.001). Peak pressures were higher with the multiorifice catheter compared with the single-orifice catheter at all delivery speeds (P<.001, for all). Using a pump designed for programmed intermittent infusion boluses, the delivery speed of saline solution through epidural catheters was directly related to the peak pressures. Future work should evaluate whether differences in the delivery speed of anesthetic solution into the epidural space correlate with differences in the duration and quality of analgesia during programmed intermittent epidural bolus delivery. Copyright © 2016 Elsevier Inc. All rights reserved.

Detection of nucleic acid sequences by invader-directed cleavage

DOEpatents

Brow, Mary Ann D.; Hall, Jeff Steven Grotelueschen; Lyamichev, Victor; Olive, David Michael; Prudent, James Robert

1999-01-01

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The 5' nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based by charge.

Hierarchical recruitment of ribosomal proteins and assembly factors remodels nucleolar pre-60S ribosomes.

PubMed

Biedka, Stephanie; Micic, Jelena; Wilson, Daniel; Brown, Hailey; Diorio-Toth, Luke; Woolford, John L

2018-04-24

Ribosome biogenesis involves numerous preribosomal RNA (pre-rRNA) processing events to remove internal and external transcribed spacer sequences, ultimately yielding three mature rRNAs. Removal of the internal transcribed spacer 2 spacer RNA is the final step in large subunit pre-rRNA processing and begins with endonucleolytic cleavage at the C 2 site of 27SB pre-rRNA. C 2 cleavage requires the hierarchical recruitment of 11 ribosomal proteins and 14 ribosome assembly factors. However, the function of these proteins in C 2 cleavage remained unclear. In this study, we have performed a detailed analysis of the effects of depleting proteins required for C 2 cleavage and interpreted these results using cryo-electron microscopy structures of assembling 60S subunits. This work revealed that these proteins are required for remodeling of several neighborhoods, including two major functional centers of the 60S subunit, suggesting that these remodeling events form a checkpoint leading to C 2 cleavage. Interestingly, when C 2 cleavage is directly blocked by depleting or inactivating the C 2 endonuclease, assembly progresses through all other subsequent steps. © 2018 Biedka et al.

Selection of hammerhead ribozymes for optimum cleavage of interleukin 6 mRNA.

PubMed Central

Hendrix, C; Anné, J; Joris, B; Van Aerschot, A; Herdewijn, P

1996-01-01

Four GUC triplets in the coding region of the MRNA of interleukin 6 (IL-6) were examined for their suitabilty to serve as a target for hammerhead ribozome-mediated cleavage. This selection procedure was performed with the intention to downregulate IL-6 production as a potential treatment of those diseases in which IL-6 overexpression is involved. Hammerhead ribozymes and their respective short synthetic substrates (19-mers) were synthesized for these four GUC triplets. Notwithstanding the identical catalytic core sequences, the difference in base composition of the helices involved in substrate binding caused substantial variation in cleavage activity. The cleavage reactions on the 1035 nucleotide IL-6 mRNA transcript revealed that two ribozymes were able to cleave this substrate, showing a decrease in catalytic efficiency to 1/30 and 1/300 of the short substrate. This study indicates that the GUC triplet located at nucleotide 510 of the mRNA of IL-6 is the best site for hammerhead ribozyme-mediated cleavage. We suggest that in future targeting of chemically modified hammerhead ribosomes for cleavage of IL-6 RNA should be directed at this location. PMID:8670082

Pyrexia's effect on the CBG-cortisol thermocouple, rather than CBG cleavage, elevates the acute free cortisol response to TNF-α in humans.

PubMed

Nenke, Marni Anne; Nielsen, Signe Tellerup; Lehrskov, Louise Lang; Lewis, John Goodwyn; Rankin, Wayne; Møller, Kirsten; Torpy, David James

2017-03-01

Corticosteroid-binding globulin (CBG) cleavage promotes local cortisol delivery in inflammation. Enzymatic cleavage of high-affinity CBG to low-affinity CBG (haCBG to laCBG) occurs at inflammatory sites and is now measurable in vivo; however, the time kinetics of haCBG depletion following an inflammatory stimulus is unknown. Hence our aim was to determine the immediate effect of the key pro-inflammatory cytokine TNF-α on CBG levels and cleavage. We performed a crossover study of 12 healthy males receiving a TNF-α versus saline infusion, measuring total CBG, haCBG, laCBG and free and total cortisol hourly for 6 h. There was no change in total CBG or haCBG levels in the first 6 h of inflammation between the groups, suggesting that CBG cleavage is not activated nor is hepatic CBG production affected by TNF-α in this time frame. There was an early increase in the ratio of free:total cortisol, in association with pyrexia. This accords with data indicating that CBG acts a thermocouple in vivo, increasing free cortisol levels independent of elastase-driven cleavage.

Effect of the timing of first cleavage on in vitro developmental potential of nuclear-transferred bovine oocytes receiving cumulus and fibroblast cells.

PubMed

Amarnath, Dasari; Kato, Yoko; Tsunoda, Yukio

2007-06-01

The aim of the present study was to examine whether cumulus and fibroblast cell nuclear-transferred oocytes, which have high and low potential to develop into normal calves, respectively, are different in terms of in their patterns of timing of first cleavage and in their relationships between timing of first cleavage and in vitro developmental potential. The timing of first cleavage was similar in both types of nuclear-transferred and in vitro fertilized oocytes. More than 86% of the oocytes cleaved within 24 h after activation or in vitro fertilization; these oocytes contributed to more than 98% of the total number of blastocysts in all three groups. The potential of oocytes that cleaved at different intervals to develop into blastocysts differed among the groups. The developmental potential of the cumulus cell nuclear-transferred oocytes and in vitro fertilized oocytes decreased with the increase in time required for cleavage. Fibroblast cell nuclear-transferred oocytes that cleaved at 20 h, an intermediate cleaving time, had higher potential to develop into blastocysts. The results of the present study suggest that the type of donor nucleus used for nuclear transfer affects the timing of first cleavage.

Functional Insights Revealed by the Kinetic Mechanism of CRISPR/Cas9.

PubMed

Raper, Austin T; Stephenson, Anthony A; Suo, Zucai

2018-02-28

The discovery of prokaryotic adaptive immunity prompted widespread use of the RNA-guided clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) endonuclease Cas9 for genetic engineering. However, its kinetic mechanism remains undefined, and details of DNA cleavage are poorly characterized. Here, we establish a kinetic mechanism of Streptococcus pyogenes Cas9 from guide-RNA binding through DNA cleavage and product release. Association of DNA to the binary complex of Cas9 and guide-RNA is rate-limiting during the first catalytic turnover, while DNA cleavage from a pre-formed ternary complex of Cas9, guide-RNA, and DNA is rapid. Moreover, an extremely slow release of DNA products essentially restricts Cas9 to be a single-turnover enzyme. By simultaneously measuring the contributions of the HNH and RuvC nuclease activities of Cas9 to DNA cleavage, we also uncovered the kinetic basis by which HNH conformationally regulates the RuvC cleavage activity. Together, our results provide crucial kinetic and functional details regarding Cas9 which will inform gene-editing experiments, guide future research to understand off-target DNA cleavage by Cas9, and aid in the continued development of Cas9 as a biotechnological tool.

Novel Functional Complexity of Polycystin-1 by GPS Cleavage In Vivo: Role in Polycystic Kidney Disease

PubMed Central

Kurbegovic, Almira; Kim, Hyunho; Xu, Hangxue; Yu, Shengqiang; Cruanès, Julie; Maser, Robin L.; Boletta, Alessandra; Trudel, Marie

2014-01-01

Polycystin-1 (Pc1) cleavage at the G protein-coupled receptor (GPCR) proteolytic site (GPS) is required for normal kidney morphology in humans and mice. We found a complex pattern of endogenous Pc1 forms by GPS cleavage. GPS cleavage generates not only the heterodimeric cleaved full-length Pc1 (Pc1cFL) in which the N-terminal fragment (NTF) remains noncovalently associated with the C-terminal fragment (CTF) but also a novel (Pc1) form (Pc1deN) in which NTF becomes detached from CTF. Uncleaved Pc1 (Pc1U) resides primarily in the endoplasmic reticulum (ER), whereas both Pc1cFL and Pc1deN traffic through the secretory pathway in vivo. GPS cleavage is not a prerequisite, however, for Pc1 trafficking in vivo. Importantly, Pc1deN is predominantly found at the plasma membrane of renal epithelial cells. By functional genetic complementation with five Pkd1 mouse models, we discovered that CTF plays a crucial role in Pc1deN trafficking. Our studies support GPS cleavage as a critical regulatory mechanism of Pc1 biogenesis and trafficking for proper kidney development and homeostasis. PMID:24958103

Propeptide cleavage conditions sortilin/neurotensin receptor-3 for ligand binding.

PubMed

Munck Petersen, C; Nielsen, M S; Jacobsen, C; Tauris, J; Jacobsen, L; Gliemann, J; Moestrup, S K; Madsen, P

1999-02-01

We recently reported the isolation and sequencing of sortilin, a new putative sorting receptor that binds receptor-associated protein (RAP). The luminal N-terminus of sortilin comprises a consensus sequence for cleavage by furin, R41WRR44, which precedes a truncation originally found in sortilin isolated from human brain. We now show that the truncation results from cellular processing. Sortilin is synthesized as a proform which, in late Golgi compartments, is converted to the mature receptor by furin-mediated cleavage of a 44 residue N-terminal propeptide. We further demonstrate that the propeptide exhibits pH-dependent high affinity binding to fully processed sortilin, that the binding is competed for by RAP and the newly discovered sortilin ligand neurotensin, and that prevention of propeptide cleavage essentially prevents binding of RAP and neurotensin. The findings evidence that the propeptide sterically hinders ligands from gaining access to overlapping binding sites in prosortilin, and that cleavage and release of the propeptide preconditions sortilin for full functional activity. Although proteolytic processing is involved in the maturation of several receptors, the described exposure of previously concealed ligand-binding sites after furin-mediated cleavage of propeptide represents a novel mechanism in receptor activation.

Propeptide cleavage conditions sortilin/neurotensin receptor-3 for ligand binding.

PubMed Central

Munck Petersen, C; Nielsen, M S; Jacobsen, C; Tauris, J; Jacobsen, L; Gliemann, J; Moestrup, S K; Madsen, P

1999-01-01

We recently reported the isolation and sequencing of sortilin, a new putative sorting receptor that binds receptor-associated protein (RAP). The luminal N-terminus of sortilin comprises a consensus sequence for cleavage by furin, R41WRR44, which precedes a truncation originally found in sortilin isolated from human brain. We now show that the truncation results from cellular processing. Sortilin is synthesized as a proform which, in late Golgi compartments, is converted to the mature receptor by furin-mediated cleavage of a 44 residue N-terminal propeptide. We further demonstrate that the propeptide exhibits pH-dependent high affinity binding to fully processed sortilin, that the binding is competed for by RAP and the newly discovered sortilin ligand neurotensin, and that prevention of propeptide cleavage essentially prevents binding of RAP and neurotensin. The findings evidence that the propeptide sterically hinders ligands from gaining access to overlapping binding sites in prosortilin, and that cleavage and release of the propeptide preconditions sortilin for full functional activity. Although proteolytic processing is involved in the maturation of several receptors, the described exposure of previously concealed ligand-binding sites after furin-mediated cleavage of propeptide represents a novel mechanism in receptor activation. PMID:9927419

Developing a capillary electrophoresis based method for dynamically monitoring enzyme cleavage activity using quantum dots-peptide assembly.

PubMed

Wang, Jianhao; Fan, Jie; Liu, Li; Ding, Shumin; Liu, Xiaoqian; Wang, Jianpeng; Gao, Liqian; Chattopadhaya, Souvik; Miao, Peng; Xia, Jiang; Qiu, Lin; Jiang, Pengju

2017-10-01

Herein, a novel assay has been developed for monitoring PreScission protease (His-PSP) mediated enzyme cleavage of ATTO 590 labeled peptide substrate (ATTO-LEV). This novel method is based on combining the use of capillary electrophoresis and fluorescence detection (CE-FL) to dynamically monitor the enzyme cleavage activity. A multivalent peptide substrate was first constructed by immobilizing His-tagged ATTO 590 labeled peptide substrate (ATTO-LEVH6) onto the surface of CdSe/ZnS quantum dots (QDs). Once successfully immobilized, the novel multivalent peptide substrate resulted in the Förster resonance energy transfer (FRET) from QDs to ATTO 590. The ATTO-LEVH6-QD assembly was then incubated with His-PSP to study the proteolytic cleavage of surface bound ATTO-LEVH6 by CE-FL. Our data suggests that PreScission-mediated proteolytic cleavage is enzyme concentration- and incubation time-dependent. By combining capillary electrophoresis, QDs and FRET, our study herein not only provides a new method for the detection and dynamically monitoring of PSP enzyme cleavage activity, but also can be extended to the detection of many other enzymes and proteases. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Imidazoline ring cleavage in 1,3,6,10-tetraazatetracyclo-(7. 3. 1. 0/sup 2,7/. 0/sup 6,13/)trideca-4,11-dienes, leading to the formation of diquinoxalino(1,2-. cap alpha. :2',3'-d)pyrrole derivatives

DOE Office of Scientific and Technical Information (OSTI.GOV)

Charushin, V.N.; Petrova, G.M.; Aleksandrov, G.G.

1987-10-01

Dibenzo(d,k)-1,3,6,10-tetraazatetracyclo(7.3.1.0/sup 2,7/.0/sup 6,13/) trideca-4,11-dienes undergo addition reactions at the C/sub (2)/ carbon atom with alcohols and thiols, accompanied by cleavage of the C-N bond of the imidazoline ring, to generate diquinoxalino(1,2-..cap alpha..:2',3'-d)pyrrole derivatives. /sup 1/H NMR spectra were recorded on Perkin-Elmer R 12B (60 MHz) and Bruker WH-90 spectrometer for CDCl/sub 3/ solutions at 40/sup 0/C and with TMS as internal standard. /sup 13/C NMR spectra were obtained on a Bruker WH-90 (22.62 MHz) spectrometer. /sup 13/C chemical shifts were measured relative to solvent signals (deltaCDCl/sub 3/ 77.0 ppm). /sup 13/C NMR spectra of compounds IIa and g were takenmore » using full spin-spin carbon-proton decoupling. In order to measure SSCC the spectrum was recorded both with proton coupling and also with selective decoupling of individual protons and their attached /sup 13/C carbon nuclei.« less

Improved Detection of Botulinum Neurotoxin Serotype A by Endopep-MS through Peptide Substrate Modification

PubMed Central

Wang, Dongxia; Baudys, Jakub; Ye, Yiming; Rees, Jon C.; Barr, John R.; Pirkle, James L.; Kalb, Suzanne R.

2015-01-01

Botulinum neurotoxins (BoNTs) are a family of seven toxin serotypes that are the most toxic substances known to man. Intoxication with BoNT causes flaccid paralysis and can lead to death if untreated with serotype specific antibodies. Supportive care, including ventilation, may be necessary. Rapid and sensitive detection of BoNT is necessary for timely clinical confirmation of clinical botulism. Previously, our laboratory developed a fast and sensitive mass spectrometry (MS) method termed the Endopep-MS assay. The BoNT serotypes are rapidly detected and differentiated by extracting the toxin with serotype specific antibodies and detecting the unique and serotype specific cleavage products of peptide substrates that mimic the sequence of the BoNT native targets. To further improve the sensitivity of the Endopep-MS assay, we report here the optimization of the substrate peptide for the detection of BoNT/A. Modifications on the terminal groups of the original peptide substrate with acetylation and amidation significantly improved the detection of BoNT/A cleavage products. The replacement of some internal amino acid residues with single or multiple substitutions led to further improvement. An optimized peptide increased assay sensitivity five fold with toxin spiked into buffer solution or different biological matrices. PMID:23017875

Shock wave emission from laser-induced cavitation bubbles in polymer solutions.

PubMed

Brujan, Emil-Alexandru

2008-09-01

The role of extensional viscosity on the acoustic emission from laser-induced cavitation bubbles in polymer solutions and near a rigid boundary is investigated by acoustic measurements. The polymer solutions consist of a 0.5% polyacrylamide (PAM) aqueous solution with a strong elastic component and a 0.5% carboxymethylcellulose (CMC) aqueous solution with a weak elastic component. A reduction of the maximum amplitude of the shock wave pressure and a prolongation of the oscillation period of the bubble were found in the elastic PAM solution. It might be caused by an increased resistance to extensional flow which is conferred upon the liquid by the polymer additive. In both polymer solutions, however, the shock pressure decays proportionally to r(-1) with increasing distance r from the emission centre.

A unifying model for elongational flow of polymer melts and solutions based on the interchain tube pressure concept

NASA Astrophysics Data System (ADS)

Wagner, Manfred Hermann; Rolón-Garrido, Víctor Hugo

2015-04-01

An extended interchain tube pressure model for polymer melts and concentrated solutions is presented, based on the idea that the pressures exerted by a polymer chain on the walls of an anisotropic confinement are anisotropic (M. Doi and S. F. Edwards, The Theory of Polymer Dynamics, Oxford University Press, New York, 1986). In a tube model with variable tube diameter, chain stretch and tube diameter reduction are related, and at deformation rates larger than the inverse Rouse time τR, the chain is stretched and its confining tube becomes increasingly anisotropic. Tube diameter reduction leads to an interchain pressure in the lateral direction of the tube, which is proportional to the 3rd power of stretch (G. Marrucci and G. Ianniruberto. Macromolecules 37, 3934-3942, 2004). In the extended interchain tube pressure (EIP) model, it is assumed that chain stretch is balanced by interchain tube pressure in the lateral direction, and by a spring force in the longitudinal direction of the tube, which is linear in stretch. The scaling relations established for the relaxation modulus of concentrated solutions of polystyrene in oligomeric styrene (M. H. Wagner, Rheol. Acta 53, 765-777, 2014, M. H. Wagner, J. Non-Newtonian Fluid Mech. http://dx.doi.org/10.1016/j.jnnfm.2014.09.017, 2014) are applied to the solutions of polystyrene (PS) in diethyl phthalate (DEP) investigated by Bhattacharjee et al. (P. K. Bhattacharjee et al., Macromolecules 35, 10131-10148, 2002) and Acharya et al. (M. V. Acharya et al. AIP Conference Proceedings 1027, 391-393, 2008). The scaling relies on the difference ΔTg between the glass-transition temperatures of the melt and the glass-transition temperatures of the solutions. ΔTg can be inferred from the reported zero-shear viscosities, and the BSW spectra of the solutions are obtained from the BSW spectrum of the reference melt with good accuracy. Predictions of the EIP model are compared to the steady-state elongational viscosity data of PS/DEP solutions. Except for a possible influence of solvent quality, linear and nonlinear viscoelasticity of entangled polystyrene solutions can thus be obtained from the linear-viscoelastic characteristics of a reference polymer melt and the shift of the glass transition temperature between melt and solution.

Experimental studies of methemoglobinemia due to percutaneous absorption of sodium nitrite.

PubMed

Saito, T; Takeichi, S; Nakajima, Y; Yukawa, N; Osawa, M

1997-01-01

Methemoglobin formation caused by a liniment solution containing sodium nitrite (30 g/L and 140 g/L) was studied in rats with normal or abraded skin, by measuring the methemoglobin concentration before and after application of liniment solutions with differing nitrite concentration. Each liniment solution (120 microL) was applied. Methemoglobin was measured for 180 minutes using a hemoximeter. Simultaneously, arterial blood pressure and cutaneous blood flow was measured by laser Doppler flowmetry and a pressure transducer. After the application of each liniment solution to normal skin, the methemoglobin concentration was not significantly modified depending on the time after application. Application of liniment solution to abraded skin (140 g/L) resulted in a marked increase in methemoglobin concentration. A remarkable decrease in arterial blood pressure and subcutaneous blood flow were observed after application of liniment solution to abraded skin (140 g/L). Each of these findings are characteristic of nitrite and they imply the percutaneous absorption of nitrite. Regardless of the nitrite concentration, the methemoglobin concentration was consistently higher in abraded skin than in normal skin.

Structure of the cleavage-activated prefusion form of the parainfluenza virus 5 fusion protein.

PubMed

Welch, Brett D; Liu, Yuanyuan; Kors, Christopher A; Leser, George P; Jardetzky, Theodore S; Lamb, Robert A

2012-10-09

The paramyxovirus parainfluenza virus 5 (PIV5) enters cells by fusion of the viral envelope with the plasma membrane through the concerted action of the fusion (F) protein and the receptor binding protein hemagglutinin-neuraminidase. The F protein folds initially to form a trimeric metastable prefusion form that is triggered to undergo large-scale irreversible conformational changes to form the trimeric postfusion conformation. It is thought that F refolding couples the energy released with membrane fusion. The F protein is synthesized as a precursor (F0) that must be cleaved by a host protease to form a biologically active molecule, F1,F2. Cleavage of F protein is a prerequisite for fusion and virus infectivity. Cleavage creates a new N terminus on F1 that contains a hydrophobic region, known as the FP, which intercalates target membranes during F protein refolding. The crystal structure of the soluble ectodomain of the uncleaved form of PIV5 F is known; here we report the crystal structure of the cleavage-activated prefusion form of PIV5 F. The structure shows minimal movement of the residues adjacent to the protease cleavage site. Most of the hydrophobic FP residues are buried in the uncleaved F protein, and only F103 at the newly created N terminus becomes more solvent-accessible after cleavage. The conformational freedom of the charged arginine residues that compose the protease recognition site increases on cleavage of F protein.

SKI2 mediates degradation of RISC 5'-cleavage fragments and prevents secondary siRNA production from miRNA targets in Arabidopsis.

PubMed

Branscheid, Anja; Marchais, Antonin; Schott, Gregory; Lange, Heike; Gagliardi, Dominique; Andersen, Stig Uggerhøj; Voinnet, Olivier; Brodersen, Peter

2015-12-15

Small regulatory RNAs are fundamental in eukaryotic and prokaryotic gene regulation. In plants, an important element of post-transcriptional control is effected by 20-24 nt microRNAs (miRNAs) and short interfering RNAs (siRNAs) bound to the ARGONAUTE1 (AGO1) protein in an RNA induced silencing complex (RISC). AGO1 may cleave target mRNAs with small RNA complementarity, but the fate of the resulting cleavage fragments remains incompletely understood. Here, we show that SKI2, SKI3 and SKI8, subunits of a cytoplasmic cofactor of the RNA exosome, are required for degradation of RISC 5', but not 3'-cleavage fragments in Arabidopsis. In the absence of SKI2 activity, many miRNA targets produce siRNAs via the RNA-dependent RNA polymerase 6 (RDR6) pathway. These siRNAs are low-abundant, and map close to the cleavage site. In most cases, siRNAs were produced 5' to the cleavage site, but several examples of 3'-spreading were also identified. These observations suggest that siRNAs do not simply derive from RDR6 action on stable 5'-cleavage fragments and hence that SKI2 has a direct role in limiting secondary siRNA production in addition to its function in mediating degradation of 5'-cleavage fragments. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Structure of the cleavage-activated prefusion form of the parainfluenza virus 5 fusion protein

PubMed Central

Welch, Brett D.; Liu, Yuanyuan; Kors, Christopher A.; Leser, George P.; Jardetzky, Theodore S.; Lamb, Robert A.

2012-01-01

The paramyxovirus parainfluenza virus 5 (PIV5) enters cells by fusion of the viral envelope with the plasma membrane through the concerted action of the fusion (F) protein and the receptor binding protein hemagglutinin-neuraminidase. The F protein folds initially to form a trimeric metastable prefusion form that is triggered to undergo large-scale irreversible conformational changes to form the trimeric postfusion conformation. It is thought that F refolding couples the energy released with membrane fusion. The F protein is synthesized as a precursor (F0) that must be cleaved by a host protease to form a biologically active molecule, F1,F2. Cleavage of F protein is a prerequisite for fusion and virus infectivity. Cleavage creates a new N terminus on F1 that contains a hydrophobic region, known as the FP, which intercalates target membranes during F protein refolding. The crystal structure of the soluble ectodomain of the uncleaved form of PIV5 F is known; here we report the crystal structure of the cleavage-activated prefusion form of PIV5 F. The structure shows minimal movement of the residues adjacent to the protease cleavage site. Most of the hydrophobic FP residues are buried in the uncleaved F protein, and only F103 at the newly created N terminus becomes more solvent-accessible after cleavage. The conformational freedom of the charged arginine residues that compose the protease recognition site increases on cleavage of F protein. PMID:23012473

Does the endolymph pass through the base of the cupula?

NASA Astrophysics Data System (ADS)

Jijiwa, H.; Watanabe, N.; Hattori, T.; Matuda, F.; Hashiba, M.; Mizuno, Y.; Shindo, M.; Watanabe, S.

2001-08-01

Whether the endolymph of the semicircular canal passes the cupular partition or not was examined using the lateral semicircular canal system of adult pigeons (Columba livia). By applying various pressures by means of injection of a dye solution through the membranous canal, it was found that the dye solution was seen to pass the cupula even under very low pressures when the pressure was increased gradually. When pulled by a magnet, the ultrafine particles of the dextran magnetite contained in the injected fluid were found to pass through the subcupular space without evident increase of the ampullary pressure.

Pressure effects on collective density fluctuations in water and protein solutions

PubMed Central

Russo, Daniela; Laloni, Alessio; Filabozzi, Alessandra; Heyden, Matthias

2017-01-01

Neutron Brillouin scattering and molecular dynamics simulations have been used to investigate protein hydration water density fluctuations as a function of pressure. Our results show significant differences between the pressure and density dependence of collective dynamics in bulk water and in concentrated protein solutions. Pressure-induced changes in the tetrahedral order of the water HB network have direct consequences for the high-frequency sound velocity and damping coefficients, which we find to be a sensitive probe for changes in the HB network structure as well as the wetting of biomolecular surfaces. PMID:29073065

FOOD IRRADIATION REACTOR

DOEpatents

Leyse, C.F.; Putnam, G.E.

1961-05-01

An irradiation apparatus is described. It comprises a pressure vessel, a neutronic reactor active portion having a substantially greater height than diameter in the pressure vessel, an annular tank surrounding and spaced from the pressure vessel containing an aqueous indium/sup 1//sup 1//sup 5/ sulfate solution of approximately 600 grams per liter concentration, means for circulating separate coolants through the active portion and the space between the annular tank and the pressure vessel, radiator means adapted to receive the materials to be irradiated, and means for flowing the indium/sup 1//sup 1//sup 5/ sulfate solution through the radiator means.

Inhibiting Effect of Additives on Pressure Solution of Calcite

NASA Astrophysics Data System (ADS)

Traskine, V.; Skvortsova, Z.; Badun, G.; Chernysheva, M.; Simonov, Ya.; Gazizullin, I.

2018-05-01

The task of protection of cultural heritage requires a better understanding of combined effects of mechanical and chemical factors involved in environmental deterioration of monuments. The present paper deals with extending some known physicochemical methods proposed for inhibiting the decay of unstressed materials to their study during water-assisted deformation. The tests have been carried out on natural limestone samples and calcite powders in CaCO3 saturated aqueous solutions under static loads causing measurable pressure solution creep. In the solutions containing 1-hydroxyethylidene-1,1-diphosphonic acid, nitrilotriacetic acid, or ethylenediaminetetraacetic acid, the creep rate decreases considerably with increasing concentration of additives. The extent of creep deceleration has been found to be proportional to the independently estimated calcite surface area occupied by adsorbed species. This fact enables us to discriminate the adsorption-induced effect from other variables controlling the pressure solution rate and may be used in screening of compounds able to minimize the environmental impact on marble and limestone objects undergoing mechanical stresses.

Least-squares finite element solution of 3D incompressible Navier-Stokes problems

NASA Technical Reports Server (NTRS)

Jiang, Bo-Nan; Lin, Tsung-Liang; Povinelli, Louis A.

1992-01-01

Although significant progress has been made in the finite element solution of incompressible viscous flow problems. Development of more efficient methods is still needed before large-scale computation of 3D problems becomes feasible. This paper presents such a development. The most popular finite element method for the solution of incompressible Navier-Stokes equations is the classic Galerkin mixed method based on the velocity-pressure formulation. The mixed method requires the use of different elements to interpolate the velocity and the pressure in order to satisfy the Ladyzhenskaya-Babuska-Brezzi (LBB) condition for the existence of the solution. On the other hand, due to the lack of symmetry and positive definiteness of the linear equations arising from the mixed method, iterative methods for the solution of linear systems have been hard to come by. Therefore, direct Gaussian elimination has been considered the only viable method for solving the systems. But, for three-dimensional problems, the computer resources required by a direct method become prohibitively large. In order to overcome these difficulties, a least-squares finite element method (LSFEM) has been developed. This method is based on the first-order velocity-pressure-vorticity formulation. In this paper the LSFEM is extended for the solution of three-dimensional incompressible Navier-Stokes equations written in the following first-order quasi-linear velocity-pressure-vorticity formulation.

High-frequency ultrasound-responsive block copolymer micelle.

PubMed

Wang, Jie; Pelletier, Maxime; Zhang, Hongji; Xia, Hesheng; Zhao, Yue

2009-11-17

Micelles of a diblock copolymer composed of poly(ethylene oxide) and poly(2-tetrahydropyranyl methacrylate) (PEO-b-PTHPMA) in aqueous solution could be disrupted by high-frequency ultrasound (1.1 MHz). It was found that, upon exposure to a high-intensity focused ultrasound (HIFU) beam at room temperature, the pH value of the micellar solution decreased over irradiation time. The infrared spectroscopic analysis of solid block copolymer samples collected from the ultrasound irradiated micellar solution revealed the formation of carboxylic acid dimers and hydroxyl groups. These characterization results suggest that the high-frequency HIFU beam could induce the hydrolysis reaction of THPMA at room temperature resulting in the cleavage of THP groups. The disruption of PEO-b-PTHPMA micelles by ultrasound was investigated by using dynamic light scattering, atomic force microscopy, and fluorescence spectroscopy. On the basis of the pH change, it was found that the disruption process was determined by a number of factors such as the ultrasound power, the micellar solution volume and the location of the focal spot of the ultrasound beam. This study shows the potential to develop ultrasound-sensitive block copolymer micelles by having labile chemical bonds in the polymer structure, and to use the high-frequency HIFU to trigger a chemical reaction for the disruption of micelles.

Combined pressure and cosolvent effects on enzyme activity - a high-pressure stopped-flow kinetic study on α-chymotrypsin.

PubMed

Luong, Trung Quan; Winter, Roland

2015-09-21

We investigated the combined effects of cosolvents and pressure on the hydrolysis of a model peptide catalysed by α-chymotrypsin. The enzymatic activity was measured in the pressure range from 0.1 to 200 MPa using a high-pressure stopped-flow systems with 10 ms time resolution. A kosmotropic (trimethalymine-N-oxide, TMAO) and chaotropic (urea) cosolvent and mixtures thereof were used as cosolvents. High pressure enhances the hydrolysis rate as a consequence of a negative activation volume, ΔV(#), which, depending on the cosolvent system, amounts to -2 to -4 mL mol(-1). A more negative activation volume can be explained by a smaller compression of the ES complex relative to the transition state. Kinetic constants, such as kcat and the Michaelis constant KM, were determined for all solution conditions as a function of pressure. With increasing pressure, kcat increases by about 35% and its pressure dependence by a factor of 1.9 upon addition of 2 M urea, whereas 1 M TMAO has no significant effect on kcat and its pressure dependence. Similarly, KM increases upon addition of urea 6-fold. Addition of TMAO compensates the urea-effect on kcat and KM to some extent. The maximum rate of the enzymatic reaction increases with increasing pressure in all solutions except in the TMAO : urea 1 : 2 mixture, where, remarkably, pressure is found to have no effect on the rate of the enzymatic reaction anymore. Our data clearly show that compatible solutes can easily override deleterious effects of harsh environmental conditions, such as high hydrostatic pressures in the 100 MPa range, which is the maximum pressure encountered in the deep biosphere on Earth.

Can sucrose cleavage enzymes serve as markers for sink strength and is sucrose a signal molecule during plant sink development?

Treesearch

C.C. Black; T. Lobodia; J.-Q Chen; Shi-Jean S. Sung

1995-01-01

Sucrose cleavage is an essential reaction for higher plant cells to initiate intermediary metabolism and to direct its carbon into the host of essential compounds derived therefrom for maintaining the cells of intact plants.This review will focus on: the concentrations of sucrose available to plant cells; some biochemical traits of sucrose cleavage enzymes; the...

Microbial cleavage of organic C-S bonds

DOEpatents

Kilbane, J.J. II.

1994-10-25

A microbial process is described for selective cleavage of organic C-S bonds which may be used for reducing the sulfur content of sulfur-containing organic carbonaceous materials. Microorganisms of Rhodococcus rhodochrous and Bacillus sphaericus have been found which have the ability of selective cleavage of organic C-S bonds. Particularly preferred microorganisms are Rhodococcus rhodochrous strain ATCC 53968 and Bacillus sphaericus strain ATCC 53969 and their derivatives.

Microbial cleavage of organic C-S bonds

DOEpatents

Kilbane, II, John J.

1994-01-01

A microbial process for selective cleavage of organic C--S bonds which may be used for reducing the sulfur content of sulfur-containing organic carbonaceous materials, Microorganisms of Rhodococcus rhodochrous and Bacillus sphaericus have been found which have the ability of selective cleavage of organic C--S bonds. Particularly preferred microorganisms are Rhodococcus rhodochrous strain ATCC 53968 and Bacillus sphaericus strain ATCC 53969 and their derivatives.

Bubble formation in water with addition of a hydrophobic solute.

PubMed

Okamoto, Ryuichi; Onuki, Akira

2015-07-01

We show that phase separation can occur in a one-component liquid outside its coexistence curve (CX) with addition of a small amount of a solute. The solute concentration at the transition decreases with increasing the difference of the solvation chemical potential between liquid and gas. As a typical bubble-forming solute, we consider O2 in ambient liquid water, which exhibits mild hydrophobicity and its critical temperature is lower than that of water. Such a solute can be expelled from the liquid to form gaseous domains while the surrounding liquid pressure is higher than the saturated vapor pressure p cx. This solute-induced bubble formation is a first-order transition in bulk and on a partially dried wall, while a gas film grows continuously on a completely dried wall. We set up a bubble free energy ΔG for bulk and surface bubbles with a small volume fraction ϕ. It becomes a function of the bubble radius R under the Laplace pressure balance. Then, for sufficiently large solute densities above a threshold, ΔG exhibits a local maximum at a critical radius and a minimum at an equilibrium radius. We also examine solute-induced nucleation taking place outside CX, where bubbles larger than the critical radius grow until attainment of equilibrium.

The highly pathogenic H7N3 avian influenza strain from July 2012 in Mexico acquired an extended cleavage site through recombination with host 28S rRNA.

PubMed

Maurer-Stroh, Sebastian; Lee, Raphael T C; Gunalan, Vithiagaran; Eisenhaber, Frank

2013-05-01

A characteristic difference between highly and non-highly pathogenic avian influenza strains is the presence of an extended, often multibasic, cleavage motif insertion in the hemagglutinin protein. Such motif is found in H7N3 strains from chicken farm outbreaks in 2012 in Mexico. Through phylogenetic, sequence and structural analysis, we try to shed light on the role, prevalence, likelihood of appearance and origin of the inserted cleavage motifs in these H7N3 avian influenza strains. The H7N3 avian influenza strain which caused outbreaks in chicken farms in June/July 2012 in Mexico has a new extended cleavage site which is the likely reason for its high pathogenicity in these birds. This cleavage site appears to have been naturally acquired and was not present in the closest low pathogenic precursors. Structural modeling shows that insertion of a productive cleavage site is quite flexible to accept insertions of different length and with sequences from different possible origins. Different from recent cleavage site insertions, the origin of the insert here is not from the viral genome but from host 28S ribosomal RNA (rRNA) instead. This is a novelty for a natural acquisition as a similar insertion has so far only been observed in a laboratory strain before. Given the abundance of viral and host RNA in infected cells, the acquisition of a pathogenicity-enhancing extended cleavage site through a similar route by other low-pathogenic avian strains in future does not seem unlikely. Important for surveillance of these H7N3 strains, the structural sites known to enhance mammalian airborne transmission are dominated by the characteristic avian residues and the risk of human to human transmission should currently be low but should be monitored for future changes accordingly. This highly pathogenic H7N3 avian influenza strain acquired a novel extended cleavage site which likely originated from recombination with 28S rRNA from the avian host. Notably, this new virus can infect humans but currently lacks critical host receptor adaptations that would facilitate human to human transmission.

Identification of a Broad-Spectrum Antiviral Small Molecule against Severe Acute Respiratory Syndrome Coronavirus and Ebola, Hendra, and Nipah Viruses by Using a Novel High-Throughput Screening Assay

PubMed Central

Elshabrawy, Hatem A.; Fan, Jilao; Haddad, Christine S.; Ratia, Kiira; Broder, Christopher C.; Caffrey, Michael

2014-01-01

ABSTRACT Severe acute respiratory syndrome coronavirus (SARS-CoV) and Ebola, Hendra, and Nipah viruses are members of different viral families and are known causative agents of fatal viral diseases. These viruses depend on cathepsin L for entry into their target cells. The viral glycoproteins need to be primed by protease cleavage, rendering them active for fusion with the host cell membrane. In this study, we developed a novel high-throughput screening assay based on peptides, derived from the glycoproteins of the aforementioned viruses, which contain the cathepsin L cleavage site. We screened a library of 5,000 small molecules and discovered a small molecule that can inhibit the cathepsin L cleavage of all viral peptides with minimal inhibition of cleavage of a host protein-derived peptide (pro-neuropeptide Y). The small molecule inhibited the entry of all pseudotyped viruses in vitro and the cleavage of SARS-CoV spike glycoprotein in an in vitro cleavage assay. In addition, the Hendra and Nipah virus fusion glycoproteins were not cleaved in the presence of the small molecule in a cell-based cleavage assay. Furthermore, we demonstrate that the small molecule is a mixed inhibitor of cathepsin L. Our broad-spectrum antiviral small molecule appears to be an ideal candidate for future optimization and development into a potent antiviral against SARS-CoV and Ebola, Hendra, and Nipah viruses. IMPORTANCE We developed a novel high-throughput screening assay to identify small molecules that can prevent cathepsin L cleavage of viral glycoproteins derived from SARS-CoV and Ebola, Hendra, and Nipah viruses that are required for their entry into the host cell. We identified a novel broad-spectrum small molecule that could block cathepsin L-mediated cleavage and thus inhibit the entry of pseudotypes bearing the glycoprotein derived from SARS-CoV or Ebola, Hendra, or Nipah virus. The small molecule can be further optimized and developed into a potent broad-spectrum antiviral drug. PMID:24501399

Identification of a broad-spectrum antiviral small molecule against severe acute respiratory syndrome coronavirus and Ebola, Hendra, and Nipah viruses by using a novel high-throughput screening assay.

PubMed

Elshabrawy, Hatem A; Fan, Jilao; Haddad, Christine S; Ratia, Kiira; Broder, Christopher C; Caffrey, Michael; Prabhakar, Bellur S

2014-04-01

Severe acute respiratory syndrome coronavirus (SARS-CoV) and Ebola, Hendra, and Nipah viruses are members of different viral families and are known causative agents of fatal viral diseases. These viruses depend on cathepsin L for entry into their target cells. The viral glycoproteins need to be primed by protease cleavage, rendering them active for fusion with the host cell membrane. In this study, we developed a novel high-throughput screening assay based on peptides, derived from the glycoproteins of the aforementioned viruses, which contain the cathepsin L cleavage site. We screened a library of 5,000 small molecules and discovered a small molecule that can inhibit the cathepsin L cleavage of all viral peptides with minimal inhibition of cleavage of a host protein-derived peptide (pro-neuropeptide Y). The small molecule inhibited the entry of all pseudotyped viruses in vitro and the cleavage of SARS-CoV spike glycoprotein in an in vitro cleavage assay. In addition, the Hendra and Nipah virus fusion glycoproteins were not cleaved in the presence of the small molecule in a cell-based cleavage assay. Furthermore, we demonstrate that the small molecule is a mixed inhibitor of cathepsin L. Our broad-spectrum antiviral small molecule appears to be an ideal candidate for future optimization and development into a potent antiviral against SARS-CoV and Ebola, Hendra, and Nipah viruses. We developed a novel high-throughput screening assay to identify small molecules that can prevent cathepsin L cleavage of viral glycoproteins derived from SARS-CoV and Ebola, Hendra, and Nipah viruses that are required for their entry into the host cell. We identified a novel broad-spectrum small molecule that could block cathepsin L-mediated cleavage and thus inhibit the entry of pseudotypes bearing the glycoprotein derived from SARS-CoV or Ebola, Hendra, or Nipah virus. The small molecule can be further optimized and developed into a potent broad-spectrum antiviral drug.

Application of chiral critical clusters to assymetric synthesis

DOEpatents

Ferrieri, Richard A.

2002-01-01

Disclosed is a composition, a method of making and a method of using critical clusters for asymmetric synthesis using substantially optically-pure chiral solvent molecules in a supercritical fluid. The solvent molecules are capable of forming a multipoint hydrogen bonded solvate as they encage at least one solute molecule. The encaged solute molecule is capable of reacting to form an optically active chiral center. In another aspect, there is disclosed a method of directing the position of bonding between a solute molecule and a ligand involving encaging the solute molecule and the ligand with polar solvent molecules in a supercritical fluid under conditions of temperature and pressure sufficient to change electric charge distribution in the solute molecule. In yet another aspect, disclosed is a method of making pharmaceutical compounds involving encaging a solute molecule, which is capable of forming a chiral center, and a ligand with polar solvent molecules in a supercritical fluid under conditions of temperature and pressure sufficient to change electric charge distribution of the solute molecule. The solute molecule and ligand are then reacted whereby the ligand bonds to the solute molecule forming a chiral center. Also disclosed is a method for racemic resolution using critical clusters involving encaging racemic mixtures of solute molecules with substantially optically-pure chiral solvent molecules in a supercritical fluid under conditions of temperature and pressure sufficient to form critical clusters. The solvent molecules are capable of multipoint hydrogen bonding with the solute molecules. The encaged solute molecules are then nonenzymatically reacted to enhance the optical purity of the solute molecules.

Observed relationships between wood density and solution uptake during pressure treatment

Treesearch

Steve Halverson; Stan Lebow

2011-01-01

A better understanding of the relationship between wood properties and solution uptake during pressure treatment could lead to improvements in treatment quality and more efficient use of preservatives. In this study several years of treatment data representing a range of wood species, charge conditions and preservative formulations were analyzed to evaluate the...

Exospheric perturbations by radiation pressure. II - Solution for orbits in the ecliptic plane

NASA Technical Reports Server (NTRS)

Chamberlain, J. W.

1980-01-01

A previous study (Chamberlain, 1979) gave solutions for the mean time rates of change of orbital elements of satellite atoms in an exosphere influenced by solar radiation pressure; each element was assumed to behave independently. In the present paper, the instantaneous rates of changes for three elements (e, Omega, and phi = omega + Omega) are integrated simultaneously for the case of the inclination i = 0. The results confirm the validity of using mean rates when the orbits are tighly bound to the planet, and serve as examples to be reproduced by the complicated numerical solutions required for arbitrary inclination. Strongly bound hydrogen atoms perturbed in earth orbit by radiation pressure do not seem a likely cause of the geotail extending in the anti-sun direction. Instead, radiation pressure will cause those particles' orbits to form a broad fan-shaped tail and to deteriorate into the earth's atmosphere.

Effects of pressure and electrical charge on macromolecular transport across bovine lens basement membrane.

PubMed

Ferrell, Nicholas; Cameron, Kathleen O; Groszek, Joseph J; Hofmann, Christina L; Li, Lingyan; Smith, Ross A; Bian, Aihua; Shintani, Ayumi; Zydney, Andrew L; Fissell, William H

2013-04-02

Molecular transport through the basement membrane is important for a number of physiological functions, and dysregulation of basement membrane architecture can have serious pathological consequences. The structure-function relationships that govern molecular transport in basement membranes are not fully understood. The basement membrane from the lens capsule of the eye is a collagen IV-rich matrix that can easily be extracted and manipulated in vitro. As such, it provides a convenient model for studying the functional relationships that govern molecular transport in basement membranes. Here we investigate the effects of increased transmembrane pressure and solute electrical charge on the transport properties of the lens basement membrane (LBM) from the bovine eye. Pressure-permeability relationships in LBM transport were governed primarily by changes in diffusive and convective contributions to solute flux and not by pressure-dependent changes in intrinsic membrane properties. The solute electrical charge had a minimal but statistically significant effect on solute transport through the LBM that was opposite of the expected electrokinetic behavior. The observed transport characteristics of the LBM are discussed in the context of established membrane transport modeling and previous work on the effects of pressure and electrical charge in other basement membrane systems. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism.

PubMed

Noble, Christian G; Maxwell, Anthony

2002-04-26

We have examined the role of the DNA gyrase B protein in cleavage and religation of DNA using site-directed mutagenesis. Three aspartate residues and a glutamate residue: E424, D498, D500 and D502, thought to co-ordinate a magnesium ion, were mutated to alanine; in addition, the glutamate residue and one aspartate residue were mutated to glutamine and asparagine, respectively. We have shown that these residues are important for the cleavage-religation reaction and are likely to be involved in magnesium ion co-ordination. On separate mutation of two of these aspartate residues to cysteine or histidine, the metal ion preference for the DNA relaxation activity of gyrase changed from magnesium to manganese (II). We present evidence to support the idea that cleavage of each DNA strand involves two or more metal ions, and suggest a scheme for the DNA cleavage chemistry of DNA gyrase involving two metal ions. (c) 2002 Elsevier Science Ltd.

Cleavage sites within the poliovirus capsid protein precursors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larsen, G.R.; Anderson, C.W.; Dorner, A.J.

1982-01-01

Partial amino-terminal sequence analysis was performed on radiolabeled poliovirus capsid proteins VP1, VP2, and VP3. A computer-assisted comparison of the amino acid sequences obtained with that predicted by the nucleotide sequence of the poliovirus genome allows assignment of the amino terminus of each capsid protein to a unique position within the virus polyprotein. Sequence analysis of trypsin-digested VP4, which has a blocked amino terminus, demonstrates that VP4 is encoded at or very near to the amino terminus of the polyprotein. The gene order of the capsid proteins is VP4-VP2-VP3-VP1. Cleavage of VP0 to VP4 and VP2 is shown to occurmore » between asparagine and serine, whereas the cleavages that separate VP2/VP3 and VP3/VP1 occur between glutamine and glycine residues. This finding supports the hypothesis that the cleavage of VP0, which occurs during virion morphogenesis, is distinct from the cleavages that separate functional regions of the polyprotein.« less

A fundamental study of the impact of pressure on the adsorption mechanism in reversed-phase liquid chromatography.

PubMed

Åsberg, Dennis; Samuelsson, Jörgen; Fornstedt, Torgny

2016-07-29

A fundamental investigation of the pressure effect on individual adsorption sites was undertaken based on adsorption energy distribution and adsorption isotherm measurements. For this purpose, we measured adsorption equilibrium data at pressures ranging from 100 to 1000bar at constant flow and over a wide concentration range for three low-molecular-weight solutes, antipyrine, sodium 2-naphthalenesulfonate, and benzyltriethylammonium chloride, on an Eternity C18 stationary phase. The adsorption energy distribution was bimodal for all solutes, remaining clearly so at all pressures. The bi-Langmuir model best described the adsorption in these systems and two types of adsorption sites were identified, one with a low and another with a high energy of interaction. Evidence exists that the low-energy interactions occur at the interface between the mobile and stationary phases and that the high-energy interactions occur nearer the silica surface, deeper in the C18 layer. The contribution of each type of adsorption site to the retention factor was calculated and the change in solute molar volume from the mobile to stationary phase during the adsorption process was estimated for each type of site. The change in solute molar volume was 2-4 times larger at the high-energy site, likely because of the greater loss of solute solvation layer when penetrating deeper into the C18 layer. The association equilibrium constant increased with increasing pressure while the saturation capacity of the low-energy site remained almost unchanged. The observed increase in saturation capacity for the high-energy site did not affect the column loading capacity, which was almost identical at 50- and 950-bar pressure drops over the column. Copyright © 2016 Elsevier B.V. All rights reserved.

High-Pressure-High-Temperature Processing Reduces Maillard Reaction and Viscosity in Whey Protein-Sugar Solutions.

PubMed

Avila Ruiz, Geraldine; Xi, Bingyan; Minor, Marcel; Sala, Guido; van Boekel, Martinus; Fogliano, Vincenzo; Stieger, Markus

2016-09-28

The aim of the study was to determine the influence of pressure in high-pressure-high-temperature (HPHT) processing on Maillard reactions and protein aggregation of whey protein-sugar solutions. Solutions of whey protein isolate containing either glucose or trehalose at pH 6, 7, and 9 were treated by HPHT processing or conventional high-temperature (HT) treatments. Browning was reduced, and early and advanced Maillard reactions were retarded under HPHT processing at all pH values compared to HT treatment. HPHT induced a larger pH drop than HT treatments, especially at pH 9, which was not associated with Maillard reactions. After HPHT processing at pH 7, protein aggregation and viscosity of whey protein isolate-glucose/trehalose solutions remained unchanged. It was concluded that HPHT processing can potentially improve the quality of protein-sugar-containing foods, for which browning and high viscosities are undesired, such as high-protein beverages.

Similar solutions for the compressible laminar boundary layer with heat transfer and pressure gradient

NASA Technical Reports Server (NTRS)

Cohen, Clarence B; Reshotko, Eli

1956-01-01

Stewartson's transformation is applied to the laminar compressible boundary-layer equations and the requirement of similarity is introduced, resulting in a set of ordinary nonlinear differential equations previously quoted by Stewartson, but unsolved. The requirements of the system are Prandtl number of 1.0, linear viscosity-temperature relation across the boundary layer, an isothermal surface, and the particular distributions of free-stream velocity consistent with similar solutions. This system admits axial pressure gradients of arbitrary magnitude, heat flux normal to the surface, and arbitrary Mach numbers. The system of differential equations is transformed to integral system, with the velocity ratio as the independent variable. For this system, solutions are found by digital computation for pressure gradients varying from that causing separation to the infinitely favorable gradient and for wall temperatures from absolute zero to twice the free-stream stagnation temperature. Some solutions for separated flows are also presented.

Dynamics of a 4x6-Meter Thin Film Elliptical Inflated Membrane for Space Applications

NASA Technical Reports Server (NTRS)

Casiano, Matthew J.; Hamidzadeh, Hamid R.; Tinker, Michael L.; McConnaughey, Paul R. (Technical Monitor)

2002-01-01

Dynamic characterization of a thin film inflatable elliptical structure is described in detail. A two-step finite element modeling approach in MSC/NASTRAN is utilized, consisting of (1) a nonlinear static pressurization procedure used to obtain the updated stiffness matrix, and (2) a modal "restart" eigen solution that uses the modified stiffness matrix. Unique problems encountered in modeling of this large Hexameter lightweight inflatable arc identified, including considerable difficulty in obtaining convergence in the nonlinear finite element pressurization solution. It was found that the extremely thin polyimide film material (.001 in or 1 mil) presents tremendous problems in obtaining a converged solution when internal pressure loading is applied. Approaches utilized to overcome these difficulties are described. Comparison of finite element predictions for frequency and mode shapes of the inflated structure with closed-form solutions for a flat pre-tensioned membrane indicate reasonable agreement.

Thermoelastic analysis of non-uniform pressurized functionally graded cylinder with variable thickness using first order shear deformation theory(FSDT) and perturbation method

NASA Astrophysics Data System (ADS)

Khoshgoftar, M. J.; Mirzaali, M. J.; Rahimi, G. H.

2015-11-01

Recently application of functionally graded materials(FGMs) have attracted a great deal of interest. These materials are composed of various materials with different micro-structures which can vary spatially in FGMs. Such composites with varying thickness and non-uniform pressure can be used in the aerospace engineering. Therefore, analysis of such composite is of high importance in engineering problems. Thermoelastic analysis of functionally graded cylinder with variable thickness under non-uniform pressure is considered. First order shear deformation theory and total potential energy approach is applied to obtain the governing equations of non-homogeneous cylinder. Considering the inner and outer solutions, perturbation series are applied to solve the governing equations. Outer solution for out of boundaries and more sensitive variable in inner solution at the boundaries are considered. Combining of inner and outer solution for near and far points from boundaries leads to high accurate displacement field distribution. The main aim of this paper is to show the capability of matched asymptotic solution for different non-homogeneous cylinders with different shapes and different non-uniform pressures. The results can be used to design the optimum thickness of the cylinder and also some properties such as high temperature residence by applying non-homogeneous material.

Melting of the precipitated ice IV in LiCl aqueous solution and polyamorphism of water.

PubMed

Mishima, Osamu

2011-12-08

Melting of the precipitated ice IV in supercooled LiCl-H(2)O solution was studied in the range of 0-0.6 MPa and 160-270 K. Emulsified solution was used to detect this metastable transition. Ice IV was precipitated from the aqueous solution of 2.0 mol % LiCl (or 4.8 mol % LiCl) in each emulsion particle at low-temperature and high-pressure conditions, and the emulsion was decompressed at different temperatures. The melting of ice IV was detected from the temperature change of the emulsified sample during the decompression. There was an apparently sudden change in the slope of the ice IV melting curve (liquidus) in the pressure-temperature diagram. At the high-pressure and high-temperature side of the change, the solute-induced freezing point depression was observed. At the low-pressure and low-temperature side, ice IV transformed into ice Ih on the decompression, and the transition was almost unrelated to the concentration of LiCl. These experimental results were roughly explained by the presumed existence of two kinds of liquid water (low-density liquid water and high-density liquid water), or polyamorphism in water, and by the simple assumption that LiCl dissolved maily in high-density liquid water. © 2011 American Chemical Society

In situ study of mass transfer in aqueous solutions under high pressures via Raman spectroscopy: A new method for the determination of diffusion coefficients of methane in water near hydrate formation conditions

USGS Publications Warehouse

Lu, W.J.; Chou, I.-Ming; Burruss, R.C.; Yang, M.Z.

2006-01-01

A new method was developed for in situ study of the diffusive transfer of methane in aqueous solution under high pressures near hydrate formation conditions within an optical capillary cell. Time-dependent Raman spectra of the solution at several different spots along the one-dimensional diffusion path were collected and thus the varying composition profile of the solution was monitored. Diffusion coefficients were estimated by the least squares method based on the variations in methane concentration data in space and time in the cell. The measured diffusion coefficients of methane in water at the liquid (L)-vapor (V) stable region and L-V metastable region are close to previously reported values determined at lower pressure and similar temperature. This in situ monitoring method was demonstrated to be suitable for the study of mass transfer in aqueous solution under high pressure and at various temperature conditions and will be applied to the study of nucleation and dissolution kinetics of methane hydrate in a hydrate-water system where the interaction of methane and water would be more complicated than that presented here for the L-V metastable condition. ?? 2006 Society for Applied Spectroscopy.

A family of analytic equilibrium solutions for the Grad-Shafranov equation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guazzotto, L.; Freidberg, J. P.

2007-11-15

A family of exact solutions to the Grad-Shafranov equation, similar to those described by Atanasiu et al. [C. V. Atanasiu, S. Guenter, K. Lackner, and I. G. Miron, Phys. Plasmas 11, 3510 (2004)], is presented. The solution allows for finite plasma aspect ratio, elongation and triangularity, while only requiring the evaluation of a small number of well-known hypergeometric functions. Plasma current, pressure, and pressure gradients are set to zero at the plasma edge. Realistic equilibria for standard and spherical tokamaks are presented.

Concentration Dependent Physical Properties of Ge1-xSnx Solid Solution

NASA Astrophysics Data System (ADS)

Jivani, A. R.; Jani, A. R.

2011-12-01

Our own proposed potential is used to investigate few physical properties like total energy, bulk modulus, pressure derivative of bulk modulus, elastic constants, pressure derivative of elastic constants, Poisson's ratio and Young's modulus of Ge1-xSnx solid solution with x is atomic concentration of α-Sn. The potential combines linear plus quadratic types of electron-ion interaction. First time screening function proposed by Sarkar et al is used to investigate the properties of the Ge-Sn solid solution system.

Varicella zoster virus DNA exists as two isomers.

PubMed Central

Ecker, J R; Hyman, R W

1982-01-01

Fragments of varicella zoster virus DNA produced by EcoRI endonuclease cleavage were cloned in vector pACYC 184 and those produced by HindIII cleavage were cloned in pBR322. Restriction enzyme cleavage maps established by double digestion and blot hybridization showed that varicella zoster virus DNA has a Mr of 80 +/- 3 x 10(6) and exists as a population of two isomers. Images PMID:6275385

Japanese traditional miso soup attenuates salt-induced hypertension and its organ damage in Dahl salt-sensitive rats.

PubMed

Yoshinaga, Mariko; Toda, Natsuko; Tamura, Yuki; Terakado, Shouko; Ueno, Mai; Otsuka, Kie; Numabe, Atsushi; Kawabata, Yukari; Uehara, Yoshio

2012-09-01

We investigated the effects of long-term miso soup drinking on salt-induced hypertension in Dahl salt-sensitive (Dahl S) rats. Dahl S rats were divided into four groups that consumed 1) water, 2) a 0.9% NaCl solution, 3) a 1.3% sodium NaCl solution, or 4) miso soup containing 1.3% NaCl. They were followed for 8 wk. Systolic blood pressure and hypertensive organ damage were determined. Systolic blood pressure increased in an age- and dose-dependent manner in Dahl S rats drinking salt solutions. The systolic blood pressure increase was significantly less in the Dahl S rats that drank miso soup, although the ultimate cumulative salt loading was greater than that in the Dahl S rats given the 1.3% NaCl solution. This blood pressure decrease was associated with a morphologic attenuation of glomerular sclerosis in the kidney and collagen infiltration in the heart. Urinary protein excretions were less in the miso group than in the rats given the 1.3% NaCl solution. The fractional excretion of sodium was increased and that of potassium was decreased in Dahl S rats given the 1.3% NaCl solution, and these effects were reversed in rats given miso soup toward the values of the control. We found that long-term miso soup drinking attenuates the blood pressure increase in salt-induced hypertension with organ damage. This may be caused by a possible retardation of sodium absorption in the gastrointestinal tract or by the direct effects of nutrients in the miso soup from soybeans. The decrease was associated with decreases in cardiovascular and renal damage. Copyright © 2012 Elsevier Inc. All rights reserved.

Mutations altering the gammaretrovirus endoproteolytic motif affect glycosylation of the envelope glycoprotein and early events of the virus life cycle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Argaw, Takele; Wilson, Carolyn A., E-mail: carolyn.wilson@fda.hhs.gov

Previously, we found that mutation of glutamine to proline in the endoproteolytic cleavage signal of the PERV-C envelope (RQKK to RPKK) resulted in non-infectious vectors. Here, we show that RPKK results in a non-infectious vector when placed in not only a PERV envelope, but also the envelope of a related gammaretrovirus, FeLV-B. The amino acid substitutions do not prevent envelope precursor cleavage, viral core and genome assembly, or receptor binding. Rather, the mutations result in the formation of hyperglycosylated glycoprotein and a reduction in the reverse transcribed minus strand synthesis and undetectable 2-LTR circular DNA in cells exposed to vectorsmore » with these mutated envelopes. Our findings suggest novel functions associated with the cleavage signal sequence that may affect trafficking through the glycosylation machinery of the cell. Further, the glycosylation status of the envelope appears to impact post-binding events of the viral life cycle, either membrane fusion, internalization, or reverse transcription. - Highlights: • Env cleavage signal impacts infectivity of gammaretroviruses. • Non-infectious mutants have hyper-glycosylated envelope that bind target cells. • Non-infectious mutants have defects in the formation of the double-stranded DNA. • Env cleavage motif has functions beyond cleavage of the env precursor.« less

Protein cleavage strategies for an improved analysis of the membrane proteome

PubMed Central

Fischer, Frank; Poetsch, Ansgar

2006-01-01

Background Membrane proteins still remain elusive in proteomic studies. This is in part due to the distribution of the amino acids lysine and arginine, which are less frequent in integral membrane proteins and almost absent in transmembrane helices. As these amino acids are cleavage targets for the commonly used protease trypsin, alternative cleavage conditions, which should improve membrane protein analysis, were tested by in silico digestion for the three organisms Saccharomyces cerevisiae, Halobacterium sp. NRC-1, and Corynebacterium glutamicum as hallmarks for eukaryotes, archea and eubacteria. Results For the membrane proteomes from all three analyzed organisms, we identified cleavage conditions that achieve better sequence and proteome coverage than trypsin. Greater improvement was obtained for bacteria than for yeast, which was attributed to differences in protein size and GRAVY. It was demonstrated for bacteriorhodopsin that the in silico predictions agree well with the experimental observations. Conclusion For all three examined organisms, it was found that a combination of chymotrypsin and staphylococcal peptidase I gave significantly better results than trypsin. As some of the improved cleavage conditions are not more elaborate than trypsin digestion and have been proven useful in practice, we suppose that the cleavage at both hydrophilic and hydrophobic amino acids should facilitate in general the analysis of membrane proteins for all organisms. PMID:16512920

Truncation of the TAR DNA-binding protein 43 is not a prerequisite for cytoplasmic relocalization, and is suppressed by caspase inhibition and by introduction of the A90V sequence variant

PubMed Central

Brandon, Nicholas J.; Moss, Stephen J.

2017-01-01

The RNA-binding and -processing protein TAR DNA-binding protein 43 (TDP-43) is heavily linked to the underlying causes and pathology of neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal lobar degeneration. In these diseases, TDP-43 is mislocalized, hyperphosphorylated, ubiquitinated, aggregated and cleaved. The importance of TDP-43 cleavage in the disease pathogenesis is still poorly understood. Here we detail the use of D-sorbitol as an exogenous stressor that causes TDP-43 cleavage in HeLa cells, resulting in a 35 kDa truncated product that accumulates in the cytoplasm within one hour of treatment. We confirm that the formation of this 35 kDa cleavage product is mediated by the activation of caspases. Inhibition of caspases blocks the cleavage of TDP-43, but does not prevent the accumulation of full-length protein in the cytoplasm. Using D-sorbitol as a stressor and caspase activator, we also demonstrate that the A90V variant of TDP-43, which lies adjacent to the caspase cleavage site within the nuclear localization sequence of TDP-43, confers partial resistance against caspase-mediated generation of the 35 kDa cleavage product. PMID:28510586

Self-cleavage of human CLCA1 protein by a novel internal metalloprotease domain controls calcium-activated chloride channel activation.

PubMed

Yurtsever, Zeynep; Sala-Rabanal, Monica; Randolph, David T; Scheaffer, Suzanne M; Roswit, William T; Alevy, Yael G; Patel, Anand C; Heier, Richard F; Romero, Arthur G; Nichols, Colin G; Holtzman, Michael J; Brett, Tom J

2012-12-07

The chloride channel calcium-activated (CLCA) family are secreted proteins that regulate both chloride transport and mucin expression, thus controlling the production of mucus in respiratory and other systems. Accordingly, human CLCA1 is a critical mediator of hypersecretory lung diseases, such as asthma, chronic obstructive pulmonary disease, and cystic fibrosis, that manifest mucus obstruction. Despite relevance to homeostasis and disease, the mechanism of CLCA1 function remains largely undefined. We address this void by showing that CLCA proteins contain a consensus proteolytic cleavage site recognized by a novel zincin metalloprotease domain located within the N terminus of CLCA itself. CLCA1 mutations that inhibit self-cleavage prevent activation of calcium-activated chloride channel (CaCC)-mediated chloride transport. CaCC activation requires cleavage to unmask the N-terminal fragment of CLCA1, which can independently gate CaCCs. Gating of CaCCs mediated by CLCA1 does not appear to involve proteolytic cleavage of the channel because a mutant N-terminal fragment deficient in proteolytic activity is able to induce currents comparable with that of the native fragment. These data provide both a mechanistic basis for CLCA1 self-cleavage and a novel mechanism for regulation of chloride channel activity specific to the mucosal interface.

Self-cleavage of Human CLCA1 Protein by a Novel Internal Metalloprotease Domain Controls Calcium-activated Chloride Channel Activation*♦

PubMed Central

Yurtsever, Zeynep; Sala-Rabanal, Monica; Randolph, David T.; Scheaffer, Suzanne M.; Roswit, William T.; Alevy, Yael G.; Patel, Anand C.; Heier, Richard F.; Romero, Arthur G.; Nichols, Colin G.; Holtzman, Michael J.; Brett, Tom J.

2012-01-01

The chloride channel calcium-activated (CLCA) family are secreted proteins that regulate both chloride transport and mucin expression, thus controlling the production of mucus in respiratory and other systems. Accordingly, human CLCA1 is a critical mediator of hypersecretory lung diseases, such as asthma, chronic obstructive pulmonary disease, and cystic fibrosis, that manifest mucus obstruction. Despite relevance to homeostasis and disease, the mechanism of CLCA1 function remains largely undefined. We address this void by showing that CLCA proteins contain a consensus proteolytic cleavage site recognized by a novel zincin metalloprotease domain located within the N terminus of CLCA itself. CLCA1 mutations that inhibit self-cleavage prevent activation of calcium-activated chloride channel (CaCC)-mediated chloride transport. CaCC activation requires cleavage to unmask the N-terminal fragment of CLCA1, which can independently gate CaCCs. Gating of CaCCs mediated by CLCA1 does not appear to involve proteolytic cleavage of the channel because a mutant N-terminal fragment deficient in proteolytic activity is able to induce currents comparable with that of the native fragment. These data provide both a mechanistic basis for CLCA1 self-cleavage and a novel mechanism for regulation of chloride channel activity specific to the mucosal interface. PMID:23112050

Determination of the protease cleavage site repertoire—The RNase H but not the RT domain is essential for foamy viral protease activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spannaus, Ralf; Bodem, Jochen, E-mail: Jochen.Bodem@vim.uni-wuerzburg.de

2014-04-15

In contrast to orthoretroviruses, the foamy virus protease is only active as a protease-reverse transcriptase fusion protein and requires viral RNA for activation. Maturation of foamy viral proteins seems to be restricted to a single cleavage site in Gag and Pol. We provide evidence that unprocessed Gag is required for optimal infectivity, which is unique among retroviruses. Analyses of the cleavage site sequences of the Gag and Pol cleavage sites revealed a high similarity compared to those of Lentiviruses. We show that positions P2' and P2 are invariant and that Gag and Pol cleavage sites are processed with similar efficiencies.more » The RNase H domain is essential for protease activity, but can functionally be substituted by RNase H domains of other retroviruses. Thus, the RNase H domain might be involved in the stabilization of the protease dimer, while the RT domain is essential for RNA dependent protease activation. - Highlights: • Unprocessed Gag is required for optimal infectivity of foamy viruses. • Positions P2 and P2' are invariant in the foamy viral cleavage sites. • The RNaseH domain is essential for protease activity. • The RNaseH domains of other retroviruses support foamy viral protease activity.« less

Single and two-phase flows of shear-thinning media in safety valves.

PubMed

Moncalvo, D; Friedel, L

2009-09-15

This study is the first one in the scientific literature to investigate the liquid and two-phase flows of shear-thinning media, here aqueous solutions of polyvinylpyrrolidone, in a fully opened safety valve. In liquid flows the volume flux at the valve seat does not show any appreciable reduction when increasing the percental weight of polymer in the solution. This result may suggest that the viscous losses in the valve do not increase sensibly from the most aqueous to the most viscous solution. The authors explain it considering that in the region between the seat and the disk, where large pressure and velocity gradients occur, large shear rates are expected. On behalf of the rheological measurements, which show that both the pseudoplasticity and the zero-shear viscosity of the solutions increase with the polymer weight, the difference between the viscosities of the most viscous and those of the most aqueous solution is between the seat and the disk far less than that existing at zero-shear condition. Therefore, the effective viscous pressure drop of the safety valve, which occurs mostly in that region, must increase only modestly with the polymer percental weight in the solution. In two-phase flows the total mass flow rate at constant quality and constant relieving pressure increases remarkably with the polymer weight. The analogy with similar results in cocurrent pipe flows suggests that air entrainment causes large velocity gradients in the liquids and strains them to very large shear rates. It suggests also that a redistribution of the gas agglomerates within the liquid must be expected when increasing the polymer weight in the solutions. In fact, the gas agglomerates react to the larger viscous drag of the liquid by compressing their volume in order to exert a higher internal pressure. The reduction of the void fraction of the mixture at constant quality and constant relieving pressure imposes an increment in the total mass flow rate, since otherwise it would lead to a reduction in the momentum of the mixture and therefore to a drop in the relieving pressure.

LBSizeCleav: improved support vector machine (SVM)-based prediction of Dicer cleavage sites using loop/bulge length.

PubMed

Bao, Yu; Hayashida, Morihiro; Akutsu, Tatsuya

2016-11-25

Dicer is necessary for the process of mature microRNA (miRNA) formation because the Dicer enzyme cleaves pre-miRNA correctly to generate miRNA with correct seed regions. Nonetheless, the mechanism underlying the selection of a Dicer cleavage site is still not fully understood. To date, several studies have been conducted to solve this problem, for example, a recent discovery indicates that the loop/bulge structure plays a central role in the selection of Dicer cleavage sites. In accordance with this breakthrough, a support vector machine (SVM)-based method called PHDCleav was developed to predict Dicer cleavage sites which outperforms other methods based on random forest and naive Bayes. PHDCleav, however, tests only whether a position in the shift window belongs to a loop/bulge structure. In this paper, we used the length of loop/bulge structures (in addition to their presence or absence) to develop an improved method, LBSizeCleav, for predicting Dicer cleavage sites. To evaluate our method, we used 810 empirically validated sequences of human pre-miRNAs and performed fivefold cross-validation. In both 5p and 3p arms of pre-miRNAs, LBSizeCleav showed greater prediction accuracy than PHDCleav did. This result suggests that the length of loop/bulge structures is useful for prediction of Dicer cleavage sites. We developed a novel algorithm for feature space mapping based on the length of a loop/bulge for predicting Dicer cleavage sites. The better performance of our method indicates the usefulness of the length of loop/bulge structures for such predictions.

The rRNA methyltransferase Bud23 shows functional interaction with components of the SSU processome and RNase MRP.

PubMed

Sardana, Richa; White, Joshua P; Johnson, Arlen W

2013-06-01

Bud23 is responsible for the conserved methylation of G1575 of 18S rRNA, in the P-site of the small subunit of the ribosome. bud23Δ mutants have severely reduced small subunit levels and show a general failure in cleavage at site A2 during rRNA processing. Site A2 is the primary cleavage site for separating the precursors of 18S and 25S rRNAs. Here, we have taken a genetic approach to identify the functional environment of BUD23. We found mutations in UTP2 and UTP14, encoding components of the SSU processome, as spontaneous suppressors of a bud23Δ mutant. The suppressors improved growth and subunit balance and restored cleavage at site A2. In a directed screen of 50 ribosomal trans-acting factors, we identified strong positive and negative genetic interactions with components of the SSU processome and strong negative interactions with components of RNase MRP. RNase MRP is responsible for cleavage at site A3 in pre-rRNA, an alternative cleavage site for separating the precursor rRNAs. The strong negative genetic interaction between RNase MRP mutants and bud23Δ is likely due to the combined defects in cleavage at A2 and A3. Our results suggest that Bud23 plays a role at the time of A2 cleavage, earlier than previously thought. The genetic interaction with the SSU processome suggests that Bud23 could be involved in triggering disassembly of the SSU processome, or of particular subcomplexes of the processome.

Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond

NASA Astrophysics Data System (ADS)

Rožman, Marko

2016-01-01

Glycosphingolipid fragmentation behavior was investigated by combining results from analysis of a series of negative ion tandem mass spectra and molecular modeling. Fragmentation patterns extracted from 75 tandem mass spectra of mainly acidic glycosphingolipid species (gangliosides) suggest prominent cleavage of the glycosidic bonds with retention of the glycosidic oxygen atom by the species formed from the reducing end (B and Y ion formation). Dominant product ions arise from dissociation of sialic acids glycosidic bonds whereas product ions resulting from cleavage of other glycosidic bonds are less abundant. Potential energy surfaces and unimolecular reaction rates of several low-energy fragmentation pathways leading to cleavage of glycosidic bonds were estimated in order to explain observed dissociation patterns. Glycosidic bond cleavage in both neutral (unsubstituted glycosyl group) and acidic glycosphingolipids was the outcome of the charge-directed intramolecular nucleophilic substitution (SN2) mechanism. According to the suggested mechanism, the nucleophile in a form of carboxylate or oxyanion attacks the carbon at position one of the sugar ring, simultaneously breaking the glycosidic bond and yielding an epoxide. For gangliosides, unimolecular reaction rates suggest that dominant product ions related to the cleavage of sialic acid glycosidic bonds are formed via direct dissociation channels. On the other hand, low abundant product ions related to the dissociation of other glycosidic bonds are more likely to be the result of sequential dissociation. Although results from this study mainly contribute to the understanding of glycosphingolipid fragmentation chemistry, some mechanistic findings regarding cleavage of the glycosidic bond may be applicable to other glycoconjugates.

H2O2 recycling during oxidation of the arylglycerol beta-aryl ether lignin structure by lignin peroxidase and glyoxal oxidase.

PubMed

Hammel, K E; Mozuch, M D; Jensen, K A; Kersten, P J

1994-11-15

Oxidative C alpha-C beta cleavage of the arylglycerol beta-aryl ether lignin model 1-(3,4-dimethoxy-phenyl)-2-phenoxypropane-1,3-diol (I) by Phanerochaete chrysosporium lignin peroxidase in the presence of limiting H2O2 was enhanced 4-5-fold by glyoxal oxidase from the same fungus. Further investigation showed that each C alpha-C beta cleavage reaction released 0.8-0.9 equiv of glycolaldehyde, a glyoxal oxidase substrate. The identification of glycolaldehyde was based on 13C NMR spectrometry of reaction product obtained from beta-, gamma-, and beta,gamma-13C-substituted I, and quantitation was based on an enzymatic NADH-linked assay. The oxidation of glycolaldehyde by glyoxal oxidase yielded 0.9 oxalate and 2.8 H2O2 per reaction, as shown by quantitation of oxalate as 2,3-dihydroxyquinoxaline after derivatization with 1,2-diaminobenzene and by quantitation of H2O2 in coupled spectrophotometric assays with veratryl alcohol and lignin peroxidase. These results suggest that the C alpha-C beta cleavage of I by lignin peroxidase in the presence of glyoxal oxidase should regenerate as many as 3 H2O2. Calculations based on the observed enhancement of LiP-catalyzed C alpha-C beta cleavage by glyoxal oxidase showed that approximately 2 H2O2 were actually regenerated per cleavage of I when both enzymes were present. The cleavage of arylglycerol beta-aryl ether structures by ligninolytic enzymes thus recycles H2O2 to support subsequent cleavage reactions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Yingying; Triscari, Joseph M.; Tseng, George C.

Data mining was performed on 28 330 unique peptide tandem mass spectra for which sequences were assigned with high confidence. By dividing the spectra into different sets based on structural features and charge states of the corresponding peptides, chemical interactions involved in promoting specific cleavage patterns in gas-phase peptides were characterized. Pairwise fragmentation maps describing cleavages at all Xxx-Zzz residue combinations for b and y ions reveal that the difference in basicity between Arg and Lys results in different dissociation patterns for singly charged Arg- and Lys-ending tryptic peptides. While one dominant protonation form (proton localized) exists for Arg-ending peptides,more » a heterogeneous population of different protonated forms or more facile interconversion of protonated forms (proton partially mobile) exists for Lys-ending peptides. Cleavage C-terminal to acidic residues dominates spectra from peptides that have a localized proton and cleavage N-terminal to Pro dominates those that have a mobile or partially mobile proton. When Pro is absent from peptides that have a mobile or partially mobile proton, cleavage at each peptide bond becomes much more prominent. Whether the above patterns can be found in b ions, y ions, or both depends on the location of the proton holder(s). Enhanced cleavages C-terminal to branched aliphatic residues (Ile, Val, Leu) are observed in both b and y ions from peptides that have a mobile proton, as well as in y ions from peptides that have a partially mobile proton; enhanced cleavages N-terminal to these residues are observed in b ions from peptides that have a partially mobile proton. Statistical tools have been designed to visualize the fragmentation maps and measure the similarity between them. The pairwise cleavage patterns observed expand our knowledge of peptide gas-phase fragmentation behaviors and should be useful in algorithm development that employs improved models to predict fragment ion intensities.« less

Determinants of the VP1/2A junction cleavage by the 3C protease in foot-and-mouth disease virus-infected cells.

PubMed

Kristensen, Thea; Normann, Preben; Gullberg, Maria; Fahnøe, Ulrik; Polacek, Charlotta; Rasmussen, Thomas Bruun; Belsham, Graham J

2017-03-01

The foot-and-mouth disease virus (FMDV) capsid precursor, P1-2A, is cleaved by FMDV 3C protease to yield VP0, VP3, VP1 and 2A. Cleavage of the VP1/2A junction is the slowest. Serotype O FMDVs with uncleaved VP1-2A (having a K210E substitution in VP1; at position P2 in cleavage site) have been described previously and acquired a second site substitution (VP1 E83K) during virus rescue. Furthermore, introduction of the VP1 E83K substitution alone generated a second site change at the VP1/2A junction (2A L2P, position P2' in cleavage site). These virus adaptations have now been analysed using next-generation sequencing to determine sub-consensus level changes in the virus; this revealed other variants within the E83K mutant virus population that changed residue VP1 K210. The construction of serotype A viruses with a blocked VP1/2A cleavage site (containing K210E) has now been achieved. A collection of alternative amino acid substitutions was made at this site, and the properties of the mutant viruses were determined. Only the presence of a positively charged residue at position P2 in the cleavage site permitted efficient cleavage of the VP1/2A junction, consistent with analyses of diverse FMDV genome sequences. Interestingly, in contrast to the serotype O virus results, no second site mutations occurred within the VP1 coding region of serotype A viruses with the blocked VP1/2A cleavage site. However, some of these viruses acquired changes in the 2C protein that is involved in enterovirus morphogenesis. These results have implications for the testing of potential antiviral agents targeting the FMDV 3C protease.

Recovery of Recombinant Crimean Congo Hemorrhagic Fever Virus Reveals a Function for Non-structural Glycoproteins Cleavage by Furin.

PubMed

Bergeron, Éric; Zivcec, Marko; Chakrabarti, Ayan K; Nichol, Stuart T; Albariño, César G; Spiropoulou, Christina F

2015-05-01

Crimean Congo hemorrhagic fever virus (CCHFV) is a negative-strand RNA virus of the family Bunyaviridae (genus: Nairovirus). In humans, CCHFV causes fever, hemorrhage, severe thrombocytopenia, and high fatality. A major impediment in precisely determining the basis of CCHFV's high pathogenicity has been the lack of methodology to produce recombinant CCHFV. We developed a reverse genetics system based on transfecting plasmids into BSR-T7/5 and Huh7 cells. In our system, bacteriophage T7 RNA polymerase produced complementary RNA copies of the viral S, M, and L segments that were encapsidated with the support, in trans, of CCHFV nucleoprotein and L polymerase. The system was optimized to systematically recover high yields of infectious CCHFV. Additionally, we tested the ability of the system to produce specifically designed CCHFV mutants. The M segment encodes a polyprotein that is processed by host proprotein convertases (PCs), including the site-1 protease (S1P) and furin-like PCs. S1P and furin cleavages are necessary for producing the non-structural glycoprotein GP38, while S1P cleavage yields structural Gn. We studied the role of furin cleavage by rescuing a recombinant CCHFV encoding a virus glycoprotein precursor lacking a functional furin cleavage motif (RSKR mutated to ASKA). The ASKA mutation blocked glycoprotein precursor's maturation to GP38, and Gn precursor's maturation to Gn was slightly diminished. Furin cleavage was not essential for replication, as blocking furin cleavage resulted only in transient reduction of CCHFV titers, suggesting that either GP38 and/or decreased Gn maturation accounted for the reduced virion production. Our data demonstrate that nairoviruses can be produced by reverse genetics, and the utility of our system uncovered a function for furin cleavage. This viral rescue system could be further used to study the CCHFV replication cycle and facilitate the development of efficacious vaccines to counter this biological and public health threat.

Recovery of Recombinant Crimean Congo Hemorrhagic Fever Virus Reveals a Function for Non-structural Glycoproteins Cleavage by Furin

PubMed Central

Bergeron, Éric; Zivcec, Marko; Chakrabarti, Ayan K.; Nichol, Stuart T.; Albariño, César G.; Spiropoulou, Christina F.

2015-01-01

Crimean Congo hemorrhagic fever virus (CCHFV) is a negative-strand RNA virus of the family Bunyaviridae (genus: Nairovirus). In humans, CCHFV causes fever, hemorrhage, severe thrombocytopenia, and high fatality. A major impediment in precisely determining the basis of CCHFV’s high pathogenicity has been the lack of methodology to produce recombinant CCHFV. We developed a reverse genetics system based on transfecting plasmids into BSR-T7/5 and Huh7 cells. In our system, bacteriophage T7 RNA polymerase produced complementary RNA copies of the viral S, M, and L segments that were encapsidated with the support, in trans, of CCHFV nucleoprotein and L polymerase. The system was optimized to systematically recover high yields of infectious CCHFV. Additionally, we tested the ability of the system to produce specifically designed CCHFV mutants. The M segment encodes a polyprotein that is processed by host proprotein convertases (PCs), including the site-1 protease (S1P) and furin-like PCs. S1P and furin cleavages are necessary for producing the non-structural glycoprotein GP38, while S1P cleavage yields structural Gn. We studied the role of furin cleavage by rescuing a recombinant CCHFV encoding a virus glycoprotein precursor lacking a functional furin cleavage motif (RSKR mutated to ASKA). The ASKA mutation blocked glycoprotein precursor’s maturation to GP38, and Gn precursor’s maturation to Gn was slightly diminished. Furin cleavage was not essential for replication, as blocking furin cleavage resulted only in transient reduction of CCHFV titers, suggesting that either GP38 and/or decreased Gn maturation accounted for the reduced virion production. Our data demonstrate that nairoviruses can be produced by reverse genetics, and the utility of our system uncovered a function for furin cleavage. This viral rescue system could be further used to study the CCHFV replication cycle and facilitate the development of efficacious vaccines to counter this biological and public health threat. PMID:25933376

Effect of Stepwise Pressure Change on Porosity Evolution during Directional Solidification in Small Cylindrical Channels

NASA Technical Reports Server (NTRS)

Grugel, R.N.; Lee, C.P.; Cox, M.C.; Blandford, B.T.; Anilkumar, A.V.

2008-01-01

Controlled directional solidification experiments were performed in capillary channels, using nitrogen-saturated succinonitrile, to examine the effect of an in-situ stepwise processing pressure increase on an isolated pore evolution. Two experiments were performed using different processing pressure input profiles. The results indicate that a processing pressure increase has a transient effect on pore growth geometry characterized by an initial phase of decreasing pore diameter, followed by a recovery phase of increasing pore diameter. The experimental results also show that processing pressure can be used as a control parameter to either increase or terminate porosity formation. A theoretical model is introduced which indicates that the pore formation process is limited by the diffusion of solute-gas through the melt, and that the observed response toa pressure increase is attributed to the re-equilibration of solute concentration in the melt associated with the increased melt pressure.

Polysulfone coating for hollow fiber artificial lungs operated at hypobaric and hyperbaric pressures.

PubMed

High, K M; Snider, M T; Panol, G R; Richard, R B; Gray, D N

1996-01-01

Carbon dioxide transfer is increased when the gas phase of a hollow fiber membrane lung is operated at hypobaric pressures. Oxygen transfer is augmented by hyperbaric pressures. However, uncoated hollow fibers transmit gas bubbles into the blood when operated at a pressure greater than 800 mmHg and may have increased plasma leakage when operated at hypobaric pressures. Ultrathin polymer coatings may avoid this problem while reducing thrombogenicity. The authors coated microporous polypropylene hollow fibers with 380 microns outer diameter and 50 microns walls using 1, 2, 3, and 4% solutions of polysulfone in tetrahydrofuran by dipping or continuous pull through. These fibers were mounted in small membrane lung prototypes having surface areas of 70 and 187 cm2. In gas-to-gas testing, the longer the exposure time to the solution and the greater the polymer concentration, the less the permeation rate. The 3% solutions blocked bulk gas flow. The coating was 1 micron thick by mass balance calculations. During water-to-gas tests, hypobaric gas pressures of 40 mmHg absolute were tolerated, but CO2 transfer was reduced to 40% of the bare fibers. Hyperbaric gas pressures of 2,100 mmHg absolute tripled O2 transfer without bubble formation.

Pressure dependence of the monoclinic phase in (1–x)Pb(Mg 1/3Nb 2/3)O 3-xPbTiO₃ solid solutions

DOE PAGES

Ahart, Muhtar; Sinogeikin, Stanislav; Shebanova, Olga; ...

2012-12-26

We combine high-pressure x-ray diffraction, high-pressure Raman scattering, and optical microscopy to investigate a series of (1–x)Pb(Mg 1/3Nb 2/3)O 3-xPbTiO₃ (PMN-xPT) solid solutions (x=0.2, 0.3, 0.33, 0.35, 0.37, 0.4) in diamond anvil cells up to 20 GPa at 300 K. The Raman spectra show a peak centered at 380 cm⁻¹ starting above 6 GPa for all samples, in agreement with previous observations. X-ray diffraction measurements are consistent with this spectral change indicating a structural phase transition; we find that the triplet at the pseudocubic (220) Bragg peak merges into a doublet above 6 GPa. Our results indicate that the morphotropicmore » phase boundary region (x=0.33–0.37) with the presence of monoclinic symmetry persists up to 7 GPa. The pressure dependence of ferroelectric domains in PMN-0.32PT single crystals was observed using a polarizing optical microscope. The domain wall density decreases with pressure and the domains disappear at a modest pressure of 3 GPa. We propose a pressure-composition phase diagram for PMN-xPT solid solutions.« less

Carbon-carbon bond cleavage of 1,2-hydroxy ethers b7 vanadium(V) dipicolinate complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hanson, Susan K; Gordon, John C; Thorn, David L

2009-01-01

The development of alternatives to current petroleum-based fuels and chemicals is becoming increasingly important due to concerns over climate change, growing world energy demand, and energy security issues. Using non-food derived biomass to produce renewable feedstocks for chemicals and fuels is a particularly attractive possibility. However, the majority of biomass is in the form of lignocellulose, which is often not fully utilized due to difficulties associated with breaking down both lignin and cellulose. Recently, a number of methods have been reported to transform cellulose directly into more valuable materials such as glucose, sorbitol, 5-(chloromethyl)furfural, and ethylene glycol. Less progress hasmore » been made with selective transformations of lignin, which is typically treated in paper and forest industries by kraft pulping (sodium hydroxide/sodium sulfide) or incineration. Our group has begun investigating aerobic oxidative C-C bond cleavage catalyzed by dipicolinate vanadium complexes, with the idea that a selective C-C cleavage reaction of this type could be used to produce valuable chemicals or intermediates from cellulose or lignin. Lignin is a randomized polymer containing methoxylated phenoxy propanol units. A number of different linkages occur naturally; one of the most prevalent is the {beta}-O-4 linkage shown in Figure 1, containing a C-C bond with 1,2-hydroxy ether substituents. While the oxidative C-C bond cleavage of 1,2-diols has been reported for a number of metals, including vanadium, iron, manganese, ruthenium, and polyoxometalate complexes, C-C bond cleavage of 1,2-hydroxy ethers is much less common. We report herein vanadium-mediated cleavage of C-C bonds between alcohol and ether functionalities in several lignin model complexes. In order to explore the scope and potential of vanadium complexes to effect oxidative C-C bond cleavage in 1,2-hydroxy ethers, we examined the reactivity of the lignin model complexes pinacol monomethyl ether (A), 2-phenoxyethanol (B), and 1,2-diphenyl-2-methoxyethanol (C) (Figure 1). Reaction of (dipic)V{sup V}(O)O{sup i}Pr (1a) or (dipic)V{sup v}(O)OEt (lb) with A, B, or C in acetonitrile yielded new vanadium(V) complexes where the alcohol-ether ligand was bound in a chelating fashion. From the reaction of 1b with pinacol monomethyl ether (A) in acetonitrile solution, (dipic)V{sup v}(O)(pinOMe) (2) (PinOMe = 2,3-dimethyl-3-methoxy-2-butanoxide) was isolated in 61 % yield. Reaction of 1b with 2-phenoxyethanol (B) in acetonitrile gave the new complex (dipic)V{sup v}(O)(OPE) (3) (OPE = 2-phenoxyethoxide), which was isolated in 76% yield. In a similar fashion, 1a reacted with 1,2-diphenyl-2-methoxyethanol (C) to give (dipic)V(O)(DPME) (4) (DPME = 1,2-diphenyl-2-methoxyethoxide), which was isolated in 39% yield. Complexes 2, 3, and 4 were characterized by {sup 1}H NMR and IR spectroscopy, elemental analysis, and X-ray crystallography. Compared to the previously reported vanadium(V) pinacolate complex (dipic)V(O)(pinOH) the X-ray structure of complex 2 reveals a slightly shorter V = O bond, 1.573(2) {angstrom} vs 1.588(2) {angstrom} for the pinOH structure. Complexes 3 and 4 display similar vanadium oxo bond distances of 1.568(2) {angstrom} and 1.576(2) {angstrom}, respectively. All three complexes show longer bonds to the ether-oxygen trans to the oxo (2.388(2) {angstrom} for 2, 2.547(2) {angstrom} for 3, and 2.438(2) {angstrom} for 4) than to the hydroxy-oxygen in the pinOH structure (2.252(2) {angstrom}).« less

Release of the glycosylphosphatidylinositol-anchored enzyme ecto-5'-nucleotidase by phospholipase C: catalytic activation and modulation by the lipid bilayer.

PubMed Central

Lehto, M T; Sharom, F J

1998-01-01

Many hydrolytic enzymes are attached to the extracellular face of the plasma membrane of eukaryotic cells by a glycosylphosphatidylinositol (GPI) anchor. Little is currently known about the consequences for enzyme function of anchor cleavage by phosphatidylinositol-specific phospholipase C. We have examined this question for the GPI-anchored protein 5'-nucleotidase (5'-ribonucleotide phosphohydrolase; EC 3.1.3.5), both in the native lymphocyte plasma membrane, and following purification and reconstitution into defined lipid bilayer vesicles, using Bacillus thuringiensis phosphatidylinositol-specific phospholipase C (PI-PLC). Membrane-bound, detergent-solubilized and cleaved 5'-nucleotidase all obeyed Michaelis-Menten kinetics, with a Km for 5'-AMP in the range 11-16 microM. The GPI anchor was removed from essentially all 5'-nucleotidase molecules, indicating that there is no phospholipase-resistant pool of enzyme. However, the phospholipase was much less efficient at cleaving the GPI anchor when 5'-nucleotidase was present in detergent solution, dimyristoyl phosphatidylcholine, egg phosphatidylethanolamine and sphingomyelin, compared with the native plasma membrane, egg phosphatidylcholine and a sphingolipid/cholesterol-rich mixture. Lipid molecular properties and bilayer packing may affect the ability of PI-PLC to gain access to the GPI anchor. Catalytic activation, characterized by an increase in Vmax, was observed following PI-PLC cleavage of reconstituted 5'-nucleotidase from vesicles of several different lipids. The highest degree of activation was noted for 5'-nucleotidase in egg phosphatidylethanolamine. An increase in Vmax was also noted for a sphingolipid/cholesterol-rich mixture, the native plasma membrane and egg phosphatidylcholine, whereas vesicles of sphingomyelin and dimyristoyl phosphatidylcholine showed little activation. Km generally remained unchanged following cleavage, except in the case of the sphingolipid/cholesterol-rich mixture. Insertion of the GPI anchor into a lipid bilayer appears to reduce the catalytic efficiency of 5'-nucleotidase, possibly via a conformational change in the enzyme, and activity is restored on release from the membrane. PMID:9576857

Pressure-dependent boron isotopic fractionation observed by column chromatography

NASA Astrophysics Data System (ADS)

Musashi, M.; Oi, T.; Matsuo, M.; Nomura, M.

2007-12-01

Boron isotopic fractionation factor ( S ) between boron taken up in strongly basic anion exchange resin and boron in aqueous solution was determined by breakthrough column chromatography at 5 and 17 MPa at 25°C, using 0.1 mmol/L boric acid solution as feed solution. The S values obtained were 1.018 and 1.012, respectively, which were smaller than the value reported by using the same chromatographic method at atmospheric pressure at 25°C with the boron concentration of 10 mmol/L, but were larger than the values at the same condition with much higher concentration of 100 and 501 mmol/L, indicating that borate-polymerization reducing the isotopic fractionation was negligible. However, calculations based on the theory of isotope distribution between two phases estimated that 21% (5MPa) and 47% (17MPa) of boron taken up in the resin phase was in the three-coordinated B(OH)3-form, instead of in the four-coordinated B(OH)4--form, at high pressures even with the very diluted solution. We discussed this discrepancy by introducing (1) hydration or (2) a partial molar volume difference between isotopic molecules. It was inferred that borate ions were partially dehydrated upon transfer from the solution phase to the resin phase at high pressures, which resulted in smaller S values compared with those at the atmospheric pressure. Alternatively, it was likely that the S value decreased with increasing pressure, because the difference of the partial isotopic molar volumes between 10B(OH)3 and 11B(OH)3 was larger than that between 10B(OH)4- and 11B(OH)4-. If either will be the case, the influence of a pressure upon the isotope effect may not be negligible for boron isotopic exchange equilibrium. This knowledge is crucial for the principle of the boron isotopic pH-metry reconstructing a chemical variation at the paleo-deep oceanic environment where the early life may have been evolved.

Textbook Forum: Equilibrium Constants of Chemical Reactions Involving Condensed Phases: Pressure Dependence and Choice of Standard State.

ERIC Educational Resources Information Center

Perlmutter-Hayman, Berta

1984-01-01

Problems of equilibria in condensed phases (particularly those involving solutes in dilute solutions) are encountered by students in their laboratory work; the thermodynamics of these equilibria is neglected in many textbooks. Therefore, several aspects of this topic are explored, focusing on pressure dependence and choice of standard state. (JN)

10 CFR 50.62 - Requirements for reduction of risk from anticipated transients without scram (ATWS) events for...

Code of Federal Regulations, 2010 CFR

2010-01-01

... into the reactor pressure vessel a borated water solution at such a flow rate, level of boron concentration and boron-10 isotope enrichment, and accounting for reactor pressure vessel volume, that the... minute of 13 weight percent sodium pentaborate decahydrate solution at the natural boron-10 isotope...

10 CFR 50.62 - Requirements for reduction of risk from anticipated transients without scram (ATWS) events for...

Code of Federal Regulations, 2012 CFR

2012-01-01

... into the reactor pressure vessel a borated water solution at such a flow rate, level of boron concentration and boron-10 isotope enrichment, and accounting for reactor pressure vessel volume, that the... minute of 13 weight percent sodium pentaborate decahydrate solution at the natural boron-10 isotope...

10 CFR 50.62 - Requirements for reduction of risk from anticipated transients without scram (ATWS) events for...

Code of Federal Regulations, 2011 CFR

2011-01-01

... into the reactor pressure vessel a borated water solution at such a flow rate, level of boron concentration and boron-10 isotope enrichment, and accounting for reactor pressure vessel volume, that the... minute of 13 weight percent sodium pentaborate decahydrate solution at the natural boron-10 isotope...

10 CFR 50.62 - Requirements for reduction of risk from anticipated transients without scram (ATWS) events for...

Code of Federal Regulations, 2013 CFR

2013-01-01

... into the reactor pressure vessel a borated water solution at such a flow rate, level of boron concentration and boron-10 isotope enrichment, and accounting for reactor pressure vessel volume, that the... minute of 13 weight percent sodium pentaborate decahydrate solution at the natural boron-10 isotope...

10 CFR 50.62 - Requirements for reduction of risk from anticipated transients without scram (ATWS) events for...

Code of Federal Regulations, 2014 CFR

2014-01-01

... into the reactor pressure vessel a borated water solution at such a flow rate, level of boron concentration and boron-10 isotope enrichment, and accounting for reactor pressure vessel volume, that the... minute of 13 weight percent sodium pentaborate decahydrate solution at the natural boron-10 isotope...

Effects of Salinity and Confining Pressure on Hydration-Induced Fracture Propagation and Permeability of Mancos Shale

NASA Astrophysics Data System (ADS)

Zhang, Shifeng; Sheng, James J.

2017-11-01

Low-salinity water imbibition was considered an enhanced recovery method in shale oil/gas reservoirs due to the resulting hydration-induced fractures, as observed at ambient conditions. To study the effect of confining pressure and salinity on hydration-induced fractures, time-elapsed computerized tomography (CT) was used to obtain cross-sectional images of shale cores. Based on the CT data of these cross-sectional images, cut faces parallel to the core axial in the middle of the core and 3D fracture images were also reconstructed. To study the effects of confining pressure and salinity on shale pore fluid flowing, shale permeability was measured with Nitrogen (N2), distilled water, 4% KCl solution, and 8% KCl solution. With confining pressures increased to 2 MPa or more, either in distilled water or in KCl solutions of different salinities, fractures were observed to close instead to propagate at the end of the tests. The intrinsic permeabilities of #1 and #2 Mancos shale cores were 60.0 and 7000 nD, respectively. When tested with distilled water, the permeability of #1 shale sample with 20.0 MPa confining pressure loaded, and #2 shale sample with 2.5 MPa confining pressure loaded, decreased to 0.45 and 15 nD, respectively. Using KCl can partly mitigate shale permeability degradation. Compared to 4% KCl, 8% KCl can decrease more permeability damage. From this point of view, high salinity KCl solution should be required for the water-based fracturing fluid.

The release and vascular action of bradykinin in the isolated perfused bovine udder

PubMed Central

Zeitlin, I J; Eshraghi, H R

2002-01-01

It has been postulated that the mammary kinin system may play a role in modulating mammary blood flow. Until the present study, the local release of bradykinin (BK) or other kinin system constituents into the mammary vasculature had not been reported and there were also conflicting findings on the action of BK on udder vasculature. Udders were removed from healthy lactating cows at slaughter. Pairs of ipsilateral quarters were perfused with Tyrode solution through the external pudendalis artery and drained via the cranial superficial epigastric vein. Mammary secretion was collected through teat cannulae. The perfusion pressure was linearly related to perfusate flux between 60 and 210 ml min−1 and the flow rate was adjusted (110-150 ml min−1) to give a basal pressure of 85 mmHg. PO2, PCO2 and pH in the venous effluent perfusate stabilised at 157 ± 10 mmHg, 50.1 ± 2.4 mmHg and 7.1 ± 0.03, respectively. The venous effluent contained immunoreactive BK and BK precursor, tissue kallikrein activity, and bradykinin-destroying enzyme. The concentration of BK stabilised at 378 ± 48 pg (ml perfusate)−1, that of trypsin-activated BK precursor was 679 ± 59 pg BK equivalents ml−1 and that of tissue kallikrein, measured as cleavage of d-Val.Leu.Arg-p-nitroanilide (d-Val.Leu.Arg-pNA), was 5.5 ± 1.7 nmol p-NA h−1 ml−1. Arterial infusion of phenylephrine (0.49-490 μM) produced increases in perfusion pressure (vasoconstriction). Acetylcholine (ACh) (0.55-55 μM) and BK (0.1-10 μM) produced only vasodilatation. BK (EC50 = 1.00±0.04 μM) was a more potent vasodilator than ACh (EC50 = 9.57±0.49 μM). The basal BK concentration was 250 times below the threshold for vasoactivity. The udder produced a milk-like secretion, which was dependent on perfusate flow and contained a concentration of BK which remained unchanged from 60 to 180 min of perfusion (231 ± 31 pg ml−1) unlike that in the venous effluent which doubled between 60 and 120 min. Thus, in addition to its secretion into milk, BK, together with its precursor and tissue kallikrein, is continuously released into the vasculature of the isolated, perfused, lactating bovine udder. PMID:12181294

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, J. Y.; E, J. C.; Huang, J. W.

Impact fracture of single-crystal Si is critical to long-term reliability of electronic devices and solar cells for its wide use as components or substrates in semiconductor industry. Single-crystal Si is loaded along two different crystallographic directions with a split Hopkinson pressure bar integrated with an in situ x-ray imaging and diffraction system. Bulk stress histories are measured, simultaneously with x-ray phase contrast imaging (XPCI) and Laue diffraction. Damage evolution is quantified with grayscale maps from XPCI. Single-crystal Si exhibits pronounced anisotropy in fracture modes, and thus fracture strengths and damage evolution. For loading along [11¯ 0] and viewing along [001],more » (1¯1¯0)[11¯ 0] cleavage is activated and induces horizontal primary cracks followed by perpendicular wing cracks. However, for loading along [011¯] and viewing along [111], random nucleation and growth of shear and tensile-splitting crack networks lead to catastrophic failure of materials with no cleavage. The primary-wing crack mode leads to a lower characteristic fracture strength due to predamage, but a more concentrated strength distribution, i.e., a higher Weibull modulus, compared to the second loading case. Furthermore, the sequential primary cracking, wing cracking and wing-crack coalescence processes result in a gradual increase of damage with time, deviating from theoretical predictions. Particle size and aspect ratios of fragments are discussed with postmortem fragment analysis, which verifies fracture modes observed in XPCI.« less

Immigration reform in France and the United States: reflections and documentation.

PubMed

Wenden, C W; Costa-lascoux, J

1984-01-01

This paper analyzes similarities and dissimilarities in French and American efforts to come to grip with irregular migration. The symbolic importance of immigration reform is argued to be a key political concern in both nations, although the politics of immigration reform has assumed a more partisan flavor in France, particularly since the municipal elections of 1983. In France, the theme of control and security, associated with the notion of preventing "automatic" immigration which would endanger the cohesion of French society, was widely utilized for political ends prior to and after May 10, 1981 (the date of Francois Mitterand's investiture). The American government, on the other hand, is confronted with the unenviable task of obtaining a legislative consensus on legalization and employer sanctions through an approach seeking to harmonize and integrate the demands articulated by various groups: employers, unions, and alien and ethnic interest groups (principally Hispanic groups divided into a hierarchy along a recently arrived/established cleavage). The American situation most sharply differs from the French case in terms of the absence of a right/left political cleavage. The real effects of clandestine immigration are to be found at the local level. In France, as in the US, the ability of local actors to exert pressure raises the fear that legalization and sanctions will change little, except in terms of symbolic legitimacy.

Mild acetosolv process to fractionate bamboo for the biorefinery: structural and antioxidant properties of the dissolved lignin.

PubMed

Li, Ming-Fei; Sun, Shao-Ni; Xu, Feng; Sun, Run-Cang

2012-02-22

Fractionation of lignocellulosic material into its constitutive components is of vital importance for the production of biofuels as well as other value-added chemicals. The conventional acetosolv processes are mainly focused on the production of pulp from woody lignocelluloses. In this study, a mild acetosolv process was developed to fractionate bamboo under atmospheric pressure to obtain cellulosic pulp, water-soluble fraction, and acetic acid lignin. The structural features of the lignins obtained under various conditions were characterized with elemental analysis, sugar analysis, alkaline nitrobenzene oxidation, gel permeation chromatography (GPC), (1)H nuclear magnetic resonance ((1)H NMR), and heteronuclear single-quantum coherence (HSQC) spectroscopy. As compared to milled wood lignin (MWL) of bamboo, acetic acid lignins had low impurities (carbohydrates 2.48-4.56%) mainly due to the cleavage of linkages between lignin and carbohydrates. In addition, acetic acid lignins showed a low proportion of syringyl (S) units. Due to the cleavage of linkages between lignin units, acetic acid lignins had weight-average molecular weights ranging from 4870 to 5210 g/mol, less than half that of MWL (13000 g/mol). In addition, acetic acid lignins showed stronger antioxidant activity mainly due to the significant increase of free phenolic hydroxyls. The lignins obtained with such low impurities, high free phenolic hydroxyls, and medium molecular weights are promising feedstocks to replace petroleum chemicals.

Thermal Decomposition Mechanism of CL-20 at Different Temperatures by ReaxFF Reactive Molecular Dynamics Simulations.

PubMed

Wang, Fuping; Chen, Lang; Geng, Deshen; Wu, Junying; Lu, Jianying; Wang, Chen

2018-04-26

Hexanitrohexaazaisowurtzitane (CL-20) has a high detonation velocity and pressure, but its sensitivity is also high, which somewhat limits its applications. Therefore, it is important to understand the mechanism and characteristics of thermal decomposition of CL-20. In this study, a ε-CL-20 supercell was constructed and ReaxFF-lg reactive molecular dynamics simulations were performed to investigate thermal decomposition of ε-CL-20 at various temperatures (2000, 2500, 2750, 3000, 3250, and 3500 K). The mechanism of thermal decomposition of CL-20 was analyzed from the aspects of potential energy evolution, the primary reactions, and the intermediate and final product species. The effect of temperature on thermal decomposition of CL-20 is also discussed. The initial reaction path of thermal decomposition of CL-20 is N-NO 2 cleavage to form NO 2 , followed by C-N cleavage, leading to the destruction of the cage structure. A small number of clusters appear in the early reactions and disappear at the end of the reactions. The initial reaction path of CL-20 decomposition is the same at different temperatures. However, as the temperature increases, the decomposition rate of CL-20 increases and the cage structure is destroyed earlier. The temperature greatly affects the rate constants of H 2 O and N 2 , but it has little effect on the rate constants of CO 2 and H 2 .

Isotope Effects as Probes for Enzyme Catalyzed Hydrogen-Transfer Reactions

PubMed Central

Roston, Daniel; Islam, Zahidul; Kohen, Amnon

2015-01-01

Kinetic Isotope effects (KIEs) have long served as a probe for the mechanisms of both enzymatic and solution reactions. Here, we discuss various models for the physical sources of KIEs, how experimentalists can use those models to interpret their data, and how the focus of traditional models has grown to a model that includes motion of the enzyme and quantum mechanical nuclear tunneling. We then present two case studies of enzymes, thymidylate synthase and alcohol dehydrogenase, and discuss how KIEs have shed light on the C-H bond cleavages those enzymes catalyze. We will show how the combination of both experimental and computational studieshas changed our notion of how these enzymes exert their catalytic powers. PMID:23673528

Aqueous photodegradation of antibiotic florfenicol: kinetics and degradation pathway studies.

PubMed

Zhang, Ya; Li, Jianhua; Zhou, Lei; Wang, Guoqing; Feng, Yanhong; Wang, Zunyao; Yang, Xi

2016-04-01

The occurrence of antibacterial agents in natural environment was of scientific concern in recent years. As endocrine disrupting chemicals, they had potential risk on ecology system and human beings. In the present study, the photodegradation kinetics and pathways of florfenicol were investigated under solar and xenon lamp irradiation in aquatic systems. Direct photolysis half-lives of florfenicol were determined as 187.29 h under solar irradiation and 22.43 h under xenon lamp irradiation, respectively. Reactive oxygen species (ROS), such as hydroxyl radical (·OH) and singlet oxygen ((1)O2) were found to play an important role in indirect photolysis process. The presence of nitrate and dissolved organic matters (DOMs) could affect photolysis of florfenicol in solutions through light screening effect, quenching effect, and photoinduced oxidization process. Photoproducts of florfenicol in DOMs solutions were identified by solid phase extraction-liquid chromatography-mass spectrometry (SPE-LC-MS) analysis techniques, and degradation pathways were proposed, including photoinduced hydrolysis, oxidation by (1)O2 and ·OH, dechlorination, and cleavage of the side chain.

Enzymatic characterization of peptidic materials isolated from aqueous solutions of ammonium cyanide (pH 9) and hydrocyanic acid (pH 6) exposed to ionizing radiation.

PubMed

Niketic, V; Draganić, Z; Nesković, S; Draganić, I

1982-01-01

The enzymatic digestion of some radiolytically produced peptidic materials was examined. The substrates were compounds isolated from 0.1 molar solutions of NH4CN (pH 9) and HCN (pH 6), after their exposure to gamma rays from a 60Co source (15-20 Mrad doses). Commercial proteolytic enzymes pronase and aminopeptidase M were used. The examined materials were of composite nature and proteolytic action was systematically observed after their subsequent purification. In some fractions the effect was found to be positive with up to 30% of peptide bonds cleaved with respect to the amino acid content. These findings support our previous conclusions on the free radical induced formation of peptidic backbones without the intervention of amino acids. Some side effects were also noted which might be of interest in observations on enzymatic cleavage of other composite peptidic materials of abiotic origin.

Dissociation of biomolecules in liquid environments during fast heavy-ion irradiation

NASA Astrophysics Data System (ADS)

Nomura, Shinji; Tsuchida, Hidetsugu; Kajiwara, Akihiro; Yoshida, Shintaro; Majima, Takuya; Saito, Manabu

2017-12-01

The effect of aqueous environment on fast heavy-ion radiation damage of biomolecules was studied by comparative experiments using liquid- and gas-phase amino acid targets. Three types of amino acids with different chemical structures were used: glycine, proline, and hydroxyproline. Ion-induced reaction products were analyzed by time-of-flight secondary-ion mass spectrometry. The results showed that fragments from the amino acids resulting from the C—Cα bond cleavage were the major products for both types of targets. For liquid-phase targets, specific products originating from chemical reactions in solutions were observed. Interestingly, multiple dissociated atomic fragments were negligible for the liquid-phase targets. We found that the ratio of multifragment to total fragment ion yields was approximately half of that for gas-phase targets. This finding agreed with the results of other studies on biomolecular cluster targets. It is concluded that the suppression of molecular multifragmentation is caused by the energy dispersion to numerous water molecules surrounding the biomolecular solutes.

Phenomenological aspects of fatigue cracking in as-received and hardened F82H modified steel exposed to lithiated water with dissolved hydrogen at 240°C

NASA Astrophysics Data System (ADS)

Maday, Marie-Françoise

2000-12-01

The low cycle fatigue (LCF) behaviour of F82H modified steel with three different degrees of hardness produced by specific thermal treatments has been investigated at 240°C under load control, in oxygen-free lithiated solutions containing either no or 2 ppm dissolved hydrogen. In all cases, it was found that the aqueous environments reduced the fatigue life of the material and promoted fracture modes different from those observed in air tests; the fracture modes comprised intergranular and transgranular quasi-cleavage separations as well as microvoid coalescence, which depended on material conditions and water chemistry. All these features were ascribed to a hydrogen-assisted-cracking (HAC) phenomenon, as the basic mechanism for controlling the fatigue behaviour of various F82H heats in lithiated solutions. The observed differences in HAC paths are discussed from the standpoint of material microstructural and substructural parameters.

Structure of Profiled Crystals Based on Solid Solutions of Bi2Te3 and Their X-Ray Diagnostics

NASA Astrophysics Data System (ADS)

Voronin, A. I.; Bublik, V. T.; Tabachkova, N. Yu.; Belov, Yu. M.

2011-05-01

In this work, we used x-ray structural diagnostic data to reveal the formation of structural regularities in profiled polycrystalline ingots based on Bi and Sb chalcogenide solid solutions. In Bi2Te3 lattice crystals, the solid phase grows such that the cleavage surfaces are perpendicular to the crystallization front. The crystallization singularity determines the nature of the growth texture. Because texture is an important factor determining the anisotropy of properties, which in turn determines the suitability of an ingot for production of modules and the possibility of figure of merit improvement, its diagnostics is an important issue for technology testing. Examples of texture analysis using the method of straight pole figure (SPF) construction for profiled crystals are provided. The structure of the surface layers in the profiled ingots was studied after electroerosion cutting. In addition, the method of estimation of the disturbed layer depth based on the nature of texture changes was used.

Ozonation of trimethoprim in aqueous solution: identification of reaction products and their toxicity.

PubMed

Kuang, Jiangmeng; Huang, Jun; Wang, Bin; Cao, Qiming; Deng, Shubo; Yu, Gang

2013-05-15

This work aimed to better understand the ozonation process of a typical antibiotic pharmaceutical, trimethoprim in aqueous solution. The parent compound was almost completely degraded with ozone dose up to 3.5 mg/L with no mineralization. Twenty one degradation products were identified using an electrospray quadrupole time-of-flight mass spectrometer. Several ozonation pathways were proposed including hydroxylation, demethylation, carbonylation, deamination and methylene group cleavage. Two species of luminescent bacteria Photobacterium phosphoreum and Vibrio qinghaiensis were selected to assess the toxicity of ozonation products. For P. phosphoreum, higher level of toxicity was observed compared to the parent compound, but a negligible toxicity change was observed for V. qinghaiensis, indicating different modes of action for the same water sample. This was further confirmed by quantitative structure-active relationship analysis. This work proves the dominant role of ozone rather than hydroxyl radicals in the reaction and the potential risk after ozonation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Condensed tannins: A novel rearrangement of procyanidins and prodelphinidins in thiolytic cleavage

Treesearch

G. Wayne McGraw; Jan P. Steynberg; Richard W. Hemingway

1993-01-01

Conditions commonly used for the thiolytic cleavage of interflavanoid bonds of condensed tannins also result in cleavage of the C4 to C10 bond of flavan units. Subsequenet lectrophilic attack of the C4 carbocation on the C2' or C6' of the B-ring, and loss of phloroglucinol (the A-ring), result in the formation of a mixture of 1,3-dithiobenzyl-2,4,s,6-...

Nanorelief of the natural cleavage surface of triglycine sulphate crystals with substitutional and interstitial impurities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belugina, N. V.; Gainutdinov, R. V.; Tolstikhina, A. L., E-mail: alla@ns.crys.ras.ru

2011-11-15

Ferroelectric triglycine sulphate crystals (TGS) with substitutional (LADTGS+ADP, DTGS) and interstitial (Cr) impurities have been studied by atomic-force microscopy, X-ray diffraction, and X-ray fluorescence. The nanorelief parameters of the mirror cleavage TGS(010) surface have been measured with a high accuracy. A correlation between the crystal defect density in the bulk and the cleavage surface nanorelief is revealed at the submicrometer level.

Copper-catalyzed transformation of ketones to amides via C(CO)-C(alkyl) bond cleavage directed by picolinamide.

PubMed

Ma, Haojie; Zhou, Xiaoqiang; Zhan, Zhenzhen; Wei, Daidong; Shi, Chong; Liu, Xingxing; Huang, Guosheng

2017-09-13

Copper catalyzed chemoselective cleavage of the C(CO)-C(alkyl) bond leading to C-N bond formation with chelation assistance of N-containing directing groups is described. Inexpensive Cu(ii)-acetate serves as a convenient catalyst for this transformation. This method highlights the emerging strategy to transform unactivated alkyl ketones into amides in organic synthesis and provides a new strategy for C-C bond cleavage.

Inhibition of the hammerhead ribozyme by neomycin.

PubMed Central

Stage, T K; Hertel, K J; Uhlenbeck, O C

1995-01-01

A series of antibiotics was tested for stimulation or inhibition of the hammerhead ribozyme cleavage reaction. Neomycin was found to be a potent inhibitor of the reaction with a Kl of 13.5 microM. Two hammerheads with well-characterized kinetics were used to determine which steps in the reaction mechanism were inhibited by neomycin. The data suggest that neomycin interacts preferentially with the enzyme-substrate complex and that this interaction leads to a reduction in the cleavage rate by stabilizing the ground state of the complex and destabilizing the transition state of the cleavage step. A comparison of neomycin with other aminoglycosides and inhibitors of hammerhead cleavage implies that the ammonium ions of neomycin are important for the antibiotic-hammerhead interaction. PMID:7489494

Bond Dissociation Free Energies (BDFEs) of the Acidic H-A Bonds in HA(*)(-) Radical Anions by Three Different Pathways.

PubMed

Zhao, Yongyu; Bordwell, Frederick G.

1996-09-20

Cleavage of radical anions, HA(*)(-), have been considered to give either H(*) + A(-) (path a) or H(-) + A(*) (path b), and factors determining the preferred mode of cleavage have been discussed. It is conceivable that cleavage to give a proton and a radical dianion, HA(*)(-) right harpoon over left harpoon H(+) + A(*)(2)(-) (path c), might also be feasible. A method, based on a thermodynamic cycle, to estimate the bond dissociation free energy (BDFE) by path c has been devised. Comparison of the BDFEs for cleavage of the radical anions derived from 24 nitroaromatic OH, SH, NH, and CH acids by paths a, b, c has shown that path c is favored thermodynamically.

Inflammatory Caspases: Activation and Cleavage of Gasdermin-D In Vitro and During Pyroptosis.

PubMed

Zhao, Yue; Shi, Jianjin; Shao, Feng

2018-01-01

Gasdermin-D (also known as GSDMD), the newly identified executioner of pyroptotic cell death, is cleaved by activated caspase-1 downstream of canonical inflammasome activation or caspase-4, 5, and 11 upon their ligation and activation by cytosolic LPS. Upon a single cleavage between the two domains in Gasdermin-D, the N-terminal domain binds to membrane lipids and lyses cells by forming pores of an inner diameter of 10-14 nm within the membrane. The inter-domain cleavage of Gasdermin-D is a reliable marker for the activation of inflammatory caspases and cell pyroptosis. Here, we describe the methods for examining Gasdermin-D cleavage by activated inflammatory caspases in vitro and upon inflammasome activation in vivo.

Thin airfoil theory based on approximate solution of the transonic flow equation

NASA Technical Reports Server (NTRS)

Spreiter, John R; Alksne, Alberta Y

1957-01-01

A method is presented for the approximate solution of the nonlinear equations transonic flow theory. Solutions are found for two-dimensional flows at a Mach number of 1 and for purely subsonic and purely supersonic flows. Results are obtained in closed analytic form for a large and significant class of nonlifting airfoils. At a Mach number of 1 general expressions are given for the pressure distribution on an airfoil of specified geometry and for the shape of an airfoil having a prescribed pressure distribution. Extensive comparisons are made with available data, particularly for a Mach number of 1, and with existing solutions.

Theoretical aspects of self-assembly of proteins: A Kirkwood-Buff-theory approach

NASA Astrophysics Data System (ADS)

Ben-Naim, Arieh

2013-06-01

A new approach to the problem of self-assembly of proteins induced by temperature, pressure, or changes in solute concentration is presented. The problem is formulated in terms of Le Chatelier principle, and a solution is sought in terms of the Kirkwood-Buff theory of solutions. In this article we focus on the pressure and solute effects on the association-dissociation equilibrium. We examine the role of both hydrophobic and hydrophilic effects. We argue that the latter are more important than the former. The solute effect, on the other hand, depends on the preferential solvation of the monomer and the aggregate with respect to solvent and co-solvent molecules. An experimental approach based on model compounds to study these effects is suggested.