Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation

PubMed Central

Nasedkin, Alexandr; Marcellini, Moreno; Religa, Tomasz L.; Freund, Stefan M.; Menzel, Andreas; Fersht, Alan R.; Jemth, Per; van der Spoel, David; Davidsson, Jan

2015-01-01

The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution. PMID:25946337

Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation.

PubMed

Nasedkin, Alexandr; Marcellini, Moreno; Religa, Tomasz L; Freund, Stefan M; Menzel, Andreas; Fersht, Alan R; Jemth, Per; van der Spoel, David; Davidsson, Jan

2015-01-01

The folding and unfolding of protein domains is an apparently cooperative process, but transient intermediates have been detected in some cases. Such (un)folding intermediates are challenging to investigate structurally as they are typically not long-lived and their role in the (un)folding reaction has often been questioned. One of the most well studied (un)folding pathways is that of Drosophila melanogaster Engrailed homeodomain (EnHD): this 61-residue protein forms a three helix bundle in the native state and folds via a helical intermediate. Here we used molecular dynamics simulations to derive sample conformations of EnHD in the native, intermediate, and unfolded states and selected the relevant structural clusters by comparing to small/wide angle X-ray scattering data at four different temperatures. The results are corroborated using residual dipolar couplings determined by NMR spectroscopy. Our results agree well with the previously proposed (un)folding pathway. However, they also suggest that the fully unfolded state is present at a low fraction throughout the investigated temperature interval, and that the (un)folding intermediate is highly populated at the thermal midpoint in line with the view that this intermediate can be regarded to be the denatured state under physiological conditions. Further, the combination of ensemble structural techniques with MD allows for determination of structures and populations of multiple interconverting structures in solution.

Role of Intermediate Filaments in Vesicular Traffic.

PubMed

Margiotta, Azzurra; Bucci, Cecilia

2016-04-25

Intermediate filaments are an important component of the cellular cytoskeleton. The first established role attributed to intermediate filaments was the mechanical support to cells. However, it is now clear that intermediate filaments have many different roles affecting a variety of other biological functions, such as the organization of microtubules and microfilaments, the regulation of nuclear structure and activity, the control of cell cycle and the regulation of signal transduction pathways. Furthermore, a number of intermediate filament proteins have been involved in the acquisition of tumorigenic properties. Over the last years, a strong involvement of intermediate filament proteins in the regulation of several aspects of intracellular trafficking has strongly emerged. Here, we review the functions of intermediate filaments proteins focusing mainly on the recent knowledge gained from the discovery that intermediate filaments associate with key proteins of the vesicular membrane transport machinery. In particular, we analyze the current understanding of the contribution of intermediate filaments to the endocytic pathway.

Nuclear networking.

PubMed

Xie, Wei; Burke, Brian

2017-07-04

Nuclear lamins are intermediate filament proteins that represent important structural components of metazoan nuclear envelopes (NEs). By combining proteomics and superresolution microscopy, we recently reported that both A- and B-type nuclear lamins form spatially distinct filament networks at the nuclear periphery of mouse fibroblasts. In particular, A-type lamins exhibit differential association with nuclear pore complexes (NPCs). Our studies reveal that the nuclear lamina network in mammalian somatic cells is less ordered and more complex than that of amphibian oocytes, the only other system in which the lamina has been visualized at high resolution. In addition, the NPC component Tpr likely links NPCs to the A-type lamin network, an association that appears to be regulated by C-terminal modification of various A-type lamin isoforms. Many questions remain, however, concerning the structure and assembly of lamin filaments, as well as with their mode of association with other nuclear components such as peripheral chromatin.

Structural and Mechanical Properties of Intermediate Filaments under Extreme Conditions and Disease

NASA Astrophysics Data System (ADS)

Qin, Zhao

Intermediate filaments are one of the three major components of the cytoskeleton in eukaryotic cells. It was discovered during the recent decades that intermediate filament proteins play key roles to reinforce cells subjected to large-deformation as well as participate in signal transduction. However, it is still poorly understood how the nanoscopic structure, as well as the biochemical properties of these protein molecules contribute to their biomechanical functions. In this research we investigate the material function of intermediate filaments under various extreme mechanical conditions as well as disease states. We use a full atomistic model and study its response to mechanical stresses. Learning from the mechanical response obtained from atomistic simulations, we build mesoscopic models following the finer-trains-coarser principles. By using this multiple-scale model, we present a detailed analysis of the mechanical properties and associated deformation mechanisms of intermediate filament network. We reveal the mechanism of a transition from alpha-helices to beta-sheets with subsequent intermolecular sliding under mechanical force, which has been inferred previously from experimental results. This nanoscale mechanism results in a characteristic nonlinear force-extension curve, which leads to a delocalization of mechanical energy and prevents catastrophic fracture. This explains how intermediate filament can withstand extreme mechanical deformation of > 1 00% strain despite the presence of structural defects. We combine computational and experimental techniques to investigate the molecular mechanism of Hutchinson-Gilford progeria syndrome, a premature aging disease. We find that the mutated lamin tail .domain is more compact and stable than the normal one. This altered structure and stability may enhance the association of intermediate filaments with the nuclear membrane, providing a molecular mechanism of the disease. We study the nuclear membrane association with intermediate filaments by focusing on the effect of calcium on the maturation process of lamin A. Our result shows that calcium plays a regulatory role in the post-translational processing of lam in A by tuning its molecular conformation and mechanics. Based on these findings we demonstrate that multiple-scale computational modeling provides a useful tool in understanding the biomechanical property and disease mechanism of intermediate filaments. We provide a perspective on research opportunities to improve the foundation for engineering the mechanical and biochemical functions of biomaterials. (Copies available exclusively from MIT Libraries, libraries.mit.edu/docs - docs@mit.edu)

The Transient Intermediate Plexiform Layer, a Plexiform Layer-like Structure Temporarily Existing in the Inner Nuclear Layer in Developing Rat Retina.

PubMed

Park, Hyung Wook; Kim, Hong-Lim; Park, Yong Soo; Kim, In-Beom

2018-02-01

The retina is a highly specialised part of the brain responsible for visual processing. It is well-laminated; three layers containing five different types of neurons are compartmentalised by two synaptic layers. Among the retinal layers, the inner nuclear layer (INL) is composed of horizontal, bipolar, and amacrine cell types. Bipolar cells form one sublayer in the distal half of the IPL, while amacrine cells form another sublayer in the proximal half, without any border-like structure. Here, we report that a plexiform layer-like structure exists temporarily in the border between the bipolar and amacrine sublayers in the INL in the rat retina during retinal development. This transient intermediate plexiform layer (TIPL) appeared at postnatal day (PD) 7 and then disappeared around PD 12. Most apoptotic cells in the INL were found near the TIPL. These results suggest that the TIPL may contribute to the formation of sublayers and the cell number limit in the INL.

The nonchromatin substructures of the nucleus: the ribonucleoprotein (RNP)-containing and RNP-depleted matrices analyzed by sequential fractionation and resinless section electron microscopy

PubMed Central

1986-01-01

The nonchromatin structure or matrix of the nucleus has been studied using an improved fractionation in concert with resinless section electron microscopy. The resinless sections show the nucleus of the intact cell to be filled with a dense network or lattice composed of soluble proteins and chromatin in addition to the structural nuclear constituents. In the first fractionation step, soluble proteins are removed by extraction with Triton X-100, and the dense nuclear lattice largely disappears. Chromatin and nonchromatin nuclear fibers are now sharply imaged. Nuclear constituents are further separated into three well-defined, distinct protein fractions. Chromatin proteins are those that require intact DNA for their association with the nucleus and are released by 0.25 M ammonium sulfate after internucleosomal DNA is cut with DNAase I. The resulting structure retains most heterogeneous nuclear ribonucleoprotein (hnRNP) and is designated the RNP-containing nuclear matrix. The proteins of hnRNP are those associated with the nucleus only if RNA is intact. These are released when nuclear RNA is briefly digested with RNAase A. Ribonuclease digestion releases 97% of the hnRNA and its associated proteins. These proteins correspond to the hnRNP described by Pederson (Pederson, T., 1974, J. Mol. Biol., 83:163- 184) and are distinct from the proteins that remain in the ribonucleoprotein (RNP)-depleted nuclear matrix. The RNP-depleted nuclear matrix is a core structure that retains lamins A and C, the intermediate filaments, and a unique set of nuclear matrix proteins (Fey, E. G., K. M. Wan, and S. Penman, 1984, J. Cell Biol. 98:1973- 1984). This core had been previously designated the nuclear matrix- intermediate filament scaffold and its proteins are a third, distinct, and nonoverlapping subset of the nuclear nonhistone proteins. Visualizing the nuclear matrix using resinless sections shows that nuclear RNA plays an important role in matrix organization. Conventional Epon-embedded electron microscopy sections show comparatively little of the RNP-containing and RNP-depleted nuclear matrix structure. In contrast, resinless sections show matrix interior to be a three-dimensional network of thick filaments bounded by the nuclear lamina. The filaments are covered with 20-30-nm electron dense particles which may contain the hnRNA. The large electron dense bodies, enmeshed in the interior matrix fibers, have the characteristic morphology of nucleoli. Treatment of the nuclear matrix with RNAase results in the aggregation of the interior fibers and the extensive loss of the 20-30-nm particles.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:3700470

Nuclear Science References Database

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

Pritychenko, B., E-mail: pritychenko@bnl.gov; Běták, E.; Singh, B.

2014-06-15

The Nuclear Science References (NSR) database together with its associated Web interface, is the world's only comprehensive source of easily accessible low- and intermediate-energy nuclear physics bibliographic information for more than 210,000 articles since the beginning of nuclear science. The weekly-updated NSR database provides essential support for nuclear data evaluation, compilation and research activities. The principles of the database and Web application development and maintenance are described. Examples of nuclear structure, reaction and decay applications are specifically included. The complete NSR database is freely available at the websites of the National Nuclear Data Center (http://www.nndc.bnl.gov/nsr) and the International Atomic Energymore » Agency (http://www-nds.iaea.org/nsr)« less

Structural Changes Associated with Transthyretin Misfolding and Amyloid Formation Revealed by Solution and Solid-State NMR

DOE PAGES

Lim, Kwang Hun; Dasari, Anvesh K. R.; Hung, Ivan; ...

2016-03-21

Elucidation of structural changes involved in protein misfolding and amyloid formation is crucial for unraveling the molecular basis of amyloid formation. We report structural analyses of the amyloidogenic intermediate and amyloid aggregates of transthyretin using solution and solid-state nuclear magnetic resonance (NMR) spectroscopy. These NMR solution results show that one of the two main β-sheet structures (CBEF β-sheet) is maintained in the aggregation-competent intermediate, while the other DAGH β-sheet is more flexible on millisecond time scales. Magic-angle-spinning solid-state NMR revealed that AB loop regions interacting with strand A in the DAGH β-sheet undergo conformational changes, leading to the destabilized DAGHmore » β-sheet.« less

Structure and antimicrobial activity of platypus 'intermediate' defensin-like peptide.

PubMed

Torres, Allan M; Bansal, Paramjit; Koh, Jennifer M S; Pagès, Guilhem; Wu, Ming J; Kuchel, Philip W

2014-05-02

The three-dimensional structure of a chemically synthesized peptide that we have called 'intermediate' defensin-like peptide (Int-DLP), from the platypus genome, was determined by nuclear magnetic resonance (NMR) spectroscopy; and its antimicrobial activity was investigated. The overall structural fold of Int-DLP was similar to that of the DLPs and β-defensins, however the presence of a third antiparallel β-strand makes its structure more similar to the β-defensins than the DLPs. Int-DLP displayed potent antimicrobial activity against Staphylococcus aureus and Pseudomonas aeruginosa. The four arginine residues at the N-terminus of Int-DLP did not affect the overall fold, but were important for its antimicrobial potency. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

Nuclear Lamins

PubMed Central

Dechat, Thomas; Adam, Stephen A.; Taimen, Pekka; Shimi, Takeshi; Goldman, Robert D.

2010-01-01

The nuclear lamins are type V intermediate filament proteins that are critically important for the structural properties of the nucleus. In addition, they are involved in the regulation of numerous nuclear processes, including DNA replication, transcription and chromatin organization. The developmentally regulated expression of lamins suggests that they are involved in cellular differentiation. Their assembly dynamic properties throughout the cell cycle, particularly in mitosis, are influenced by posttranslational modifications. Lamins may regulate nuclear functions by direct interactions with chromatin and determining the spatial organization of chromosomes within the nuclear space. They may also regulate chromatin functions by interacting with factors that epigenetically modify the chromatin or directly regulate replication or transcription. PMID:20826548

Structure of cold nuclear matter at subnuclear densities by quantum molecular dynamics

NASA Astrophysics Data System (ADS)

Watanabe, Gentaro; Sato, Katsuhiko; Yasuoka, Kenji; Ebisuzaki, Toshikazu

2003-09-01

Structure of cold nuclear matter at subnuclear densities for the proton fraction x=0.5, 0.3, and 0.1 is investigated by quantum molecular dynamics (QMD) simulations. We demonstrate that the phases with slablike and rodlike nuclei, etc. can be formed dynamically from hot uniform nuclear matter without any assumptions on nuclear shape, and also systematically analyze the structure of cold matter using two-point correlation functions and Minkowski functionals. In our simulations, we also observe intermediate phases, which have complicated nuclear shapes. It has been found out that these phases can be characterized as those with negative Euler characteristic. Our result implies the existence of these kinds of phases in addition to the simple “pasta” phases in neutron star crusts and supernova inner cores. In addition, we investigate the properties of the effective QMD interaction used in the present work to examine the validity of our results. The resultant energy per nucleon ɛn of the pure neutron matter, the proton chemical μ(0)p in pure neutron matter and the nuclear surface tension Esurf are generally reasonable in comparison with other nuclear interactions.

Intermediate-energy inverse-kinematics one-proton pickup reactions on neutron-deficient fp-shell nuclei

NASA Astrophysics Data System (ADS)

McDaniel, S.; Gade, A.; Tostevin, J. A.; Baugher, T.; Bazin, D.; Brown, B. A.; Cook, J. M.; Glasmacher, T.; Grinyer, G. F.; Ratkiewicz, A.; Weisshaar, D.

2012-01-01

Background: Thick-target-induced nucleon-adding transfer reactions onto energetic rare-isotope beams are an emerging spectroscopic tool. Their sensitivity to single-particle structure complements one-nucleon removal reaction capabilities in the quest to reveal the evolution of nuclear shell structure in very exotic nuclei. Purpose: Our purpose is to add intermediate-energy, carbon-target-induced one-proton pickup reactions to the arsenal of γ-ray-tagged direct reactions applicable in the regime of low beam intensities and to apply these for the first time to fp-shell nuclei. Methods: Inclusive and partial cross sections were measured for the 12C(48Cr,49Mn+γ)X and 12C(50Fe,51Co+γ)X proton pickup reactions at 56.7 and 61.2 MeV/nucleon, respectively, using coincident particle-γ spectroscopy at the National Superconducting Cyclotron Laboratory. The results are compared to reaction theory calculations using fp-shell-model nuclear structure input. For comparison with our previous work, the same reactions were measured on 9Be targets. Results: The measured partial cross sections confirm the specific population pattern predicted by theory, with pickup into high-ℓ orbitals being strongly favored, driven by linear and angular momentum matching. Conclusion: Carbon-target-induced pickup reactions are well suited, in the regime of modest beam intensity, to study the evolution of nuclear structure, with specific sensitivities that are well described by theory.

Intermediate introns in nuclear genes of euglenids - are they a distinct type?

PubMed

Milanowski, Rafał; Gumińska, Natalia; Karnkowska, Anna; Ishikawa, Takao; Zakryś, Bożena

2016-02-29

Nuclear genes of euglenids contain two major types of introns: conventional spliceosomal and nonconventional introns. The latter are characterized by variable non-canonical borders, RNA secondary structure that brings intron ends together, and an unknown mechanism of removal. Some researchers also distinguish intermediate introns, which combine features of both types. They form a stable RNA secondary structure and are classified into two subtypes depending on whether they contain one (intermediate/nonconventional subtype) or both (conventional/intermediate subtype) canonical spliceosomal borders. However, it has been also postulated that most introns classified as intermediate could simply be special cases of conventional or nonconventional introns. Sequences of tubB, hsp90 and gapC genes from six strains of Euglena agilis were obtained. They contain four, six, and two or three introns, respectively (the third intron in the gapC gene is unique for just one strain). Conventional introns were present at three positions: two in the tubB gene (at one position conventional/intermediate introns were also found) and one in the gapC gene. Nonconventional introns are present at ten positions: two in the tubB gene (at one position intermediate/nonconventional introns were also found), six in hsp90 (at four positions intermediate/nonconventional introns were also found), and two in the gapC gene. Sequence and RNA secondary structure analyses of nonconventional introns confirmed that their most strongly conserved elements are base pairing nucleotides at positions +4, +5 and +6/ -8, -7 and -6 (in most introns CAG/CTG nucleotides were observed). It was also confirmed that the presence of the 5' GT/C end in intermediate/nonconventional introns is not the result of kinship with conventional introns, but is due to evolutionary pressure to preserve the purine at the 5' end. However, an example of a nonconventional intron with GC-AG ends was shown, suggesting the possibility of intron type conversion between nonconventional and conventional. Furthermore, an analysis of conventional introns revealed that the ability to form a stable RNA secondary structure by some introns is probably not a result of their relationship with nonconventional introns. It was also shown that acquisition of new nonconventional introns is an ongoing process and can be observed at the level of a single species. In the recently acquired intron in the gapC gene an extended direct repeats at the intron-exon junctions are present, suggesting that double-strand break repair process could be the source of new nonconventional introns.

Demonstration of mechanical connections between integrins, cytoskeletal filaments, and nucleoplasm that stabilize nuclear structure

NASA Technical Reports Server (NTRS)

Maniotis, A. J.; Chen, C. S.; Ingber, D. E.

1997-01-01

We report here that living cells and nuclei are hard-wired such that a mechanical tug on cell surface receptors can immediately change the organization of molecular assemblies in the cytoplasm and nucleus. When integrins were pulled by micromanipulating bound microbeads or micropipettes, cytoskeletal filaments reoriented, nuclei distorted, and nucleoli redistributed along the axis of the applied tension field. These effects were specific for integrins, independent of cortical membrane distortion, and were mediated by direct linkages between the cytoskeleton and nucleus. Actin microfilaments mediated force transfer to the nucleus at low strain; however, tearing of the actin gel resulted with greater distortion. In contrast, intermediate filaments effectively mediated force transfer to the nucleus under both conditions. These filament systems also acted as molecular guy wires to mechanically stiffen the nucleus and anchor it in place, whereas microtubules acted to hold open the intermediate filament lattice and to stabilize the nucleus against lateral compression. Molecular connections between integrins, cytoskeletal filaments, and nuclear scaffolds may therefore provide a discrete path for mechanical signal transfer through cells as well as a mechanism for producing integrated changes in cell and nuclear structure in response to changes in extracellular matrix adhesivity or mechanics.

Insight into the functional organization of nuclear lamins in health and disease.

PubMed

Tatli, Meltem; Medalia, Ohad

2018-05-22

Lamins are the main component of the nuclear lamina, a protein meshwork at the inner nuclear membrane which primarily provide mechanical stability to the nucleus. Lamins, type V intermediate filament proteins, are also involved in many nuclear activities. Structural analysis of nuclei revealed that lamins form 3.5nm thick filaments often interact with nuclear pore complexes. Mutations in the LMNA gene, encoding A-type lamins, have been associated with at least 15 distinct diseases collectively termed laminopathies, including muscle, metabolic and neurological disorders, and premature aging syndrome. It is unclear how laminopathic mutations lead to such a wide array of diseases, essentially affecting almost all tissues. Copyright © 2018 Elsevier Ltd. All rights reserved.

Solution structures and backbone dynamics of Escherichia coli rhodanese PspE in its sulfur-free and persulfide-intermediate forms: implications for the catalytic mechanism of rhodanese.

PubMed

Li, Hongwei; Yang, Fan; Kang, Xue; Xia, Bin; Jin, Changwen

2008-04-15

Rhodanese catalyzes the sulfur-transfer reaction that transfers sulfur from thiosulfate to cyanide by a double-displacement mechanism, in which an active cysteine residue plays a central role. Previous studies indicated that the phage-shock protein E (PspE) from Escherichia coli is a rhodanese composed of a single active domain and is the only accessible rhodanese among the three single-domain rhodaneses in E. coli. To understand the catalytic mechanism of rhodanese at the molecular level, we determined the solution structures of the sulfur-free and persulfide-intermediate forms of PspE by nuclear magnetic resonance (NMR) spectroscopy and identified the active site by NMR titration experiments. To obtain further insights into the catalytic mechanism, we studied backbone dynamics by NMR relaxation experiments. Our results demonstrated that the overall structures in both sulfur-free and persulfide-intermediate forms are highly similar, suggesting that no significant conformational changes occurred during the catalytic reaction. However, the backbone dynamics revealed that the motional properties of PspE in its sulfur-free form are different from the persulfide-intermediate state. The conformational exchanges are largely enhanced in the persulfide-intermediate form of PspE, especially around the active site. The present structural and biochemical studies in combination with backbone dynamics provide further insights in understanding the catalytic mechanism of rhodanese.

Fission yeast Lem2 and Man1 perform fundamental functions of the animal cell nuclear lamina.

PubMed

Gonzalez, Yanira; Saito, Akira; Sazer, Shelley

2012-01-01

In animal cells the nuclear lamina, which consists of lamins and lamin-associated proteins, serves several functions: it provides a structural scaffold for the nuclear envelope and tethers proteins and heterochromatin to the nuclear periphery. In yeast, proteins and large heterochromatic domains including telomeres are also peripherally localized, but there is no evidence that yeast have lamins or a fibrous nuclear envelope scaffold. Nonetheless, we found that the Lem2 and Man1 proteins of the fission yeast Schizosaccharomyces pombe, evolutionarily distant relatives of the Lap2/Emerin/Man1 (LEM) sub-family of animal cell lamin-associated proteins, perform fundamental functions of the animal cell lamina. These integral inner nuclear membrane localized proteins, with nuclear localized DNA binding Helix-Extension-Helix (HEH) domains, impact nuclear envelope structure and integrity, are essential for the enrichment of telomeres at the nuclear periphery and by means of their HEH domains anchor chromatin, most likely transcriptionally repressed heterochromatin, to the nuclear periphery. These data indicate that the core functions of the nuclear lamina are conserved between fungi and animal cells and can be performed in fission yeast, without lamins or other intermediate filament proteins.

Intermediate-energy nuclear chemistry workshop

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

Butler, G.W.; Giesler, G.C.; Liu, L.C.

1981-05-01

This report contains the proceedings of the LAMPF Intermediate-Energy Nuclear Chemistry Workshop held in Los Alamos, New Mexico, June 23-27, 1980. The first two days of the Workshop were devoted to invited review talks highlighting current experimental and theoretical research activities in intermediate-energy nuclear chemistry and physics. Working panels representing major topic areas carried out indepth appraisals of present research and formulated recommendations for future research directions. The major topic areas were Pion-Nucleus Reactions, Nucleon-Nucleus Reactions and Nuclei Far from Stability, Mesonic Atoms, Exotic Interactions, New Theoretical Approaches, and New Experimental Techniques and New Nuclear Chemistry Facilities.

Mechanism for circularization of linear DNAs: circular parvovirus MVM DNA is formed by a "noose" sliding in a "lasso"-like DNA structure.

PubMed

Bratosin, S; Laub, O; Tal, J; Aloni, Y

1979-09-01

During an electron-microscopic survey with the aim of identifying the parvovirus MVM transcription template, we observed previously unidentified structures of MVM DNA in lysates of virus-infected cells. These included double-stranded "lasso"-like structures and relaxed circles. Both structures were of unit length MVM DNA, indicating that they were not intermediates formed during replication; they each represented about 5% of the total nuclear MVM DNA. The proportion of these structures was unchanged after digestion with sodium dodecyl sulfate/Pronase and RNase and after mild denaturation treatment. Cleavage of the "lasso" structures with EcoRI restriction endonuclease indicated that the "noose" part of the "lasso" structure is located on the 5' side of the genomic single-stranded MVM DNA. A model is presented for the molecular nature of the circularization process of MVM DNA in which the "lasso" structures are identified as intermediates during circle formation. This model proposes a mechanism for circularization of linear DNAs.

Physics Division annual review, 1 April 1980-31 March 1981

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

Not Available

1982-06-01

Progress in nuclear physics research is reported in the following areas: medium-energy physics (pion reaction mechanisms, high-resolution studies and nuclear structure, and two-nucleon physics with pions and electrons); heavy-ion research at the tandem and superconducting linear accelerator (resonant structure in heavy-ion reactions, fusion cross sections, high angular momentum states in nuclei, and reaction mechanisms and distributions of reaction strengths); charged-particle research; neutron and photonuclear physics; theoretical physics (heavy-ion direct-reaction theory, nuclear shell theory and nuclear structure, nuclear matter and nuclear forces, intermediate-energy physics, microscopic calculations of high-energy collisions of heavy ions, and light ion direct reactions); the superconducting linac; acceleratormore » operations; and GeV electron linac. Progress in atomic and molecular physics research is reported in the following areas: dissociation and other interactions of energetic molecular ions in solid and gaseous targets, beam-foil research and collision dynamics of heavy ions, photoionization- photoelectron research, high-resolution laser rf spectroscopy with atomic and molecular beams, moessbauer effect research, and theoretical atomic physics. Studies on interactions of energetic particles with solids are also described. Publications are listed. (WHK)« less

Retrospection of Chernobyl nuclear accident for decision analysis concerning remedial actions in Ukraine

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

Georgievskiy, Vladimir

2007-07-01

It is considered the efficacy of decisions concerning remedial actions when of-site radiological monitoring in the early and (or) in the intermediate phases was absent or was not informative. There are examples of such situations in the former Soviet Union where many people have been exposed: releases of radioactive materials from 'Krasnoyarsk-26' into Enisey River, releases of radioactive materials from 'Chelabinsk-65' (the Kishtim accident), nuclear tests at the Semipalatinsk Test Site, the Chernobyl nuclear accident etc. If monitoring in the early and (or) in the intermediate phases is absent the decisions concerning remedial actions are usually developed on the basemore » of permanent monitoring. However decisions of this kind may be essentially erroneous. For these cases it is proposed to make retrospection of radiological data of the early and intermediate phases of nuclear accident and to project decisions concerning remedial actions on the base of both retrospective data and permanent monitoring data. In this Report the indicated problem is considered by the example of the Chernobyl accident for Ukraine. Their of-site radiological monitoring in the early and intermediate phases was unsatisfactory. In particular, the pasture-cow-milk monitoring had not been made. All official decisions concerning dose estimations had been made on the base of measurements of {sup 137}Cs in body (40 measurements in 135 days and 55 measurements in 229 days after the Chernobyl accident). For the retrospection of radiological data of the Chernobyl accident dynamic model has been developed. This model has structure similar to the structure of Pathway model and Farmland model. Parameters of the developed model have been identified for agricultural conditions of Russia and Ukraine. By means of this model dynamics of 20 radionuclides in pathways and dynamics of doses have been estimated for the early, intermediate and late phases of the Chernobyl accident. The main results are following: - During the first year after the Chernobyl accident 75-93% of Commitment Effective Dose had been formed; - During the first year after the Chernobyl accident 85-90% of damage from radiation exposure had been formed. During the next 50 years (the late phase of accident) only 10-15% of damage from radiation exposure will have been formed; - Remedial actions (agricultural remedial actions as most effective) in Ukraine are intended for reduction of the damage from consumption of production which is contaminated in the late phase of accident. I.e. agricultural remedial actions have been intended for minimization only 10 % of the total damage from radiation exposure; - Medical countermeasures can minimize radiation exposure damage by an order of magnitude greater than agricultural countermeasures. - Thus, retrospection of nuclear accident has essentially changed type of remedial actions and has given a chance to increase effectiveness of spending by an order of magnitude. This example illustrates that in order to optimize remedial actions it is required to use data of retrospection of nuclear accidents in all cases when monitoring in the early and (or) intermediate phases is unsatisfactory. (author)« less

The investigation of order–disorder transition process of ZSM-5 induced by spark plasma sintering

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

Wang, Liang; Wang, Lianjun, E-mail: wanglj@dhu.edu.cn; Jiang, Wan

2014-04-01

Based on the amorphization of zeolites, an order–disorder transition method was used to prepare silica glass via Spark Plasma Sintering (SPS). In order to get a better understanding about the mechanism of amorphization induced by SPS, the intermediate products in this process were prepared and characterized by different characterization techniques. X-ray diffraction and High-energy synchrotron X-ray scattering show a gradual transformation from ordered crystal to glass. Local structural changes in glass network including Si–O bond length, O–Si–O bond angle, size of rings, coordination were detected by Infrared spectroscopy and {sup 29}Si magic-angle spinning nuclear magnetic resonance (NMR) spectroscopy. Topologically ordered,more » amorphous material with a different intermediate-range structure can be obtained by precise control of intermediate process which can be expected to optimize and design material. - Graphical abstract: Low-density, ordered zeolites collapse to the rigid amorphous glass through spark plasma sintering. The intermediate-range structure formed in the process of order–disorder transition may give rise to specific property. - Highlights: • Order–disorder transition process of ZSM-5 induced by spark plasma sintering was investigated using several methods including XRD, High-energy synchrotron X-ray scattering, SAXS, IR, NMR, ect. • Order–disorder transition induced by SPS was compared with TIA and PIA. • Three stages has been divided during the whole process. • The collapse temperature range which may give rise to intermediate-range structure has been located.« less

Electron microscopic observations of mouse sperm whole mounts after extraction for nuclear matrix and intermediate filaments.

PubMed

Markova, M D

2001-01-01

Nuclear matrix and intermediate filaments (NM-IF) can be isolated by sequential treatment with non-ionic detergent, high salt. and nuclease. Extracted cells are easily observed by unembedded whole-mount transmission electron microscopy. Different somatic cell types have been subjected to this procedure and retained their essential architecture. To our knowledge, this work describes the first application of NM-IF extraction to sperm. After chemical dissection the general appearance of mouse sperm cells was preserved, except for head-from-neck separation in some cases. The cell membrane, acrosome and mitochondria were not present. The nucleus showed no apparent changes and revealed no details excepting pore complexes in the posterior part. Tissue-specific cytoskeletal elements (perforatorium, postacrosomal sheath, capitulum, segmented columns, outer dense fibers, submitochondrial reticulum, annulus, and fibrous sheath) were retained, which permitted a parallel between them and intermediate filaments of somatic cells. Tail microtubules were also relatively well preserved, showing high intrinsic stability. Cell structures could be observed well, with some details in the tail even better visible than in ultrathin sections. Observation of mouse sperm whole mounts after NM-IF extraction not only revealed intermediate filament-like properties of their cytoskeletal elements but also offered an additional viewpoint to sperm ultrastructure.

The INF (Intermediate-Range Nuclear Forces) Controversy: A Confluence of Foreign and Domestic Interests.

DTIC Science & Technology

1986-09-01

AD-R175 303 THE INF (INTERMEDIRTE-RANSE NUCLEAR FORCES) 1/2 CONTROVERSY: A CONFLUENCE OF FOREIGN AND DOMESTIC INTERESTS(U) NAVAL POSTGRADUATE SCHOOL...on reverse if necessary and identify by block number) F:ELD I GROUP SUB-GROUP INF (Intermediate-Range Nuclear Forces, NATO, European Nuclear Capability...the United Kingdom, and several non- nuclear members of 14ATO are examined and analyzed. The analysis is concerned with alliance and transnational

Mechanisms of nuclear pore complex assembly - two different ways of building one molecular machine.

PubMed

Otsuka, Shotaro; Ellenberg, Jan

2018-02-01

The nuclear pore complex (NPC) mediates all macromolecular transport across the nuclear envelope. In higher eukaryotes that have an open mitosis, NPCs assemble at two points in the cell cycle: during nuclear assembly in late mitosis and during nuclear growth in interphase. How the NPC, the largest nonpolymeric protein complex in eukaryotic cells, self-assembles inside cells remained unclear. Recent studies have started to uncover the assembly process, and evidence has been accumulating that postmitotic and interphase NPC assembly use fundamentally different mechanisms; the duration, structural intermediates, and regulation by molecular players are different and different types of membrane deformation are involved. In this Review, we summarize the current understanding of these two modes of NPC assembly and discuss the structural and regulatory steps that might drive the assembly processes. We furthermore integrate understanding of NPC assembly with the mechanisms for rapid nuclear growth in embryos and, finally, speculate on the evolutionary origin of the NPC implied by the presence of two distinct assembly mechanisms. © 2017 The Authors. FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.

Electron-deuteron deep-inelastic scattering with spectator nucleon tagging and final-state interactions at intermediate x

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

Strikman, Mark; Weiss, Christian

We consider electron-deuteron deep-inelastic scattering (DIS) with detection of a proton in the nuclear fragmentation region ("spectator tagging") as a method for extracting the free neutron structure functions and studying their nuclear modifications. Such measurements could be performed at a future Electron-Ion Collider (EIC) with suitable forward detectors. The measured proton recoil momentum (≲ 100 MeV in the deuteron rest frame) specifies the deuteron configuration during the high-energy process and permits a controlled theoretical treatment of nuclear effects. Nuclear and nucleonic structure are separated using methods of light-front quantum mechanics. The impulse approximation (IA) to the tagged DIS cross sectionmore » contains the free neutron pole, which can be reached by on-shell extrapolation in the recoil momentum. Final-state interactions (FSI) distort the recoil momentum distribution away from the pole. In the intermediate-x region 0.1 < x < 0.5 FSI arise predominantly from interactions of the spectator proton with slow hadrons produced in the DIS process on the neutron (rest frame momenta ≲1 GeV, target fragmentation region). We construct a schematic model describing this effect, using final-state hadron distributions measured in nucleon DIS experiments and low-energy hadron scattering amplitudes. We investigate the magnitude of FSI, their dependence on the recoil momentum (angular dependence, forward/backward regions), their analytic properties, and their effect on the on-shell extrapolation. We comment on the prospects for neutron structure extraction in tagged DIS with EIC. Finally, we discuss possible extensions of the FSI model to other kinematic regions (large/small x). In tagged DIS at x << 0.1 FSI resulting from diffractive scattering on the nucleons become important and require separate treatment.« less

Electron-deuteron deep-inelastic scattering with spectator nucleon tagging and final-state interactions at intermediate x

NASA Astrophysics Data System (ADS)

Strikman, M.; Weiss, C.

2018-03-01

We consider electron-deuteron deep-inelastic scattering (DIS) with detection of a proton in the nuclear fragmentation region ("spectator tagging") as a method for extracting the free neutron structure functions and studying their nuclear modifications. Such measurements could be performed at a future electron-ion collider (EIC) with suitable forward detectors. The measured proton recoil momentum (≲100 MeV in the deuteron rest frame) specifies the deuteron configuration during the high-energy process and permits a controlled theoretical treatment of nuclear effects. Nuclear and nucleonic structure are separated using methods of light-front quantum mechanics. The impulse approximation to the tagged DIS cross section contains the free neutron pole, which can be reached by on-shell extrapolation in the recoil momentum. Final-state interactions (FSIs) distort the recoil momentum distribution away from the pole. In the intermediate-x region 0.1

Electron-deuteron deep-inelastic scattering with spectator nucleon tagging and final-state interactions at intermediate x

DOE PAGES

Strikman, Mark; Weiss, Christian

2018-03-27

We consider electron-deuteron deep-inelastic scattering (DIS) with detection of a proton in the nuclear fragmentation region ("spectator tagging") as a method for extracting the free neutron structure functions and studying their nuclear modifications. Such measurements could be performed at a future Electron-Ion Collider (EIC) with suitable forward detectors. The measured proton recoil momentum (≲ 100 MeV in the deuteron rest frame) specifies the deuteron configuration during the high-energy process and permits a controlled theoretical treatment of nuclear effects. Nuclear and nucleonic structure are separated using methods of light-front quantum mechanics. The impulse approximation (IA) to the tagged DIS cross sectionmore » contains the free neutron pole, which can be reached by on-shell extrapolation in the recoil momentum. Final-state interactions (FSI) distort the recoil momentum distribution away from the pole. In the intermediate-x region 0.1 < x < 0.5 FSI arise predominantly from interactions of the spectator proton with slow hadrons produced in the DIS process on the neutron (rest frame momenta ≲1 GeV, target fragmentation region). We construct a schematic model describing this effect, using final-state hadron distributions measured in nucleon DIS experiments and low-energy hadron scattering amplitudes. We investigate the magnitude of FSI, their dependence on the recoil momentum (angular dependence, forward/backward regions), their analytic properties, and their effect on the on-shell extrapolation. We comment on the prospects for neutron structure extraction in tagged DIS with EIC. Finally, we discuss possible extensions of the FSI model to other kinematic regions (large/small x). In tagged DIS at x << 0.1 FSI resulting from diffractive scattering on the nucleons become important and require separate treatment.« less

Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site.

PubMed

Wang, Lu; Fried, Stephen D; Boxer, Steven G; Markland, Thomas E

2014-12-30

Enzymes use protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here, we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen-bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active-site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen-bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen-bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds.

Systematics of intermediate-energy single-nucleon removal cross sections

NASA Astrophysics Data System (ADS)

Tostevin, J. A.; Gade, A.

2014-11-01

There is now a large and increasing body of experimental data and theoretical analyses for reactions that remove a single nucleon from an intermediate-energy beam of neutron- or proton-rich nuclei. In each such measurement, one obtains the inclusive cross section for the population of all bound final states of the mass A -1 reaction residue. These data, from different regions of the nuclear chart, and that involve weakly and strongly bound nucleons, are compared with theoretical expectations. These calculations include an approximate treatment of the reaction dynamics and shell-model descriptions of the projectile initial state, the bound final states of the residues, and the single-particle strengths computed from their overlap functions. The results are discussed in the light of recent data, more exclusive tests of the eikonal dynamical description, and calculations that take input from more microscopic nuclear structure models.

Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site

PubMed Central

Wang, Lu; Fried, Stephen D.; Boxer, Steven G.; Markland, Thomas E.

2014-01-01

Enzymes use protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here, we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen-bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active-site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen-bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen-bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds. PMID:25503367

Elucidation of the iron(IV)–oxo intermediate in the non-haem iron halogenase SyrB2

PubMed Central

Wong, Shaun D.; Srnec, Martin; Matthews, Megan L.; Liu, Lei V.; Kwak, Yeonju; Park, Kiyoung; Bell, Caleb B.; Alp, E. Ercan; Zhao, Jiyong; Yoda, Yoshitaka; Kitao, Shinji; Seto, Makoto; Krebs, Carsten; Bollinger, J. Martin; Solomon, Edward I.

2013-01-01

SUMMARY Mononuclear non-haem iron (NHFe) enzymes catalyse a wide variety of oxidative reactions including halogenation, hydroxylation, ring closure, desaturation, and aromatic ring cleavage. These are highly important for mammalian somatic processes such as phenylalanine metabolism, production of neurotransmitters, hypoxic response, and the biosynthesis of natural products.1–3 The key reactive intermediate in the catalytic cycles of these enzymes is an S = 2 FeIV=O species, which has been trapped for a number of NHFe enzymes4–8 including the halogenase SyrB2, the subject of this study. Computational studies to understand the reactivity of the enzymatic NHFe FeIV=O intermediate9–13 are limited in applicability due to the paucity of experimental knowledge regarding its geometric and electronic structures, which determine its reactivity. Synchrotron-based nuclear resonance vibrational spectroscopy (NRVS) is a sensitive and effective method that defines the dependence of the vibrational modes of Fe on the nature of the FeIV=O active site.14–16 Here we present the first NRVS structural characterisation of the reactive FeIV=O intermediate of a NHFe enzyme. This FeIV=O intermediate reacts via an initial H-atom abstraction step, with its subsquent halogenation (native) or hydroxylation (non-native) rebound reactivity being dependent on the substrate.17 A correlation of the experimental NRVS data to electronic structure calculations indicates that the substrate is able to direct the orientation of the FeIV=O intermediate, presenting specific frontier molecular orbitals (FMOs) which can activate the selective halogenation versus hydroxylation reactivity. PMID:23868262

Correlation and nuclear distortion effects of Cr-substituted ZnSe.

PubMed

Tablero, C

2007-04-28

There is a great deal of interest in the effect of the correlation and effect of the atomic distortion in materials with a metallic intermediate band. This band, situated within the semiconductor band gaps, would be split, thus creating two bands, a full one below the Fermi energy and an empty one above it, i.e., a metal-insulator transition. This basic electronic band structure corresponds to intermediate band materials and is characteristic of transparent-conducting oxides, up and down converters, and intermediate band solar cells. A sufficiently high density of Cr in ZnSe substituting the Zn atoms leads to a microscopic intermediate band, in which these effects will be analyzed. A Hubbard term has been included to improve the description of the many-body effect. This term modifies the bandwidth of the intermediate band, the Fermi energy, and breaks the orbital-occupation degeneracy. From the results, the intermediate band is not split within the range of Hubbard term values analyzed and for Cr substituting Zn from 0.463% to 3.125% of Cr atomic concentration.

Nuclear lamina builds tissues from the stem cell niche.

PubMed

Chen, Haiyang; Zheng, Yixian

2014-01-01

Recent studies show that nuclear lamins, the type V intermediate filament proteins, are required for proper building of at least some organs. As the major structural components of the nuclear lamina found underneath the inner nuclear membranes, lamins are ubiquitously expressed in all animal cells. How the broadly expressed lamins support the building of specific tissues is not understood. By studying Drosophila testis, we have uncovered a mechanism by which lamin-B functions in the cyst stem cell (CySC) and its differentiated cyst cell, the cell types known to form the niche/microenvironment for the germline stem cells (GSC) and the developing germ line, to ensure testis organogenesis (1). In this extra view, we discuss some remaining questions and the implications of our findings in the understanding of how the ubiquitous nuclear lamina regulates tissue building in a context-dependent manner.

NMR analysis of a kinetically trapped intermediate of a disulfide-deficient mutant of the starch-binding domain of glucoamylase.

PubMed

Sugimoto, Hayuki; Noda, Yasuo; Segawa, Shin-ichi

2011-09-16

A thermally unfolded disulfide-deficient mutant of the starch-binding domain of glucoamylase refolds into a kinetically trapped metastable intermediate when subjected to a rapid lowering of temperature. We attempted to characterise this intermediate using multidimensional NMR spectroscopy. The (1)H-(15)N heteronuclear single quantum coherence spectrum after a rapid temperature decrease (the spectrum of the intermediate) showed good chemical shift dispersion but was significantly different from that of the native state, suggesting that the intermediate adopts a nonnative but well-structured conformation. Large chemical shift changes for the backbone amide protons between the native and the intermediate states were observed for residues in the β-sheet consisting of strands 2, 3, 5, 6, and 7 as well as in the C-terminal region. These residues were found to be in close proximity to aromatic residues, suggesting that the chemical shift changes are mainly due to ring current shifts caused by the aromatic residues. The two-dimensional nuclear Overhauser enhancement (NOE) spectroscopy experiments showed that the intermediate contained substantial, native-like NOE connectivities, although there were fewer cross peaks in the spectrum of the intermediate compared with that of the native state. It was also shown that there were native-like interresidue NOEs for residues buried in the protein, whereas many of the NOE cross peaks were lost for the residues involved in a surface-exposed aromatic cluster. These results suggest that, in the intermediate, the aromatic cluster at the surface is structurally less organised, whereas the interior of the protein has relatively rigid, native-like side-chain packing. Copyright © 2011 Elsevier Ltd. All rights reserved.

Cell Pleomorphism and Cytoskeleton Disorganization in Human Liver Cancer.

PubMed

Cheng, Chiung-Chi; Lai, Yen-Chang Clark; Lai, Yih-Shyong; Chao, Wei-Ting; Tseng, Yu-Hui; Hsu, Yung-Hsiang; Chen, You-Yin; Liu, Yi-Hsiang

Nucleoskeleton maintains the framework of a cell nucleus that is required for a variety of nuclear functions. However, the nature of nucleoskeleton structure has not been yet clearly elucidated due to microscopy visualization limitations. Plectin, a nuclear pore-permeable component of cytoskeleton, exhibits a role of cross-linking between cytoplasmic intermediate filaments and nuclear lamins. Presumably, plectin is also a part of nucleoskeleton. Previously, we demonstrated that pleomorphism of hepatoma cells is the consequence of cytoskeletal changes mediated by plectin deficiency. In this study, we applied a variety of technologies to detect the cytoskeletons in liver cells. The images of confocal microscopy did not show the existence of plectin, intermediate filaments, microfilaments and microtubules in hepatic nuclei. However, in the isolated nuclear preparation, immunohistochemical staining revealed positive results for plectin and cytoskeletal proteins that may contribute to the contamination derived from cytoplasmic residues. Therefore, confocal microscopy provides a simple and effective technology to observe the framework of nucleoskeleton. Accordingly, we verified that cytoskeletons are not found in hepatic cell nuclei. Furthermore, the siRNA-mediated knockdown of plectin in liver cells leads to collapsed cytoskeleton, cell transformation and pleomorphic nuclei. Plectin and cytoskeletons were not detected in the nuclei of liver cells compared to the results of confocal microscopy. Despite the absence of nuclear plectin and cytoskeletal filaments, the evidence provided support that nuclear pleomorphism of cancer cells is correlated with the cytoplasmic disorganization of cytoskeleton. Copyright © 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Plectin isoforms as organizers of intermediate filament cytoarchitecture

PubMed Central

Winter, Lilli

2011-01-01

Intermediate filaments (IFs) form cytoplamic and nuclear networks that provide cells with mechanical strength. Perturbation of this structural support causes cell and tissue fragility and accounts for a number of human genetic diseases. In recent years, important additional roles, nonmechanical in nature, were ascribed to IFs, including regulation of signaling pathways that control survival and growth of the cells, and vectorial processes such as protein targeting in polarized cellular settings. The cytolinker protein plectin anchors IF networks to junctional complexes, the nuclear envelope and cytoplasmic organelles and it mediates their cross talk with the actin and tubulin cytoskeleton. These functions empower plectin to wield significant influence over IF network cytoarchitecture. Moreover, the unusual diversity of plectin isoforms with different N termini and a common IF-binding (C-terminal) domain enables these isoforms to specifically associate with and thereby bridge IF networks to distinct cellular structures. Here we review the evidence for IF cytoarchitecture being controlled by specific plectin isoforms in different cell systems, including fibroblasts, endothelial cells, lens fibers, lymphocytes, myocytes, keratinocytes, neurons and astrocytes, and discuss what impact the absence of these isoforms has on IF cytoarchitecture-dependent cellular functions. PMID:21866256

Investigating resonances above and below the threshold in nuclear reactions of astrophysical interest and beyond

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

La Cognata, M., E-mail: lacognata@lns.infn.it; Kiss, G. G.; Mukhamedzhanov, A. M.

2015-10-15

Resonances in nuclear cross sections dramatically change their trends. Therefore, the presence of unexpected resonances might lead to unpredicted consequences on astrophysics and nuclear physics. In nuclear physics, resonances allow one to study states in the intermediate compound systems, to evaluate their cluster structure, for instance, especially in the energy regions approaching particle decay thresholds. In astrophysics, resonances might lead to changes in the nucleosynthesis flow, determining different isotopic compositions of the nuclear burning ashes. For these reasons, the Trojan Horse method has been modified to investigate resonant reactions. Thanks to this novel approach, for the first time normalization tomore » direct data might be avoided. Moreover, in the case of sub threshold resonances, the Trojan Horse method modified to investigate resonances allows one to deduce the asymptotic normalization coefficient, showing the close connection between the two indirect approaches.« less

Inner/Outer nuclear membrane fusion in nuclear pore assembly: biochemical demonstration and molecular analysis.

PubMed

Fichtman, Boris; Ramos, Corinne; Rasala, Beth; Harel, Amnon; Forbes, Douglass J

2010-12-01

Nuclear pore complexes (NPCs) are large proteinaceous channels embedded in double nuclear membranes, which carry out nucleocytoplasmic exchange. The mechanism of nuclear pore assembly involves a unique challenge, as it requires creation of a long-lived membrane-lined channel connecting the inner and outer nuclear membranes. This stabilized membrane channel has little evolutionary precedent. Here we mapped inner/outer nuclear membrane fusion in NPC assembly biochemically by using novel assembly intermediates and membrane fusion inhibitors. Incubation of a Xenopus in vitro nuclear assembly system at 14°C revealed an early pore intermediate where nucleoporin subunits POM121 and the Nup107-160 complex were organized in a punctate pattern on the inner nuclear membrane. With time, this intermediate progressed to diffusion channel formation and finally to complete nuclear pore assembly. Correct channel formation was blocked by the hemifusion inhibitor lysophosphatidylcholine (LPC), but not if a complementary-shaped lipid, oleic acid (OA), was simultaneously added, as determined with a novel fluorescent dextran-quenching assay. Importantly, recruitment of the bulk of FG nucleoporins, characteristic of mature nuclear pores, was not observed before diffusion channel formation and was prevented by LPC or OA, but not by LPC+OA. These results map the crucial inner/outer nuclear membrane fusion event of NPC assembly downstream of POM121/Nup107-160 complex interaction and upstream or at the time of FG nucleoporin recruitment.

Laminopathies and the long strange trip from basic cell biology to therapy

PubMed Central

Worman, Howard J.; Fong, Loren G.; Muchir, Antoine; Young, Stephen G.

2009-01-01

The main function of the nuclear lamina, an intermediate filament meshwork lying primarily beneath the inner nuclear membrane, is to provide structural scaffolding for the cell nucleus. However, the lamina also serves other functions, such as having a role in chromatin organization, connecting the nucleus to the cytoplasm, gene transcription, and mitosis. In somatic cells, the main protein constituents of the nuclear lamina are lamins A, C, B1, and B2. Interest in the nuclear lamins increased dramatically in recent years with the realization that mutations in LMNA, the gene encoding lamins A and C, cause a panoply of human diseases (“laminopathies”), including muscular dystrophy, cardiomyopathy, partial lipodystrophy, and progeroid syndromes. Here, we review the laminopathies and the long strange trip from basic cell biology to therapeutic approaches for these diseases. PMID:19587457

Recent advances in biosynthetic modeling of nitric oxide reductases and insights gained from nuclear resonance vibrational and other spectroscopic studies

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

Chakraborty, Saumen; Reed, Julian; Sage, Timothy

This Forum Article focuses on recent advances in structural and spectroscopic studies of biosynthetic models of nitric oxide reductases (NORs). NORs are complex metalloenzymes found in the denitrification pathway of Earth's nitrogen cycle where they catalyze the proton-dependent twoelectron reduction of nitric oxide (NO) to nitrous oxide (N 2O). While much progress has been made in biochemical and biophysical studies of native NORs and their variants, a. clear mechanistic understanding of this important metalloenzyme related to its function is still elusive. We report herein UV vis and nuclear resonance vibrational spectroscopy (NRVS) studies of mononitrosylated intermediates of the NOR reactionmore » of a biosynthetic model. The ability to selectively substitute metals at either heme or nonheme metal sites allows the introduction of independent 57Fe probe atoms at either site, as well as allowing the preparation of analogues of stable reaction intermediates by replacing either metal with a redox inactive metal. Together with previous structural and spectroscopic results, we summarize insights gained from studying these biosynthetic models toward understanding structural features responsible for the NOR activity and its mechanism. As a result, the outlook on NOR modeling is also discussed, with an emphasis on the design of models capable of catalytic turnovers designed based on close mimics of the secondary coordination sphere of native NORs.« less

Structure–function mapping of a heptameric module in the nuclear pore complex

PubMed Central

Fernandez-Martinez, Javier; Phillips, Jeremy; Sekedat, Matthew D.; Diaz-Avalos, Ruben; Velazquez-Muriel, Javier; Franke, Josef D.; Williams, Rosemary; Stokes, David L.; Chait, Brian T.

2012-01-01

The nuclear pore complex (NPC) is a multiprotein assembly that serves as the sole mediator of nucleocytoplasmic exchange in eukaryotic cells. In this paper, we use an integrative approach to determine the structure of an essential component of the yeast NPC, the ∼600-kD heptameric Nup84 complex, to a precision of ∼1.5 nm. The configuration of the subunit structures was determined by satisfaction of spatial restraints derived from a diverse set of negative-stain electron microscopy and protein domain–mapping data. Phenotypic data were mapped onto the complex, allowing us to identify regions that stabilize the NPC’s interaction with the nuclear envelope membrane and connect the complex to the rest of the NPC. Our data allow us to suggest how the Nup84 complex is assembled into the NPC and propose a scenario for the evolution of the Nup84 complex through a series of gene duplication and loss events. This work demonstrates that integrative approaches based on low-resolution data of sufficient quality can generate functionally informative structures at intermediate resolution. PMID:22331846

Equation of state of dense nuclear matter and neutron star structure from nuclear chiral interactions

NASA Astrophysics Data System (ADS)

Bombaci, Ignazio; Logoteta, Domenico

2018-02-01

Aims: We report a new microscopic equation of state (EOS) of dense symmetric nuclear matter, pure neutron matter, and asymmetric and β-stable nuclear matter at zero temperature using recent realistic two-body and three-body nuclear interactions derived in the framework of chiral perturbation theory (ChPT) and including the Δ(1232) isobar intermediate state. This EOS is provided in tabular form and in parametrized form ready for use in numerical general relativity simulations of binary neutron star merging. Here we use our new EOS for β-stable nuclear matter to compute various structural properties of non-rotating neutron stars. Methods: The EOS is derived using the Brueckner-Bethe-Goldstone quantum many-body theory in the Brueckner-Hartree-Fock approximation. Neutron star properties are next computed solving numerically the Tolman-Oppenheimer-Volkov structure equations. Results: Our EOS models are able to reproduce the empirical saturation point of symmetric nuclear matter, the symmetry energy Esym, and its slope parameter L at the empirical saturation density n0. In addition, our EOS models are compatible with experimental data from collisions between heavy nuclei at energies ranging from a few tens of MeV up to several hundreds of MeV per nucleon. These experiments provide a selective test for constraining the nuclear EOS up to 4n0. Our EOS models are consistent with present measured neutron star masses and particularly with the mass M = 2.01 ± 0.04 M⊙ of the neutron stars in PSR J0348+0432.

Selective binding of meiosis-specific yeast Hop1 protein to the holliday junctions distorts the DNA structure and its implications for junction migration and resolution.

PubMed

Tripathi, Pankaj; Anuradha, S; Ghosal, Gargi; Muniyappa, K

2006-12-08

Saccharomyces cerevisiae HOP1, which encodes a component of synaptonemal complex (SC), plays an important role in both gene conversion and crossing over between homologs, as well as enforces meiotic recombination checkpoint control over the progression of recombination intermediates. In hop1Delta mutants, meiosis-specific double-strand breaks (DSBs) are reduced to 10% of the wild-type level, and at aberrantly late times, these DSBs are processed into inter-sister recombination intermediates. However, the underlying mechanism by which Hop1 protein regulates these nuclear events remains obscure. Here we show that Hop1 protein interacts selectively with the Holliday junction, changes its global conformation and blocks the dissolution of the junction by a RecQ helicase. The Holliday junction-Hop1 protein complexes are significantly more stable at higher ionic strengths and molar excess of unlabeled competitor DNA than complexes containing other recombination intermediates. Structural analysis of the Holliday junction using 2-aminopurine fluorescence emission, DNase I footprinting and KMnO4 probing provide compelling evidence that Hop1 protein binding induces significant distortion at the center of the Holliday junction. We propose that Hop1 protein might coordinate the physical monitoring of meiotic recombination intermediates with the process of branch migration of Holliday junction.

Corrosion behaviour of steel rebars embedded in a concrete designed for the construction of an intermediate-level radioactive waste disposal facility

NASA Astrophysics Data System (ADS)

Duffó, G. S.; Arva, E. A.; Schulz, F. M.; Vazquez, D. R.

2013-07-01

The National Atomic Energy Commission of the Argentine Republic is developing a nuclear waste disposal management programme that contemplates the design and construction of a facility for the final disposal of intermediate-level radioactive wastes. The repository is based on the use of multiple, independent and redundant barriers. The major components are made in reinforced concrete so, the durability of these structures is an important aspect for the facility integrity. This work presents an investigation performed on an instrumented reinforced concrete prototype specifically designed for this purpose, to study the behaviour of an intermediate level radioactive waste disposal facility from the rebar corrosion point of view. The information obtained will be used for the final design of the facility in order to guarantee a service life more or equal than the foreseen durability for this type of facilities.

Durability of a reinforced concrete designed for the construction of an intermediate-level radioactive waste disposal facility

NASA Astrophysics Data System (ADS)

Duffó, G. S.; Arva, E. A.; Schulz, F. M.; Vazquez, D. R.

2012-01-01

The National Atomic Energy Commission of the Argentine Republic is developing a nuclear waste disposal management programme that contemplates the design and construction of a facility for the final disposal of intermediate-level radioactive wastes. The repository is based on the use of multiple, independent and redundant barriers. The major components are made in reinforced concrete so, the durability of these structures is an important aspect for the facility integrity. This work presents an investigation performed on a reinforced concrete specifically designed for this purpose, to predict the service life of the intermediate level radioactive waste disposal facility from data obtained with several techniques. Results obtained with corrosion sensors embedded in a concrete prototype are also included. The information obtained will be used for the final design of the facility in order to guarantee a service life more or equal than the foreseen durability for this type of facilities.

INF (Intermediate Range Nuclear Forces) Treaty and flexible response. Research report

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

Lewis, J.W.

1988-03-01

This paper examines how the Intermediate Range Nuclear Forces (INF) Treaty affects NATO's military strategy of flexible response. A discussion of flexible response strategy is provided as background for the reader. Then, relevant terms of the INF treaty are addressed followed by an assessment of the treaty's impact on the military strategy of the alliance.

Intermediate Nuclear Structure for 2v 2{beta} Decay of {sup 48}Ca Studied by (p, n) and (n, p) Reactions at 300 MeV

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

Sakai, H.; Yako, K.

2009-08-26

Angular distributions of the double differential cross sections for the {sup 48}Ca(p,n) and the {sup 48}Ti(n,p) reactions were measured at 300 MeV. A multipole decomposition technique was applied to the spectra to extract the Gamow-Teller (GT) transition strengths. In the (n, p) spectrum beyond 8 MeV excitation energy extra B(GT{sup +}) strengths which are not predicted by the shell model calculation. This extra B(GT{sup +}) strengths significantly contribute to the nuclear matrix element of the 2v2{beta}-decay.

Electronic Structure of the Ferryl Intermediate in the α-Ketoglutarate Dependent Non-Heme Iron Halogenase SyrB2: Contributions to H Atom Abstraction Reactivity.

PubMed

Srnec, Martin; Wong, Shaun D; Matthews, Megan L; Krebs, Carsten; Bollinger, J Martin; Solomon, Edward I

2016-04-20

Low temperature magnetic circular dichroism (LT MCD) spectroscopy in combination with quantum-chemical calculations are used to define the electronic structure associated with the geometric structure of the Fe(IV)═O intermediate in SyrB2 that was previously determined by nuclear resonance vibrational spectroscopy. These studies elucidate key frontier molecular orbitals (FMOs) and their contribution to H atom abstraction reactivity. The VT MCD spectra of the enzymatic S = 2 Fe(IV)═O intermediate with Br(-) ligation contain information-rich features that largely parallel the corresponding spectra of the S = 2 model complex (TMG3tren)Fe(IV)═O (Srnec, M.; Wong, S. D.; England, J; Que, L; Solomon, E. I. Proc. Natl. Acad. Sci. USA 2012, 109, 14326-14331). However, quantitative differences are observed that correlate with π-anisotropy and oxo donor strength that perturb FMOs and affect reactivity. Due to π-anisotropy, the Fe(IV)═O active site exhibits enhanced reactivity in the direction of the substrate cavity that proceeds through a π-channel that is controlled by perpendicular orientation of the substrate C-H bond relative to the halide-Fe(IV)═O plane. Also, the increased intrinsic reactivity of the SyrB2 intermediate relative to the ferryl model complex is correlated to a higher oxyl character of the Fe(IV)═O at the transition states resulting from the weaker ligand field of the halogenase.

Automation of NMR structure determination of proteins.

PubMed

Altieri, Amanda S; Byrd, R Andrew

2004-10-01

The automation of protein structure determination using NMR is coming of age. The tedious processes of resonance assignment, followed by assignment of NOE (nuclear Overhauser enhancement) interactions (now intertwined with structure calculation), assembly of input files for structure calculation, intermediate analyses of incorrect assignments and bad input data, and finally structure validation are all being automated with sophisticated software tools. The robustness of the different approaches continues to deal with problems of completeness and uniqueness; nevertheless, the future is very bright for automation of NMR structure generation to approach the levels found in X-ray crystallography. Currently, near completely automated structure determination is possible for small proteins, and the prospect for medium-sized and large proteins is good. Copyright 2004 Elsevier Ltd.

Physiological and Pathological Aging Affects Chromatin Dynamics, Structure and Function at the Nuclear Edge

PubMed Central

Robin, Jérôme D.; Magdinier, Frédérique

2016-01-01

Lamins are intermediate filaments that form a complex meshwork at the inner nuclear membrane. Mammalian cells express two types of Lamins, Lamins A/C and Lamins B, encoded by three different genes, LMNA, LMNB1, and LMNB2. Mutations in the LMNA gene are associated with a group of phenotypically diverse diseases referred to as laminopathies. Lamins interact with a large number of binding partners including proteins of the nuclear envelope but also chromatin-associated factors. Lamins not only constitute a scaffold for nuclear shape, rigidity and resistance to stress but also contribute to the organization of chromatin and chromosomal domains. We will discuss here the impact of A-type Lamins loss on alterations of chromatin organization and formation of chromatin domains and how disorganization of the lamina contributes to the patho-physiology of premature aging syndromes. PMID:27602048

Relevance of β-delayed neutron data for reactor, nuclear physics and astrophysics applications

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

Kratz, Karl-Ludwig

Initially, yields (or abundances) and branching ratios of β-delayed neutrons (βdn) from fission products (P{sub n}-values) have had their main importance in nuclear reactor control. At that time, the six-group mathematical approximation of the time-dependence of βdn-data in terms of the so-called 'Keepin groups' was generally accepted. Later, with the development of high-resolution neutron spectroscopy, βdn data have provided important information on nuclear-structure properties at intermediate excitation energy in nuclei far from stability, as well as in nuclear astrophysics. In this paper, I will present some examples of the βdn-studies performed by the Kernchemie Mainz group during the past threemore » decades. This work has been recognized as an example of 'broad scientific diversity' which has led to my nomination for the 2014 Hans A. Bethe prize.« less

Tiopronin Gold Nanoparticle Precursor Forms Aurophilic Ring Tetramer

PubMed Central

Simpson, Carrie A.; Farrow, Christopher L.; Tian, Peng; Billinge, Simon J.L.; Huffman, Brian J.; Harkness, Kellen M.; Cliffel, David E.

2010-01-01

In the two step synthesis of thiolate-monolayer protected clusters (MPCs), the first step of the reaction is a mild reduction of gold(III) by thiols that generates gold(I) thiolate complexes as intermediates. Using tiopronin (Tio) as the thiol reductant, the characterization of the intermediate Au4Tio4 complex was accomplished with various analytical and structural techniques. Nuclear magnetic resonance (NMR), elemental analysis, thermogravimetric analysis (TGA), and matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) were all consistent with a cyclic gold(I)-thiol tetramer structure, and final structural analysis was gathered through the use of powder diffraction and pair distribution functions (PDF). Crystallographic data has proved challenging for almost all previous gold(I)-thiolate complexes. Herein, a novel characterization technique when combined with standard analytical assessment to elucidate structure without crystallographic data proved invaluable to the study of these complexes. This in conjunction with other analytical techniques, in particular mass spectrometry, can elucidate a structure when crystallographic data is unavailable. In addition, luminescent properties provided evidence of aurophilicity within the molecule. The concept of aurophilicity has been introduced to describe a select group of gold-thiolate structures, which possess unique characteristics, mainly red photoluminescence and a distinct Au-Au intramolecular distance indicating a weak metal-metal bond as also evidenced by the structural model of the tetramer. Significant features of both the tetrameric and aurophilic properties of the intermediate gold(I) tiopronin complex are retained after borohydride reduction to form the MPC, including gold(I) tiopronin partial rings as capping motifs, or “staples”, and weak red photoluminescence that extends into the Near Infrared region. PMID:21067183

Iso standardization of theoretical activity evaluation method for low and intermediate level activated waste generated at nuclear power plants

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

Makoto Kashiwagi; Garamszeghy, Mike; Lantes, Bertrand

Disposal of low-and intermediate-level activated waste generated at nuclear power plants is being planned or carried out in many countries. The radioactivity concentrations and/or total quantities of long-lived, difficult-to-measure nuclides (DTM nuclides), such as C-14, Ni-63, Nb-94, α emitting nuclides etc., are often restricted by the safety case for a final repository as determined by each country's safety regulations, and these concentrations or amounts are required to be known and declared. With respect to waste contaminated by contact with process water, the Scaling Factor method (SF method), which is empirically based on sampling and analysis data, has been applied asmore » an important method for determining concentrations of DTM nuclides. This method was standardized by the International Organization for Standardization (ISO) and published in 2007 as ISO21238 'Scaling factor method to determine the radioactivity of low and intermediate-level radioactive waste packages generated at nuclear power plants' [1]. However, for activated metal waste with comparatively high concentrations of radioactivity, such as may be found in reactor control rods and internal structures, direct sampling and radiochemical analysis methods to evaluate the DTM nuclides are limited by access to the material and potentially high personnel radiation exposure. In this case, theoretical calculation methods in combination with empirical methods based on remote radiation surveys need to be used to best advantage for determining the disposal inventory of DTM nuclides while minimizing exposure to radiation workers. Pursuant to this objective a standard for the theoretical evaluation of the radioactivity concentration of DTM nuclides in activated waste, is in process through ISO TC85/SC5 (ISO Technical Committee 85: Nuclear energy, nuclear technologies, and radiological protection; Subcommittee 5: Nuclear fuel cycle). The project team for this ISO standard was formed in 2011 and is composed of experts from 11 countries. The project team has been conducting technical discussions on theoretical methods for determining concentrations of radioactivity, and has developed the draft International Standard of ISO16966 'Theoretical activation calculation method to evaluate the radioactivity of activated waste generated at nuclear reactors' [2]. This paper describes the international standardization process developed by the ISO project team, and outlines the following two theoretical activity evaluation methods:? Point method? Range method. (authors)« less

A-type Lamins Form Distinct Filamentous Networks with Differential Nuclear Pore Complex Associations.

PubMed

Xie, Wei; Chojnowski, Alexandre; Boudier, Thomas; Lim, John S Y; Ahmed, Sohail; Ser, Zheng; Stewart, Colin; Burke, Brian

2016-10-10

The nuclear lamina is a universal feature of metazoan nuclear envelopes (NEs) [1]. In mammalian cells, it appears as a 10-30 nm filamentous layer at the nuclear face of the inner nuclear membrane (INM) and is composed primarily of A- and B-type lamins, members of the intermediate filament family [2]. While providing structural integrity to the NE, the lamina also represents an important signaling and regulatory platform [3]. Two A-type lamin isoforms, lamins A and C (LaA and LaC), are expressed in most adult human cells. Encoded by a single gene, these proteins are largely identical, diverging only in their C-terminal tail domains. By contrast with that of LaC, the unique LaA tail undergoes extensive processing, including farnesylation and endo-proteolysis [4, 5]. However, functional differences between LaA and LaC are still unclear. Compounding this uncertainty, the structure of the lamina remains ill defined. In this study, we used BioID, an in vivo proximity-labeling method to identify differential interactors of A-type lamins [6]. One of these, Tpr, a nuclear pore complex (NPC) protein, is highlighted by its selective association with LaC. By employing superresolution microscopy, we demonstrate that this Tpr association is mirrored in enhanced interaction of LaC with NPCs. Further superresolution studies visualizing both endogenous A- and B-type lamins have allowed us to construct a nanometer-scale model of the mammalian nuclear lamina. Our data indicate that different A- and B-type lamin species assemble into separate filament networks that together form an extended composite structure at the nuclear periphery providing attachment sites for NPCs, thereby regulating their distribution. Copyright © 2016 Elsevier Ltd. All rights reserved.

Definition of the intermediates and mechanism of the anticancer drug bleomycin using nuclear resonance vibrational spectroscopy and related methods

PubMed Central

Liu, Lei V.; Bell, Caleb B.; Wong, Shaun D.; Wilson, Samuel A.; Kwak, Yeonju; Chow, Marina S.; Zhao, Jiyong; Hodgson, Keith O.; Hedman, Britt; Solomon, Edward I.

2010-01-01

Bleomycin (BLM) is a glycopeptide anticancer drug capable of effecting single- and double-strand DNA cleavage. The last detectable intermediate prior to DNA cleavage is a low spin FeIII peroxy level species, termed activated bleomycin (ABLM). DNA strand scission is initiated through the abstraction of the C-4′ hydrogen atom of the deoxyribose sugar unit. Nuclear resonance vibrational spectroscopy (NRVS) aided by extended X-ray absorption fine structure spectroscopy and density functional theory (DFT) calculations are applied to define the natures of FeIIIBLM and ABLM as (BLM)FeIII─OH and (BLM)FeIII(η1─OOH) species, respectively. The NRVS spectra of FeIIIBLM and ABLM are strikingly different because in ABLM the δFe─O─O bending mode mixes with, and energetically splits, the doubly degenerate, intense O─Fe─Nax transaxial bends. DFT calculations of the reaction of ABLM with DNA, based on the species defined by the NRVS data, show that the direct H-atom abstraction by ABLM is thermodynamically favored over other proposed reaction pathways. PMID:21149675

NMR Crystallography of a Carbanionic Intermediate in Tryptophan Synthase: Chemical Structure, Tautomerization, and Reaction Specificity.

PubMed

Caulkins, Bethany G; Young, Robert P; Kudla, Ryan A; Yang, Chen; Bittbauer, Thomas J; Bastin, Baback; Hilario, Eduardo; Fan, Li; Marsella, Michael J; Dunn, Michael F; Mueller, Leonard J

2016-11-23

Carbanionic intermediates play a central role in the catalytic transformations of amino acids performed by pyridoxal-5'-phosphate (PLP)-dependent enzymes. Here, we make use of NMR crystallography-the synergistic combination of solid-state nuclear magnetic resonance, X-ray crystallography, and computational chemistry-to interrogate a carbanionic/quinonoid intermediate analogue in the β-subunit active site of the PLP-requiring enzyme tryptophan synthase. The solid-state NMR chemical shifts of the PLP pyridine ring nitrogen and additional sites, coupled with first-principles computational models, allow a detailed model of protonation states for ionizable groups on the cofactor, substrates, and nearby catalytic residues to be established. Most significantly, we find that a deprotonated pyridine nitrogen on PLP precludes formation of a true quinonoid species and that there is an equilibrium between the phenolic and protonated Schiff base tautomeric forms of this intermediate. Natural bond orbital analysis indicates that the latter builds up negative charge at the substrate C α and positive charge at C4' of the cofactor, consistent with its role as the catalytic tautomer. These findings support the hypothesis that the specificity for β-elimination/replacement versus transamination is dictated in part by the protonation states of ionizable groups on PLP and the reacting substrates and underscore the essential role that NMR crystallography can play in characterizing both chemical structure and dynamics within functioning enzyme active sites.

NMR Crystallography of a Carbanionic Intermediate in Tryptophan Synthase: Chemical Structure, Tautomerization, and Reaction Specificity

PubMed Central

2016-01-01

Carbanionic intermediates play a central role in the catalytic transformations of amino acids performed by pyridoxal-5′-phosphate (PLP)-dependent enzymes. Here, we make use of NMR crystallography—the synergistic combination of solid-state nuclear magnetic resonance, X-ray crystallography, and computational chemistry—to interrogate a carbanionic/quinonoid intermediate analogue in the β-subunit active site of the PLP-requiring enzyme tryptophan synthase. The solid-state NMR chemical shifts of the PLP pyridine ring nitrogen and additional sites, coupled with first-principles computational models, allow a detailed model of protonation states for ionizable groups on the cofactor, substrates, and nearby catalytic residues to be established. Most significantly, we find that a deprotonated pyridine nitrogen on PLP precludes formation of a true quinonoid species and that there is an equilibrium between the phenolic and protonated Schiff base tautomeric forms of this intermediate. Natural bond orbital analysis indicates that the latter builds up negative charge at the substrate Cα and positive charge at C4′ of the cofactor, consistent with its role as the catalytic tautomer. These findings support the hypothesis that the specificity for β-elimination/replacement versus transamination is dictated in part by the protonation states of ionizable groups on PLP and the reacting substrates and underscore the essential role that NMR crystallography can play in characterizing both chemical structure and dynamics within functioning enzyme active sites. PMID:27779384

Lamina-independent lamins in the nuclear interior serve important functions.

PubMed

Dechat, T; Gesson, K; Foisner, R

2010-01-01

Nuclear lamins were originally described as the main constituents of the nuclear lamina, a filamentous meshwork closely associated with the inner nuclear membrane. However, within recent years, it has become increasingly evident that a fraction of lamins also resides throughout the nuclear interior. As intermediate-filament-type proteins, lamins have been suggested to fulfill mainly structural functions such as providing shape and mechanical stability to the nucleus. But recent findings show that both peripheral and nucleoplasmic lamins also have important roles in essential cellular processes such as transcription, DNA replication, cell cycle progression, and chromatin organization. Furthermore, more than 300 mutations in the gene encoding A-type lamins have been associated with several human diseases now generally termed laminopathies and comprising muscular dystrophies, lipodystrophies, cardiomyopathies, and premature aging diseases. This review focuses on the lamina-independent pool of lamins in the nuclear interior, which surprisingly has not been studied in much detail so far. We discuss the properties and regulation of nucleoplasmic lamins during the cell cycle, their interaction partners, and their potential involvement in cellular processes and the development of laminopathies.

Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027

DOE PAGES

Huang, Tingting; Chang, Chin -Yuan; Lohman, Jeremy R.; ...

2016-10-01

Comparative analysis of the enediyne biosynthetic gene clusters revealed sets of conserved genes serving as outstanding candidates for the enediyne core. Here we report the crystal structures of SgcJ and its homologue NCS-Orf16, together with gene inactivation and site-directed mutagenesis studies, to gain insight into enediyne core biosynthesis. Gene inactivation in vivo establishes that SgcJ is required for C-1027 production in Streptomyces globisporus. SgcJ and NCS-Orf16 share a common structure with the nuclear transport factor 2-like superfamily of proteins, featuring a putative substrate binding or catalytic active site. Site-directed mutagenesis of the conserved residues lining this site allowed us tomore » propose that SgcJ and its homologues may play a catalytic role in transforming the linear polyene intermediate, along with other enediyne polyketide synthase-associated enzymes, into an enzyme-sequestered enediyne core intermediate. In conclusion, these findings will help formulate hypotheses and design experiments to ascertain the function of SgcJ and its homologues in nine-membered enediyne core biosynthesis.« less

Protein Folding—How and Why: By Hydrogen Exchange, Fragment Separation, and Mass Spectrometry

PubMed Central

Englander, S. Walter; Mayne, Leland; Kan, Zhong-Yuan; Hu, Wenbing

2017-01-01

Advanced hydrogen exchange (HX) methodology can now determine the structure of protein folding intermediates and their progression in folding pathways. Key developments over time include the HX pulse labeling method with nuclear magnetic resonance analysis, development of the fragment separation method, the addition to it of mass spectrometric (MS) analysis, and recent improvements in the HX MS technique and data analysis. Also, the discovery of protein foldons and their role supplies an essential interpretive link. Recent work using HX pulse labeling with HX MS analysis finds that a number of proteins fold by stepping through a reproducible sequence of native-like intermediates in an ordered pathway. The stepwise nature of the pathway is dictated by the cooperative foldon unit construction of the protein. The pathway order is determined by a sequential stabilization principle; prior native-like structure guides the formation of adjacent native-like structure. This view does not match the funneled energy landscape paradigm of a very large number of folding tracks, which was framed before foldons were known. PMID:27145881

Proton elastic scattering from stable and unstable nuclei - Extraction of nuclear densities

NASA Astrophysics Data System (ADS)

Sakaguchi, H.; Zenihiro, J.

2017-11-01

Progress in proton elastic scattering at intermediate energies to determine nuclear density distributions is reviewed. After challenges of about 15 years to explain proton elastic scattering and associated polarization phenomena at intermediate energies, we have reached to some conclusions regarding proton elastic scattering as a means of obtaining nuclear densities. During this same period, physics of unstable nuclei has become of interest, and the density distributions of protons and neutrons play more important roles in unstable nuclei, since the differences in proton and neutron numbers and densities are expected to be significant. As such, proton elastic scattering experiments at intermediate energies using the inverse kinematic method have started to determine density distributions of unstable nuclei. In the region of unstable nuclei, we are confronted with a new problem when attempting to find proton and neutron densities separately from elastic proton scattering data, since electron scattering data for unstable nuclei are not presently available. We introduce a new means of determining proton and neutron densities separately by double-energy proton elastic scattering at intermediate energies.

The physics of solid-state neutron detector materials and geometries.

PubMed

Caruso, A N

2010-11-10

Detection of neutrons, at high total efficiency, with greater resolution in kinetic energy, time and/or real-space position, is fundamental to the advance of subfields within nuclear medicine, high-energy physics, non-proliferation of special nuclear materials, astrophysics, structural biology and chemistry, magnetism and nuclear energy. Clever indirect-conversion geometries, interaction/transport calculations and modern processing methods for silicon and gallium arsenide allow for the realization of moderate- to high-efficiency neutron detectors as a result of low defect concentrations, tuned reaction product ranges, enhanced effective omnidirectional cross sections and reduced electron-hole pair recombination from more physically abrupt and electronically engineered interfaces. Conversely, semiconductors with high neutron cross sections and unique transduction mechanisms capable of achieving very high total efficiency are gaining greater recognition despite the relative immaturity of their growth, lithographic processing and electronic structure understanding. This review focuses on advances and challenges in charged-particle-based device geometries, materials and associated mechanisms for direct and indirect transduction of thermal to fast neutrons within the context of application. Calorimetry- and radioluminescence-based intermediate processes in the solid state are not included.

L-tyrosine and L-DOPA as hormone-like regulators of melanocytes functions

PubMed Central

Slominski, Andrzej; Zmijewski, Michal; Pawelek, John

2011-01-01

Summary Evidence reveals that L-tyrosine and L-DOPA, besides serving as substrates and intermediates of melanogenesis, are also bioregulatory agents acting not only as inducers and positive regulators of melanogenesis but also as regulators of other cellular functions. These can be mediated through action on specific receptors or through non-receptor mediated mechanisms. The substrate induced (L-tyrosine and/or L-DOPA) melanogenic pathway would autoregulate itself as well as it would regulate the melanocyte functions through activity of its structural or regulatory proteins and through intermediates of melanogenesis and melanin itself. Dissection of regulatory and autoregulatory elements of this process may elucidate how substrate induced autoregulatory pathways have evolved from prokaryotic or simple eukaryotic organisms to complex systems in vertebrates. This could substantiate older theory proposing that receptors for amino-acid derived hormones arose from the receptors for those amino acids, and that nuclear receptors evolved from primitive intracellular receptors binding nutritional factors or metabolic intermediates. PMID:21834848

Mechanism of intermediate filament recognition by plakin repeat domains revealed by envoplakin targeting of vimentin

NASA Astrophysics Data System (ADS)

Fogl, Claudia; Mohammed, Fiyaz; Al-Jassar, Caezar; Jeeves, Mark; Knowles, Timothy J.; Rodriguez-Zamora, Penelope; White, Scott A.; Odintsova, Elena; Overduin, Michael; Chidgey, Martyn

2016-03-01

Plakin proteins form critical connections between cell junctions and the cytoskeleton; their disruption within epithelial and cardiac muscle cells cause skin-blistering diseases and cardiomyopathies. Envoplakin has a single plakin repeat domain (PRD) which recognizes intermediate filaments through an unresolved mechanism. Herein we report the crystal structure of envoplakin's complete PRD fold, revealing binding determinants within its electropositive binding groove. Four of its five internal repeats recognize negatively charged patches within vimentin via five basic determinants that are identified by nuclear magnetic resonance spectroscopy. Mutations of the Lys1901 or Arg1914 binding determinants delocalize heterodimeric envoplakin from intracellular vimentin and keratin filaments in cultured cells. Recognition of vimentin is abolished when its residues Asp112 or Asp119 are mutated. The latter slot intermediate filament rods into basic PRD domain grooves through electrosteric complementarity in a widely applicable mechanism. Together this reveals how plakin family members form dynamic linkages with cytoskeletal frameworks.

Sustainable Thorium Nuclear Fuel Cycles: A Comparison of Intermediate and Fast Neutron Spectrum Systems

DOE PAGES

Brown, Nicholas R.; Powers, Jeffrey J.; Feng, B.; ...

2015-05-21

This paper presents analyses of possible reactor representations of a nuclear fuel cycle with continuous recycling of thorium and produced uranium (mostly U-233) with thorium-only feed. The analysis was performed in the context of a U.S. Department of Energy effort to develop a compendium of informative nuclear fuel cycle performance data. The objective of this paper is to determine whether intermediate spectrum systems, having a majority of fission events occurring with incident neutron energies between 1 eV and 10 5 eV, perform as well as fast spectrum systems in this fuel cycle. The intermediate spectrum options analyzed include tight latticemore » heavy or light water-cooled reactors, continuously refueled molten salt reactors, and a sodium-cooled reactor with hydride fuel. All options were modeled in reactor physics codes to calculate their lattice physics, spectrum characteristics, and fuel compositions over time. Based on these results, detailed metrics were calculated to compare the fuel cycle performance. These metrics include waste management and resource utilization, and are binned to accommodate uncertainties. The performance of the intermediate systems for this selfsustaining thorium fuel cycle was similar to a representative fast spectrum system. However, the number of fission neutrons emitted per neutron absorbed limits performance in intermediate spectrum systems.« less

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

Huang, Tingting; Chang, Chin -Yuan; Lohman, Jeremy R.

Comparative analysis of the enediyne biosynthetic gene clusters revealed sets of conserved genes serving as outstanding candidates for the enediyne core. Here we report the crystal structures of SgcJ and its homologue NCS-Orf16, together with gene inactivation and site-directed mutagenesis studies, to gain insight into enediyne core biosynthesis. Gene inactivation in vivo establishes that SgcJ is required for C-1027 production in Streptomyces globisporus. SgcJ and NCS-Orf16 share a common structure with the nuclear transport factor 2-like superfamily of proteins, featuring a putative substrate binding or catalytic active site. Site-directed mutagenesis of the conserved residues lining this site allowed us tomore » propose that SgcJ and its homologues may play a catalytic role in transforming the linear polyene intermediate, along with other enediyne polyketide synthase-associated enzymes, into an enzyme-sequestered enediyne core intermediate. In conclusion, these findings will help formulate hypotheses and design experiments to ascertain the function of SgcJ and its homologues in nine-membered enediyne core biosynthesis.« less

Radiation shielding estimates for manned Mars space flight.

PubMed

Dudkin, V E; Kovalev, E E; Kolomensky, A V; Sakovich, V A; Semenov, V F; Demin, V P; Benton, E V

1992-01-01

In the analysis of the required radiation shielding protection of spacecraft during a Mars flight, specific effects of solar activity (SA) on the intensity of galactic and solar cosmic rays were taken into consideration. Three spaceflight periods were considered: (1) maximum SA; (2) minimum SA; and (3) intermediate SA, when intensities of both galactic and solar cosmic rays are moderately high. Scenarios of spaceflights utilizing liquid-propellant rocket engines, low- and intermediate-thrust nuclear electrojet engines, and nuclear rocket engines, all of which have been designed in the Soviet Union, are reviewed. Calculations were performed on the basis of a set of standards for radiation protection approved by the U.S.S.R. State Committee for Standards. It was found that the lowest estimated mass of a Mars spacecraft, including the radiation shielding mass, obtained using a combination of a liquid propellant engine with low and intermediate thrust nuclear electrojet engines, would be 500-550 metric tons.

Overexpression of the lamina proteins Lamin and Kugelkern induces specific ultrastructural alterations in the morphology of the nuclear envelope of intestinal stem cells and enterocytes.

PubMed

Petrovsky, Roman; Krohne, Georg; Großhans, Jörg

2018-03-01

The nuclear envelope has a stereotypic morphology consisting of a flat double layer of the inner and outer nuclear membrane, with interspersed nuclear pores. Underlying and tightly linked to the inner nuclear membrane is the nuclear lamina, a proteinous layer of intermediate filament proteins and associated proteins. Physiological, experimental or pathological alterations in the constitution of the lamina lead to changes in nuclear morphology, such as blebs and lobulations. It has so far remained unclear whether the morphological changes depend on the differentiation state and the specific lamina protein. Here we analysed the ultrastructural morphology of the nuclear envelope in intestinal stem cells and differentiated enterocytes in adult Drosophila flies, in which the proteins Lam, Kugelkern or a farnesylated variant of LamC were overexpressed. Surprisingly, we detected distinct morphological features specific for the respective protein. Lam induced envelopes with multiple layers of membrane and lamina, surrounding the whole nucleus whereas farnesylated LamC induced the formation of a thick fibrillary lamina. In contrast, Kugelkern induced single-layered and double-layered intranuclear membrane structures, which are likely be derived from infoldings of the inner nuclear membrane or of the double layer of the envelope. Copyright © 2018 Elsevier GmbH. All rights reserved.

Electron microscopy of intermediate filaments: teaming up with atomic force and confocal laser scanning microscopy.

PubMed

Kreplak, Laurent; Richter, Karsten; Aebi, Ueli; Herrmann, Harald

2008-01-01

Intermediate filaments (IFs) were originally discovered and defined by electron microscopy in myoblasts. In the following it was demonstrated and confirmed that they constitute, in addition to microtubules and microfilaments, a third independent, general filament system in the cytoplasm of most metazoan cells. In contrast to the other two systems, IFs are present in cells in two principally distinct cytoskeletal forms: (i) extended and free-running filament arrays in the cytoplasm that are integrated into the cytoskeleton by associated proteins of the plakin type; and (ii) a membrane- and chromatin-bound thin 'lamina' of a more or less regular network of interconnected filaments made from nuclear IF proteins, the lamins, which differ in several important structural aspects from cytoplasmic IF proteins. In man, more than 65 genes code for distinct IF proteins that are expressed during embryogenesis in various routes of differentiation in a tightly controlled manner. IF proteins exhibit rather limited sequence identity implying that the different types of IFs have distinct biochemical properties. Hence, to characterize the structural properties of the various IFs, in vitro assembly regimes have been developed in combination with different visualization methods such as transmission electron microscopy of fixed and negatively stained samples as well as methods that do not use staining such as scanning transmission electron microscopy (STEM) and cryoelectron microscopy as well as atomic force microscopy. Moreover, with the generation of both IF-type specific antibodies and chimeras of fluorescent proteins and IF proteins, it has become possible to investigate the subcellular organization of IFs by correlative fluorescence and electron microscopic methods. The combination of these powerful methods should help to further develop our understanding of nuclear architecture, in particular how nuclear subcompartments are organized and in which way lamins are involved.

The nuclear spin response to intermediate energy protons

NASA Astrophysics Data System (ADS)

Baker, F. T.; Bimbot, L.; Castel, B.; Fergerson, R. W.; Glashausser, C.; Green, A.; Hausser, O.; Hicks, K.; Jones, K.; Miller, C. A.; Nanda, S. K.; Smith, R. D.; Vetterli, M.; Wambach, J.; Abegg, R.; Beatty, D.; Cupps, V.; Djalali, C.; Henderson, R.; Jackson, K. P.; Jeppeson, R.; Lisantti, J.; Morlet, M.; Sawafta, R.; Unkelbach, W.; Willis, A.; Yen, S.

1990-03-01

Measurements of the spin-flip probability Snn for inclusive inelastic proton scattering around 300 MeV from nuclei between 12C and 90Zr show that an enhanced spin response near 40 MeV excitation at q ∼ 100 MeV/ c is a general feature of nuclear structure. Data for 40Ca at 800 MeV confirm that the enhancement is not a peculiarity of 300 MeV scattering. In addition, measurements in 44Ca up to 75 MeV show that the enhancement cannot be attributed solely to a relatively narrow resonance. Continuum RPA calculations suggest that the enhancement is due to the exhaustion of most S = 0 strength at lower energy and a shift of S = 1 strength to higher energy.

What are the effects of arms control on Norway and northern waters. Research report

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

Furnes, R.H.

1990-04-01

Norway occupies a strategic position between the two superpowers. Her close proximity to the Soviet Union and the military bases on the Kola Peninsula make her territory attractive to both NATO and the Soviet Union. Buildups of the Soviet North Fleet and the naval base on Kola and the United States naval strategy of forward deployment, have increased the activity and the importance of northern waters. This increased importance of northern waters could challenge the Norwegian security policy. Arms reduction could make Norwegian territory relatively more important for the Soviet Union to defend her interests on Kola and in northernmore » waters and for the United States to project a threat to the Soviet interests in the area. (1) A reduction of strategic nuclear missile forces will focus on survivability. Northern waters offers excellent protection to Soviet submarines. A relative shift to SLBM could be the result of reducing the strategic nuclear missile forces. (2) The INF does not comprise sea launched intermediate nuclear missiles. Hence the elimination of land-based intermediate nuclear forces could cause a shift to sea launched nuclear missiles. START negotiations and the INF treaty could relatively increase the number of sea based strategic and intermediate nuclear forces which would relatively increase the activity and the importance of northern waters. Thus, Norway and her security policy would be affected.« less

Geometric and electronic structure contributions to function in non-heme iron enzymes.

PubMed

Solomon, Edward I; Light, Kenneth M; Liu, Lei V; Srnec, Martin; Wong, Shaun D

2013-11-19

Mononuclear non-heme Fe (NHFe) enzymes play key roles in DNA repair, the biosynthesis of antibiotics, the response to hypoxia, cancer therapy, and many other biological processes. These enzymes catalyze a diverse range of oxidation reactions, including hydroxylation, halogenation, ring closure, desaturation, and electrophilic aromatic substitution (EAS). Most of these enzymes use an Fe(II) site to activate dioxygen, but traditional spectroscopic methods have not allowed researchers to insightfully probe these ferrous active sites. We have developed a methodology that provides detailed geometric and electronic structure insights into these NHFe(II) active sites. Using these data, we have defined a general mechanistic strategy that many of these enzymes use: they control O2 activation (and limit autoxidation and self-hydroxylation) by allowing Fe(II) coordination unsaturation only in the presence of cosubstrates. Depending on the type of enzyme, O2 activation either involves a 2e(-) reduced Fe(III)-OOH intermediate or a 4e(-) reduced Fe(IV)═O intermediate. Nuclear resonance vibrational spectroscopy (NRVS) has provided the geometric structure of these intermediates, and magnetic circular dichroism (MCD) has defined the frontier molecular orbitals (FMOs), the electronic structure that controls reactivity. This Account emphasizes that experimental spectroscopy is critical in evaluating the results of electronic structure calculations. Therefore these data are a key mechanistic bridge between structure and reactivity. For the Fe(III)-OOH intermediates, the anticancer drug activated bleomycin (BLM) acts as the non-heme Fe analog of compound 0 in heme (e.g., P450) chemistry. However BLM shows different reactivity: the low-spin (LS) Fe(III)-OOH can directly abstract a H atom from DNA. The LS and high-spin (HS) Fe(III)-OOHs have fundamentally different transition states. The LS transition state goes through a hydroxyl radical, but the HS transition state is activated for EAS without O-O cleavage. This activation is important in one class of NHFe enzymes that utilizes a HS Fe(III)-OOH intermediate in dioxygenation. For Fe(IV)═O intermediates, the LS form has a π-type FMO activated for attack perpendicular to the Fe-O bond. However, the HS form (present in the NHFe enzymes) has a π FMO activated perpendicular to the Fe-O bond and a σ FMO positioned along the Fe-O bond. For the NHFe enzymes, the presence of π and σ FMOs enables enzymatic control in determining the type of reactivity: EAS or H-atom extraction for one substrate with different enzymes and halogenation or hydroxylation for one enzyme with different substrates.

Investigations into the Structure and Dynamics of Chalcogenide Glasses using High-Resolution Nuclear Magnetic Resonance Spectroscopy

NASA Astrophysics Data System (ADS)

Kaseman, Derrick Charles

Chalcogenide glasses constitute an important class of materials that are sulfides, selenides or tellurides of group IV and/or V elements, namely Ge, As, P and Si with minor concentrations of other elements such as Ga, Sb, In. Because of their infrared transparency that can be tuned by changing chemistry and can be actively altered by exposure to band gap irradiation, chalcogenide glasses find use in passive and active optical devices for applications in the areas of photonics, remote sensing and memory technology. Therefore, it is important to establish predictive models of structure-property relationships for these materials for optimization of their physical properties for various applications. Structural elucidation of chalcogenide glasses is experimentally challenging and in order to make predictive structural models, structural units at both short and intermediate -range length scales must be identified and quantified. Nuclear Magnetic Resonance (NMR) spectroscopy is an element-specific structural probe that is uniquely suited for this task, but resolution and sensitivity issues have severely limited the applications of such techniques in the past. The recent development of multi-dimensional solid-state NMR techniques, such as Phase Adjusted Spinning Sidebands (PASS) and Magic Angle Turning (MAT) can potentially alleviate such issues. In this study novel two-dimensional, high-resolution 77Se and 125Te MATPASS NMR spectroscopic techniques are utilized to elucidate quantitatively the compositional evolution of the short- and intermediate- range atomic structure in three binary chalcogenide glass-forming systems, namely: GexSe100-x, AsxSe100-x , and AsxTe100-x. The spectroscopic results provide unambiguous site speciation and quantification for short- and intermediate-range structural motifs present in these glasses. In turn, for all systems, robust structural models and the corresponding structure-property relationships are successfully established as a function of composition. The results indicate that the physical properties are intimately tied to the topology and chemical order present in each system. Finally, a dynamic version of the two-dimensional 31P PASS NMR spectroscopy is used to study the molecular motion in a supercooled chalcogenide liquid of composition P5Se3. The results clearly display the presence of isotropic rotational reorientation of the constituent molecules at timescales significantly decoupled from that of the structural relaxation near and above Tg. This behavior is atypical of conventional molecular glasses in organic systems in which rotational and translational dynamics remain coupled near Tg. When taken together with previous reports on the dynamics of other globular inorganic molecules, the results support the existence of a "plastic glass" phase where the molecules perform rapid rotation without significant translation.

THE CENTRAL MOLECULAR GAS STRUCTURE IN LINERS WITH LOW-LUMINOSITY ACTIVE GALACTIC NUCLEI: EVIDENCE FOR GRADUAL DISAPPEARANCE OF THE TORUS

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

Mueller-Sanchez, F.; Prieto, M. A.; Mezcua, M.

2013-01-20

We present observations of the molecular gas in the nuclear environment of three prototypical low-luminosity active galactic nuclei (LLAGNs), based on VLT/SINFONI AO-assisted integral-field spectroscopy of H{sub 2} 1-0 S(1) emission at angular resolutions of {approx}0.''17. On scales of 50-150 pc, the spatial distribution and kinematics of the molecular gas are consistent with a rotating thin disk, where the ratio of rotation (V) to dispersion ({sigma}) exceeds unity. However, in the central 50 pc, the observations reveal a geometrically and optically thick structure of molecular gas (V/{sigma} < 1 and N{sub H} > 10{sup 23} cm{sup -2}) that is likelymore » to be associated with the outer extent of any smaller scale obscuring structure. In contrast to Seyfert galaxies, the molecular gas in LLAGNs has a V/{sigma} < 1 over an area that is {approx}9 times smaller and column densities that are on average {approx}3 times smaller. We interpret these results as evidence for a gradual disappearance of the nuclear obscuring structure. While a disk wind may not be able to maintain a thick rotating structure at these luminosities, inflow of material into the nuclear region could provide sufficient energy to sustain it. In this context, LLAGNs may represent the final phase of accretion in current theories of torus evolution. While the inflow rate is considerable during the Seyfert phase, it is slowly decreasing, and the collisional disk is gradually transitioning to become geometrically thin. Furthermore, the nuclear region of these LLAGNs is dominated by intermediate-age/old stellar populations (with little or no ongoing star formation), consistent with a late stage of evolution.« less

Concentration-dependent Effects of Nuclear Lamins on Nuclear Size in Xenopus and Mammalian Cells*

PubMed Central

Jevtić, Predrag; Edens, Lisa J.; Li, Xiaoyang; Nguyen, Thang; Chen, Pan; Levy, Daniel L.

2015-01-01

A fundamental question in cell biology concerns the regulation of organelle size. While nuclear size is exquisitely controlled in different cell types, inappropriate nuclear enlargement is used to diagnose and stage cancer. Clarifying the functional significance of nuclear size necessitates an understanding of the mechanisms and proteins that control nuclear size. One structural component implicated in the regulation of nuclear morphology is the nuclear lamina, a meshwork of intermediate lamin filaments that lines the inner nuclear membrane. However, there has not been a systematic investigation of how the level and type of lamin expression influences nuclear size, in part due to difficulties in precisely controlling lamin expression levels in vivo. In this study, we circumvent this limitation by studying nuclei in Xenopus laevis egg and embryo extracts, open biochemical systems that allow for precise manipulation of lamin levels by the addition of recombinant proteins. We find that nuclear growth and size are sensitive to the levels of nuclear lamins, with low and high concentrations increasing and decreasing nuclear size, respectively. Interestingly, each type of lamin that we tested (lamins B1, B2, B3, and A) similarly affected nuclear size whether added alone or in combination, suggesting that total lamin concentration, and not lamin type, is more critical to determining nuclear size. Furthermore, we show that altering lamin levels in vivo, both in Xenopus embryos and mammalian tissue culture cells, also impacts nuclear size. These results have implications for normal development and carcinogenesis where both nuclear size and lamin expression levels change. PMID:26429910

Characterization of Aptamer BC 007 Substance and Product Using Circular Dichroism and Nuclear Magnetic Resonance Spectroscopy.

PubMed

Weisshoff, Hardy; Wenzel, Katrin; Schulze-Rothe, Sarah; Nikolenko, Heike; Davideit, Hanna; Becker, Niels-Peter; Göttel, Peter; Srivatsa, G Susan; Dathe, Margitta; Müller, Johannes; Haberland, Annekathrin

2018-04-18

Possible unwanted folding of biopharmaceuticals during manufacturing and storage has resulted in analysis schemes compared to small molecules that include bioanalytical characterization besides chemical characterization. Whether bioanalytical characterization is required for nucleotide-based drugs, may be decided on a case-by-case basis. Nucleotide-based pharmaceuticals, if chemically synthesized, occupy an intermediate position between small-molecule drugs and biologics. Here, we tested whether a physicochemical characterization of a nucleotide-based drug substance, BC 007, was adequate, using circular dichroism (CD) spectroscopy. Nuclear magnetic resonance confirmed CD data in one experimental setup. BC 007 forms a quadruplex structure under specific external conditions, which was characterized for its stability and structural appearance also after denaturation using CD and nuclear magnetic resonance. The amount of the free energy (ΔG 0 ) involved in quadruplex formation of BC 007 was estimated at +8.7 kJ/mol when dissolved in water and +1.4 kJ/mol in 154 mM NaCl, indicating structural instability under these conditions. However, dissolution of the substance in 5 mM of KCl reduced the ΔG 0 to -5.6 kJ/mol due to the stabilizing effect of cations. These results show that positive ΔG 0 of quadruplex structure formation in water and aqueous NaCl prevents BC 007 from preforming stable 3-dimensional structures, which could potentially affect drug function. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Nuclear reactor control column

DOEpatents

Bachovchin, Dennis M.

1982-01-01

The nuclear reactor control column comprises a column disposed within the nuclear reactor core having a variable cross-section hollow channel and containing balls whose vertical location is determined by the flow of the reactor coolant through the column. The control column is divided into three basic sections wherein each of the sections has a different cross-sectional area. The uppermost section of the control column has the greatest cross-sectional area, the intermediate section of the control column has the smallest cross-sectional area, and the lowermost section of the control column has the intermediate cross-sectional area. In this manner, the area of the uppermost section can be established such that when the reactor coolant is flowing under normal conditions therethrough, the absorber balls will be lifted and suspended in a fluidized bed manner in the upper section. However, when the reactor coolant flow falls below a predetermined value, the absorber balls will fall through the intermediate section and into the lowermost section, thereby reducing the reactivity of the reactor core and shutting down the reactor.

Formation of single-walled aluminosilicate nanotubes from molecular precursors and curved nanoscale intermediates.

PubMed

Yucelen, G Ipek; Choudhury, Rudra Prosad; Vyalikh, Anastasia; Scheler, Ulrich; Beckham, Haskell W; Nair, Sankar

2011-04-13

We report the identification and elucidation of the mechanistic role of molecular precursors and nanoscale (1-3 nm) intermediates with intrinsic curvature in the formation of single-walled aluminosilicate nanotubes. We characterize the structural and compositional evolution of molecular and nanoscale species over a length scale of 0.1-100 nm by electrospray ionization mass spectrometry, nuclear magnetic resonance spectroscopy ((27)Al liquid-state, (27)Al and (29)Si solid-state MAS), and dynamic light scattering. Together with structural optimization of key experimentally identified species by solvated density functional theory calculations, this study reveals the existence of intermediates with bonding environments, as well as intrinsic curvature, similar to the structure of the final nanotube product. We show that "proto-nanotube-like" intermediates with inherent curvature form in aqueous synthesis solutions immediately after initial hydrolysis of reactants, disappear from the solution upon heating to 95 °C due to condensation accompanied by an abrupt pH decrease, and finally form ordered single-walled aluminosilicate nanotubes. Detailed quantitative analysis of NMR and ESI-MS spectra from the relevant aluminosilicate, aluminate, and silicate solutions reveals the presence of a variety of monomeric and polymeric aluminate and aluminosilicate species (Al(1)Si(x)-Al(13)Si(x)), such as Keggin ions [AlO(4)Al(12)(OH)(24)(H(2)O)(12)](7+) and polynuclear species with a six-membered Al oxide ring unit. Our study also directly reveals the complexation of aluminate and aluminosilicate species with perchlorate species that most likely inhibit the formation of larger condensates or nontubular structures. Integration of all of our results leads to the construction of the first molecular-level mechanism of single-walled metal oxide nanotube formation, incorporating the role of monomeric and polymeric aluminosilicate species as well as larger nanoparticles. © 2011 American Chemical Society

A brief review of intermediate controlled nuclear syntheses (ICNS) without harmful radiations

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

Lanjewar, R. B.

Hadronic mechanics gave birth to new magnecular fuels. The present day demand is of clean energy source that is cheap and abundant. Clean energy can be obtained by harnessing renewable energy sources like solar, wind etc. Nuclear energy conventionally produced by fission reactions emits hazardous radiation and radioactive waste. The requirements of clean and safe energy gets fulfilled by novel fuel that achieved by elevating the traditional quantum mechanics to hadronic mechanics and to hadronic chemistry. In the present paper, a comprehensive review on both the theoretical and experimental aspect of the Intermediate Controlled Nuclear Synthesis (ICNS) as developed bymore » Italian American Scientist Professor R. M. Santilli.« less

Efficient near-field wireless energy transfer using adiabatic system variations

DOEpatents

Hamam, Rafif E.; Karalis, Aristeidis; Joannopoulos, John D.; Soljacic, Marin

2013-01-29

Disclosed is a method for transferring energy wirelessly including transferring energy wirelessly from a first resonator structure to an intermediate resonator structure, wherein the coupling rate between the first resonator structure and the intermediate resonator structure is .kappa..sub.1B, transferring energy wirelessly from the intermediate resonator structure to a second resonator structure, wherein the coupling rate between the intermediate resonator structure and the second resonator structure is .kappa..sub.B2, and during the wireless energy transfers, adjusting at least one of the coupling rates .kappa..sub.1B and .kappa..sub.B2 to reduce energy accumulation in the intermediate resonator structure and improve wireless energy transfer from the first resonator structure to the second resonator structure through the intermediate resonator structure.

Efficient near-field wireless energy transfer using adiabatic system variations

DOEpatents

Hamam, Rafif E; Karalis, Aristeidis; Joannopoulos, John D; Soljacic, Marin

2014-09-16

Disclosed is a method for transferring energy wirelessly including transferring energy wirelessly from a first resonator structure to an intermediate resonator structure, wherein the coupling rate between the first resonator structure and the intermediate resonator structure is .kappa..sub.1B, transferring energy wirelessly from the intermediate resonator structure to a second resonator structure, wherein the coupling rate between the intermediate resonator structure and the second resonator structure is .kappa..sub.B2, and during the wireless energy transfers, adjusting at least one of the coupling rates .kappa..sub.1B and .kappa..sub.B2 to reduce energy accumulation in the intermediate resonator structure and improve wireless energy transfer from the first resonator structure to the second resonator structure through the intermediate resonator structure.

Preconceptual design of a fluoride high temperature salt-cooled engineering demonstration reactor: Motivation and overview

DOE PAGES

Qualls, A. Louis; Betzler, Benjamin R.; Brown, Nicholas R.; ...

2016-12-21

Engineering demonstration reactors are nuclear reactors built to establish proof of concept for technology options that have never been built. Examples of engineering demonstration reactors include Peach Bottom 1 for high temperature gas-cooled reactors (HTGRs) and Experimental Breeder Reactor-II (EBR-II) for sodium-cooled fast reactors. Historically, engineering demonstrations have played a vital role in advancing the technology readiness level of reactor technologies. Our paper details a preconceptual design for a fluoride salt-cooled engineering demonstration reactor. The fluoride salt-cooled high-temperature reactor (FHR) demonstration reactor (DR) is a concept for a salt-cooled reactor with 100 megawatts of thermal output (MWt). It would usemore » tristructural-isotropic (TRISO) particle fuel within prismatic graphite blocks. FLiBe (2 7LiF-BeF2) is the reference primary coolant. The FHR DR is designed to be small, simple, and affordable. Development of the FHR DR is a necessary intermediate step to enable near-term commercial FHRs. The design philosophy of the FHR DR was focused on safety, near-term deployment, and flexibility. Lower risk technologies are purposely included in the initial FHR DR design to ensure that the reactor can be built, licensed, and operated as an engineering demonstration with minimal risk and cost. These technologies include TRISO particle fuel, replaceable core structures, and consistent structural material selection for core structures and the primary and intermediate loops, and tube-and-shell primary-to-intermediate heat exchangers. Important capabilities to be demonstrated by building and operating the FHR DR include fabrication and operation of high temperature reactors; heat exchanger performance (including passive decay heat removal); pump performance; and reactivity control; salt chemistry control to maximize vessel life; tritium management; core design methodologies; salt procurement, handling, maintenance and ultimate disposal. It is recognized that non-nuclear separate and integral test efforts (e.g., heated salt loops or loops using simulant fluids) are necessary to develop the technologies that will be demonstrated in the FHR DR.« less

Preconceptual design of a fluoride high temperature salt-cooled engineering demonstration reactor: Motivation and overview

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

Qualls, A. Louis; Betzler, Benjamin R.; Brown, Nicholas R.

Engineering demonstration reactors are nuclear reactors built to establish proof of concept for technology options that have never been built. Examples of engineering demonstration reactors include Peach Bottom 1 for high temperature gas-cooled reactors (HTGRs) and Experimental Breeder Reactor-II (EBR-II) for sodium-cooled fast reactors. Historically, engineering demonstrations have played a vital role in advancing the technology readiness level of reactor technologies. Our paper details a preconceptual design for a fluoride salt-cooled engineering demonstration reactor. The fluoride salt-cooled high-temperature reactor (FHR) demonstration reactor (DR) is a concept for a salt-cooled reactor with 100 megawatts of thermal output (MWt). It would usemore » tristructural-isotropic (TRISO) particle fuel within prismatic graphite blocks. FLiBe (2 7LiF-BeF2) is the reference primary coolant. The FHR DR is designed to be small, simple, and affordable. Development of the FHR DR is a necessary intermediate step to enable near-term commercial FHRs. The design philosophy of the FHR DR was focused on safety, near-term deployment, and flexibility. Lower risk technologies are purposely included in the initial FHR DR design to ensure that the reactor can be built, licensed, and operated as an engineering demonstration with minimal risk and cost. These technologies include TRISO particle fuel, replaceable core structures, and consistent structural material selection for core structures and the primary and intermediate loops, and tube-and-shell primary-to-intermediate heat exchangers. Important capabilities to be demonstrated by building and operating the FHR DR include fabrication and operation of high temperature reactors; heat exchanger performance (including passive decay heat removal); pump performance; and reactivity control; salt chemistry control to maximize vessel life; tritium management; core design methodologies; salt procurement, handling, maintenance and ultimate disposal. It is recognized that non-nuclear separate and integral test efforts (e.g., heated salt loops or loops using simulant fluids) are necessary to develop the technologies that will be demonstrated in the FHR DR.« less

Simultaneous and spectroscopic redox molecular imaging of multiple free radical intermediates using dynamic nuclear polarization-magnetic resonance imaging.

PubMed

Hyodo, Fuminori; Ito, Shinji; Yasukawa, Keiji; Kobayashi, Ryoma; Utsumi, Hideo

2014-08-05

Redox reactions that generate free radical intermediates are essential to metabolic processes. However, their intermediates can produce reactive oxygen species, which may promote diseases related to oxidative stress. We report here the use of dynamic nuclear polarization-magnetic resonance imaging (DNP-MRI) to conduct redox molecular imaging. Using DNP-MRI, we obtained simultaneous images of free radical intermediates generated from the coenzyme Q10 (CoQ10), flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD) involved in the mitochondrial electron transport chain as well as the radicals derived from vitamins E and K1. Each of these free radicals was imaged in real time in a phantom comprising a mixture of free radicals localized in either lipophilic or aqueous environments. Changing the frequency of electron spin resonance (ESR) irradiation also allowed each of the radical species to be distinguished in the spectroscopic images. This study is the first to report the spectroscopic DNP-MRI imaging of free radical intermediates that are derived from endogenous species involved in metabolic processes.

Molecular characterization of the major membrane skeletal protein in the ciliate Tetrahymena pyriformis suggests n-plication of an early evolutionary intermediate filament protein subdomain.

PubMed

Bouchard, P; Chomilier, J; Ravet, V; Mornon, J P; Viguès, B

2001-01-01

Epiplasmin C is the major protein component of the membrane skeleton in the ciliate Tetrahymena pyriformis. Cloning and analysis of the gene encoding epiplasmin C showed this protein to be a previously unrecognized protein. In particular, epiplasmin C was shown to lack the canonical features of already known epiplasmic proteins in ciliates and flagellates. By means of hydrophobic cluster analysis (HCA), it has been shown that epiplasmin C is constituted of a repeat of 25 domains of 40 residues each. These domains are related and can be grouped in two families called types I and types II. Connections between types I and types II present rules that can be evidenced in the sequence itself, thus enforcing the validity of the splitting of the domains. Using these repeated domains as queries, significant structural similarities were demonstrated with an extra six heptads shared by nuclear lamins and invertebrate cytoplasmic intermediate filament proteins and deleted in the cytoplasmic intermediate filament protein lineage at the protostome-deuterostome branching in the eukaryotic phylogenetic tree.

Dedifferentiation rescues senescence of progeria cells but only while pluripotent.

PubMed

Niedernhofer, Laura J; Glorioso, Joseph C; Robbins, Paul D

2011-06-01

Hutchinson-Gilford progeria syndrome (HGPS) is a genetic disease in which children develop pathologies associated with old age. HGPS is caused by a mutation in the LMNA gene, resulting in the formation of a dominant negative form of the intermediate filament, nuclear structural protein lamin A, termed progerin. Expression of progerin alters the nuclear architecture and heterochromatin, affecting cell cycle progression and genomic stability. Two groups recently reported the successful generation and characterization of induced pluripotent stem cells (iPSCs) from HGPS fibroblasts. Remarkably, progerin expression and senescence phenotypes are lost in iPSCs but not in differentiated progeny. These new HGPS iPSCs are valuable for characterizing the role of progerin in driving HGPS and aging and for screening therapeutic strategies to prevent or delay cell senescence.

Genomic relationship between SINE retrotransposons, Pol III–Pol II transcription, and chromatin organization: the journey from junk to jewel

PubMed Central

Lunyak, Victoria V.; Atallah, Michelle

2013-01-01

A typical eukaryotic genome harbors a rich variety of repetitive elements. The most abundant are retrotransposons, mobile retroelements that utilize reverse transcriptase and an RNA intermediate to relocate to a new location within the cellular genomes. A vast majority of the repetitive mammalian genome content has originated from the retrotransposition of SINE (100–300 bp short interspersed nuclear elements that are derived from the structural 7SL RNA or tRNA), LINE (7kb long interspersed nuclear element), and LTR (2–3 kb long terminal repeats) transposable element superfamilies. Broadly labeled as “evolutionary junkyard” or “fossils”, this enigmatic “dark matter” of the genome possesses many yet to be discovered properties. PMID:21916613

Efficient near-field wireless energy transfer using adiabatic system variations

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

Hamam, Rafif E.; Karalis, Aristeidis; Joannopoulos, John D.

Disclosed is a method for transferring energy wirelessly including transferring energy wirelessly from a first resonator structure to an intermediate resonator structure, wherein the coupling rate between the first resonator structure and the intermediate resonator structure is .kappa..sub.1B, transferring energy wirelessly from the intermediate resonator structure to a second resonator structure, wherein the coupling rate between the intermediate resonator structure and the second resonator structure is .kappa..sub.B2, and during the wireless energy transfers, adjusting at least one of the coupling rates .kappa..sub.1B and .kappa..sub.B2 to reduce energy accumulation in the intermediate resonator structure and improve wireless energy transfer from themore » first resonator structure to the second resonator structure through the intermediate resonator structure.« less

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

Jorgens, Danielle M.; Inman, Jamie L.; Wojcik, Michal

The importance of context in regulation of gene expression is now an accepted principle; yet the mechanism by which the microenvironment communicates with the nucleus and chromatin in healthy tissues is poorly understood. A functional role for nuclear and cytoskeletal architecture is suggested by the phenotypic differences observed between epithelial and mesenchymal cells. Capitalizing on recent advances in cryogenic techniques, volume electron microscopy and super-resolution light microscopy, we studied human mammary epithelial cells in three-dimensional (3D) cultures forming growtharrested acini. Intriguingly, we found deep nuclear invaginations and tunnels traversing the nucleus, encasing cytoskeletal actin and/or intermediate filaments, which connect tomore » the outer nuclear envelope. Also, the cytoskeleton is connected both to other cells through desmosome adhesion complexes and to the extracellular matrix through hemidesmosomes. This finding supports a physical and/or mechanical link from the desmosomes and hemidesmosomes to the nucleus, which had previously been hypothesized but now is visualized for the first time. These unique structures, including the nuclear invaginations and the cytoskeletal connectivity to the cell nucleus, are consistent with a dynamic reciprocity between the nucleus and the outside of epithelial cells and tissues.« less

Deep nuclear invaginations are linked to cytoskeletal filaments – integrated bioimaging of epithelial cells in 3D culture

PubMed Central

Inman, Jamie L.; Wojcik, Michal; Robertson, Claire; Tsai, Wen-Ting; Huang, Haina; Bruni-Cardoso, Alexandre; López, Claudia S.; Bissell, Mina J.; Xu, Ke

2017-01-01

ABSTRACT The importance of context in regulation of gene expression is now an accepted principle; yet the mechanism by which the microenvironment communicates with the nucleus and chromatin in healthy tissues is poorly understood. A functional role for nuclear and cytoskeletal architecture is suggested by the phenotypic differences observed between epithelial and mesenchymal cells. Capitalizing on recent advances in cryogenic techniques, volume electron microscopy and super-resolution light microscopy, we studied human mammary epithelial cells in three-dimensional (3D) cultures forming growth-arrested acini. Intriguingly, we found deep nuclear invaginations and tunnels traversing the nucleus, encasing cytoskeletal actin and/or intermediate filaments, which connect to the outer nuclear envelope. The cytoskeleton is also connected both to other cells through desmosome adhesion complexes and to the extracellular matrix through hemidesmosomes. This finding supports a physical and/or mechanical link from the desmosomes and hemidesmosomes to the nucleus, which had previously been hypothesized but now is visualized for the first time. These unique structures, including the nuclear invaginations and the cytoskeletal connectivity to the cell nucleus, are consistent with a dynamic reciprocity between the nucleus and the outside of epithelial cells and tissues. PMID:27505896

Deep nuclear invaginations are linked to cytoskeletal filaments – integrated bioimaging of epithelial cells in 3D culture

DOE PAGES

Jorgens, Danielle M.; Inman, Jamie L.; Wojcik, Michal; ...

2016-08-05

The importance of context in regulation of gene expression is now an accepted principle; yet the mechanism by which the microenvironment communicates with the nucleus and chromatin in healthy tissues is poorly understood. A functional role for nuclear and cytoskeletal architecture is suggested by the phenotypic differences observed between epithelial and mesenchymal cells. Capitalizing on recent advances in cryogenic techniques, volume electron microscopy and super-resolution light microscopy, we studied human mammary epithelial cells in three-dimensional (3D) cultures forming growtharrested acini. Intriguingly, we found deep nuclear invaginations and tunnels traversing the nucleus, encasing cytoskeletal actin and/or intermediate filaments, which connect tomore » the outer nuclear envelope. Also, the cytoskeleton is connected both to other cells through desmosome adhesion complexes and to the extracellular matrix through hemidesmosomes. This finding supports a physical and/or mechanical link from the desmosomes and hemidesmosomes to the nucleus, which had previously been hypothesized but now is visualized for the first time. These unique structures, including the nuclear invaginations and the cytoskeletal connectivity to the cell nucleus, are consistent with a dynamic reciprocity between the nucleus and the outside of epithelial cells and tissues.« less

G-triplex structure and formation propensity

PubMed Central

Cerofolini, Linda; Amato, Jussara; Giachetti, Andrea; Limongelli, Vittorio; Novellino, Ettore; Parrinello, Michele; Fragai, Marco; Randazzo, Antonio; Luchinat, Claudio

2014-01-01

The occurrence of a G-triplex folding intermediate of thrombin binding aptamer (TBA) has been recently predicted by metadynamics calculations, and experimentally supported by Nuclear Magnetic Resonance (NMR), Circular Dichroism (CD) and Differential Scanning Calorimetry (DSC) data collected on a 3′ end TBA-truncated 11-mer oligonucleotide (11-mer-3′-t-TBA). Here we present the solution structure of 11-mer-3′-t-TBA in the presence of potassium ions. This structure is the first experimental example of a G-triplex folding, where a network of Hoogsteen-like hydrogen bonds stabilizes six guanines to form two G:G:G triad planes. The G-triplex folding of 11-mer-3′-t-TBA is stabilized by the potassium ion and destabilized by increasing the temperature. The superimposition of the experimental structure with that predicted by metadynamics shows a great similarity, with only significant differences involving two loops. These new structural data show that 11-mer-3′-t-TBA assumes a G-triplex DNA conformation as its stable form, reinforcing the idea that G-triplex folding intermediates may occur in vivo in human guanine-rich sequences. NMR and CD screening of eight different constructs obtained by removing from one to four bases at either the 3′ and the 5′ ends show that only the 11-mer-3′-t-TBA yields a relatively stable G-triplex. PMID:25378342

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

Thayer, K.J.

The past year has seen several of the Physics Division`s new research projects reach major milestones with first successful experiments and results: the atomic physics station in the Basic Energy Sciences Research Center at the Argonne Advanced Photon Source was used in first high-energy, high-brilliance x-ray studies in atomic and molecular physics; the Short Orbit Spectrometer in Hall C at the Thomas Jefferson National Accelerator (TJNAF) Facility that the Argonne medium energy nuclear physics group was responsible for, was used extensively in the first round of experiments at TJNAF; at ATLAS, several new beams of radioactive isotopes were developed andmore » used in studies of nuclear physics and nuclear astrophysics; the new ECR ion source at ATLAS was completed and first commissioning tests indicate excellent performance characteristics; Quantum Monte Carlo calculations of mass-8 nuclei were performed for the first time with realistic nucleon-nucleon interactions using state-of-the-art computers, including Argonne`s massively parallel IBM SP. At the same time other future projects are well under way: preparations for the move of Gammasphere to ATLAS in September 1997 have progressed as planned. These new efforts are imbedded in, or flowing from, the vibrant ongoing research program described in some detail in this report: nuclear structure and reactions with heavy ions; measurements of reactions of astrophysical interest; studies of nucleon and sub-nucleon structures using leptonic probes at intermediate and high energies; atomic and molecular structure with high-energy x-rays. The experimental efforts are being complemented with efforts in theory, from QCD to nucleon-meson systems to structure and reactions of nuclei. Finally, the operation of ATLAS as a national users facility has achieved a new milestone, with 5,800 hours beam on target for experiments during the past fiscal year.« less

Epithelial cytoskeletal framework and nuclear matrix-intermediate filament scaffold: three-dimensional organization and protein composition.

PubMed

Fey, E G; Wan, K M; Penman, S

1984-06-01

Madin-Darby canine kidney (MDCK) cells grow as differentiated, epithelial colonies that display tissue-like organization. We examined the structural elements underlying the colony morphology in situ using three consecutive extractions that produce well-defined fractions for both microscopy and biochemical analysis. First, soluble proteins and phospholipid were removed with Triton X-100 in a physiological buffer. The resulting skeletal framework retained nuclei, dense cytoplasmic filament networks, intercellular junctional complexes, and apical microvillar structures. Scanning electron microscopy showed that the apical cell morphology is largely unaltered by detergent extraction. Residual desmosomes, as can be seen in thin sections, were also well-preserved. The skeletal framework was visualized in three dimensions as an unembedded whole mount that revealed the filament networks that were masked in Epon-embedded thin sections of the same preparation. The topography of cytoskeletal filaments was relatively constant throughout the epithelial sheet, particularly across intercellular borders. This ordering of epithelial skeletal filaments across contiguous cell boundaries was in sharp contrast to the more independent organization of networks in autonomous cells such as fibroblasts. Further extraction removed the proteins of the salt-labile cytoskeleton and the chromatin as separate fractions, and left the nuclear matrix-intermediate filament (NM-IF) scaffold. The NM-IF contained only 5% of total cellular protein, but whole mount transmission electron microscopy and immunofluorescence showed that this scaffold was organized as in the intact epithelium. Immunoblots demonstrate that vimentin, cytokeratins, desmosomal proteins, and a 52,000-mol-wt nuclear matrix protein were found almost exclusively in the NM-IF scaffold. Vimentin was largely perinuclear while the cytokeratins were localized at the cell borders. The 52,000-mol-wt nuclear matrix protein was confined to the chromatin-depleted matrix and the desmosomal proteins were observed in punctate polygonal arrays at intercellular junctions. The filaments of the NM-IF were seen to be interconnected, via the desmosomes, over the entire epithelial colony. The differentiated epithelial morphology was reflected in both the cytoskeletal framework and the NM-IF scaffold.

Epithelial cytoskeletal framework and nuclear matrix-intermediate filament scaffold: three-dimensional organization and protein composition

PubMed Central

1984-01-01

Madin-Darby canine kidney (MDCK) cells grow as differentiated, epithelial colonies that display tissue-like organization. We examined the structural elements underlying the colony morphology in situ using three consecutive extractions that produce well-defined fractions for both microscopy and biochemical analysis. First, soluble proteins and phospholipid were removed with Triton X-100 in a physiological buffer. The resulting skeletal framework retained nuclei, dense cytoplasmic filament networks, intercellular junctional complexes, and apical microvillar structures. Scanning electron microscopy showed that the apical cell morphology is largely unaltered by detergent extraction. Residual desmosomes, as can be seen in thin sections, were also well- preserved. The skeletal framework was visualized in three dimensions as an unembedded whole mount that revealed the filament networks that were masked in Epon-embedded thin sections of the same preparation. The topography of cytoskeletal filaments was relatively constant throughout the epithelial sheet, particularly across intercellular borders. This ordering of epithelial skeletal filaments across contiguous cell boundaries was in sharp contrast to the more independent organization of networks in autonomous cells such as fibroblasts. Further extraction removed the proteins of the salt-labile cytoskeleton and the chromatin as separate fractions, and left the nuclear matrix-intermediate filament (NM-IF) scaffold. The NM-IF contained only 5% of total cellular protein, but whole mount transmission electron microscopy and immunofluorescence showed that this scaffold was organized as in the intact epithelium. Immunoblots demonstrate that vimentin, cytokeratins, desmosomal proteins, and a 52,000-mol-wt nuclear matrix protein were found almost exclusively in the NM-IF scaffold. Vimentin was largely perinuclear while the cytokeratins were localized at the cell borders. The 52,000-mol-wt nuclear matrix protein was confined to the chromatin- depleted matrix and the desmosomal proteins were observed in punctate polygonal arrays at intercellular junctions. The filaments of the NM-IF were seen to be interconnected, via the desmosomes, over the entire epithelial colony. The differentiated epithelial morphology was reflected in both the cytoskeletal framework and the NM-IF scaffold. PMID:6202700

Flexible response and the INF (Intermediate-range Nuclear Force) Treaty: what next. Study project

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

Williams, H.A.

1988-03-14

The prospect of the Intermediate-range Nuclear Force (INF) Treaty led the former Supreme Allied Commander, Europe, GEN Bernard Rogers, to claim that NATO would lose weapons vital to the Alliance's defense when Pershing II (PII) and Ground-Launched Cruise Missiles (GLCM) were withdrawn from Europe. Nuclear weapons and the NATO strategy of flexible response are inseparably dependent upon each other. GEN Rogers' comments focus directly on the capability which PII and GLCM provided NATO to strike Soviet territory in event of conflict and if such an escalatory step was deemed necessary. Various sources were researched to determine if the INF Treatymore » will cripple the flexible response strategy; while it should not, certain changes in NATO's approach to defense are suggested. Specifically, conventional and nuclear improvements, the latter within the terms of the INF Treaty, are suggested, as are conventional force reduction negotiations and the Europeanization of NATO.« less

Proteomic analysis in giant axonal neuropathy: new insights into disease mechanisms.

PubMed

Mussche, Silke; De Paepe, Boel; Smet, Joél; Devreese, Katrien; Lissens, Willy; Rasic, Vedrana Milic; Murnane, Matthew; Devreese, Bart; Van Coster, Rudy

2012-08-01

Giant axonal neuropathy (GAN) is a progressive hereditary disease that affects the peripheral and central nervous systems. It is characterized morphologically by aggregates of intermediate filaments in different tissues. Mutations have been reported in the gene that codes for gigaxonin. Nevertheless, the underlying molecular mechanism remains obscure. Cell lines from 4 GAN patients and 4 controls were analyzed by iTRAQ. Among the dysregulated proteins were ribosomal protein L29, ribosomal protein L37, galectin-1, glia-derived nexin, and aminopeptidase N. Also, nuclear proteins linked to formin-binding proteins were found to be dysregulated. Although the major role of gigaxonin is reported to be degradation of cytoskeleton-associated proteins, the amount of 76 structural cytoskeletal proteins was unaltered. Several of the dysregulated proteins play a role in cytoskeletal reorganization. Based on these findings, we speculate that disturbed cytoskeletal regulation is responsible for formation of aggregates of intermediate filaments. Copyright © 2012 Wiley Periodicals, Inc.

Y-12 PLANT NUCLEAR SAFETY HANDBOOK

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

Wachter, J.W. ed.; Bailey, M.L.; Cagle, T.J.

1963-03-27

Information needed to solve nuclear safety problems is condensed into a reference book for use by persons familiar with the field. Included are a glossary of terms; useful tables; nuclear constants; criticality calculations; basic nuclear safety limits; solution geometries and critical values; metal critical values; criticality values for intermediate, heterogeneous, and interacting systems; miscellaneous and related information; and report number, author, and subject indexes. (C.H.)

Evolutionary history of two endemic Appalachian conifers revealed using microsatellite markers

Treesearch

Kevin M. Potter; John Frampton; Sedley A. Josserand; C. Dana Nelson

2010-01-01

Fraser fir (Abies fraseri [Pursh] Poir.) and intermediate fir (Abies balsamea [L.] Mill. var. phanerolepis Fern.) exist in small populations in the Appalachian highlands of the southeastern United States. We used ten nuclear microsatellite markers to quantify genetic variation within Fraser fir and intermediate...

Does Explosive Nuclear Burning Occur in Tidal Disruption Events of White Dwarfs by Intermediate-mass Black Holes?

NASA Astrophysics Data System (ADS)

Tanikawa, Ataru; Sato, Yushi; Nomoto, Ken'ichi; Maeda, Keiichi; Nakasato, Naohito; Hachisu, Izumi

2017-04-01

We investigate nucleosynthesis in tidal disruption events (TDEs) of white dwarfs (WDs) by intermediate-mass black holes. We consider various types of WDs with different masses and compositions by means of three-dimensional (3D) smoothed particle hydrodynamics (SPH) simulations. We model these WDs with different numbers of SPH particles, N, from a few 104 to a few 107 in order to check mass resolution convergence, where SPH simulations with N > 107 (or a space resolution of several 106 cm) have unprecedentedly high resolution in this kind of simulation. We find that nuclear reactions become less active with increasing N and that these nuclear reactions are excited by spurious heating due to low resolution. Moreover, we find no shock wave generation. In order to investigate the reason for the absence of a shock wave, we additionally perform one-dimensional (1D) SPH and mesh-based simulations with a space resolution ranging from 104 to 107 cm, using a characteristic flow structure extracted from the 3D SPH simulations. We find shock waves in these 1D high-resolution simulations, one of which triggers a detonation wave. However, we must be careful of the fact that, if the shock wave emerged in an outer region, it could not trigger the detonation wave due to low density. Note that the 1D initial conditions lack accuracy to precisely determine where a shock wave emerges. We need to perform 3D simulations with ≲106 cm space resolution in order to conclude that WD TDEs become optical transients powered by radioactive nuclei.

Industrial Program of Waste Management - Cigeo Project - 13033

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

Butez, Marc; Bartagnon, Olivier; Gagner, Laurent

2013-07-01

The French Planning Act of 28 June 2006 prescribed that a reversible repository in a deep geological formation be chosen as the reference solution for the long-term management of high-level and intermediate-level long-lived radioactive waste. It also entrusted the responsibility of further studies and design of the repository (named Cigeo) upon the French Radioactive Waste Management Agency (Andra), in order for the review of the creation-license application to start in 2015 and, subject to its approval, the commissioning of the repository to take place in 2025. Andra is responsible for siting, designing, implementing, operating the future geological repository, including operationalmore » and long term safety and waste acceptance. Nuclear operators (Electricite de France (EDF), AREVA NC, and the French Commission in charge of Atomic Energy and Alternative Energies (CEA) are technically and financially responsible for the waste they generate, with no limit in time. They provide Andra, on one hand, with waste packages related input data, and on the other hand with their long term industrial experiences of high and intermediate-level long-lived radwaste management and nuclear operation. Andra, EDF, AREVA and CEA established a cooperation agreement for strengthening their collaborations in these fields. Within this agreement Andra and the nuclear operators have defined an industrial program for waste management. This program includes the waste inventory to be taken into account for the design of the Cigeo project and the structural hypothesis underlying its phased development. It schedules the delivery of the different categories of waste and defines associated flows. (authors)« less

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

Moon, Chang-Bum, E-mail: cbmoon@hoseo.edu

This paper outlines the new physics possibilities that fall within the field of nuclear structure and astrophysics based on experiments with radioactive ion beams at the future Rare Isotope Beams Accelerator facility in Korea. This ambitious multi-beam facility has both an Isotope Separation On Line (ISOL) and fragmentation capability to produce rare isotopes beams (RIBs) and will be capable of producing and accelerating beams of wide range mass of nuclides with energies of a few to hundreds MeV per nucleon. The large dynamic range of reaccelerated RIBs will allow the optimization in each nuclear reaction case with respect to crossmore » section and channel opening. The low energy RIBs around Coulomb barrier offer nuclear reactions such as elastic resonance scatterings, one or two particle transfers, Coulomb multiple-excitations, fusion-evaporations, and direct capture reactions for the study of the very neutron-rich and proton-rich nuclides. In contrast, the high energy RIBs produced by in-flight fragmentation with reaccelerated ions from the ISOL enable to explore the study of neutron drip lines in intermediate mass regions. The proposed studies aim at investigating the exotic nuclei near and beyond the nucleon drip lines, and to explore how nuclear many-body systems change in such extreme regions by addressing the following topics: the evolution of shell structure in areas of extreme proton to neutron imbalance; the study of the weak interaction in exotic decay schemes such as beta-delayed two-neutron or two-proton emission; the change of isospin symmetry in isobaric mirror nuclei at the drip lines; two protons or two neutrons radioactivity beyond the drip lines; the role of the continuum states including resonant states above the particle-decay threshold in exotic nuclei; and the effects of nuclear reaction rates triggered by the unbound proton-rich nuclei on nuclear astrophysical processes.« less

The structure of a ring-opened proliferating cell nuclear antigen-replication factor C complex revealed by fluorescence energy transfer.

PubMed

Zhuang, Zhihao; Yoder, Bonita L; Burgers, Peter M J; Benkovic, Stephen J

2006-02-21

Numerous proteins that function in DNA metabolic pathways are known to interact with the proliferating cell nuclear antigen (PCNA). The important function of PCNA in stimulating various cellular activities requires its topological linkage with DNA. Loading of the circular PCNA onto duplex DNA requires the activity of a clamp-loader [replication factor C (RFC)] complex and the energy derived from ATP hydrolysis. The mechanistic and structural details regarding PCNA loading by the RFC complex are still developing. In particular, the positive identification of a long-hypothesized structure of an open clamp-RFC complex as an intermediate in loading has remained elusive. In this study, we capture an open yeast PCNA clamp in a complex with RFC through fluorescence energy transfer experiments. We also follow the topological transitions of PCNA in the various steps of the clamp-loading pathway through both steady-state and stopped-flow fluorescence studies. We find that ATP effectively drives the clamp-loading process to completion with the formation of the closed PCNA bound to DNA, whereas ATPgammaS cannot. The information derived from this work complements that obtained from previous structural and mechanistic studies and provides a more complete picture of a eukaryotic clamp-loading pathway using yeast as a paradigm.

The ubiquitin ligase MuRF1 regulates PPARα activity in the heart by enhancing nuclear export via monoubiquitination

PubMed Central

Rodríguez, Jessica E.; Liao, Jie-Ying; He, Jun; Schisler, Jonathan C.; Newgard, Christopher B.; Drujan, Doreen; Glass, David L.; Frederick, C.Brandon; Yoder, Bryan C.; Lalush, David S.; Patterson, Cam; Willis, Monte S.

2015-01-01

The transcriptional regulation of peroxisome proliferator-activated receptor (PPAR) α by post-translational modification, such as ubiquitin, has not been described. We report here for the first time an ubiquitin ligase (muscle ring finger-1/MuRF1) that inhibits fatty acid oxidation by inhibiting PPARα, but not PPARβ/δ or PPARγ in cardiomyocytes in vitro. Similarly, MuRF1 Tg+ hearts showed significant decreases in nuclear PPARα activity and acyl-carnitine intermediates, while MuRF1−/− hearts exhibited increased PPARα activity and acyl-carnitine intermediates. MuRF1 directly interacts with PPARα, mono-ubiquitinates it, and targets it for nuclear export to inhibit fatty acid oxidation in a proteasome independent manner. We then identified a previously undescribed nuclear export sequence in PPARα, along with three specific lysines (292, 310, 388) required for MuRF1s targeting of nuclear export. These studies identify the role of ubiquitination in regulating cardiac PPARα, including the ubiquitin ligase that may be responsible for this critical regulation of cardiac metabolism in heart failure. PMID:26116825

Effect of the timing of the first cleavage on the developmental potential of nuclear-transferred mouse oocytes receiving embryonic stem cells.

PubMed

Kobayashi, T; Kato, Y; Tsunoda, Y

2004-09-01

The present study examined whether the timing of the first cleavage has an effect on the in vitro and in vivo developmental potential of nuclear-transferred mouse oocytes receiving embryonic stem cells. First, the timing of the first cleavage and the developmental potential of nuclear-transferred oocytes were examined every hour from 12 to 24 h after the start of culture and compared with in vitro-fertilized oocytes. The developmental potential of in vitro-fertilized oocytes decreased gradually according to the time required for cleavage (84% (32/38) for 15 h to 50% (1/2) for 20 h), but intermediate-cleaved (15-16 h) nuclear-transferred oocytes had a higher potential to develop into blastocysts (55% (17/31) to 67% (45/67) versus 0-43% (6/14)]. Second the nuclear-transferred oocytes were divided into three groups according to the timing of the first cleavage; each group was cultured to blastocysts in vitro, and then transferred to recipients. The potential of intermediate-cleaved oocytes (15-16 h) to develop into blastocysts was significantly higher than fast-cleaved (before 15 h) and slow-cleaved (after 16 h) oocytes (65, 46, and 37%). The proportion of fetuses on Day 10.5 of pregnancy was highest in the intermediate-cleaved group (4 versus 2 and 1%, respectively) and a full-term fetus was obtained from this group. The present study demonstrated that the timing of the first cleavage could be used to determine the potential of nuclear-transferred oocytes with embryonic stem cells to develop to the blastocyst stage in vitro, but not to determine post-implantation viability after transfer to recipients.

Maskelynite formation via solid-state transformation: Evidence of infrared and x-ray anisotropy

DOE PAGES

Jaret, Steven J.; Ehm, Lars; Woerner, William R.; ...

2015-03-24

We present optical microscopy, micro-Raman spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, high-energy X-ray total scattering experiments, and micro-Fourier transform infrared (micro-FTIR) spectroscopy on shocked labradorite from the Lonar Crater, India. We show that maskelynite of shock class 2 is structurally more similar to fused glass than to crystalline plagioclase. However, there are slight but significant differences – preservation of original pre-impact igneous zoning, anisotropy at Infrared wavelengths, X-ray anisotropy, and preservation of some intermediate range order – which are all consistent with a solid-state transformation formation of maskelynite.

Quantum and isotope effects in lithium metal

NASA Astrophysics Data System (ADS)

Ackland, Graeme J.; Dunuwille, Mihindra; Martinez-Canales, Miguel; Loa, Ingo; Zhang, Rong; Sinogeikin, Stanislav; Cai, Weizhao; Deemyad, Shanti

2017-06-01

The crystal structure of elements at zero pressure and temperature is the most fundamental information in condensed matter physics. For decades it has been believed that lithium, the simplest metallic element, has a complicated ground-state crystal structure. Using synchrotron x-ray diffraction in diamond anvil cells and multiscale simulations with density functional theory and molecular dynamics, we show that the previously accepted martensitic ground state is metastable. The actual ground state is face-centered cubic (fcc). We find that isotopes of lithium, under similar thermal paths, exhibit a considerable difference in martensitic transition temperature. Lithium exhibits nuclear quantum mechanical effects, serving as a metallic intermediate between helium, with its quantum effect-dominated structures, and the higher-mass elements. By disentangling the quantum kinetic complexities, we prove that fcc lithium is the ground state, and we synthesize it by decompression.

Deep nuclear invaginations are linked to cytoskeletal filaments - integrated bioimaging of epithelial cells in 3D culture.

PubMed

Jorgens, Danielle M; Inman, Jamie L; Wojcik, Michal; Robertson, Claire; Palsdottir, Hildur; Tsai, Wen-Ting; Huang, Haina; Bruni-Cardoso, Alexandre; López, Claudia S; Bissell, Mina J; Xu, Ke; Auer, Manfred

2017-01-01

The importance of context in regulation of gene expression is now an accepted principle; yet the mechanism by which the microenvironment communicates with the nucleus and chromatin in healthy tissues is poorly understood. A functional role for nuclear and cytoskeletal architecture is suggested by the phenotypic differences observed between epithelial and mesenchymal cells. Capitalizing on recent advances in cryogenic techniques, volume electron microscopy and super-resolution light microscopy, we studied human mammary epithelial cells in three-dimensional (3D) cultures forming growth-arrested acini. Intriguingly, we found deep nuclear invaginations and tunnels traversing the nucleus, encasing cytoskeletal actin and/or intermediate filaments, which connect to the outer nuclear envelope. The cytoskeleton is also connected both to other cells through desmosome adhesion complexes and to the extracellular matrix through hemidesmosomes. This finding supports a physical and/or mechanical link from the desmosomes and hemidesmosomes to the nucleus, which had previously been hypothesized but now is visualized for the first time. These unique structures, including the nuclear invaginations and the cytoskeletal connectivity to the cell nucleus, are consistent with a dynamic reciprocity between the nucleus and the outside of epithelial cells and tissues. © 2017. Published by The Company of Biologists Ltd.

SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets.

PubMed

Mao, Hongliang; Wang, Hao

2017-03-01

Short Interspersed Nuclear Elements (SINEs) are transposable elements (TEs) that amplify through a copy-and-paste mode via RNA intermediates. The computational identification of new SINEs are challenging because of their weak structural signals and rapid diversification in sequences. Here we report SINE_Scan, a highly efficient program to predict SINE elements in genomic DNA sequences. SINE_Scan integrates hallmark of SINE transposition, copy number and structural signals to identify a SINE element. SINE_Scan outperforms the previously published de novo SINE discovery program. It shows high sensitivity and specificity in 19 plant and animal genome assemblies, of which sizes vary from 120 Mb to 3.5 Gb. It identifies numerous new families and substantially increases the estimation of the abundance of SINEs in these genomes. The code of SINE_Scan is freely available at http://github.com/maohlzj/SINE_Scan , implemented in PERL and supported on Linux. wangh8@fudan.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets

PubMed Central

Mao, Hongliang

2017-01-01

Abstract Motivation: Short Interspersed Nuclear Elements (SINEs) are transposable elements (TEs) that amplify through a copy-and-paste mode via RNA intermediates. The computational identification of new SINEs are challenging because of their weak structural signals and rapid diversification in sequences. Results: Here we report SINE_Scan, a highly efficient program to predict SINE elements in genomic DNA sequences. SINE_Scan integrates hallmark of SINE transposition, copy number and structural signals to identify a SINE element. SINE_Scan outperforms the previously published de novo SINE discovery program. It shows high sensitivity and specificity in 19 plant and animal genome assemblies, of which sizes vary from 120 Mb to 3.5 Gb. It identifies numerous new families and substantially increases the estimation of the abundance of SINEs in these genomes. Availability and Implementation: The code of SINE_Scan is freely available at http://github.com/maohlzj/SINE_Scan, implemented in PERL and supported on Linux. Contact: wangh8@fudan.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28062442

Pulsed-High Field/High-Frequency EPR Spectroscopy

NASA Astrophysics Data System (ADS)

Fuhs, Michael; Moebius, Klaus

Pulsed high-field/high-frequency electron paramagnetic resonance (EPR) spectroscopy is used to disentangle many kinds of different effects often obscured in continuous wave (cw) EPR spectra at lower magnetic fields/microwave frequencies. While the high magnetic field increases the resolution of G tensors and of nuclear Larmor frequencies, the high frequencies allow for higher time resolution for molecular dynamics as well as for transient paramagnetic intermediates studied with time-resolved EPR. Pulsed EPR methods are used for example for relaxation-time studies, and pulsed Electron Nuclear DOuble Resonance (ENDOR) is used to resolve unresolved hyperfine structure hidden in inhomogeneous linewidths. In the present article we introduce the basic concepts and selected applications to structure and mobility studies on electron transfer systems, reaction centers of photosynthesis as well as biomimetic models. The article concludes with an introduction to stochastic EPR which makes use of an other concept for investigating resonance systems in order to increase the excitation bandwidth of pulsed EPR. The limited excitation bandwidth of pulses at high frequency is one of the main limitations which, so far, made Fourier transform methods hardly feasible.

The nucleoporins Nup170p and Nup157p are essential for nuclear pore complex assembly

PubMed Central

Makio, Tadashi; Stanton, Leslie H.; Lin, Cheng-Chao; Goldfarb, David S.; Weis, Karsten

2009-01-01

We have established that two homologous nucleoporins, Nup170p and Nup157p, play an essential role in the formation of nuclear pore complexes (NPCs) in Saccharomyces cerevisiae. By regulating their synthesis, we showed that the loss of these nucleoporins triggers a decrease in NPCs caused by a halt in new NPC assembly. Preexisting NPCs are ultimately lost by dilution as cells grow, causing the inhibition of nuclear transport and the loss of viability. Significantly, the loss of Nup170p/Nup157p had distinct effects on the assembly of different architectural components of the NPC. Nucleoporins (nups) positioned on the cytoplasmic face of the NPC rapidly accumulated in cytoplasmic foci. These nup complexes could be recruited into new NPCs after reinitiation of Nup170p synthesis, and may represent a physiological intermediate. Loss of Nup170p/Nup157p also caused core and nucleoplasmically positioned nups to accumulate in NPC-like structures adjacent to the inner nuclear membrane, which suggests that these nucleoporins are required for formation of the pore membrane and the incorporation of cytoplasmic nups into forming NPCs. PMID:19414608

Feasible variants for intermediate storage of the spent fuel obtained at NPP Cernavoda, Romania

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

Radu, M.; Popescu, G.

1993-12-31

The 5 CANDU-PHW Reactors of 600 Standard type of Cernavoda Nuclear Power Plant are under construction and the first unit is expected to be commissioned in 1995, group 2 following after 2 years, and then groups 3, 4 and 5 one each year. In this study there are presented feasible variants for intermediate storage of spent fuel, obtained during 30 years of operation from the stations at Cernavoda. From the solutions applied worldwide, both dry and wet storage have been taken into account. In any of the two variants, a unique intermediate storage will be provided and the storage buildingmore » was proposed to be built in 4 different stages. As a first estimation, considering the fact that, by now Romania has only one nuclear plant of CANDU fuel type the dry variant seems to be the best.« less

Thermodynamic studies of studtite thermal decomposition pathways via amorphous intermediates UO 3, U 2O 7, and UO 4

DOE PAGES

Guo, Xiaofeng; Wu, Di; Xu, Hongwu; ...

2016-09-01

The thermal decomposition of studtite (UO 2)O 2(H 2O) 2·2H 2O results in a series of intermediate X-ray amorphous materials with general composition UO 3+x (x = 0, 0.5, 1). As an extension of a structural study on U 2O 7, this work provides detailed calorimetric data on these amorphous oxygen-rich materials since their energetics and thermal stability are unknown. These were characterized in situ by thermogravimetry, and mass spectrometry. Ex situ X-ray diffraction and infrared spectroscopy characterized their chemical bonding and local structures. This detailed characterization formed the basis for obtaining formation enthalpies by high temperature oxide melt solutionmore » calorimetry. The thermodynamic data demonstrate the metastability of the amorphous UO 3+x materials, and explain their irreversible and spontaneous reactions to generate oxygen and form metaschoepite. Thus, formation of studtite in the nuclear fuel cycle, followed by heat treatment, can produce metastable amorphous UO 3+x materials that pose the risk of significant O 2 gas. Quantitative knowledge of the energy landscape of amorphous UO 3+x was provided for stability analysis and assessment of conditions for decomposition.« less

Characterization of the Environmentally Induced Chemical Transformations of Uranium Tetrafluoride

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

Wellons, M.

A key challenge with nuclear safeguards environmental sampling is identification of the materials post release due to subsequent chemical reactions with ambient water and oxygen. Uranium Tetrafluoride (UF4) is of interest as an intermediate in both the upstream and downstream portions of uranium feedstock and metal production processes used in nuclear fuel production; however minimal published research exists relating to UF4 hydrolysis. FY16 efforts were dedicated to in-situ Raman spectroscopy and X-ray diffraction characterization of UF4 during exposure to various relative humidity conditions. This effort mapped several hydrolysis reaction pathways and identified both intermediate, and terminal progeny species.

Double probing of human spermatozoa for persistent histones, surplus cytoplasm, apoptosis and DNA fragmentation.

PubMed

Sati, Leyla; Ovari, Laszlo; Bennett, David; Simon, Stephen D; Demir, Ramazan; Huszar, Gabor

2008-04-01

Individual spermatozoa were assessed with pairs of probes for persistent histones and cytoplasmic retention, persistent histones and DNA fragmentation, and persistent histones and apoptotic markers. The individual spermatozoa were treated sequentially with combinations of probes for these cytoplasmic and nuclear biochemical markers. Sperm fields were recorded with computer-assisted imaging, and staining patterns with the two probes in the same spermatozoa were examined and scored as light, intermediate or dark (mature to arrested-maturity spermatozoa). The effects of arrested sperm maturation were similar with respect to the cytoplasmic and nuclear characteristics of spermatozoa in 84% of cells, indicating that cytoplasmic and nuclear attributes of arrested sperm maturation are related. However, there were moderate (intermediate-dark or intermediate-light patterns, 14.5% of cells) or major (light-dark patterns, 1.6% of cells) discrepancies in the intensity of the double staining patterns. Thus, testing with single maturity markers may not be fully reliable. These findings are important with respect to: (i) arrested sperm maturation; (ii) potential efficacy of antioxidant and similar therapeutic strategies in subfertile men, as spermatozoa with infrastructure defects due to mismaturation or maturation arrest are unlikely to respond to interventions; and (iii) detection of adverse male environmental exposures.

Core filaments of the nuclear matrix

PubMed Central

1990-01-01

The nuclear matrix is concealed by a much larger mass of chromatin, which can be removed selectively by digesting nuclei with DNase I followed by elution of chromatin with 0.25 M ammonium sulfate. This mild procedure removes chromatin almost completely and preserves nuclear matrix morphology. The complete nuclear matrix consists of a nuclear lamina with an interior matrix composed of thick, polymorphic fibers and large masses that resemble remnant nucleoli. Further extraction of the nuclear matrices of HeLa or MCF-7 cells with 2 M sodium chloride uncovered a network of core filaments. A few dark masses remained enmeshed in the filament network and may be remnants of the nuclear matrix thick fibers and nucleoli. The highly branched core filaments had diameters of 9 and 13 nm measured relative to the intermediate filaments. They may serve as the core structure around which the matrix is constructed. The core filaments retained 70% of nuclear RNA. This RNA consisted both of ribosomal RNA precursors and of very high molecular weight hnRNA with a modal size of 20 kb. Treatment with RNase A removed the core filaments. When 2 M sodium chloride was used directly to remove chromatin after DNase I digestion without a preceding 0.25 M ammonium sulfate extraction, the core filaments were not revealed. Instead, the nuclear interior was filled with amorphous masses that may cover the filaments. This reflected a requirement for a stepwise increase in ionic strength because gradual addition of sodium chloride to a final concentration of 2 M without an 0.25 M ammonium sulfate extraction uncovered core filaments. PMID:2307700

Nuclear Methods for Transmutation of Nuclear Waste: Problems, Perspextives, Cooperative Research - Proceedings of the International Workshop

NASA Astrophysics Data System (ADS)

Khankhasayev, Zhanat B.; Kurmanov, Hans; Plendl, Mikhail Kh.

1996-12-01

The Table of Contents for the full book PDF is as follows: * Preface * I. Review of Current Status of Nuclear Transmutation Projects * Accelerator-Driven Systems — Survey of the Research Programs in the World * The Los Alamos Accelerator-Driven Transmutation of Nuclear Waste Concept * Nuclear Waste Transmutation Program in the Czech Republic * Tentative Results of the ISTC Supported Study of the ADTT Plutonium Disposition * Recent Neutron Physics Investigations for the Back End of the Nuclear Fuel Cycle * Optimisation of Accelerator Systems for Transmutation of Nuclear Waste * Proton Linac of the Moscow Meson Factory for the ADTT Experiments * II. Computer Modeling of Nuclear Waste Transmutation Methods and Systems * Transmutation of Minor Actinides in Different Nuclear Facilities * Monte Carlo Modeling of Electro-nuclear Processes with Nonlinear Effects * Simulation of Hybrid Systems with a GEANT Based Program * Computer Study of 90Sr and 137Cs Transmutation by Proton Beam * Methods and Computer Codes for Burn-Up and Fast Transients Calculations in Subcritical Systems with External Sources * New Model of Calculation of Fission Product Yields for the ADTT Problem * Monte Carlo Simulation of Accelerator-Reactor Systems * III. Data Basis for Transmutation of Actinides and Fission Products * Nuclear Data in the Accelerator Driven Transmutation Problem * Nuclear Data to Study Radiation Damage, Activation, and Transmutation of Materials Irradiated by Particles of Intermediate and High Energies * Radium Institute Investigations on the Intermediate Energy Nuclear Data on Hybrid Nuclear Technologies * Nuclear Data Requirements in Intermediate Energy Range for Improvement of Calculations of ADTT Target Processes * IV. Experimental Studies and Projects * ADTT Experiments at the Los Alamos Neutron Science Center * Neutron Multiplicity Distributions for GeV Proton Induced Spallation Reactions on Thin and Thick Targets of Pb and U * Solid State Nuclear Track Detector and Radiochemical Studies on the Transmutation of Nuclei Using Relativistic Heavy Ions * Experimental and Theoretical Study of Radionuclide Production on the Electronuclear Plant Target and Construction Materials Irradiated by 1.5 GeV and 130 MeV Protons * Neutronics and Power Deposition Parameters of the Targets Proposed in the ISTC Project 17 * Multicycle Irradiation of Plutonium in Solid Fuel Heavy-Water Blanket of ADS * Compound Neutron Valve of Accelerator-Driven System Sectioned Blanket * Subcritical Channel-Type Reactor for Weapon Plutonium Utilization * Accelerator Driven Molten-Fluoride Reactor with Modular Heat Exchangers on PB-BI Eutectic * A New Conception of High Power Ion Linac for ADTT * Pions and Accelerator-Driven Transmutation of Nuclear Waste? * V. Problems and Perspectives * Accelerator-Driven Transmutation Technologies for Resolution of Long-Term Nuclear Waste Concerns * Closing the Nuclear Fuel-Cycle and Moving Toward a Sustainable Energy Development * Workshop Summary * List of Participants

Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy.

PubMed

Baird, Nathan J; Ludtke, Steven J; Khant, Htet; Chiu, Wah; Pan, Tao; Sosnick, Tobin R

2010-11-24

RNA folding occurs via a series of transitions between metastable intermediate states. It is unknown whether folding intermediates are discrete structures folding along defined pathways or heterogeneous ensembles folding along broad landscapes. We use cryo-electron microscopy and single-particle image reconstruction to determine the structure of the major folding intermediate of the specificity domain of a ribonuclease P ribozyme. Our results support the existence of a discrete conformation for this folding intermediate.

Nuclear microsatellite variation in Malagasy baobabs (Adansonia, Bombacoideae, Malvaceae) reveals past hybridization and introgression.

PubMed

Leong Pock Tsy, Jean-Michel; Lumaret, Roselyne; Flaven-Noguier, Elodie; Sauve, Mathieu; Dubois, Marie-Pierre; Danthu, Pascal

2013-12-01

Adansonia comprises nine species, six of which are endemic to Madagascar. Genetic relationships between the Malagasy species remain unresolved due to conflicting results between nuclear and plastid DNA variation. Morphologically intermediate individuals between distinct species have been identified, indicative of interspecific hybridization. In this paper, microsatellite data are used to identify potential cases of hybridization and to provide insights into the evolutionary history of the genus on Madagascar. Eleven microsatellites amplified with new primers developed for Adansonia rubrostipa were used to analyse 672 individuals collected at 27 sites for the six Malagasy species and morphologically intermediate individuals. Rates of individual admixture were examined using three Bayesian clustering programs, STRUCTURE, BAPS and NewHybrids, with no a priori species assignment. Population differentiation was coherent, with recognized species boundaries. In the four Malagasy species of section Longitubae, 8·0, 9·0 and 9·5 % of individuals with mixed genotypes were identified by BAPS, NewHybrids and STRUCTURE, respectively. At sites with sympatric populations of A. rubrostipa and A. za, NewHybrids indicated these individuals to be F2 and, predominantly, backcrosses with both parental species. In northern Madagascar, two populations of trees combining A. za and A. perrieri morphology and microsatellite alleles were identified in the current absence of the parental species. The clear genetic differentiation observed between the six species may reflect their adaptation to different assortments of climate regimes and habitats during the colonization of the island. Microsatellite variation reveals that hybridization probably occurred in secondary contact between species of section Longitubae. This type of hybridization may also have been involved in the differentiation of a local new stabilized entity showing specific microsatellite alleles and morphological characters, suggesting a potential role of hybridization in the recent history of diversification on Madagascar.

Micropillar displacements by cell traction forces are mechanically correlated with nuclear dynamics

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

Li, Qingsen; Makhija, Ekta; Hameed, F.M.

2015-05-29

Cells sense physical cues at the level of focal adhesions and transduce them to the nucleus by biochemical and mechanical pathways. While the molecular intermediates in the mechanical links have been well studied, their dynamic coupling is poorly understood. In this study, fibroblast cells were adhered to micropillar arrays to probe correlations in the physical coupling between focal adhesions and nucleus. For this, we used novel imaging setup to simultaneously visualize micropillar deflections and EGFP labeled chromatin structure at high spatial and temporal resolution. We observed that micropillar deflections, depending on their relative positions, were positively or negatively correlated tomore » nuclear and heterochromatin movements. Our results measuring the time scales between micropillar deflections and nucleus centroid displacement are suggestive of a strong elastic coupling that mediates differential force transmission to the nucleus. - Highlights: • Correlation between focal adhesions and nucleus studied using novel imaging setup. • Micropillar and nuclear displacements were measured at high resolution. • Correlation timescales show strong elastic coupling between cell edge and nucleus.« less

Hydroxylation and hydrolysis: two main metabolic ways of spiramycin I in anaerobic digestion.

PubMed

Zhu, Pei; Chen, Daijie; Liu, Wenbin; Zhang, Jianbin; Shao, Lei; Li, Ji-an; Chu, Ju

2014-02-01

The anaerobic degradation behaviors of five macrolides including spiramycin I, II, III, midecamycin and josamycin by sludge were investigated. Within 32days, 95% of spiramycin I, II or III was degraded, while the remove rate of midecamycin or josamycin was 75%. SPM I degradation was much higher in nutrition supplementation than that just in sludge. The degradation products and processes of spiramycin I were further characterized. Three molecules, designated P-1, P-2 and P-3 according to their order of occurrence, were obtained and purified. Structural determination was then performed by nuclear magnetic resonance and MS/MS spectra, and data indicated that hydroxylation and hydrolysis were main reactions during the anaerobic digestion of spiramycin I. P-1 is the intermediate of hydroxylation, and P-2 is the intermediate of hydrolysis. P-3 is the final product of the both reaction. This study revealed a hydroxylation and hydrolysis mechanism of macrolide in anaerobic digestion. Copyright © 2013 Elsevier Ltd. All rights reserved.

Cryo-EM structures of two bovine adenovirus type 3 intermediates

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

Cheng, Lingpeng; Huang, Xiaoxing; Li, Xiaomin

2014-02-15

Adenoviruses (Ads) infect hosts from all vertebrate species and have been investigated as vaccine vectors. We report here near-atomic structures of two bovine Ad type 3 (BAd3) intermediates obtained by cryo-electron microscopy. A comparison between the two intermediate structures reveals that the differences are localized in the fivefold vertex region, while their facet structures are identical. The overall facet structure of BAd3 exhibits a similar structure to human Ads; however, BAd3 protein IX has a unique conformation. Mass spectrometry and cryo-electron tomography analyses indicate that one intermediate structure represents the stage during DNA encapsidation, whilst the other intermediate structure representsmore » a later stage. These results also suggest that cleavage of precursor protein VI occurs during, rather than after, the DNA encapsidation process. Overall, our results provide insights into the mechanism of Ad assembly, and allow the first structural comparison between human and nonhuman Ads at backbone level. - Highlights: • First structure of bovine adenovirus type 3. • Some channels are located at the vertex of intermediate during DNA encapsidation. • Protein IX exhibits a unique conformation of trimeric coiled–coiled structure. • Cleavage of precursor protein VI occurs during the DNA encapsidation process.« less

Comparative analysis of compact heat exchangers for application as the intermediate heat exchanger for advanced nuclear reactors

DOE PAGES

Bartel, N.; Chen, M.; Utgikar, V. P.; ...

2015-04-04

A comparative evaluation of alternative compact heat exchanger designs for use as the intermediate heat exchanger in advanced nuclear reactor systems is presented in this article. Candidate heat exchangers investigated included the Printed circuit heat exchanger (PCHE) and offset strip-fin heat exchanger (OSFHE). Both these heat exchangers offer high surface area to volume ratio (a measure of compactness [m2/m3]), high thermal effectiveness, and overall low pressure drop. Helium–helium heat exchanger designs for different heat exchanger types were developed for a 600 MW thermal advanced nuclear reactor. The wavy channel PCHE with a 15° pitch angle was found to offer optimummore » combination of heat transfer coefficient, compactness and pressure drop as compared to other alternatives. The principles of the comparative analysis presented here will be useful for heat exchanger evaluations in other applications as well.« less

Comparative analysis of compact heat exchangers for application as the intermediate heat exchanger for advanced nuclear reactors

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

Bartel, N.; Chen, M.; Utgikar, V. P.

A comparative evaluation of alternative compact heat exchanger designs for use as the intermediate heat exchanger in advanced nuclear reactor systems is presented in this article. Candidate heat exchangers investigated included the Printed circuit heat exchanger (PCHE) and offset strip-fin heat exchanger (OSFHE). Both these heat exchangers offer high surface area to volume ratio (a measure of compactness [m2/m3]), high thermal effectiveness, and overall low pressure drop. Helium–helium heat exchanger designs for different heat exchanger types were developed for a 600 MW thermal advanced nuclear reactor. The wavy channel PCHE with a 15° pitch angle was found to offer optimummore » combination of heat transfer coefficient, compactness and pressure drop as compared to other alternatives. The principles of the comparative analysis presented here will be useful for heat exchanger evaluations in other applications as well.« less

Does Explosive Nuclear Burning Occur in Tidal Disruption Events of White Dwarfs by Intermediate-mass Black Holes?

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

Tanikawa, Ataru; Sato, Yushi; Hachisu, Izumi

We investigate nucleosynthesis in tidal disruption events (TDEs) of white dwarfs (WDs) by intermediate-mass black holes. We consider various types of WDs with different masses and compositions by means of three-dimensional (3D) smoothed particle hydrodynamics (SPH) simulations. We model these WDs with different numbers of SPH particles, N , from a few 10{sup 4} to a few 10{sup 7} in order to check mass resolution convergence, where SPH simulations with N > 10{sup 7} (or a space resolution of several 10{sup 6} cm) have unprecedentedly high resolution in this kind of simulation. We find that nuclear reactions become less activemore » with increasing N and that these nuclear reactions are excited by spurious heating due to low resolution. Moreover, we find no shock wave generation. In order to investigate the reason for the absence of a shock wave, we additionally perform one-dimensional (1D) SPH and mesh-based simulations with a space resolution ranging from 10{sup 4} to 10{sup 7} cm, using a characteristic flow structure extracted from the 3D SPH simulations. We find shock waves in these 1D high-resolution simulations, one of which triggers a detonation wave. However, we must be careful of the fact that, if the shock wave emerged in an outer region, it could not trigger the detonation wave due to low density. Note that the 1D initial conditions lack accuracy to precisely determine where a shock wave emerges. We need to perform 3D simulations with ≲10{sup 6} cm space resolution in order to conclude that WD TDEs become optical transients powered by radioactive nuclei.« less

Intermediate-range nuclear forces (INF) treaty: an operational error

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

Caldwell, W.B.

1988-05-12

The purpose of this paper is to examine the operational impact of the INF treaty and what it means for the future of NATO. At this writing, there is considerable debate going on as to whether or not the US Congress should ratify the INF treaty. The political issues are well known and under careful examination. A critical element that still needs to be addressed is the operational impact of the INF treaty. This area may have been neglected because nuclear weapons are viewed primarily as an element of deterrence. Therefore, their warfighting potential is given only minimal consideration. Thismore » paper begins with a discussion of the historical use of nuclear weapons in NATO's defensive Alliance. It follows through to the decision in 1979 to modernize NATO's nuclear force. This decision resulted in the deployment of the Pershing II and ground-launched cruise missile (GLCM) systems in Europe. The Soviet warfighting concept for Europe is addressed next to place the intermediate-range nuclear forces in their proper perspective. This is followed by a discussion on the operational implications of the INF treaty. The paper concludes by briefly mentioning a few of the defensive proposals for the post-INF period.« less

A statistical image analysis framework for pore-free islands derived from heterogeneity distribution of nuclear pore complexes.

PubMed

Mimura, Yasuhiro; Takemoto, Satoko; Tachibana, Taro; Ogawa, Yutaka; Nishimura, Masaomi; Yokota, Hideo; Imamoto, Naoko

2017-11-24

Nuclear pore complexes (NPCs) maintain cellular homeostasis by mediating nucleocytoplasmic transport. Although cyclin-dependent kinases (CDKs) regulate NPC assembly in interphase, the location of NPC assembly on the nuclear envelope is not clear. CDKs also regulate the disappearance of pore-free islands, which are nuclear envelope subdomains; this subdomain gradually disappears with increase in homogeneity of the NPC in response to CDK activity. However, a causal relationship between pore-free islands and NPC assembly remains unclear. Here, we elucidated mechanisms underlying NPC assembly from a new perspective by focusing on pore-free islands. We proposed a novel framework for image-based analysis to automatically determine the detailed 'landscape' of pore-free islands from a large quantity of images, leading to the identification of NPC intermediates that appear in pore-free islands with increased frequency in response to CDK activity. Comparison of the spatial distribution between simulated and the observed NPC intermediates within pore-free islands showed that their distribution was spatially biased. These results suggested that the disappearance of pore-free islands is highly related to de novo NPC assembly and indicated the existence of specific regulatory mechanisms for the spatial arrangement of NPC assembly on nuclear envelopes.

Mechanisms for pressure-induced crystal-crystal transition, amorphization, and devitrification of SnI{sub 4}

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

Liu, H.; Tse, J. S., E-mail: john.tse@usask.ca; Hu, M. Y.

2015-10-28

The pressure-induced amorphization and subsequent recrystallization of SnI{sub 4} have been investigated using first principles molecular dynamics calculations together with high-pressure {sup 119}Sn nuclear resonant inelastic x-ray scattering measurements. Above ∼8 GPa, we observe a transformation from an ambient crystalline phase to an intermediate crystal structure and a subsequent recrystallization into a cubic phase at ∼64 GPa. The crystalline-to-amorphous transition was identified on the basis of elastic compatibility criteria. The measured tin vibrational density of states shows large amplitude librations of SnI{sub 4} under ambient conditions. Although high pressure structures of SnI{sub 4} were thought to be determined by randommore » packing of equal-sized spheres, we detected electron charge transfer in each phase. This charge transfer results in a crystal structure packing determined by larger than expected iodine atoms.« less

Mechanisms for pressure-induced crystal-crystal transition, amorphization, and devitrification of Snl 4

DOE PAGES

Liu, Hanyu; Tse, John S.; Hu, Michael Y.; ...

2015-10-27

The pressure-induced amorphization and subsequent recrystallization of SnI 4 have been investigated using first principles molecular dynamics calculations together with high-pressure 119Sn nuclear resonant inelastic x-ray scattering measurements. Above ~8 GPa, we observe a transformation from an ambient crystalline phase to an intermediate crystal structure and a subsequent recrystallization into a cubic phase at ~64 GPa. The crystalline-to-amorphous transition was identified on the basis of elastic compatibility criteria. The measured tin vibrational density of states shows large amplitude librations of SnI 4 under ambient conditions. Although high pressure structures of SnI 4 were thought to be determined by random packingmore » of equal-sized spheres, we detected electron charge transfer in each phase. As a result, this charge transfer results in a crystal structure packing determined by larger than expected iodine atoms. (C) 2015 AIP Publishing LLC.« less

Structural characterization of a non-heme iron active site in zeolites that hydroxylates methane

DOE PAGES

Snyder, Benjamin E. R.; Bottger, Lars H.; Bols, Max L.; ...

2018-04-02

Iron-containing zeolites exhibit unprecedented reactivity in the low-temperature hydroxylation of methane to form methanol. Reactivity occurs at a mononuclear ferrous active site, α-Fe(II), that is activated by N 2O to form the reactive intermediate α-O. This has been defined as an Fe(IV)=O species. Using nuclear resonance vibrational spectroscopy coupled to X-ray absorption spectroscopy, we probe the bonding interaction between the iron center, its zeolite lattice-derived ligands, and the reactive oxygen. α-O is found to contain an unusually strong Fe(IV)=O bond resulting from a constrained coordination geometry enforced by the zeolite lattice. As a result, density functional theory calculations clarify howmore » the experimentally determined geometric structure of the active site leads to an electronic structure that is highly activated to perform H-atom abstraction.« less

Structural characterization of a non-heme iron active site in zeolites that hydroxylates methane

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

Snyder, Benjamin E. R.; Bottger, Lars H.; Bols, Max L.

Iron-containing zeolites exhibit unprecedented reactivity in the low-temperature hydroxylation of methane to form methanol. Reactivity occurs at a mononuclear ferrous active site, α-Fe(II), that is activated by N 2O to form the reactive intermediate α-O. This has been defined as an Fe(IV)=O species. Using nuclear resonance vibrational spectroscopy coupled to X-ray absorption spectroscopy, we probe the bonding interaction between the iron center, its zeolite lattice-derived ligands, and the reactive oxygen. α-O is found to contain an unusually strong Fe(IV)=O bond resulting from a constrained coordination geometry enforced by the zeolite lattice. As a result, density functional theory calculations clarify howmore » the experimentally determined geometric structure of the active site leads to an electronic structure that is highly activated to perform H-atom abstraction.« less

Mechanisms for pressure-induced crystal-crystal transition, amorphization, and devitrification of SnI4.

PubMed

Liu, H; Tse, J S; Hu, M Y; Bi, W; Zhao, J; Alp, E E; Pasternak, M; Taylor, R D; Lashley, J C

2015-10-28

The pressure-induced amorphization and subsequent recrystallization of SnI4 have been investigated using first principles molecular dynamics calculations together with high-pressure (119)Sn nuclear resonant inelastic x-ray scattering measurements. Above ∼8 GPa, we observe a transformation from an ambient crystalline phase to an intermediate crystal structure and a subsequent recrystallization into a cubic phase at ∼64 GPa. The crystalline-to-amorphous transition was identified on the basis of elastic compatibility criteria. The measured tin vibrational density of states shows large amplitude librations of SnI4 under ambient conditions. Although high pressure structures of SnI4 were thought to be determined by random packing of equal-sized spheres, we detected electron charge transfer in each phase. This charge transfer results in a crystal structure packing determined by larger than expected iodine atoms.

NATO (North Atlantic Treaty Organization) deterrence and defense after the INF (Intermediate-Range Nuclear Forces) treaty. Final report, June 1988-June 1989

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

Garrett, S.A.

1989-06-21

The treaty between the Soviet Union and the United States eliminating a whole class of intermediate-range nuclear forces (INF) in Europe raises a number of questions about NATO's future ability to deter Warsaw Pact aggression. Future choices on Alliance strategy and doctrine will be influenced by a variety of factors, including the image of new thinking in Soviet security policy enunciated by General Secretary Gorbachev, changing West European opinion toward the use of nuclear weapons for NATO deterrence, the complications inherent in further nuclear and conventional arms-control negotiations, assessments of the current conventional arms balance in Europe, and ongoing questionsmore » about NATO cohesion as well as the continued coupling of American security with that of her European allies. In the post-INF environment it may well be that U.S. Navy nuclear assets will assume an increasingly important role, particularly the Tomahawk Land Attack Missile/Nuclear (TLAM/N). The TLAM/N has many attractive attributes that can be supportive of NATO deterrence of the WTO, but there are also a number of unresolved questions to be addressed concerning this particular weapons system. Modernization of NATO's land-based short-range nuclear forces (SNF), such as the Lance missile, is also seen by many as critical to the maintenance of Alliance security in the aftermath of INF.« less

Bcs1p can rescue a large and productive cytochrome bc(1) complex assembly intermediate in the inner membrane of yeast mitochondria.

PubMed

Conte, Laura; Trumpower, Bernard L; Zara, Vincenzo

2011-01-01

The yeast cytochrome bc(1) complex, a component of the mitochondrial respiratory chain, is composed of ten distinct protein subunits. In the assembly of the bc(1) complex, some ancillary proteins, such as the chaperone Bcs1p, are actively involved. The deletion of the nuclear gene encoding this chaperone caused the arrest of the bc(1) assembly and the formation of a functionally inactive bc(1) core structure of about 500-kDa. This immature bc(1) core structure could represent, on the one hand, a true assembly intermediate or, on the other hand, a degradation product and/or an incorrect product of assembly. The experiments here reported show that the gradual expression of Bcs1p in the yeast strain lacking this protein was progressively able to rescue the bc(1) core structure leading to the formation of the functional homodimeric bc(1) complex. Following Bcs1p expression, the mature bc(1) complex was also progressively converted into two supercomplexes with the cytochrome c oxidase complex. The capability of restoring the bc(1) complex and the supercomplexes was also possessed by the mutated yeast R81C Bcsp1. Notably, in the human ortholog BCS1L, the corresponding point mutation (R45C) was instead the cause of a severe bc(1) complex deficiency. Differently from the yeast R81C Bcs1p, two other mutated Bcs1p's (K192P and F401I) were unable to recover the bc(1) core structure in yeast. This study identifies for the first time a productive assembly intermediate of the yeast bc(1) complex and gives new insights into the molecular mechanisms involved in the last steps of bc(1) assembly. Copyright © 2010 Elsevier B.V. All rights reserved.

Heat exchanger with intermediate evaporating and condensing fluid

DOEpatents

Fraas, Arthur P.

1978-01-01

A shell and tube-type heat exchanger, such as a liquid sodium-operated steam generator for use in nuclear reactors, comprises a shell containing a primary fluid tube bundle, a secondary fluid tube bundle at higher elevation, and an intermediate fluid vaporizing at the surface of the primary fluid tubes and condensing at the surface of the secondary fluid tubes.

High-lying intermediate excitations in the nuclear effective interaction with a super-soft-core potential

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

Goode, P.R.; Barrett, B.R.; Portilho, O.

1979-02-01

The earlier calculations of Goode and Barrett are repeated using the super-soft-core potential of Gogny, Pires, and de Tourreil. The particular third-order folded diagram which they calculated now converges in its intermediate-state energy summation, because of the suppression of the strong short-range repulsive effects present in earlier calculations.

Plastid-to-Nucleus Retrograde Signals Are Essential for the Expression of Nuclear Starch Biosynthesis Genes during Amyloplast Differentiation in Tobacco BY-2 Cultured Cells1[W][OA

PubMed Central

Enami, Kazuhiko; Ozawa, Tomoki; Motohashi, Noriko; Nakamura, Masayuki; Tanaka, Kan; Hanaoka, Mitsumasa

2011-01-01

Amyloplasts, a subtype of plastid, are found in nonphotosynthetic tissues responsible for starch synthesis and storage. When tobacco (Nicotiana tabacum) Bright Yellow-2 cells are cultured in the presence of cytokinin instead of auxin, their plastids differentiate from proplastids to amyloplasts. In this program, it is well known that the expression of nucleus-encoded starch biosynthesis genes, such as ADP-Glucose Pyrophosphorylase (AgpS) and Granule-Bound Starch Synthase (GBSS), is specifically induced. In this study, we investigated the roles of plastid gene expression in amyloplast differentiation. Microarray analysis of plastid genes revealed that no specific transcripts were induced in amyloplasts. Nevertheless, amyloplast development accompanied with starch biosynthesis was drastically inhibited in the presence of plastid transcription/translation inhibitors. Surprisingly, the expression of nuclear AgpS and GBSS was significantly repressed by the addition of these inhibitors, suggesting that a plastid-derived signal(s) that reflects normal plastid gene expression was essential for nuclear gene expression. A series of experiments was performed to examine the effects of intermediates and inhibitors of tetrapyrrole biosynthesis, since some of the intermediates have been characterized as candidates for plastid-to-nucleus retrograde signals. Addition of levulinic acid, an inhibitor of tetrapyrrole biosynthesis, resulted in the up-regulation of nuclear AgpS and GBSS gene expression as well as starch accumulation, while the addition of heme showed opposite effects. Thus, these results indicate that plastid transcription and/or translation are required for normal amyloplast differentiation, regulating the expression of specific nuclear genes by unknown signaling mechanisms that can be partly mediated by tetrapyrrole intermediates. PMID:21771917

Critical Intermediate Structure That Directs the Crystalline Texture and Surface Morphology of Organo-Lead Trihalide Perovskite.

PubMed

Chia, Hao-Chung; Sheu, Hwo-Shuenn; Hsiao, Yu-Yun; Li, Shao-Sian; Lan, Yi-Kang; Lin, Chung-Yao; Chang, Je-Wei; Kuo, Yen-Chien; Chen, Chia-Hao; Weng, Shih-Chang; Su, Chun-Jen; Su, An-Chung; Chen, Chun-Wei; Jeng, U-Ser

2017-10-25

We have identified an often observed yet unresolved intermediate structure in a popular processing with dimethylformamide solutions of lead chloride and methylammonium iodide for perovskite solar cells. With subsecond time-resolved grazing-incidence X-ray scattering and X-ray photoemission spectroscopy, supplemental with ab initio calculation, the resolved intermediate structure (CH 3 NH 3 ) 2 PbI 2 Cl 2 ·CH 3 NH 3 I features two-dimensional (2D) perovskite bilayers of zigzagged lead-halide octahedra and sandwiched CH 3 NH 3 I layers. Such intermediate structure reveals a hidden correlation between the intermediate phase and the composition of the processing solution. Most importantly, the 2D perovskite lattice of the intermediate phase is largely crystallographically aligned with the [110] planes of the three-dimensional perovskite cubic phase; consequently, with sublimation of Cl ions from the organo-lead octahedral terminal corners in prolonged annealing, the zigzagged octahedral layers of the intermediate phase can merge with the intercalated methylammonium iodide layers for templated growth of perovskite crystals. Regulated by annealing temperature and the activation energies of the intermediate and perovskite, deduced from analysis of temperature-dependent structural kinetics, the intermediate phase is found to selectively mature first and then melt along the layering direction for epitaxial conversion into perovskite crystals. The unveiled epitaxial conversion under growth kinetics controls might be general for solution-processed and intermediate-templated perovskite formation.

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

Sherrett, R.R.

This study investigates the relationship between NATO's decision to approach the problem created by the intermediate-range nuclear force superiority of the Soviets and the eventual signing of the INF Treaty by the United States and the Soviet Union. The concept presented is that by adopting the dual track decision, (a track for negotiations and a simultaneous track for fielding U.S. INF missiles), the United States was eventually able to conduct arms negotiations from a position of strength. In this way a significant contribution to the INF Treaty negotiation process was made. The study examines the position of each principal priormore » to the dual track decision, examines the role each played in that decision, and looks at the actions taken following the implementation of the dual track decision. The study also presents the nuclear background of NATO, and also examines the INF negotiations in some detail. The conclusions provide the current status of the INF Treaty implementation and outlines some lessons which could be applied to future negotiations of this type. Intermediate-range Nuclear Forces, INF Treaty, GLCM, PIT, Pershing II missiles, Ground Launched Cruise Missiles, Dual Track Decision, Nuclear arms negotiations.« less

Reaction intermediates in the catalytic Gif-type oxidation from nuclear inelastic scattering

NASA Astrophysics Data System (ADS)

Rajagopalan, S.; Asthalter, T.; Rabe, V.; Laschat, S.

2016-12-01

Nuclear inelastic scattering (NIS) of synchrotron radiation, also known as nuclear resonant vibrational spectroscopy (NRVS), has been shown to provide valuable insights into metal-centered vibrations at Mössbauer-active nuclei. We present a study of the iron-centered vibrational density of states (VDOS) during the first step of the Gif-type oxidation of cyclohexene with a novel trinuclear Fe3(μ 3-O) complex as catalyst precursor. The experiments were carried out on shock-frozen solutions for different combinations of reactants: Fe3(μ 3-O) in pyridine solution, Fe3(μ 3-O) plus Zn/acetic acid in pyridine without and with addition of either oxygen or cyclohexene, and Fe3(μ 3-O)/Zn/acetic acid/pyridine/cyclohexene (reaction mixture) for reaction times of 1 min, 5 min, and 30 min. The projected VDOS of the Fe atoms was calculated on the basis of pseudopotential density functional calculations. Two possible reaction intermediates were identified as [Fe(III)(C5H5N)2(O2CCH3)2]+ and Fe(II)(C5H5N)4(O2CCH3)2, yielding evidence that NIS (NRVS) allows to identify the presence of iron-centered intermediates also in complex reaction mixtures.

Studies concerning the durability of concrete vaults for intermediate level radioactive waste disposal: Electrochemical monitoring and corrosion aspects

NASA Astrophysics Data System (ADS)

Duffó, G. S.; Farina, S. B.; Arva, E. A.; Giordano, C. M.; Lafont, C. J.

2006-11-01

The Argentine Atomic Energy Commission (CNEA) is responsible of the development of a management nuclear waste disposal programme. This programme contemplates the design and construction of a facility for the final disposal of intermediate-level radioactive waste. The proposed concept is the near-surface monolithic repository similar to those in operation in El Cabril, Spain. The design of this type of repository is based on the use of multiple, independent and redundant barriers. Since the vault and cover are major components of the engineered barriers, the durability of these concrete structures is an important aspect for the facilities integrity. This work presents a laboratory and field investigation performed for the last 6 years on reinforced concrete specimens, in order to predict the service life of the intermediate level radioactive waste disposal vaults from data obtained from electrochemical techniques. On the other hand, the development of sensors that allow on-line measurements of rebar corrosion potential and corrosion current density; incoming oxygen flow that reaches the metal surface; concrete electrical resistivity and chloride concentration is shown. Those sensors, properly embedded in a new full scale vault (nowadays in construction), will allow the monitoring of the corrosion process of the steel rebars embedded in thestructure.

Implications for the Origin of Early-type Dwarf Galaxies: A Detailed Look at the Isolated Rotating Early-type Dwarf Galaxy LEDA 2108986 (CG 611), Ramifications for the Fundamental Plane’s {S}_{K}^{2} Kinematic Scaling, and the Spin-Ellipticity Diagram

NASA Astrophysics Data System (ADS)

Graham, Alister W.; Janz, Joachim; Penny, Samantha J.; Chilingarian, Igor V.; Ciambur, Bogdan C.; Forbes, Duncan A.; Davies, Roger L.

2017-05-01

Selected from a sample of nine, isolated, dwarf early-type galaxies (ETGs) with the same range of kinematic properties as dwarf ETGs in clusters, we use LEDA 2108986 (CG 611) to address the nature versus nurture debate regarding the formation of dwarf ETGs. The presence of faint disk structures and rotation within some cluster dwarf ETGs has often been heralded as evidence that they were once late-type spiral or dwarf irregular galaxies prior to experiencing a cluster-induced transformation into an ETG. However, CG 611 also contains significant stellar rotation (≈20 km s-1) over its inner half-light radius ({R}{{e},{maj}}=0.71 kpc), and its stellar structure and kinematics resemble those of cluster ETGs. In addition to hosting a faint young nuclear spiral within a possible intermediate-scale stellar disk, CG 611 has accreted an intermediate-scale, counter-rotating gas disk. It is therefore apparent that dwarf ETGs can be built by accretion events, as opposed to disk-stripping scenarios. We go on to discuss how both dwarf and ordinary ETGs with intermediate-scale disks, whether under (de)construction or not, are not fully represented by the kinematic scaling {S}0.5=\\sqrt{0.5 {V}{rot}2+{σ }2}, and we also introduce a modified spin-ellipticity diagram λ (R)-ɛ (R) with the potential to track galaxies with such disks.

Rapid flow-induced responses in endothelial cells

NASA Technical Reports Server (NTRS)

Stamatas, G. N.; McIntire, L. V.

2001-01-01

Endothelial cells alter their morphology, growth rate, and metabolism in response to fluid shear stress. To study rapid flow-induced responses in the 3D endothelial cell morphology and calcium distribution, coupled fluorescence microscopy with optical sectioning, digital imaging, and numerical deconvolution techniques have been utilized. Results demonstrate that within the first minutes of flow application nuclear calcium is increasing. In the same time frame whole cell height and nuclear height are reduced by about 1 microm. Whole cell height changes may facilitate reduction of shear stress gradients on the luminal surface, whereas nuclear structural changes may be important for modulating endothelial growth rate and metabolism. To study the role of the cytoskeleton in these responses, endothelial cells have been treated with specific disrupters (acrylamide, cytochalasin D, and colchicine) of each of the cytoskeleton elements (intermediate filaments, microfilaments, and microtubules, respectively). None of these compounds had any effect on the shear-induced calcium response. Cytochalasin D and acrylamide did not affect the shear-induced nuclear morphology changes. Colchicine, however, completely abrogated the response, indicating that microtubules may be implicated in force transmission from the plasma membrane to the nucleus. A pedagogical model based on tensegrity theory principles is presented that is consistent with the results on the 3D endothelial morphology.

Structural damping results from vibration tests of straight piping sections

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

Ware, A.G.; Thinnes, G.L.

EG and G Idaho is assisting the USNRC and the Pressure Vessel Research Committee in supporting a final position on revised damping values for structural analyses of nuclear piping systems. As part of this program, a series of vibrational tests on 76-mm and 203-mm (3-in. amd 8-in.) Schedule 40 carbon steel piping was conducted to determine the changes in structural damping due to various parametric effects. The 10-m (33-ft) straight sections of piping were rigidly supported at the ends. Spring, rod, and constant force hangers, as well as a sway brace and snubbers were included as intermediate supports. Excitation wasmore » provided by low-force level hammer inpacts, a hydraulic shaker, and a 445-kN (50-ton) overhead crane. Data was recorded using acceleration, strain, and displacement time histories. This paper presents results from the testing showing the effect of stress level and type of supports on structural damping in piping.« less

Conformational Heterogeneity in a Fully Complementary DNA Three-Way Junction with a GC-Rich Branchpoint.

PubMed

Toulmin, Anita; Baltierra-Jasso, Laura E; Morten, Michael J; Sabir, Tara; McGlynn, Peter; Schröder, Gunnar F; Smith, Brian O; Magennis, Steven W

2017-09-19

DNA three-way junctions (3WJs) are branched structures that serve as important biological intermediates and as components in DNA nanostructures. We recently derived the global structure of a fully complementary 3WJ and found that it contained unpaired bases at the branchpoint, which is consistent with previous observations of branch flexibility and branchpoint reactivity. By combining high-resolution single-molecule Förster resonance energy transfer, molecular modeling, time-resolved ensemble fluorescence spectroscopy, and the first 19 F nuclear magnetic resonance observations of fully complementary 3WJs, we now show that the 3WJ structure can adopt multiple distinct conformations depending upon the sequence at the branchpoint. A 3WJ with a GC-rich branchpoint adopts an open conformation with unpaired bases at the branch and at least one additional conformation with an increased number of base interactions at the branchpoint. This structural diversity has implications for branch interactions and processing in vivo and for technological applications.

A Novel Lamin A Mutant Responsible for Congenital Muscular Dystrophy Causes Distinct Abnormalities of the Cell Nucleus.

PubMed

Barateau, Alice; Vadrot, Nathalie; Vicart, Patrick; Ferreiro, Ana; Mayer, Michèle; Héron, Delphine; Vigouroux, Corinne; Buendia, Brigitte

2017-01-01

A-type lamins, the intermediate filament proteins participating in nuclear structure and function, are encoded by LMNA. LMNA mutations can lead to laminopathies such as lipodystrophies, premature aging syndromes (progeria) and muscular dystrophies. Here, we identified a novel heterozygous LMNA p.R388P de novo mutation in a patient with a non-previously described severe phenotype comprising congenital muscular dystrophy (L-CMD) and lipodystrophy. In culture, the patient's skin fibroblasts entered prematurely into senescence, and some nuclei showed a lamina honeycomb pattern. C2C12 myoblasts were transfected with a construct carrying the patient's mutation; R388P-lamin A (LA) predominantly accumulated within the nucleoplasm and was depleted at the nuclear periphery, altering the anchorage of the inner nuclear membrane protein emerin and the nucleoplasmic protein LAP2-alpha. The mutant LA triggered a frequent and severe nuclear dysmorphy that occurred independently of prelamin A processing, as well as increased histone H3K9 acetylation. Nuclear dysmorphy was not significantly improved when transfected cells were treated with drugs disrupting microtubules or actin filaments or modifying the global histone acetylation pattern. Therefore, releasing any force exerted at the nuclear envelope by the cytoskeleton or chromatin did not rescue nuclear shape, in contrast to what was previously shown in Hutchinson-Gilford progeria due to other LMNA mutations. Our results point to the specific cytotoxic effect of the R388P-lamin A mutant, which is clinically related to a rare and severe multisystemic laminopathy phenotype.

Geographic structure of European anchovy: A nuclear-DNA study

NASA Astrophysics Data System (ADS)

Bouchenak-Khelladi, Yanis; Durand, Jean-Dominique; Magoulas, Antonios; Borsa, Philippe

2008-08-01

Atlantic-Mediterranean anchovies were genetically characterized at two polymorphic nuclear loci (intron 6 of two creatine-kinase genes) and compared to reference Engraulis albidus and E. encrasicolus samples from the northern Western Mediterranean to provide new insights into their geographic structure. Northeastern Atlantic anchovy, represented by one sample from the Canary archipelago and one sample from the Alboran Sea, were genetically distinct from Mediterranean E. encrasicolus (Weir and Cockerham's ^θ = 0.027-0.311), indicating geographic isolation from either side of the Almería-Oran oceanographic front. Generally smaller genetic differences were evident among anchovy populations from different sub-basins in the Mediterranean ( ^θ = - 0.019-0.116), the genetic differences between Black Sea and Ionian Sea/Aegean Sea anchovies being the strongest ( ^θ = 0.002-0.116). There was no evidence of the presence of E. albidus in our samples outside Camargue (northern shore of the Western Mediterranean). However, a sample from the southern Western Mediterranean appeared to be genetically intermediate between E. albidus and Mediterranean E. encrasicolus, indicating possible hybridization. Anchovy from the Benguela current system off southern Africa possessed allele frequencies characteristic of E. albidus at one locus and Northeastern Atlantic anchovy at the other locus, suggesting past introgression.

Cost-effectiveness of measuring fractional flow reserve to guide coronary interventions.

PubMed

Fearon, William F; Yeung, Alan C; Lee, David P; Yock, Paul G; Heidenreich, Paul A

2003-05-01

Most patients come to the catheterization laboratory without prior functional tests, which makes the cost-effective treatment of patients with intermediate coronary lesions a practical challenge. We developed a decision model to compare the long-term costs and benefits of 3 strategies for treating patients with an intermediate coronary lesion and no prior functional study: 1) deferring the decision for percutaneous coronary intervention (PCI) to obtain a nuclear stress imaging study (NUC strategy); 2) measuring fractional flow reserve (FFR) at the time of angiography to help guide the decision for PCI (FFR strategy); and 3) stenting all intermediate lesions (STENT strategy). On the basis of the literature, we estimated that 40% of intermediate lesions would produce ischemia, 70% of patients treated with PCI and 30% of patients treated medically would be free of angina after 4 years, and the quality-of-life adjustment for living with angina was 0.9 (1.0 = perfect health). We estimated the cost of FFR to be 761 dollars, the cost of nuclear stress imaging to be 1093 dollars, and the cost of medical treatment for angina to be 1775 dollars per year. The extra cost of splitting the angiogram and PCI as dictated by the NUC strategy was 3886 dollars by use of hospital cost-accounting data. Sensitivity and threshold analyses were performed to determine which variables affected our results. The FFR strategy saved 1795 dollars per patient compared with the NUC strategy and 3830 dollars compared with the STENT strategy. Quality-adjusted life expectancy was similar among the 3 strategies (NUC-FFR = 0.8 quality-adjusted days, FFR-STENT = 6 quality-adjusted life days). Compared with the FFR strategy, the NUC strategy was expensive (>800,000 dollars per quality-adjusted life year gained). Both screening strategies were superior to (less cost, better outcomes) the STENT strategy. Sensitivity analysis indicated that the NUC strategy would only become attractive (<50,000 dollars/quality-adjusted life years compared with FFR) if the specificity of nuclear stress imaging was >25% better than FFR. Our results were not altered significantly by changing the other assumptions. In patients with an intermediate coronary lesion and no prior functional study, measuring FFR to guide the decision to perform PCI may lead to significant cost savings compared with performing nuclear stress imaging or with simply stenting lesions in all patients.

Coupled biopolymer networks

NASA Astrophysics Data System (ADS)

Schwarz, J. M.; Zhang, Tao

2015-03-01

The actin cytoskeleton provides the cell with structural integrity and allows it to change shape to crawl along a surface, for example. The actin cytoskeleton can be modeled as a semiflexible biopolymer network that modifies its morphology in response to both external and internal stimuli. Just inside the inner nuclear membrane of a cell exists a network of filamentous lamin that presumably protects the heart of the cell nucleus--the DNA. Lamins are intermediate filaments that can also be modeled as semiflexible biopolymers. It turns out that the actin cytoskeletal biopolymer network and the lamin biopolymer network are coupled via a sequence of proteins that bridge the outer and inner nuclear membranes. We, therefore, probe the consequences of such a coupling via numerical simulations to understand the resulting deformations in the lamin network in response to perturbations in the cytoskeletal network. Such study could have implications for mechanical mechanisms of the regulation of transcription, since DNA--yet another semiflexible polymer--contains lamin-binding domains, and, thus, widen the field of epigenetics.

Method for passive cooling liquid metal cooled nuclear reactors, and system thereof

DOEpatents

Hunsbedt, Anstein; Busboom, Herbert J.

1991-01-01

A liquid metal cooled nuclear reactor having a passive cooling system for removing residual heat resulting from fuel decay during reactor shutdown. The passive cooling system comprises a plurality of partitions surrounding the reactor vessel in spaced apart relation forming intermediate areas for circulating heat transferring fluid which remove and carry away heat from the reactor vessel.

Cobalt spin states and hyperfine interactions in LaCoO3 investigated by LDA+U calculations

NASA Astrophysics Data System (ADS)

Hsu, Han; Blaha, Peter; Wentzcovitch, Renata M.; Leighton, C.

2010-09-01

With a series of local-density approximation plus Hubbard U calculations, we have demonstrated that for lanthanum cobaltite (LaCoO3) , the electric field gradient at the cobalt nucleus can be used as a fingerprint to identify the spin state of the cobalt ion. Therefore, in principle, the spin state of the cobalt ion can be unambiguously determined from nuclear magnetic resonance spectra. Our calculations also suggest that a crossover from the low-spin to intermediate-spin state in the temperature range of 0-90 K is unlikely, based on the half-metallic band structure associated with isolated IS Co ions, which is incompatible with the measured conductivity.

Structural studies on Desulfovibrio gigas cytochrome c3 by two-dimensional 1H-nuclear-magnetic-resonance spectroscopy.

PubMed Central

Piçarra-Pereira, M A; Turner, D L; LeGall, J; Xavier, A V

1993-01-01

Several aromatic amino acid residues and haem resonances in the fully reduced form of Desulfovibrio gigas cytochrome c3 are assigned, using two-dimensional 1H n.m.r., on the basis of the interactions between the protons of the aromatic amino acids and the haem protons as well as the intrahaem distances known from the X-ray structure [Kissinger (1989) Ph.D. Thesis, Washington State University]. The interhaem interactions observed in the n.m.r. spectra are in full agreement with the D. gigas X-ray structure and also with the n.m.r. data from Desulfovibrio vulgaris (Hildenborough) [Turner, Salgueiro, LeGall and Xavier (1992) Eur. J. Biochem. 210, 931-936]. The good correlation between the calculated ring-current shifts and the observed chemical shifts strongly supports the present assignments. Observation of the two-dimensional nuclear-Overhauser-enhancement spectra of the protein in the reduced, intermediate and fully oxidized stages led to the ordering of the haems in terms of their midpoint redox potentials and their identification in the X-ray structure. The first haem to oxidize is haem I, followed by haems II, III and IV, numbered according to the Cys ligand positions in the amino acid sequences [Mathews (1985) Prog. Biophys. Mol. Biol. 54, 1-56]. Although the haem core architecture is the same for the different Desulfovibrio cytochromes c3, the order of redox potentials is different. PMID:8397514

Curcumin Modulates α-Synuclein Aggregation and Toxicity

PubMed Central

2012-01-01

In human beings, Parkinson’s disease (PD) is associated with the oligomerization and amyloid formation of α-synuclein (α-Syn). The polyphenolic Asian food ingredient curcumin has proven to be effective against a wide range of human diseases including cancers and neurological disorders. While curcumin has been shown to significantly reduce cell toxicity of α-Syn aggregates, its mechanism of action remains unexplored. Here, using a series of biophysical techniques, we demonstrate that curcumin reduces toxicity by binding to preformed oligomers and fibrils and altering their hydrophobic surface exposure. Further, our fluorescence and two-dimensional nuclear magnetic resonance (2D-NMR) data indicate that curcumin does not bind to monomeric α-Syn but binds specifically to oligomeric intermediates. The degree of curcumin binding correlates with the extent of α-Syn oligomerization, suggesting that the ordered structure of protein is required for effective curcumin binding. The acceleration of aggregation by curcumin may decrease the population of toxic oligomeric intermediates of α-Syn. Collectively; our results suggest that curcumin and related polyphenolic compounds can be pursued as candidate drug targets for treatment of PD and other neurological diseases. PMID:23509976

KIFC1-Like Motor Protein Associates with the Cephalopod Manchette and Participates in Sperm Nuclear Morphogenesis in Octopus tankahkeei

PubMed Central

Tan, Fu-Qing; Yang, Wan-Xi

2010-01-01

Background Nuclear morphogenesis is one of the most fundamental cellular transformations taking place during spermatogenesis. In rodents, a microtubule-based perinuclear structure, the manchette, and a C-terminal kinesin motor KIFC1 are believed to play crucial roles in this process. Spermatogenesis in Octopus tankahkeei is a good model system to explore whether evolution has created a cephalopod prototype of mammalian manchette-based and KIFC1-dependent sperm nuclear shaping machinery. Methodology/Principal Findings We detected the presence of a KIFC1-like protein in the testis, muscle, and liver of O. tankahkeei by Western Blot. Then we tracked its dynamic localization in spermatic cells at various stages using Immunofluorescence and Immunogold Electron Microscopy. The KIFC1-like protein was not expressed at early stages of spermatogenesis when no significant morphological changes occur, began to be present in early spermatid, localized around and in the nucleus of intermediate and late spermatids where the nucleus was dramatically elongated and compressed, and concentrated at one end of final spermatid. Furthermore, distribution of the motor protein during nuclear elongation and condensation overlapped with that of the cephalopod counterpart of manchette at a significant level. Conclusions/Significance The results support the assumption that the protein is actively involved in sperm nuclear morphogenesis in O. tankahkeei possibly through bridging the manchette-like perinuclear microtubules to the nucleus and assisting in the nucleocytoplasmic trafficking of specific cargoes. This study represents the first description of the role of a motor protein in sperm nuclear shaping in cephalopod. PMID:21187923

Radical SAM catalysis via an organometallic intermediate with an Fe-[5'-C]-deoxyadenosyl bond.

PubMed

Horitani, Masaki; Shisler, Krista; Broderick, William E; Hutcheson, Rachel U; Duschene, Kaitlin S; Marts, Amy R; Hoffman, Brian M; Broderick, Joan B

2016-05-13

Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to cleave SAM to initiate diverse radical reactions. These reactions are thought to involve the 5'-deoxyadenosyl radical intermediate, which has not yet been detected. We used rapid freeze-quenching to trap a catalytically competent intermediate in the reaction catalyzed by the radical SAM enzyme pyruvate formate-lyase activating enzyme. Characterization of the intermediate by electron paramagnetic resonance and (13)C, (57)Fe electron nuclear double-resonance spectroscopies reveals that it contains an organometallic center in which the 5' carbon of a SAM-derived deoxyadenosyl moiety forms a bond with the unique iron site of the [4Fe-4S] cluster. Discovery of this intermediate extends the list of enzymatic bioorganometallic centers to the radical SAM enzymes, the largest enzyme superfamily known, and reveals intriguing parallels to B12 radical enzymes. Copyright © 2016, American Association for the Advancement of Science.

Final Technical Report - Nuclear Studies with Intermediate Energy Probes

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

Norum, Blaine

During the almost 20 year period of this grant research was carried out on atomic nuclei and their constituents using both photons and electrons. Research was carried out at the electron accelerator facility of the Netherlands Institute for Nuclear and High Energy Physics (NIKHEFK, Amsterdam) until the electron accelerator facility was closed in 1998. Subsequently, research was carried out at the Laser-Electron Gamma Source (LEGS) of the National Synchrotron Light Source (NSLS) located at the Brookhaven National Laboratory (BNL) until the LEGS was closed at the end of 2006. During the next several years research was carried out at bothmore » the Thomas Jefferson National Accelerator Facility (JLAB) and the High Intensity Gamma Source (HIGS) of the Tri-Universities Nuclear Laboratory (TUNL) located on the campus of Duke University. Since approximately 2010 the principal focus was on research at TUNL, although analysis of data from previous research at other facilities continued. The principal early focus of the research was on the role of pions in nuclei. This was studied by studying the production of pions using both photons (at LEGS) and electrons (at NIKHEF-K and JLAB). Measurements of charged pion photoproduction from deuterium at LEGS resulted in the most interesting result of these two decades of work. By measuring the production of a charged pion (p + ) in coincidence with an emitted photon we observed structures in the residual two-nucleon system. These indicated the existence of long-lived states not explicable by standard nuclear theory; they suggest a set of configurations not explicable in terms of a nucleon-nucleon pair. The existence of such “exotic” structures has formed the foundation for most of the work that has ensued.« less

Intraspecific Genetic Admixture and the Morphological Diversification of an Estuarine Fish Population Complex

PubMed Central

Legault, Michel

2015-01-01

The North-east American Rainbow smelt (Osmerus mordax) is composed of two glacial races first identified through the spatial distribution of two distinct mtDNA lineages. Contemporary breeding populations of smelt in the St. Lawrence estuary comprise contrasting mixtures of both lineages, suggesting that the two races came into secondary contact in this estuary. The overall objective of this study was to assess the role of intraspecific genetic admixture in the morphological diversification of the estuarine rainbow smelt population complex. The morphology of mixed-ancestry populations varied as a function of the relative contribution of the two races to estuarine populations, supporting the hypothesis of genetic admixture. Populations comprising both ancestral mtDNA races did not exhibit intermediate morphologies relative to pure populations but rather exhibited many traits that exceeded the parental trait values, consistent with the hypothesis of transgressive segregation. Evidence for genetic admixture at the level of the nuclear gene pool, however, provided only partial support for this hypothesis. Variation at nuclear AFLP markers revealed clear evidence of the two corresponding mtDNA glacial races. The admixture of the two races at the nuclear level is only pronounced in mixed-ancestry populations dominated by one of the mtDNA lineages, the same populations showing the greatest degree of morphological diversification and population structure. In contrast, mixed-ancestry populations dominated by the alternate mtDNA lineage showed little evidence of introgression of the nuclear genome, little morphological diversification and little contemporary population genetic structure. These results only partially support the hypothesis of transgressive segregation and may be the result of the differential effects of natural selection acting on admixed genomes from different sources. PMID:25856193

In medium dispersion relation effects in nuclear inclusive reactions at intermediate and low energies

NASA Astrophysics Data System (ADS)

Nieves, Juan; Sobczyk, Joanna E.

2017-08-01

In a well-established many-body framework, successful in modeling a great variety of nuclear processes, we analyze the role of the spectral functions (SFs) accounting for the modifications of the dispersion relation of nucleons embedded in a nuclear medium. We concentrate in processes mostly governed by one-body mechanisms, and study possible approximations to evaluate the particle-hole propagator using SFs. We also investigate how to include together SFs and long-range RPA-correlation corrections in the evaluation of nuclear response functions, discussing the existing interplay between both type of nuclear effects. At low energy transfers (≤ 50 MeV), we compare our predictions for inclusive muon and radiative pion captures in nuclei, and charge-current (CC) neutrino-nucleus cross sections with experimental results. We also present an analysis of intermediate energy quasi-elastic neutrino scattering for various targets and both neutrino and antineutrino CC driven processes. In all cases, we pay special attention to estimate the uncertainties affecting the theoretical predictions. In particular, we show that errors on the σμ /σe ratio are much smaller than 5%, and also much smaller than the size of the SF+RPA nuclear corrections, which produce significant effects, not only in the individual cross sections, but also in their ratio for neutrino energies below 400 MeV. These latter nuclear corrections, beyond Pauli blocking, turn out to be thus essential to achieve a correct theoretical understanding of this ratio of cross sections of interest for appearance neutrino oscillation experiments. We also briefly compare our SF and RPA results to predictions obtained within other representative approaches.

Cluster Analysis of Time-Dependent Crystallographic Data: Direct Identification of Time-Independent Structural Intermediates

PubMed Central

Kostov, Konstantin S.; Moffat, Keith

2011-01-01

The initial output of a time-resolved macromolecular crystallography experiment is a time-dependent series of difference electron density maps that displays the time-dependent changes in underlying structure as a reaction progresses. The goal is to interpret such data in terms of a small number of crystallographically refinable, time-independent structures, each associated with a reaction intermediate; to establish the pathways and rate coefficients by which these intermediates interconvert; and thereby to elucidate a chemical kinetic mechanism. One strategy toward achieving this goal is to use cluster analysis, a statistical method that groups objects based on their similarity. If the difference electron density at a particular voxel in the time-dependent difference electron density (TDED) maps is sensitive to the presence of one and only one intermediate, then its temporal evolution will exactly parallel the concentration profile of that intermediate with time. The rationale is therefore to cluster voxels with respect to the shapes of their TDEDs, so that each group or cluster of voxels corresponds to one structural intermediate. Clusters of voxels whose TDEDs reflect the presence of two or more specific intermediates can also be identified. From such groupings one can then infer the number of intermediates, obtain their time-independent difference density characteristics, and refine the structure of each intermediate. We review the principles of cluster analysis and clustering algorithms in a crystallographic context, and describe the application of the method to simulated and experimental time-resolved crystallographic data for the photocycle of photoactive yellow protein. PMID:21244840

Elucidation of the Flavonoid Catabolism Pathway in Pseudomonas putida PML2 by Comparative Metabolic Profiling

PubMed Central

Pillai, Bhinu V. S.; Swarup, Sanjay

2002-01-01

Flavonoids are 15-carbon plant secondary metabolites exuded in the rhizosphere that hosts several flavonoid-degrading bacteria. We studied flavonoid catabolism in a plant growth-promoting rhizobacterial strain of Pseudomonas by using a combination of biochemical and genetic approaches. Transposants carrying mini-Tn5gfp insertions were screened for flavonoid auxotrophy, and these mutant strains were found to be unable to grow in the flavonols naringenin and quercetin, while their growth in glycerol was comparable to that of the parental strain. In order to understand flavonoid catabolism, culture supernatants, whole-cell fractions, cell lysate, and cell debris of the wild-type and mutant strains were analyzed. Intermediates that accumulated intracellularly and those secreted in the medium were identified by a combination of reversed-phase high-pressure liquid chromatography and electrospray ionization-mass spectrometry. Structures of four key intermediates were confirmed by one-dimensional nuclear magnetic resonance spectroscopy. Comparative metabolic profiling of the compounds in the wild-type and mutant strains allowed us to understand the degradation events and to identify six metabolic intermediates. The first step in the pathway involves 3,3′-didehydroxylation, followed by hydrolysis and cleavage of the C-ring, leading via subsequent oxidations to the formation of protocatechuate. This is the first report on quercetin dehydroxylation in aerobic conditions leading to naringenin accumulation. PMID:11772620

Characterization of two distinct beta2-microglobulin unfolding intermediates that may lead to amyloid fibrils of different morphology.

PubMed

Armen, Roger S; Daggett, Valerie

2005-12-13

The self-assembly of beta(2)-microglobulin into fibrils leads to dialysis-related amyloidosis. pH-mediated partial unfolding is required for the formation of the amyloidogenic intermediate that then self-assembles into amyloid fibrils. Two partially folded intermediates of beta(2)-microglobulin have been identified experimentally and linked to the formation of fibrils of distinct morphology, yet it remains difficult to characterize these partially unfolded states at high resolution using experimental approaches. Consequently, we have performed molecular dynamics simulations at neutral and low pH to determine the structures of these partially unfolded amyloidogenic intermediates. In the low-pH simulations, we observed the formation of alpha-sheet structure, which was first proposed by Pauling and Corey. Multiple simulations were performed, and two distinct intermediate state ensembles were identified that may account for the different fibril morphologies. The predominant early unfolding intermediate was nativelike in structure, in agreement with previous NMR studies. The late unfolding intermediate was significantly disordered, but it maintained an extended elongated structure, with hydrophobic clusters and residual alpha-extended chain strands in specific regions of the sequence that map to amyloidogenic peptides. We propose that the formation of alpha-sheet facilitates self-assembly into partially unfolded prefibrillar amyloidogenic intermediates.

Crystallographic and spectroscopic snapshots reveal a dehydrogenase in action

DOE PAGES

Huo, Lu; Davis, Ian; Liu, Fange; ...

2015-01-07

Aldehydes are ubiquitous intermediates in metabolic pathways and their innate reactivity can often make them quite unstable. There are several aldehydic intermediates in the metabolic pathway for tryptophan degradation that can decay into neuroactive compounds that have been associated with numerous neurological diseases. An enzyme of this pathway, 2-aminomuconate-6-semialdehyde dehydrogenase, is responsible for ‘disarming’ the final aldehydic intermediate. Here we show the crystal structures of a bacterial analogue enzyme in five catalytically relevant forms: resting state, one binary and two ternary complexes, and a covalent, thioacyl intermediate. We also report the crystal structures of a tetrahedral, thiohemiacetal intermediate, a thioacylmore » intermediate and an NAD +-bound complex from an active site mutant. These covalent intermediates are characterized by single-crystal and solution-state electronic absorption spectroscopy. The crystal structures reveal that the substrate undergoes an E/Z isomerization at the enzyme active site before an sp 3-to-sp 2 transition during enzyme-mediated oxidation.« less

Nuclear microsatellite variation in Malagasy baobabs (Adansonia, Bombacoideae, Malvaceae) reveals past hybridization and introgression

PubMed Central

Leong Pock Tsy, Jean-Michel; Lumaret, Roselyne; Flaven-Noguier, Elodie; Sauve, Mathieu; Dubois, Marie-Pierre; Danthu, Pascal

2013-01-01

Background and Aims Adansonia comprises nine species, six of which are endemic to Madagascar. Genetic relationships between the Malagasy species remain unresolved due to conflicting results between nuclear and plastid DNA variation. Morphologically intermediate individuals between distinct species have been identified, indicative of interspecific hybridization. In this paper, microsatellite data are used to identify potential cases of hybridization and to provide insights into the evolutionary history of the genus on Madagascar. Methods Eleven microsatellites amplified with new primers developed for Adansonia rubrostipa were used to analyse 672 individuals collected at 27 sites for the six Malagasy species and morphologically intermediate individuals. Rates of individual admixture were examined using three Bayesian clustering programs, STRUCTURE, BAPS and NewHybrids, with no a priori species assignment. Key Results Population differentiation was coherent, with recognized species boundaries. In the four Malagasy species of section Longitubae, 8·0, 9·0 and 9·5 % of individuals with mixed genotypes were identified by BAPS, NewHybrids and STRUCTURE, respectively. At sites with sympatric populations of A. rubrostipa and A. za, NewHybrids indicated these individuals to be F2 and, predominantly, backcrosses with both parental species. In northern Madagascar, two populations of trees combining A. za and A. perrieri morphology and microsatellite alleles were identified in the current absence of the parental species. Conclusions The clear genetic differentiation observed between the six species may reflect their adaptation to different assortments of climate regimes and habitats during the colonization of the island. Microsatellite variation reveals that hybridization probably occurred in secondary contact between species of section Longitubae. This type of hybridization may also have been involved in the differentiation of a local new stabilized entity showing specific microsatellite alleles and morphological characters, suggesting a potential role of hybridization in the recent history of diversification on Madagascar. PMID:24187031

Structure of a low-population intermediate state in the release of an enzyme product.

PubMed

De Simone, Alfonso; Aprile, Francesco A; Dhulesia, Anne; Dobson, Christopher M; Vendruscolo, Michele

2015-01-09

Enzymes can increase the rate of biomolecular reactions by several orders of magnitude. Although the steps of substrate capture and product release are essential in the enzymatic process, complete atomic-level descriptions of these steps are difficult to obtain because of the transient nature of the intermediate conformations, which makes them largely inaccessible to standard structure determination methods. We describe here the determination of the structure of a low-population intermediate in the product release process by human lysozyme through a combination of NMR spectroscopy and molecular dynamics simulations. We validate this structure by rationally designing two mutations, the first engineered to destabilise the intermediate and the second to stabilise it, thus slowing down or speeding up, respectively, product release. These results illustrate how product release by an enzyme can be facilitated by the presence of a metastable intermediate with transient weak interactions between the enzyme and product.

Determination of an ensemble of structures representing the intermediate state of the bacterial immunity protein Im7.

PubMed

Gsponer, Joerg; Hopearuoho, Harri; Whittaker, Sara B-M; Spence, Graham R; Moore, Geoffrey R; Paci, Emanuele; Radford, Sheena E; Vendruscolo, Michele

2006-01-03

We present a detailed structural characterization of the intermediate state populated during the folding and unfolding of the bacterial immunity protein Im7. We achieve this result by incorporating a variety of experimental data available for this species in molecular dynamics simulations. First, we define the structure of the exchange-competent intermediate state of Im7 by using equilibrium hydrogen-exchange protection factors. Second, we use this ensemble to predict Phi-values and compare the results with the experimentally determined Phi-values of the kinetic refolding intermediate. Third, we predict chemical-shift measurements and compare them with the measured chemical shifts of a mutational variant of Im7 for which the kinetic folding intermediate is the most stable state populated at equilibrium. Remarkably, we found that the properties of the latter two species are predicted with high accuracy from the exchange-competent intermediate that we determined, suggesting that these three states are characterized by a similar architecture in which helices I, II, and IV are aligned in a native-like, but reorganized, manner. Furthermore, the structural ensemble that we obtained enabled us to rationalize the results of tryptophan fluorescence experiments in the WT protein and a series of mutational variants. The results show that the integration of diverse sets of experimental data at relatively low structural resolution is a powerful approach that can provide insights into the structural organization of this conformationally heterogeneous three-helix intermediate with unprecedented detail and highlight the importance of both native and non-native interactions in stabilizing its structure.

Design and structure of an equilibrium protein folding intermediate: a hint into dynamical regions of proteins.

PubMed

Ayuso-Tejedor, Sara; Angarica, Vladimir Espinosa; Bueno, Marta; Campos, Luis A; Abián, Olga; Bernadó, Pau; Sancho, Javier; Jiménez, M Angeles

2010-07-23

Partly unfolded protein conformations close to the native state may play important roles in protein function and in protein misfolding. Structural analyses of such conformations which are essential for their fully physicochemical understanding are complicated by their characteristic low populations at equilibrium. We stabilize here with a single mutation the equilibrium intermediate of apoflavodoxin thermal unfolding and determine its solution structure by NMR. It consists of a large native region identical with that observed in the X-ray structure of the wild-type protein plus an unfolded region. Small-angle X-ray scattering analysis indicates that the calculated ensemble of structures is consistent with the actual degree of expansion of the intermediate. The unfolded region encompasses discontinuous sequence segments that cluster in the 3D structure of the native protein forming the FMN cofactor binding loops and the binding site of a variety of partner proteins. Analysis of the apoflavodoxin inner interfaces reveals that those becoming destabilized in the intermediate are more polar than other inner interfaces of the protein. Natively folded proteins contain hydrophobic cores formed by the packing of hydrophobic surfaces, while natively unfolded proteins are rich in polar residues. The structure of the apoflavodoxin thermal intermediate suggests that the regions of natively folded proteins that are easily responsive to thermal activation may contain cores of intermediate hydrophobicity. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Identification of persisten anionic surfactant-derived chemicals in sewage effluent and groundwater

USGS Publications Warehouse

Field, J.A.; Leenheer, J.A.; Thorn, K.A.; Barber, L.B.; Rostad, C.; Macalady, D.L.; Daniel, S.R.

1992-01-01

Preparative isolation and fractionation procedures coupled with spectrometric analyses were used to identify surfactant-derived contaminants in sewage effluent and sewage-contaminated groundwater from a site located on Cape Cod, Massachusetts. Anionic surfactants and their biodegradation intermediates were isolated from field samples by ion exchange and fractionated by solvent extraction and adsorption chromatography. Fractions were analyzed by 13C nuclear magnetic resonance spectrometry and gas chromatography-mass spectrometry. Carboxylated residues of alkylphenol polyethoxylate surfactants were detected in sewage effluent and contaminated groundwater. Linear alkylbenzenesulfonates (LAS) were identified in sewage effluent and groundwater. Groundwater LAS composition suggested preferential removal of select isomers and homologs due to processes of biodegradation and partitioning. Tetralin and indane sulfonates (DATS), alicyclic analogs of LAS, were also identified in field samples. Although DATS are a minor portion of LAS formulations, equivalent concentrations of LAS and DATS in groundwater suggested persistence of alicyclic contaminant structures over those of linear structure. Sulfophenyl-carboxylated (SPC) LAS biodegradation intermediates were determined in sewage effluent and groundwater. Homolog distributions suggested that SPC containing 3-10 alkyl-chain carbons persist during infiltration and groundwater transport. Surfactant-derived residues detected in well F300-50 groundwater have a minimum residence time in the range of 2.7-4.6 yr. LAS detected in groundwater at 500 m from infiltration has been stable over an estimated 50-500 half lives.

Identification of persistent anionic surfactant-derived chemicals in sewage effluent and groundwater

USGS Publications Warehouse

Field, Jennifer A.; Leenheer, Jerry A.; Thorn, Kevin A.; Barber, Larry B.; Rostad, Colleen; Macalady, Donald L.; Daniel, Stephen R.

1992-01-01

Preparative isolation and fractionation procedures coupled with spectrometric analyses were used to identify surfactant-derived contaminants in sewage effluent and sewage-contaminated groundwater from a site located on Cape Cod, Massachusetts. Anionic surfactants and their biodegradation intermediates were isolated from field samples by ion exchange and fractionated by solvent extraction and adsorption chromatography. Fractions were analyzed by 13C nuclear magnetic resonance spectrometry and gas chromatography-mass spectrometry. Carboxylated residues of alkylphenol polyethoxylate surfactants were detected in sewage effluent and contaminated groundwater. Linear alkylbenzenesulfonates (LAS) were identified in sewage effluent and groundwater. Groundwater LAS composition suggested preferential removal of select isomers and homologs due to processes of biodegradation and partitioning. Tetralin and indane sulfonates (DATS), alicyclic analogs of LAS, were also identified in field samples. Although DATS are a minor portion of LAS formulations, equivalent concentrations of LAS and DATS in groundwater suggested persistence of alicyclic contaminant structures over those of linear structure. Sulfophenyl-carboxylated (SPC) LAS biodegradation intermediates were determined in sewage effluent and groundwater. Homolog distributions suggested that SPC containing 3–10 alkyl-chain carbons persist during infiltration and groundwater transport. Surfactant-derived residues detected in well F300-50 groundwater have a minimum residence time in the range of 2.7–4.6 yr. LAS detected in groundwater at 500 m from infiltration has been stable over an estimated 50–500 half lives.

Novel ATPase activity of the polyprotein intermediate, Viral Protein genome-linked-Nuclear Inclusion-a protease, of Pepper vein banding potyvirus

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

Mathur, Chhavi; Savithri, Handanahal S., E-mail: bchss@biochem.iisc.ernet.in

2012-10-12

Highlights: Black-Right-Pointing-Pointer Pepper vein banding potyvirus VPg harbors Walker motifs. Black-Right-Pointing-Pointer VPg exhibits ATPase activity in the presence of NIa-Pro. Black-Right-Pointing-Pointer Plausible structural and functional interplay between VPg and NIa-Pro. Black-Right-Pointing-Pointer Functional relevance of prolonged presence of VPg-Pro during infection. -- Abstract: Potyviruses temporally regulate their protein function by polyprotein processing. Previous studies have shown that VPg (Viral Protein genome-linked) of Pepper vein banding virus interacts with the NIa-Pro (Nuclear Inclusion-a protease) domain, and modulates the kinetics of the protease. In the present study, we report for the first time that VPg harbors the Walker motifs A and B, andmore » the presence of NIa-Pro, especially in cis (cleavage site (E191A) VPg-Pro mutant), is essential for manifestation of the ATPase activity. Mutation of Lys47 (Walker motif A) and Asp88:Glu89 (Walker motif B) to alanine in E191A VPg-Pro lead to reduced ATPase activity, confirming that this activity was inherent to VPg. We propose that potyviral VPg, established as an intrinsically disordered domain, undergoes plausible structural alterations upon interaction with globular NIa-Pro which induces the ATPase activity.« less

When transcription goes on Holliday: Double Holliday junctions block RNA polymerase II transcription in vitro.

PubMed

Pipathsouk, Anne; Belotserkovskii, Boris P; Hanawalt, Philip C

2017-02-01

Non-canonical DNA structures can obstruct transcription. This transcription blockage could have various biological consequences, including genomic instability and gratuitous transcription-coupled repair. Among potential structures causing transcription blockage are Holliday junctions (HJs), which can be generated as intermediates in homologous recombination or during processing of stalled replication forks. Of particular interest is the double Holliday junction (DHJ), which contains two HJs. Topological considerations impose the constraint that the total number of helical turns in the DNA duplexes between the junctions cannot be altered as long as the flanking DNA duplexes are intact. Thus, the DHJ structure should strongly resist transient unwinding during transcription; consequently, it is predicted to cause significantly stronger blockage than single HJ structures. The patterns of transcription blockage obtained for RNA polymerase II transcription in HeLa cell nuclear extracts were in accordance with this prediction. However, we did not detect transcription blockage with purified T7 phage RNA polymerase; we discuss a possible explanation for this difference. In general, our findings implicate naturally occurring Holliday junctions in transcription arrest. Copyright © 2016 Elsevier B.V. All rights reserved.

INF and IAEA: A comparative analysis of verification strategy

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

Scheinman, L.; Kratzer, M.

1992-07-01

This is the final report of a study on the relevance and possible lessons of Intermediate Range Nuclear Force (INF) verification to the International Atomic Energy Agency (IAEA) international safeguards activities.

Multiplicity dependence of charged pion, kaon, and (anti)proton production at large transverse momentum in p-Pb collisions at √{sNN} = 5.02 TeV

NASA Astrophysics Data System (ADS)

Adam, J.; Adamová, D.; Aggarwal, M. M.; Aglieri Rinella, G.; Agnello, M.; Agrawal, N.; Ahammed, Z.; Ahmad, S.; Ahn, S. U.; Aiola, S.; Akindinov, A.; Alam, S. N.; Aleksandrov, D.; Alessandro, B.; Alexandre, D.; Alfaro Molina, R.; Alici, A.; Alkin, A.; Almaraz, J. R. M.; Alme, J.; Alt, T.; Altinpinar, S.; Altsybeev, I.; Alves Garcia Prado, C.; Andrei, C.; Andronic, A.; Anguelov, V.; Antičić, T.; Antinori, F.; Antonioli, P.; Aphecetche, L.; Appelshäuser, H.; Arcelli, S.; Arnaldi, R.; Arnold, O. W.; Arsene, I. C.; Arslandok, M.; Audurier, B.; Augustinus, A.; Averbeck, R.; Azmi, M. D.; Badalà, A.; Baek, Y. W.; Bagnasco, S.; Bailhache, R.; Bala, R.; Balasubramanian, S.; Baldisseri, A.; Baral, R. C.; Barbano, A. M.; Barbera, R.; Barile, F.; Barnaföldi, G. G.; Barnby, L. S.; Barret, V.; Bartalini, P.; Barth, K.; Bartke, J.; Bartsch, E.; Basile, M.; Bastid, N.; Basu, S.; Bathen, B.; Batigne, G.; Batista Camejo, A.; Batyunya, B.; Batzing, P. C.; Bearden, I. G.; Beck, H.; Bedda, C.; Behera, N. K.; Belikov, I.; Bellini, F.; Bello Martinez, H.; Bellwied, R.; Belmont, R.; Belmont-Moreno, E.; Belyaev, V.; Benacek, P.; Bencedi, G.; Beole, S.; Berceanu, I.; Bercuci, A.; Berdnikov, Y.; Berenyi, D.; Bertens, R. A.; Berzano, D.; Betev, L.; Bhasin, A.; Bhat, I. R.; Bhati, A. K.; Bhattacharjee, B.; Bhom, J.; Bianchi, L.; Bianchi, N.; Bianchin, C.; Bielčík, J.; Bielčíková, J.; Bilandzic, A.; Biro, G.; Biswas, R.; Biswas, S.; Bjelogrlic, S.; Blair, J. T.; Blau, D.; Blume, C.; Bock, F.; Bogdanov, A.; Bøggild, H.; Boldizsár, L.; Bombara, M.; Book, J.; Borel, H.; Borissov, A.; Borri, M.; Bossú, F.; Botta, E.; Bourjau, C.; Braun-Munzinger, P.; Bregant, M.; Breitner, T.; Broker, T. A.; Browning, T. A.; Broz, M.; Brucken, E. J.; Bruna, E.; Bruno, G. E.; Budnikov, D.; Buesching, H.; Bufalino, S.; Buncic, P.; Busch, O.; Buthelezi, Z.; Butt, J. B.; Buxton, J. T.; Caffarri, D.; Cai, X.; Caines, H.; Calero Diaz, L.; Caliva, A.; Calvo Villar, E.; Camerini, P.; Carena, F.; Carena, W.; Carnesecchi, F.; Castillo Castellanos, J.; Castro, A. J.; Casula, E. A. R.; Ceballos Sanchez, C.; Cerello, P.; Cerkala, J.; Chang, B.; Chapeland, S.; Chartier, M.; Charvet, J. L.; Chattopadhyay, S.; Chattopadhyay, S.; Chauvin, A.; Chelnokov, V.; Cherney, M.; Cheshkov, C.; Cheynis, B.; Chibante Barroso, V.; Chinellato, D. D.; Cho, S.; Chochula, P.; Choi, K.; Chojnacki, M.; Choudhury, S.; Christakoglou, P.; Christensen, C. H.; Christiansen, P.; Chujo, T.; Chung, S. U.; Cicalo, C.; Cifarelli, L.; Cindolo, F.; Cleymans, J.; Colamaria, F.; Colella, D.; Collu, A.; Colocci, M.; Conesa Balbastre, G.; Conesa Del Valle, Z.; Connors, M. E.; Contreras, J. G.; Cormier, T. M.; Corrales Morales, Y.; Cortés Maldonado, I.; Cortese, P.; Cosentino, M. R.; Costa, F.; Crochet, P.; Cruz Albino, R.; Cuautle, E.; Cunqueiro, L.; Dahms, T.; Dainese, A.; Danisch, M. C.; Danu, A.; Das, D.; Das, I.; Das, S.; Dash, A.; Dash, S.; de, S.; de Caro, A.; de Cataldo, G.; de Conti, C.; de Cuveland, J.; de Falco, A.; de Gruttola, D.; De Marco, N.; de Pasquale, S.; Deisting, A.; Deloff, A.; Dénes, E.; Deplano, C.; Dhankher, P.; di Bari, D.; di Mauro, A.; di Nezza, P.; Diaz Corchero, M. A.; Dietel, T.; Dillenseger, P.; Divià, R.; Djuvsland, Ø.; Dobrin, A.; Domenicis Gimenez, D.; Dönigus, B.; Dordic, O.; Drozhzhova, T.; Dubey, A. K.; Dubla, A.; Ducroux, L.; Dupieux, P.; Ehlers, R. J.; Elia, D.; Endress, E.; Engel, H.; Epple, E.; Erazmus, B.; Erdemir, I.; Erhardt, F.; Espagnon, B.; Estienne, M.; Esumi, S.; Eum, J.; Evans, D.; Evdokimov, S.; Eyyubova, G.; Fabbietti, L.; Fabris, D.; Faivre, J.; Fantoni, A.; Fasel, M.; Feldkamp, L.; Feliciello, A.; Feofilov, G.; Ferencei, J.; Fernández Téllez, A.; Ferreiro, E. G.; Ferretti, A.; Festanti, A.; Feuillard, V. J. G.; Figiel, J.; Figueredo, M. A. S.; Filchagin, S.; Finogeev, D.; Fionda, F. M.; Fiore, E. M.; Fleck, M. G.; Floris, M.; Foertsch, S.; Foka, P.; Fokin, S.; Fragiacomo, E.; Francescon, A.; Frankenfeld, U.; Fronze, G. G.; Fuchs, U.; Furget, C.; Furs, A.; Fusco Girard, M.; Gaardhøje, J. J.; Gagliardi, M.; Gago, A. M.; Gallio, M.; Gangadharan, D. R.; Ganoti, P.; Gao, C.; Garabatos, C.; Garcia-Solis, E.; Gargiulo, C.; Gasik, P.; Gauger, E. F.; Germain, M.; Gheata, A.; Gheata, M.; Ghosh, P.; Ghosh, S. K.; Gianotti, P.; Giubellino, P.; Giubilato, P.; Gladysz-Dziadus, E.; Glässel, P.; Goméz Coral, D. M.; Gomez Ramirez, A.; Gonzalez, V.; González-Zamora, P.; Gorbunov, S.; Görlich, L.; Gotovac, S.; Grabski, V.; Grachov, O. A.; Graczykowski, L. K.; Graham, K. L.; Grelli, A.; Grigoras, A.; Grigoras, C.; Grigoriev, V.; Grigoryan, A.; Grigoryan, S.; Grinyov, B.; Grion, N.; Gronefeld, J. M.; Grosse-Oetringhaus, J. F.; Grossiord, J.-Y.; Grosso, R.; Guber, F.; Guernane, R.; Guerzoni, B.; Gulbrandsen, K.; Gunji, T.; Gupta, A.; Gupta, R.; Haake, R.; Haaland, Ø.; Hadjidakis, C.; Haiduc, M.; Hamagaki, H.; Hamar, G.; Hamon, J. C.; Harris, J. W.; Harton, A.; Hatzifotiadou, D.; Hayashi, S.; Heckel, S. T.; Helstrup, H.; Herghelegiu, A.; Herrera Corral, G.; Hess, B. A.; Hetland, K. F.; Hillemanns, H.; Hippolyte, B.; Horak, D.; Hosokawa, R.; Hristov, P.; Huang, M.; Humanic, T. J.; Hussain, N.; Hussain, T.; Hutter, D.; Hwang, D. S.; Ilkaev, R.; Inaba, M.; Incani, E.; Ippolitov, M.; Irfan, M.; Ivanov, M.; Ivanov, V.; Izucheev, V.; Jacazio, N.; Jacobs, P. M.; Jadhav, M. B.; Jadlovska, S.; Jadlovsky, J.; Jahnke, C.; Jakubowska, M. J.; Jang, H. J.; Janik, M. A.; Jayarathna, P. H. S. Y.; Jena, C.; Jena, S.; Jimenez Bustamante, R. T.; Jones, P. G.; Jusko, A.; Kalinak, P.; Kalweit, A.; Kamin, J.; Kang, J. H.; Kaplin, V.; Kar, S.; Karasu Uysal, A.; Karavichev, O.; Karavicheva, T.; Karayan, L.; Karpechev, E.; Kebschull, U.; Keidel, R.; Keijdener, D. L. D.; Keil, M.; Mohisin Khan, M.; Khan, P.; Khan, S. A.; Khanzadeev, A.; Kharlov, Y.; Kileng, B.; Kim, D. W.; Kim, D. J.; Kim, D.; Kim, H.; Kim, J. S.; Kim, M.; Kim, S.; Kim, T.; Kirsch, S.; Kisel, I.; Kiselev, S.; Kisiel, A.; Kiss, G.; Klay, J. L.; Klein, C.; Klein, J.; Klein-Bösing, C.; Klewin, S.; Kluge, A.; Knichel, M. L.; Knospe, A. G.; Kobdaj, C.; Kofarago, M.; Kollegger, T.; Kolojvari, A.; Kondratiev, V.; Kondratyeva, N.; Kondratyuk, E.; Konevskikh, A.; Kopcik, M.; Kostarakis, P.; Kour, M.; Kouzinopoulos, C.; Kovalenko, O.; Kovalenko, V.; Kowalski, M.; Koyithatta Meethaleveedu, G.; Králik, I.; Kravčáková, A.; Kretz, M.; Krivda, M.; Krizek, F.; Kryshen, E.; Krzewicki, M.; Kubera, A. M.; Kučera, V.; Kuhn, C.; Kuijer, P. G.; Kumar, A.; Kumar, J.; Kumar, L.; Kumar, S.; Kurashvili, P.; Kurepin, A.; Kurepin, A. B.; Kuryakin, A.; Kweon, M. J.; Kwon, Y.; La Pointe, S. L.; La Rocca, P.; Ladron de Guevara, P.; Lagana Fernandes, C.; Lakomov, I.; Langoy, R.; Lara, C.; Lardeux, A.; Lattuca, A.; Laudi, E.; Lea, R.; Leardini, L.; Lee, G. R.; Lee, S.; Lehas, F.; Lemmon, R. C.; Lenti, V.; Leogrande, E.; León Monzón, I.; León Vargas, H.; Leoncino, M.; Lévai, P.; Li, S.; Li, X.; Lien, J.; Lietava, R.; Lindal, S.; Lindenstruth, V.; Lippmann, C.; Lisa, M. A.; Ljunggren, H. M.; Lodato, D. F.; Loenne, P. I.; Loginov, V.; Loizides, C.; Lopez, X.; López Torres, E.; Lowe, A.; Luettig, P.; Lunardon, M.; Luparello, G.; Lutz, T. H.; Maevskaya, A.; Mager, M.; Mahajan, S.; Mahmood, S. M.; Maire, A.; Majka, R. D.; Malaev, M.; Maldonado Cervantes, I.; Malinina, L.; Mal'Kevich, D.; Malzacher, P.; Mamonov, A.; Manko, V.; Manso, F.; Manzari, V.; Marchisone, M.; Mareš, J.; Margagliotti, G. V.; Margotti, A.; Margutti, J.; Marín, A.; Markert, C.; Marquard, M.; Martin, N. A.; Martin Blanco, J.; Martinengo, P.; Martínez, M. I.; Martínez García, G.; Martinez Pedreira, M.; Mas, A.; Masciocchi, S.; Masera, M.; Masoni, A.; Massacrier, L.; Mastroserio, A.; Matyja, A.; Mayer, C.; Mazer, J.; Mazzoni, M. A.; McDonald, D.; Meddi, F.; Melikyan, Y.; Menchaca-Rocha, A.; Meninno, E.; Mercado Pérez, J.; Meres, M.; Miake, Y.; Mieskolainen, M. M.; Mikhaylov, K.; Milano, L.; Milosevic, J.; Minervini, L. M.; Mischke, A.; Mishra, A. N.; Miśkowiec, D.; Mitra, J.; Mitu, C. M.; Mohammadi, N.; Mohanty, B.; Molnar, L.; Montaño Zetina, L.; Montes, E.; Moreira de Godoy, D. A.; Moreno, L. A. P.; Moretto, S.; Morreale, A.; Morsch, A.; Muccifora, V.; Mudnic, E.; Mühlheim, D.; Muhuri, S.; Mukherjee, M.; Mulligan, J. D.; Munhoz, M. G.; Munzer, R. H.; Murakami, H.; Murray, S.; Musa, L.; Musinsky, J.; Naik, B.; Nair, R.; Nandi, B. K.; Nania, R.; Nappi, E.; Naru, M. U.; Natal da Luz, H.; Nattrass, C.; Navarro, S. R.; Nayak, K.; Nayak, R.; Nayak, T. K.; Nazarenko, S.; Nedosekin, A.; Nellen, L.; Ng, F.; Nicassio, M.; Niculescu, M.; Niedziela, J.; Nielsen, B. S.; Nikolaev, S.; Nikulin, S.; Nikulin, V.; Noferini, F.; Nomokonov, P.; Nooren, G.; Noris, J. C. C.; Norman, J.; Nyanin, A.; Nystrand, J.; Oeschler, H.; Oh, S.; Oh, S. K.; Ohlson, A.; Okatan, A.; Okubo, T.; Olah, L.; Oleniacz, J.; Oliveira da Silva, A. C.; Oliver, M. H.; Onderwaater, J.; Oppedisano, C.; Orava, R.; Ortiz Velasquez, A.; Oskarsson, A.; Otwinowski, J.; Oyama, K.; Ozdemir, M.; Pachmayer, Y.; Pagano, P.; Paić, G.; Pal, S. K.; Pan, J.; Pandey, A. K.; Papikyan, V.; Pappalardo, G. S.; Pareek, P.; Park, W. J.; Parmar, S.; Passfeld, A.; Paticchio, V.; Patra, R. N.; Paul, B.; Pei, H.; Peitzmann, T.; Pereira da Costa, H.; Peresunko, D.; Pérez Lara, C. E.; Perez Lezama, E.; Peskov, V.; Pestov, Y.; Petráček, V.; Petrov, V.; Petrovici, M.; Petta, C.; Piano, S.; Pikna, M.; Pillot, P.; Pimentel, L. O. D. L.; Pinazza, O.; Pinsky, L.; Piyarathna, D. B.; Płoskoń, M.; Planinic, M.; Pluta, J.; Pochybova, S.; Podesta-Lerma, P. L. M.; Poghosyan, M. G.; Polichtchouk, B.; Poljak, N.; Poonsawat, W.; Pop, A.; Porteboeuf-Houssais, S.; Porter, J.; Pospisil, J.; Prasad, S. K.; Preghenella, R.; Prino, F.; Pruneau, C. A.; Pshenichnov, I.; Puccio, M.; Puddu, G.; Pujahari, P.; Punin, V.; Putschke, J.; Qvigstad, H.; Rachevski, A.; Raha, S.; Rajput, S.; Rak, J.; Rakotozafindrabe, A.; Ramello, L.; Rami, F.; Raniwala, R.; Raniwala, S.; Räsänen, S. S.; Rascanu, B. T.; Rathee, D.; Read, K. F.; Redlich, K.; Reed, R. J.; Rehman, A.; Reichelt, P.; Reidt, F.; Ren, X.; Renfordt, R.; Reolon, A. R.; Reshetin, A.; Revol, J.-P.; Reygers, K.; Riabov, V.; Ricci, R. A.; Richert, T.; Richter, M.; Riedler, P.; Riegler, W.; Riggi, F.; Ristea, C.; Rocco, E.; Rodríguez Cahuantzi, M.; Rodriguez Manso, A.; Røed, K.; Rogochaya, E.; Rohr, D.; Röhrich, D.; Romita, R.; Ronchetti, F.; Ronflette, L.; Rosnet, P.; Rossi, A.; Roukoutakis, F.; Roy, A.; Roy, C.; Roy, P.; Rubio Montero, A. J.; Rui, R.; Russo, R.; Ryabinkin, E.; Ryabov, Y.; Rybicki, A.; Sadovsky, S.; Šafařík, K.; Sahlmuller, B.; Sahoo, P.; Sahoo, R.; Sahoo, S.; Sahu, P. K.; Saini, J.; Sakai, S.; Saleh, M. A.; Salzwedel, J.; Sambyal, S.; Samsonov, V.; Šándor, L.; Sandoval, A.; Sano, M.; Sarkar, D.; Sarma, P.; Scapparone, E.; Scarlassara, F.; Schiaua, C.; Schicker, R.; Schmidt, C.; Schmidt, H. R.; Schuchmann, S.; Schukraft, J.; Schulc, M.; Schuster, T.; Schutz, Y.; Schwarz, K.; Schweda, K.; Scioli, G.; Scomparin, E.; Scott, R.; Šefčík, M.; Seger, J. E.; Sekiguchi, Y.; Sekihata, D.; Selyuzhenkov, I.; Senosi, K.; Senyukov, S.; Serradilla, E.; Sevcenco, A.; Shabanov, A.; Shabetai, A.; Shadura, O.; Shahoyan, R.; Shahzad, M. I.; Shangaraev, A.; Sharma, A.; Sharma, M.; Sharma, M.; Sharma, N.; Shigaki, K.; Shtejer, K.; Sibiriak, Y.; Siddhanta, S.; Sielewicz, K. M.; Siemiarczuk, T.; Silvermyr, D.; Silvestre, C.; Simatovic, G.; Simonetti, G.; Singaraju, R.; Singh, R.; Singha, S.; Singhal, V.; Sinha, B. C.; Sinha, T.; Sitar, B.; Sitta, M.; Skaali, T. B.; Slupecki, M.; Smirnov, N.; Snellings, R. J. M.; Snellman, T. W.; Søgaard, C.; Song, J.; Song, M.; Song, Z.; Soramel, F.; Sorensen, S.; de Souza, R. D.; Sozzi, F.; Spacek, M.; Spiriti, E.; Sputowska, I.; Spyropoulou-Stassinaki, M.; Stachel, J.; Stan, I.; Stankus, P.; Stefanek, G.; Stenlund, E.; Steyn, G.; Stiller, J. H.; Stocco, D.; Strmen, P.; Suaide, A. A. P.; Sugitate, T.; Suire, C.; Suleymanov, M.; Suljic, M.; Sultanov, R.; Šumbera, M.; Szabo, A.; Szanto de Toledo, A.; Szarka, I.; Szczepankiewicz, A.; Szymanski, M.; Tabassam, U.; Takahashi, J.; Tambave, G. J.; Tanaka, N.; Tangaro, M. A.; Tarhini, M.; Tariq, M.; Tarzila, M. G.; Tauro, A.; Tejeda Muñoz, G.; Telesca, A.; Terasaki, K.; Terrevoli, C.; Teyssier, B.; Thäder, J.; Thomas, D.; Tieulent, R.; Timmins, A. R.; Toia, A.; Trogolo, S.; Trombetta, G.; Trubnikov, V.; Trzaska, W. H.; Tsuji, T.; Tumkin, A.; Turrisi, R.; Tveter, T. S.; Ullaland, K.; Uras, A.; Usai, G. L.; Utrobicic, A.; Vajzer, M.; Vala, M.; Valencia Palomo, L.; Vallero, S.; van der Maarel, J.; van Hoorne, J. W.; van Leeuwen, M.; Vanat, T.; Vande Vyvre, P.; Varga, D.; Vargas, A.; Vargyas, M.; Varma, R.; Vasileiou, M.; Vasiliev, A.; Vauthier, A.; Vechernin, V.; Veen, A. M.; Veldhoen, M.; Velure, A.; Venaruzzo, M.; Vercellin, E.; Vergara Limón, S.; Vernet, R.; Verweij, M.; Vickovic, L.; Viesti, G.; Viinikainen, J.; Vilakazi, Z.; Villalobos Baillie, O.; Villatoro Tello, A.; Vinogradov, A.; Vinogradov, L.; Vinogradov, Y.; Virgili, T.; Vislavicius, V.; Viyogi, Y. P.; Vodopyanov, A.; Völkl, M. A.; Voloshin, K.; Voloshin, S. A.; Volpe, G.; von Haller, B.; Vorobyev, I.; Vranic, D.; Vrláková, J.; Vulpescu, B.; Wagner, B.; Wagner, J.; Wang, H.; Wang, M.; Watanabe, D.; Watanabe, Y.; Weber, M.; Weber, S. G.; Weiser, D. F.; Wessels, J. P.; Westerhoff, U.; Whitehead, A. M.; Wiechula, J.; Wikne, J.; Wilk, G.; Wilkinson, J.; Williams, M. C. S.; Windelband, B.; Winn, M.; Yang, H.; Yang, P.; Yano, S.; Yasin, Z.; Yin, Z.; Yokoyama, H.; Yoo, I.-K.; Yoon, J. H.; Yurchenko, V.; Yushmanov, I.; Zaborowska, A.; Zaccolo, V.; Zaman, A.; Zampolli, C.; Zanoli, H. J. C.; Zaporozhets, S.; Zardoshti, N.; Zarochentsev, A.; Závada, P.; Zaviyalov, N.; Zbroszczyk, H.; Zgura, I. S.; Zhalov, M.; Zhang, H.; Zhang, X.; Zhang, Y.; Zhang, C.; Zhang, Z.; Zhao, C.; Zhigareva, N.; Zhou, D.; Zhou, Y.; Zhou, Z.; Zhu, H.; Zhu, J.; Zichichi, A.; Zimmermann, A.; Zimmermann, M. B.; Zinovjev, G.; Zyzak, M.; Alice Collaboration

2016-09-01

The production of charged pions, kaons and (anti)protons has been measured at mid-rapidity (- 0.5 < y < 0) in p-Pb collisions at √{sNN} = 5.02 TeV using the ALICE detector at the LHC. Exploiting particle identification capabilities at high transverse momentum (pT), the previously published pT spectra have been extended to include measurements up to 20 GeV/c for seven event multiplicity classes. The pT spectra for pp collisions at √{ s} = 7 TeV, needed to interpolate a pp reference spectrum, have also been extended up to 20 GeV/c to measure the nuclear modification factor (RpPb) in non-single diffractive p-Pb collisions. At intermediate transverse momentum (2 10 GeV / c), the particle ratios are consistent with those reported for pp and Pb-Pb collisions at the LHC energies. At intermediate pT the (anti)proton RpPb shows a Cronin-like enhancement, while pions and kaons show little or no nuclear modification. At high pT the charged pion, kaon and (anti)proton RpPb are consistent with unity within statistical and systematic uncertainties.

Multiplicity dependence of charged pion, kaon, and (anti)proton production at large transverse momentum in p–Pb collisions at s NN = 5.02  TeV

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

Adam, J.; Adamová, D.; Aggarwal, M. M.

The production of charged pions, kaons and (anti)protons has been measured at mid-rapidity (-0.5 < y < 0) in p–Pb collisions at s NN =5.02 TeV using the ALICE detector at the LHC. Exploiting particle identification capabilities at high transverse momentum (p T ), the previously published p T spectra have been extended to include measurements up to 20 GeV/c for seven event multiplicity classes. The p T spectra for pp collisions at s=7 TeV, needed to interpolate a pp reference spectrum, have also been extended up to 20 GeV/c to measure the nuclear modification factor (R pPb ) in non-single diffractivemore » p–Pb collisions. At intermediate transverse momentum (2 < p T < 10 GeV/c) the proton-to-pion ratio increases with multiplicity in p–Pb collisions, a similar effect is not present in the kaon-to-pion ratio. The p T dependent structure of such increase is qualitatively similar to those observed in pp and heavy-ion collisions. At high p T ( > 10 GeV/c), the particle ratios are consistent with those reported for pp and Pb–Pb collisions at the LHC energies. At intermediate p T the (anti)proton R pPb shows a Cronin-like enhancement, while pions and kaons show little or no nuclear modification. At high p T the charged pion, kaon and (anti)proton R pPb are consistent with unity within statistical and systematic uncertainties.« less

Multiplicity dependence of charged pion, kaon, and (anti)proton production at large transverse momentum in p–Pb collisions at s NN = 5.02  TeV

DOE PAGES

Adam, J.; Adamová, D.; Aggarwal, M. M.; ...

2016-07-22

The production of charged pions, kaons and (anti)protons has been measured at mid-rapidity (-0.5 < y < 0) in p–Pb collisions at s NN =5.02 TeV using the ALICE detector at the LHC. Exploiting particle identification capabilities at high transverse momentum (p T ), the previously published p T spectra have been extended to include measurements up to 20 GeV/c for seven event multiplicity classes. The p T spectra for pp collisions at s=7 TeV, needed to interpolate a pp reference spectrum, have also been extended up to 20 GeV/c to measure the nuclear modification factor (R pPb ) in non-single diffractivemore » p–Pb collisions. At intermediate transverse momentum (2 < p T < 10 GeV/c) the proton-to-pion ratio increases with multiplicity in p–Pb collisions, a similar effect is not present in the kaon-to-pion ratio. The p T dependent structure of such increase is qualitatively similar to those observed in pp and heavy-ion collisions. At high p T ( > 10 GeV/c), the particle ratios are consistent with those reported for pp and Pb–Pb collisions at the LHC energies. At intermediate p T the (anti)proton R pPb shows a Cronin-like enhancement, while pions and kaons show little or no nuclear modification. At high p T the charged pion, kaon and (anti)proton R pPb are consistent with unity within statistical and systematic uncertainties.« less

Separate roles for chromatin and lamins in nuclear mechanics.

PubMed

Stephens, Andrew D; Banigan, Edward J; Marko, John F

2018-01-01

The cell nucleus houses, protects, and arranges the genome within the cell. Therefore, nuclear mechanics and morphology are important for dictating gene regulation, and these properties are perturbed in many human diseases, such as cancers and progerias. The field of nuclear mechanics has long been dominated by studies of the nuclear lamina, the intermediate filament shell residing just beneath the nuclear membrane. However, a growing body of work shows that chromatin and chromatin-related factors within the nucleus are an essential part of the mechanical response of the cell nucleus to forces. Recently, our group demonstrated that chromatin and the lamina provide distinct mechanical contributions to nuclear mechanical response. The lamina is indeed important for robust response to large, whole-nucleus stresses, but chromatin dominates the short-extension response. These findings offer a clarifying perspective on varied nuclear mechanics measurements and observations, and they suggest several new exciting possibilities for understanding nuclear morphology, organization, and mechanics.

Ionization cross section, pressure shift and isotope shift measurements of osmium

NASA Astrophysics Data System (ADS)

Hirayama, Yoshikazu; Mukai, Momo; Watanabe, Yutaka; Oyaizu, Michihiro; Ahmed, Murad; Kakiguchi, Yutaka; Kimura, Sota; Miyatake, Hiroari; Schury, Peter; Wada, Michiharu; Jeong, Sun-Chan

2017-11-01

In-gas-cell laser resonance ionization spectroscopy of neutral osmium atoms was performed with the use of a two-color two-step laser resonance ionization technique. Saturation curves for the ionization scheme were measured, and the ionization cross section was experimentally determined by solving the rate equations for the ground, intermediate and ionization continuum populations. The pressure shift and pressure broadening in the resonance spectra of the excitation transition were measured. The electronic factor {F}247 for the transition {λ }1=247.7583 nm to the intermediate state was deduced from the measured isotope shifts of stable {}{188,189,{190,192}}Os isotopes. The efficient ionization scheme, pressure shift, nuclear isotope shift and {F}247 are expected to be useful for applications of laser ion sources to unstable nuclei and for nuclear spectroscopy based on laser ionization techniques.

Report of the Defense Science Board Task Force on Nuclear Deterrence Skills

DTIC Science & Technology

2008-09-01

entail modeling and simulation capability analogous to that for weapon design. A minimum “national” nuclear weapons effects simulator enterprise...systems programs (design, develop, produce, deploy, and sustain) relies 18 I C HA P TE R 3 upon a variety of management models . For example, the Air...entry vehicle design, modeling and simulation efforts, command and control, launch system infrastructure, intermediate-range missile concepts, advanced

Cross section for the subthreshold fission of 236U

NASA Astrophysics Data System (ADS)

Alekseev, A. A.; Bergman, A. A.; Berlev, A. I.; Koptelov, E. A.; Samylin, B. F.; Trufanov, A. M.; Fursov, B. I.; Shorin, V. S.

2008-08-01

The cross section for 236U fission in the neutron-energy range E n = 0.001 20 keV was measured by using the INR RAS (Institute of Nuclear Research, Russian Academy of Sciences, Moscow) LSDS-100 neutron spectrometer of the lead slowing-down spectrometer type. The resonance fission areas of the resonances at 5.45 eV and 1.28 keV were found, and the fission widths of these resonances were evaluated. The cross section for the 238U( n, f) fission process was measured, and the threshold sensitivity of the LSDS-100 to small values of fission cross sections was estimated. The well-known intermediate structure in the cross section for the neutron-induced subbarrier fission of 236U was confirmed.

INF and IAEA: A comparative analysis of verification strategy. [Final report

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

Scheinman, L.; Kratzer, M.

1992-07-01

This is the final report of a study on the relevance and possible lessons of Intermediate Range Nuclear Force (INF) verification to the International Atomic Energy Agency (IAEA) international safeguards activities.

Kinetically trapped metastable intermediate of a disulfide-deficient mutant of the starch-binding domain of glucoamylase.

PubMed

Sugimoto, Hayuki; Nakaura, Miho; Nishimura, Shigenori; Karita, Shuichi; Miyake, Hideo; Tanaka, Akiyoshi

2009-08-01

Refolding of a thermally unfolded disulfide-deficient mutant of the starch-binding domain of glucoamylase was investigated using differential scanning calorimetry, isothermal titration calorimetry, CD, and (1)H NMR. When the protein solution was rapidly cooled from a higher temperature, a kinetic intermediate was formed during refolding. The intermediate was unexpectedly stable compared with typical folding intermediates that have short half-lives. It was shown that this intermediate contained substantial secondary structure and tertiary packing and had the same binding ability with beta-cyclodextrin as the native state, suggesting that the intermediate is highly-ordered and native-like on the whole. These characteristics differ from those of partially folded intermediates such as molten globule states. Far-UV CD spectra showed that the secondary structure was once disrupted during the transition from the intermediate to the native state. These results suggest that the intermediate could be an off-pathway type, possibly a misfolded state, that has to undergo unfolding on its way to the native state.

Nuclear localization of the DNA repair scaffold XRCC1: Uncovering the functional role of a bipartite NLS

DOE PAGES

Kirby, Thomas W.; Gassman, Natalie R.; Smith, Cassandra E.; ...

2015-08-25

We have characterized the nuclear localization signal (NLS) of XRCC1 structurally using X-ray crystallography and functionally using fluorescence imaging. Crystallography and binding studies confirm the bipartite nature of the XRCC1 NLS interaction with Importin α (Impα) in which the major and minor binding motifs are separated by >20 residues, and resolve previous inconsistent determinations. Binding studies of peptides corresponding to the bipartite NLS, as well as its major and minor binding motifs, to both wild-type and mutated forms of Impα reveal pronounced cooperative binding behavior that is generated by the proximity effect of the tethered major and minor motifs ofmore » the NLS. The cooperativity stems from the increased local concentration of the second motif near its cognate binding site that is a consequence of the stepwise binding behavior of the bipartite NLS. We predict that the stepwise dissociation of the NLS from Impα facilitates unloading by providing a partially complexed intermediate that is available for competitive binding by Nup50 or the Importin β binding domain. This behavior gives a basis for meeting the intrinsically conflicting high affinity and high flux requirements of an efficient nuclear transport system.« less

Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR

PubMed Central

NISHIMURA, Chiaki

2017-01-01

The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H. The improved strategy for the analysis of the kinetic intermediate was developed to include (1) the dimethyl sulfoxide method, (2) data processing with the various labeling times, and (3) a new in-house mixer. Particularly, the rapid mixing revealed that helices A and G were significantly more protected at the earlier stage (400 µs) of the intermediate (former-phase intermediate) than the other helices. Mutation studies, where each hydrophobic residue was replaced with an alanine in helices A, B, E, F, G and H, indicated that both non-native and native-like structures exist in the latter-phase folding intermediate. The N-terminal part of helix B is a weak point in the intermediate, and the docking of helix E residues to the core of the A, B, G and H helices was interrupted by a premature helix B, resulting in the accumulation of the intermediate composed of helices A, B, G and H. The prediction-based protein engineering produced important mutants: Helix F in a P88K/A90L/S92K/A94L mutant folded in the latter-phase intermediate, although helix F in the wild type does not fold even at the native state. Furthermore, in the L11G/W14G/A70L/G73W mutant, helix A did not fold but helix E did, which is similar to what was observed in the kinetic intermediate of apoleghemoglobin. Thus, this protein engineering resulted in a changed structure for the apomyoglobin folding intermediate. PMID:28077807

Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR.

PubMed

Nishimura, Chiaki

2017-01-01

The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H. The improved strategy for the analysis of the kinetic intermediate was developed to include (1) the dimethyl sulfoxide method, (2) data processing with the various labeling times, and (3) a new in-house mixer. Particularly, the rapid mixing revealed that helices A and G were significantly more protected at the earlier stage (400 µs) of the intermediate (former-phase intermediate) than the other helices. Mutation studies, where each hydrophobic residue was replaced with an alanine in helices A, B, E, F, G and H, indicated that both non-native and native-like structures exist in the latter-phase folding intermediate. The N-terminal part of helix B is a weak point in the intermediate, and the docking of helix E residues to the core of the A, B, G and H helices was interrupted by a premature helix B, resulting in the accumulation of the intermediate composed of helices A, B, G and H. The prediction-based protein engineering produced important mutants: Helix F in a P88K/A90L/S92K/A94L mutant folded in the latter-phase intermediate, although helix F in the wild type does not fold even at the native state. Furthermore, in the L11G/W14G/A70L/G73W mutant, helix A did not fold but helix E did, which is similar to what was observed in the kinetic intermediate of apoleghemoglobin. Thus, this protein engineering resulted in a changed structure for the apomyoglobin folding intermediate.

Applications of Multiple Nuclear Genes to the Molecular Phylogeny, Population Genetics and Hybrid Identification in the Mangrove Genus Rhizophora.

PubMed

Chen, Yongmei; Hou, Yansong; Guo, Zixiao; Wang, Wenqing; Zhong, Cairong; Zhou, Renchao; Shi, Suhua

2015-01-01

The genus Rhizophora is one of the most important components of mangrove forests. It is an ideal system for studying biogeography, molecular evolution, population genetics, hybridization and conservation genetics of mangroves. However, there are no sufficient molecular markers to address these topics. Here, we developed 77 pairs of nuclear gene primers, which showed successful PCR amplifications across all five Rhizophora species and sequencing in R. apiculata. Here, we present three tentative applications using a subset of the developed nuclear genes to (I) reconstruct the phylogeny, (II) examine the genetic structure and (III) identify natural hybridization in Rhizophora. Phylogenetic analyses support the hypothesis that Rhizophora had disappeared in the Atlantic-East Pacific (AEP) region and was re-colonized from the IWP region approximately 12.7 Mya. Population genetics analyses in four natural populations of R. apiculata in Hainan, China, revealed extremely low genetic diversity, strong population differentiation and extensive admixture, suggesting that the Pleistocene glaciations, particularly the last glacial maximum, greatly influenced the population dynamics of R. apiculata in Hainan. We also verified the hybrid status of a morphologically intermediate individual between R. apiculata and R. stylosa in Hainan. Based on the sequences of five nuclear genes and one chloroplast intergenic spacer, this individual is likely to be an F1 hybrid, with R. stylosa as its maternal parent. The nuclear gene markers developed in this study should be of great value for characterizing the hybridization and introgression patterns in other cases of this genus and testing the role of natural selection using population genomics approaches.

Intranuclear inclusions of meningioma associated with abnormal cytoskeletal protein expression.

PubMed

Yoshida, T; Hirato, J; Sasaki, A; Yokoo, H; Nakazato, Y; Kurachi, H

1999-01-01

We describe a case of meningothelial meningioma with a large number of intranuclear inclusions. Morphologically, these are divided into cytoplasmic inclusions and nuclear vacuoles. The cytoplasmic inclusion has a limiting membrane with cell organelles and filaments. Inclusions of this type are generally eosinophilic, like the cytoplasm. However, there are many inclusions that are more eosinophilic than the cytoplasm or that have a ground-glass appearance. Some of them may contain fine or coarse granules. On the other hand, the nuclear vacuole lacks a limiting membrane and appears empty. In most of the inclusions of this type, there is a faintly basophilic substance in the margin. Generally, the cytoplasmic inclusions are as immunopositive as cytoplasm with vimentin, but some of these cytoplasmic inclusions are more reactive. Under the electron microscope, abnormal aggregation of intermediate filaments is recognized in the cytoplasmic inclusions. It is considered that a strong reaction of cytoplasmic inclusions with vimentin immunostaining is due to abnormal aggregation of intermediate filaments. The present study distinctly demonstrates abnormal localization of intermediate filaments in the cytoplasmic inclusions, and it is suggested that the cytoskeleton participates in the evolution of the cytoplasmic inclusions.

Cooperative alpha-helix formation of beta-lactoglobulin induced by sodium n-alkyl sulfates.

PubMed

Chamani, J; Moosavi-Movahedi, A A; Rajabi, O; Gharanfoli, M; Momen-Heravi, M; Hakimelahi, G H; Neamati-Baghsiah, A; Varasteh, A R

2006-01-01

It is generally assumed that folding intermediates contain partially formed native-like secondary structures. However, if we consider the fact that the conformational stability of the intermediate state is simpler than that of the native state, it would be expected that the secondary structures in a folding intermediate would not necessarily be similar to those of the native state. beta-Lactoglobulin is a predominantly beta-sheet protein, although it has a markedly high intrinsic preference for alpha-helical structure. The formation of non-native alpha-helical intermediate of beta-lactoglobulin was induced by n-alkyl sulfates including sodium octyl sulfate, SOS; sodium decyl sulfate, SDeS; sodium dodecyl sulfate, SDS; and sodium tetradecyl sulfate, STS at special condition. The effect of n-alkyl sulfates on the structure of native beta-lactoglobulin at pH 2 was utilized to investigate the contribution of hydrophobic interactions to the stability of non-native alpha-helical intermediate. The addition of various concentrations of n-alkyl sulfates to the native state of beta-lactoglobulin (pH 2) appears to support the stabilized form of non-native alpha-helical intermediate at pH 2. The m values of the intermediate state of beta-lactoglobulin by SOS, SDeS, SDS and STS showed substantial variation. The enhancement of m values as the stability criterion of non-native alpha-helical intermediate state corresponded with increasing chain length of the cited n-alkyl sulfates. The present results suggest that the folding reaction of beta-lactoglobulin follows a non-hierarchical mechanism and hydrophobic interactions play important roles in stabilizing the non-native alpha-helical intermediate state.

Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase

DOE PAGES

Knoot, Cory J.; Purpero, Vincent M.; Lipscomb, John D.

2014-12-29

Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe 3+ to activate O 2 and catecholic substrates for reaction. The inability of Fe 3+ to directly bind O 2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated in this paper using the alternative substrate 4-fluorocatechol. This substrate is found to slow the reaction at several steps throughout the mechanistic cycle, allowing the intermediates to be detected in solution studies. When the reaction was initiated in an enzyme crystal, it was found to halt at one of two intermediates depending on the pH of the surroundingmore » solution. The X-ray crystal structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe 3+ species, and the anhydride-Fe 3+ intermediate was found for a crystal reacted at pH 8.5. Intermediates of these types have not been structurally characterized for intradiol dioxygenases, and they validate four decades of spectroscopic, kinetic, and computational studies. In contrast to our similar in crystallo crystallographic studies of an Fe 2+-containing extradiol dioxygenase, no evidence for a superoxo or peroxo intermediate preceding the alkylperoxo was found. This observation and the lack of spectroscopic evidence for an Fe 2+ intermediate that could bind O 2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Finally, structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage.« less

CONSIDERATION OF REACTION INTERMEDIATES IN STRUCTURE-ACTIVITY RELATIONSHIPS: A KEY TO UNDERSTANDING AND PREDICTION

EPA Science Inventory

Consideration of Reaction Intermediates in Structure- Activity Relationships: A Key to Understanding and Prediction

A structure-activity relationship (SAR) represents an empirical means for generalizing chemical information relative to biological activity, and is frequent...

Vertical nanopillars for in situ probing of nuclear mechanics in adherent cells

PubMed Central

Hanson, Lindsey; Zhao, Wenting; Lou, Hsin-Ya; Lin, Ziliang Carter; Lee, Seok Woo; Chowdary, Praveen; Cui, Yi; Cui, Bianxiao

2016-01-01

The mechanical stability and deformability of the cell nucleus are crucial to many biological processes, including migration, proliferation and polarization. In vivo, the cell nucleus is frequently subjected to deformation on a variety of length and time scales, but current techniques for studying nuclear mechanics do not provide access to subnuclear deformation in live functioning cells. Here we introduce arrays of vertical nanopillars as a new method for the in situ study of nuclear deformability and the mechanical coupling between the cell membrane and the nucleus in live cells. Our measurements show that nanopillar-induced nuclear deformation is determined by nuclear stiffness, as well as opposing effects from actin and intermediate filaments. Furthermore, the depth, width and curvature of nuclear deformation can be controlled by varying the geometry of the nanopillar array. Overall, vertical nanopillar arrays constitute a novel approach for non-invasive, subcellular perturbation of nuclear mechanics and mechanotransduction in live cells. PMID:25984833

The experimental nuclear reaction data (EXFOR): Extended computer database and Web retrieval system

DOE PAGES

Zerkin, V. V.; Pritychenko, B.

2018-02-04

The EXchange FORmat (EXFOR) experimental nuclear reaction database and the associated Web interface provide access to the wealth of low- and intermediate-energy nuclear reaction physics data. This resource is based on numerical data sets and bibliographical information of ~22,000 experiments since the beginning of nuclear science. The principles of the computer database organization, its extended contents and Web applications development are described. New capabilities for the data sets uploads, renormalization, covariance matrix, and inverse reaction calculations are presented in this paper. The EXFOR database, updated monthly, provides an essential support for nuclear data evaluation, application development, and research activities. Finally,more » it is publicly available at the websites of the International Atomic Energy Agency Nuclear Data Section, http://www-nds.iaea.org/exfor, the U.S. National Nuclear Data Center, http://www.nndc.bnl.gov/exfor, and the mirror sites in China, India and Russian Federation.« less

The experimental nuclear reaction data (EXFOR): Extended computer database and Web retrieval system

NASA Astrophysics Data System (ADS)

Zerkin, V. V.; Pritychenko, B.

2018-04-01

The EXchange FORmat (EXFOR) experimental nuclear reaction database and the associated Web interface provide access to the wealth of low- and intermediate-energy nuclear reaction physics data. This resource is based on numerical data sets and bibliographical information of ∼22,000 experiments since the beginning of nuclear science. The principles of the computer database organization, its extended contents and Web applications development are described. New capabilities for the data sets uploads, renormalization, covariance matrix, and inverse reaction calculations are presented. The EXFOR database, updated monthly, provides an essential support for nuclear data evaluation, application development, and research activities. It is publicly available at the websites of the International Atomic Energy Agency Nuclear Data Section, http://www-nds.iaea.org/exfor, the U.S. National Nuclear Data Center, http://www.nndc.bnl.gov/exfor, and the mirror sites in China, India and Russian Federation.

The experimental nuclear reaction data (EXFOR): Extended computer database and Web retrieval system

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

Zerkin, V. V.; Pritychenko, B.

The EXchange FORmat (EXFOR) experimental nuclear reaction database and the associated Web interface provide access to the wealth of low- and intermediate-energy nuclear reaction physics data. This resource is based on numerical data sets and bibliographical information of ~22,000 experiments since the beginning of nuclear science. The principles of the computer database organization, its extended contents and Web applications development are described. New capabilities for the data sets uploads, renormalization, covariance matrix, and inverse reaction calculations are presented in this paper. The EXFOR database, updated monthly, provides an essential support for nuclear data evaluation, application development, and research activities. Finally,more » it is publicly available at the websites of the International Atomic Energy Agency Nuclear Data Section, http://www-nds.iaea.org/exfor, the U.S. National Nuclear Data Center, http://www.nndc.bnl.gov/exfor, and the mirror sites in China, India and Russian Federation.« less

Complex chromatin condensation patterns and nuclear protein transitions during spermiogenesis: examples from mollusks.

PubMed

Chiva, M; Saperas, N; Ribes, E

2011-12-01

In this paper we review and analyze the chromatin condensation pattern during spermiogenesis in several species of mollusks. Previously, we had described the nuclear protein transitions during spermiogenesis in these species. The results of our study show two types of condensation pattern: simple patterns and complex patterns, with the following general characteristics: (a) When histones (always present in the early spermatid nucleus) are directly replaced by SNBP (sperm nuclear basic proteins) of the protamine type, the spermiogenic chromatin condensation pattern is simple. However, if the replacement is not direct but through intermediate proteins, the condensation pattern is complex. (b) The intermediate proteins found in mollusks are precursor molecules that are processed during spermiogenesis to the final protamine molecules. Some of these final protamines represent proteins with the highest basic amino acid content known to date, which results in the establishment of a very strong electrostatic interaction with DNA. (c) In some instances, the presence of complex patterns of chromatin condensation clearly correlates with the acquisition of specialized forms of the mature sperm nuclei. In contrast, simple condensation patterns always lead to rounded, oval or slightly cylindrical nuclei. (d) All known cases of complex spermiogenic chromatin condensation patterns are restricted to species with specialized sperm cells (introsperm). At the time of writing, we do not know of any report on complex condensation pattern in species with external fertilization and, therefore, with sperm cells of the primitive type (ect-aquasperm). (e) Some of the mollusk an spermiogenic chromatin condensation patterns of the complex type are very similar (almost identical) to those present in other groups of animals. Interestingly, the intermediate proteins involved in these cases can be very different.In this study, we discuss the biological significance of all these features and conclude that the appearance of precursor (intermediate) molecules facilitated the development of complex patterns of condensation and, as a consequence, a great diversity of forms in the sperm cell nuclei Copyright © 2011 Elsevier Ltd. All rights reserved.

NUCLEAR FLASH TYPE STEAM GENERATOR

DOEpatents

Johns, F.L.; Gronemeyer, E.C.; Dusbabek, M.R.

1962-09-01

A nuclear steam generating apparatus is designed so that steam may be generated from water heated directly by the nuclear heat source. The apparatus comprises a pair of pressure vessels mounted one within the other, the inner vessel containing a nuclear reactor heat source in the lower portion thereof to which water is pumped. A series of small ports are disposed in the upper portion of the inner vessel for jetting heated water under pressure outwardly into the atmosphere within the interior of the outer vessel, at which time part of the jetted water flashes into steam. The invention eliminates the necessity of any intermediate heat transfer medium and components ordinarily required for handling that medium. (AEC)

Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values.

PubMed

Geierhaas, Christian D; Salvatella, Xavier; Clarke, Jane; Vendruscolo, Michele

2008-03-01

It has been suggested that Phi-values, which allow structural information about transition states (TSs) for protein folding to be obtained, are most reliably interpreted when divided into three classes (high, medium and low). High Phi-values indicate almost completely folded regions in the TS, intermediate Phi-values regions with a detectable amount of structure and low Phi-values indicate mostly unstructured regions. To explore the extent to which this classification can be used to characterise in detail the structure of TSs for protein folding, we used Phi-values divided into these classes as restraints in molecular dynamics simulations. This type of procedure is related to that used in NMR spectroscopy to define the structure of native proteins from the measurement of inter-proton distances derived from nuclear Overhauser effects. We illustrate this approach by determining the TS ensembles of five proteins and by showing that the results are similar to those obtained by using as restraints the actual numerical Phi-values measured experimentally. Our results indicate that the simultaneous consideration of a set of low-resolution Phi-values can provide sufficient information for characterising the architecture of a TS for folding of a protein.

Characterisation of transition state structures for protein folding using ‘high’, ‘medium’ and ‘low’ Φ-values

PubMed Central

Geierhaas, Christian D.; Salvatella, Xavier; Clarke, Jane; Vendruscolo, Michele

2008-01-01

It has been suggested that Φ-values, which allow structural information about transition states (TSs) for protein folding to be obtained, are most reliably interpreted when divided into three classes (high, medium and low). High Φ-values indicate almost completely folded regions in the TS, intermediate Φ-values regions with a detectable amount of structure and low Φ-values indicate mostly unstructured regions. To explore the extent to which this classification can be used to characterise in detail the structure of TSs for protein folding, we used Φ-values divided into these classes as restraints in molecular dynamics simulations. This type of procedure is related to that used in NMR spectroscopy to define the structure of native proteins from the measurement of inter-proton distances derived from nuclear Overhauser effects. We illustrate this approach by determining the TS ensembles of five proteins and by showing that the results are similar to those obtained by using as restraints the actual numerical Φ-values measured experimentally. Our results indicate that the simultaneous consideration of a set of low-resolution Φ-values can provide sufficient information for characterising the architecture of a TS for folding of a protein. PMID:18299294

Structural evolution of the methane cation in subfemtosecond photodynamics

NASA Astrophysics Data System (ADS)

Mondal, T.; Varandas, A. J. C.

2015-07-01

An ab initio quantum dynamics study has been performed to explore the structural rearrangement of ground state CH 4+ in subfemtosecond resolved photodynamics. The method utilizes time-dependent wave-packet propagation on the X ˜ 2 T 2 electronic manifold of the title cation in full dimensionality, including nonadiabatic coupling of the three electronic sheets. Good agreement is obtained with recent experiments [Baker et al., Science 312, 424 (2006)] which use high-order harmonic generation to probe the attosecond proton dynamics. The novel results provide direct theoretical support of the observations while unravelling the underlying details. With the geometrical changes obtained by calculating the expectation values of the nuclear coordinates as a function of time, the structural evolution is predicted to begin through activation of the totally symmetric a1 and doubly degenerate e modes. While the former retains the original Td symmetry of the cation, the Jahn-Teller active e mode conducts it to a D2d structure. At ˜1.85 fs, the intermediate D2d structure is further predicted to rearrange to local C2v minimum geometry via Jahn-Teller active bending vibrations of t2 symmetry.

Correlation between structure and physical properties of chalcogenide glasses in the AsxSe1-x system

NASA Astrophysics Data System (ADS)

Yang, Guang; Bureau, Bruno; Rouxel, Tanguy; Gueguen, Yann; Gulbiten, Ozgur; Roiland, Claire; Soignard, Emmanuel; Yarger, Jeffery L.; Troles, Johann; Sangleboeuf, Jean-Christophe; Lucas, Pierre

2010-11-01

Physical properties of chalcogenide glasses in the AsxSe1-x system have been measured as a function of composition including the Young’s modulus E , shear modulus G , bulk modulus K , Poisson’s ratio ν , the density ρ , and the glass transition Tg . All these properties exhibit a relatively sharp extremum at the average coordination number ⟨r⟩=2.4 . The structural origin of this trend is investigated by Raman spectroscopy and nuclear magnetic resonance. It is shown that the reticulation of the glass structure increases continuously until x=0.4 following the “chain crossing model” and then undergoes a transition toward a lower dimension pyramidal network containing an increasing number of molecular inclusions at x>0.4 . Simple theoretical estimates of the network bonding energy confirm a mismatch between the values of mechanical properties measured experimentally and the values predicted from a continuously reticulated structure, therefore corroborating the formation of a lower dimension network at high As content. The evolution of a wide range of physical properties is consistent with this sharp structural transition and suggests that there is no intermediate phase in these glasses at room temperature.

Model Independent Determination of Electron Fraction for Individual SNIa

NASA Astrophysics Data System (ADS)

De, Soma; Timmes, F.; Hawley, W.; Chamulak, D.; Athanassiadou, T.; Jack, D.; Calder, A.; Brown, E.; Townsley, D.

2013-01-01

Ye of individual supernova Type Ia at the time of explosion by using the silicon, sulfur, and calcium features from single epoch and multi-epoch spectra near maximum light. Most one-dimensional Chandrasekhar mass models of supernova Type Ia in the single-degenerate scenario produce their intermediate-mass elements in a burn to quasi-nuclear statistical equilibrium between the mass shells 0.8 and 1.1 M. We find a near linear dependence of the intermediate-mass element nuclear yields on the white dwarf’s initial metallicity from such SNe Ia explosion models, and the effect this dependence has on synthetic spectra near maximum light. We demonstrate that these metallicity signatures are only due to material achieving the necessary thermodynamic conditions. In addition, we find that global abundance of silicon is insensitive to change in metallicity but sulfur and calcium abundances change significantly

Novel origin of lamin-derived cytoplasmic intermediate filaments in tardigrades.

PubMed

Hering, Lars; Bouameur, Jamal-Eddine; Reichelt, Julian; Magin, Thomas M; Mayer, Georg

2016-02-03

Intermediate filament (IF) proteins, including nuclear lamins and cytoplasmic IF proteins, are essential cytoskeletal components of bilaterian cells. Despite their important role in protecting tissues against mechanical force, no cytoplasmic IF proteins have been convincingly identified in arthropods. Here we show that the ancestral cytoplasmic IF protein gene was lost in the entire panarthropod (onychophoran + tardigrade + arthropod) rather than arthropod lineage and that nuclear, lamin-derived proteins instead acquired new cytoplasmic roles at least three times independently in collembolans, copepods, and tardigrades. Transcriptomic and genomic data revealed three IF protein genes in the tardigrade Hypsibius dujardini, one of which (cytotardin) occurs exclusively in the cytoplasm of epidermal and foregut epithelia, where it forms belt-like filaments around each epithelial cell. These results suggest that a lamin derivative has been co-opted to enhance tissue stability in tardigrades, a function otherwise served by cytoplasmic IF proteins in all other bilaterians.

NATO without INF (Intermediate-Range Nuclear Forces). Research report

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

Modlin, S.L.

1988-05-01

This paper was written in the Winter 1987-1988, during the time of the signing of the Intermediate-range Nuclear Forces (INF) signed in Washington, D.C. on 8 December 1987. The paper was written to look ahead to the implications that the treaty, assuming congressional ratification without major change, would have on NATO. Discussed are the historical background of NATO and U.S. national interests in maintaining a balance of power in Europe. NATO strategies of massive retaliation, mutual assured destruction and flexible response are surveyed with respect to the political and military decisions to deploy, and negotiate the removal of INF frommore » Europe. The paper addresses the dual-track decision and the results leading to the INF treaty. The implications of the treaty are then discussed, with a renewed look at U.S. national interests, and suggestions for future U.S. involvement with NATO are provided.« less

The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutant.

PubMed

Ma, Buyong; Nussinov, Ruth

2006-05-15

The structure and stabilities of the intermediates affect protein folding as well as misfolding and amyloid formation. By applying Kramer's theory of barrier crossing and a Morse-function-like energy landscape, we show that intermediates with medium stability dramatically increase the rate of amyloid formation; on the other hand, very stable and very unstable intermediates sharply decrease amyloid formation. Remarkably, extensive molecular dynamics simulations and conformational energy landscape analysis of Abeta25-35 and its N27Q mutant corroborate the mathematical description. Both experimental and current simulation results indicate that the core of the amyloid structure of Abeta25-35 formed from residues 28-35. A single mutation of N27Q of Abeta25-35 makes the Abeta25-35 N27Q amyloid-free. Energy landscape calculations show that Abeta25-35 has extended intermediates with medium stability that are prone to form amyloids, whereas the extended intermediates for Abeta25-35 N27Q split into stable and very unstable species that are not disposed to form amyloids. The results explain the contribution of both alpha-helical and beta-strand intermediates to amyloid formation. The results also indicate that the structure and stability of the intermediates, as well as of the native folded and the amyloid states can be targeted in drug design. One conceivable approach is to stabilize the intermediates to deter amyloid formation.

Genetic variability and haplotypes of Echinococcus isolates from Tunisia.

PubMed

Boufana, Belgees; Lahmar, Samia; Rebaï, Waël; Ben Safta, Zoubeir; Jebabli, Leïla; Ammar, Adel; Kachti, Mahmoud; Aouadi, Soufia; Craig, Philip S

2014-11-01

The species/genotypes of Echinococcus infecting a range of intermediate, canid and human hosts were examined as well as the intraspecific variation and population structure of Echinococcus granulosus sensu lato (s.l.) within these hosts. A total of 174 Echinococcus isolates from humans and ungulate intermediate hosts and adult tapeworms from dogs and jackals were used. Genomic DNA was used to amplify a fragment within a mitochondrial gene and a nuclear gene, coding for cytochrome c oxidase subunit 1 (cox1; 828 bp) and elongation factor 1-alpha (ef1a; 656 bp), respectively. E. granulosus sensu stricto was identified from all host species examined, E. canadensis (G6) in a camel and, for the first time, fertile cysts of E. granulosus (s.s.) and E. equinus in equids (donkeys) and E. granulosus (s.s.) from wild boars and goats. Considerable genetic variation was seen only for the cox1 sequences of E. granulosus (s.s.). The pairwise fixation index (Fst) for cox1 E. granulosus (s.s.) sequences from donkeys was high and was statistically significant compared with that of E. granulosus populations from other intermediate hosts. A single haplotype (EqTu01) was identified for the cox1 nucleotide sequences of E. equinus. The role of donkeys in the epidemiology of echinococcosis in Tunisia requires further investigation. © The Author 2014. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Coherent vector meson photoproduction from deuterium at intermediate energies

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

Rogers, T.C.; Strikman, M.I.; Sargsian, M.M.

2006-04-15

We analyze the cross section for vector meson photoproduction off a deuteron for the intermediate range of photon energies starting at a few giga-electron-volts above the threshold and higher. We reproduce the steps in the derivation of the conventional nonrelativistic Glauber expression based on an effective diagrammatic method while making corrections for Fermi motion and intermediate-energy kinematic effects. We show that, for intermediate-energy vector meson production, the usual Glauber factorization breaks down, and we derive corrections to the usual Glauber method to linear order in longitudinal nucleon momentum. The purpose of our analysis is to establish methods for probing interestingmore » physics in the production mechanism for {phi} mesons and heavier vector mesons. We demonstrate how neglecting the breakdown of Glauber factorization can lead to errors in measurements of basic cross sections extracted from nuclear data.« less

Viral oncolysis that targets Raf-1 signaling control of nuclear transport.

PubMed

Riolobos, Laura; Valle, Noelia; Hernando, Eva; Maroto, Beatriz; Kann, Michael; Almendral, José M

2010-02-01

The central role of Raf protein kinase isoforms in human cancer demands specific anti-Raf therapeutic inhibitors. Parvoviruses are currently used in experimental cancer therapy due to their natural oncotropism and lytic life cycle. In searching for mechanisms underlying parvovirus oncolysis, we found that trimers of the major structural protein (VP) of the parvovirus minute virus of mice (MVM), which have to be imported into the nucleus for capsid assembly, undergo phosphorylation by the Raf-1 kinase. Purified Raf-1 phosphorylated the capsid subunits in vitro to the two-dimensional pattern found in natural MVM infections. VP trimers isolated from mammalian cells translocated into the nucleus of digitonin-permeabilized human cells. In contrast, VP trimers isolated from insect cells, which are devoid of Raf-1, were neither phosphorylated nor imported into the mammalian nucleus. However, the coexpression of a constitutively active Raf-1 kinase in insect cells restored VP trimer phosphorylation and nuclear transport competence. In MVM-infected normal and transformed cells, Raf-1 inhibition resulted in cytoplasmic retention of capsid proteins, preventing their nuclear assembly and progeny virus maturation. The level of Raf-1 activity in cancer cells was consistent with the extent of VP specific phosphorylation and with the permissiveness to MVM infection. Thus, Raf-1 control of nuclear translocation of MVM capsid assembly intermediates provides a novel target for viral oncolysis. MVM may reinforce specific therapies against frequent human cancers with deregulated Raf signaling.

Computational Pathology to Discriminate Benign from Malignant Intraductal Proliferations of the Breast

PubMed Central

Oh, Eun-Yeong; Lerwill, Melinda F.; Brachtel, Elena F.; Jones, Nicholas C.; Knoblauch, Nicholas W.; Montaser-Kouhsari, Laleh; Johnson, Nicole B.; Rao, Luigi K. F.; Faulkner-Jones, Beverly; Wilbur, David C.; Schnitt, Stuart J.; Beck, Andrew H.

2014-01-01

The categorization of intraductal proliferative lesions of the breast based on routine light microscopic examination of histopathologic sections is in many cases challenging, even for experienced pathologists. The development of computational tools to aid pathologists in the characterization of these lesions would have great diagnostic and clinical value. As a first step to address this issue, we evaluated the ability of computational image analysis to accurately classify DCIS and UDH and to stratify nuclear grade within DCIS. Using 116 breast biopsies diagnosed as DCIS or UDH from the Massachusetts General Hospital (MGH), we developed a computational method to extract 392 features corresponding to the mean and standard deviation in nuclear size and shape, intensity, and texture across 8 color channels. We used L1-regularized logistic regression to build classification models to discriminate DCIS from UDH. The top-performing model contained 22 active features and achieved an AUC of 0.95 in cross-validation on the MGH data-set. We applied this model to an external validation set of 51 breast biopsies diagnosed as DCIS or UDH from the Beth Israel Deaconess Medical Center, and the model achieved an AUC of 0.86. The top-performing model contained active features from all color-spaces and from the three classes of features (morphology, intensity, and texture), suggesting the value of each for prediction. We built models to stratify grade within DCIS and obtained strong performance for stratifying low nuclear grade vs. high nuclear grade DCIS (AUC = 0.98 in cross-validation) with only moderate performance for discriminating low nuclear grade vs. intermediate nuclear grade and intermediate nuclear grade vs. high nuclear grade DCIS (AUC = 0.83 and 0.69, respectively). These data show that computational pathology models can robustly discriminate benign from malignant intraductal proliferative lesions of the breast and may aid pathologists in the diagnosis and classification of these lesions. PMID:25490766

16th International Conference on Nuclear Structure: NS2016

DOE PAGES

Galindo-Uribarri, Alfredo

2016-10-28

Every two years the Nuclear Structure (NS) conference series brings together researchers from an international community of experimental and theoretical nuclear physicists to present and discuss their latest results in nuclear structure. This biennial conference covered the latest results on experimental and theoretical research into the structure of nuclei at the extremes of isospin, excitation energy, mass, and angular momentum. Topics included many of the most exciting areas of modern nuclear structure research such as transitional behavior, nuclear structure and its evolution across the nuclear landscape, shell structure, collectivity, nuclear structure with radioactive beams, and macroscopic and microscopic approaches tomore » nuclear structure.« less

16th International Conference on Nuclear Structure: NS2016

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

Galindo-Uribarri, Alfredo

Every two years the Nuclear Structure (NS) conference series brings together researchers from an international community of experimental and theoretical nuclear physicists to present and discuss their latest results in nuclear structure. This biennial conference covered the latest results on experimental and theoretical research into the structure of nuclei at the extremes of isospin, excitation energy, mass, and angular momentum. Topics included many of the most exciting areas of modern nuclear structure research such as transitional behavior, nuclear structure and its evolution across the nuclear landscape, shell structure, collectivity, nuclear structure with radioactive beams, and macroscopic and microscopic approaches tomore » nuclear structure.« less

Intracellular gene transfer in action: Dual transcription and multiple silencings of nuclear and mitochondrial cox2 genes in legumes

PubMed Central

Adams, Keith L.; Song, Keming; Roessler, Philip G.; Nugent, Jacqueline M.; Doyle, Jane L.; Doyle, Jeff J.; Palmer, Jeffrey D.

1999-01-01

The respiratory gene cox2, normally present in the mitochondrion, was previously shown to have been functionally transferred to the nucleus during flowering plant evolution, possibly during the diversification of legumes. To search for novel intermediate stages in the process of intracellular gene transfer and to assess the evolutionary timing and frequency of cox2 transfer, activation, and inactivation, we examined nuclear and mitochondrial (mt) cox2 presence and expression in over 25 legume genera and mt cox2 presence in 392 genera. Transfer and activation of cox2 appear to have occurred during recent legume evolution, more recently than previously inferred. Many intermediate stages of the gene transfer process are represented by cox2 genes in the studied legumes. Nine legumes contain intact copies of both nuclear and mt cox2, although transcripts could not be detected for some of these genes. Both cox2 genes are transcribed in seven legumes that are phylogenetically interspersed with species displaying only nuclear or mt cox2 expression. Inactivation of cox2 in each genome has taken place multiple times and in a variety of ways, including loss of detectable transcripts or transcript editing and partial to complete gene loss. Phylogenetic evidence shows about the same number (3–5) of separate inactivations of nuclear and mt cox2, suggesting that there is no selective advantage for a mt vs. nuclear location of cox2 in plants. The current distribution of cox2 presence and expression between the nucleus and mitochondrion in the studied legumes is probably the result of chance mutations silencing either cox2 gene. PMID:10570164

Secuencias evolutivas e isocronas para estrellas de baja masa e intermedia

NASA Astrophysics Data System (ADS)

Panei, J.; Baume, G.

2016-08-01

We present theoretical evolutionary sequences for low- and intermediate-mass stars. The masses calculated range from 1.7 to 10 M. The initial chemical composition is . In addition, we have taken into account a nuclear network with 17 isotopes and 34 nuclear reactions. With respect to the mix, we considered overshooting with a parameter . The evolutionary calculations were initialized from the region of instability of Hayashi, in order to calculate isochrones of pre-sequence, too.

Widths of transverse momentum distributions in intermediate-energy heavy-ion collisions.

PubMed

Khan, F; Townsend, L W

1993-08-01

The need to include dynamical collision momentum transfer contributions, arising from interacting nuclear and Coulomb fields, to estimates of fragment momentum distributions is discussed. Methods based upon an optical potential model are presented. Comparisons with recent experimental data of the Siegen group for variances of transverse momentum distributions for gold nuclei at 980 A MeV fragmenting on silver foil and plastic nuclear track detector targets are made. The agreement between theory and experiment is good.

New developments in high field electron paramagnetic resonance with applications in structural biology

NASA Astrophysics Data System (ADS)

Bennati, Marina; Prisner, Thomas F.

2005-02-01

Recent developments in microwave technologies have led to a renaissance of electron paramagnetic resonance (EPR) due to the implementation of new spectrometers operating at frequencies >=90 GHz. EPR at high fields and high frequencies (HF-EPR) has been established up to THz (very high frequency (VHF) EPR) in continuous wave (cw) operation and up to about 300 GHz in pulsed operation. To date, its most prominent application field is structural biology. This review article first gives an overview of the theoretical basics and the technical aspects of HF-EPR methodologies, such as cw and pulsed HF-EPR, as well as electron nuclear double resonance at high fields (HF-ENDOR). In the second part, the article illustrates different application areas of HF-EPR in studies of protein structure and function. In particular, HF-EPR has delivered essential contributions to disentangling complex spectra of radical cofactors or reaction intermediates in photosynthetic reaction centres, radical enzymes (such as ribonucleotide reductase) and in metalloproteins. Furthermore, HF-EPR combined with site-directed spin labelling in membranes and soluble proteins provides new methods of investigating complex molecular dynamics and intermolecular distances.

Hyperpolarized 89Y NMR spectroscopic detection of yttrium ion and DOTA macrocyclic ligand complexation: pH dependence and Y-DOTA intermediates

NASA Astrophysics Data System (ADS)

Ferguson, Sarah; Kiswandhi, Andhika; Niedbalski, Peter; Parish, Christopher; Kovacs, Zoltan; Lumata, Lloyd

Dissolution dynamic nuclear polarization (DNP) is a rapidly emerging physics technique used to enhance the signal strength in nuclear magnetic resonance (NMR) and imaging (MRI) experiments for nuclear spins such as yttrium-89 by >10,000-fold. One of the most common and stable MRI contrast agents used in the clinic is Gd-DOTA. In this work, we have investigated the binding of the yttrium and DOTA ligand as a model for complexation of Gd ion and DOTA ligand. The macrocyclic ligand DOTA is special because its complexation with lanthanide ions such as Gd3+ or Y3+ is highly pH dependent. Using this physics technology, we have tracked the complexation kinetics of hyperpolarized Y-triflate and DOTA ligand in real-time and detected the Y-DOTA intermediates. Different kinds of buffers were used (lactate, acetate, citrate, oxalate) and the pseudo-first order complexation kinetic calculations will be discussed. The authors would like to acknowledge the support by US Dept of Defense Award No. W81XWH-14-1-0048 and Robert A. Welch Foundation Grant No. AT-1877.

The Structure and Function of a Microbial Allantoin Racemase Reveal the Origin and Conservation of a Catalytic Mechanism.

PubMed

Cendron, Laura; Ramazzina, Ileana; Puggioni, Vincenzo; Maccacaro, Eleonora; Liuzzi, Anastasia; Secchi, Andrea; Zanotti, Giuseppe; Percudani, Riccardo

2016-11-22

The S enantiomer of allantoin is an intermediate of purine degradation in several organisms and the final product of uricolysis in nonhominoid mammals. Bioinformatics indicated that proteins of the Asp/Glu racemase superfamily could be responsible for the allantoin racemase (AllR) activity originally described in Pseudomonas species. In these proteins, a cysteine of the catalytic dyad is substituted with glycine, yet the recombinant enzyme displayed racemization activity with a similar efficiency (k cat /K M ≈ 5 × 10 4 M -1 s -1 ) for the R and S enantiomers of allantoin. The protein crystal structure identified a glutamate residue located three residues downstream (E78) that can functionally replace the missing cysteine; the catalytic role of E78 was confirmed by site-directed mutagenesis. Allantoin can undergo racemization through formation of a bicyclic intermediate (faster) or proton exchange at the chiral center (slower). By monitoring the two alternative mechanisms by 13 C and 1 H nuclear magnetic resonance, we found that the velocity of the faster reaction is unaffected by the enzyme, whereas the velocity of the slower reaction is increased by 7 orders of magnitude. Protein phylogenies trace the origin of the racemization mechanism in enzymes acting on glutamate, a substrate for which proton exchange is the only viable reaction mechanism. This mechanism was inherited by allantoin racemase through divergent evolution and conserved in spite of the substitution of catalytic residues.

Trp-cage: folding free energy landscape in explicit water.

PubMed

Zhou, Ruhong

2003-11-11

Trp-cage is a 20-residue miniprotein, which is believed to be the fastest folder known so far. In this study, the folding free energy landscape of Trp-cage has been explored in explicit solvent by using an OPLSAA force field with periodic boundary condition. A highly parallel replica exchange molecular dynamics method is used for the conformation space sampling, with the help of a recently developed efficient molecular dynamics algorithm P3ME/RESPA (particle-particle particle-mesh Ewald/reference system propagator algorithm). A two-step folding mechanism is proposed that involves an intermediate state where two correctly formed partial hydrophobic cores are separated by an essential salt-bridge between residues Asp-9 and Arg-16 near the center of the peptide. This metastable intermediate state provides an explanation for the superfast folding process. The free energy landscape is found to be rugged at low temperatures, and then becomes smooth and funnel-like above 340 K. The lowest free energy structure at 300 K is only 1.50 A Calpha-RMSD (Calpha-rms deviation) from the NMR structures. The simulated nuclear Overhauser effect pair distances are in excellent agreement with the raw NMR data. The temperature dependence of the Trp-cage population, however, is found to be significantly different from experiment, with a much higher melting transition temperature above 400 K (experimental 315 K), indicating that the current force fields, parameterized at room temperature, need to be improved to correctly predict the temperature dependence.

Trp-cage: Folding free energy landscape in explicit water

NASA Astrophysics Data System (ADS)

Zhou, Ruhong

2003-11-01

Trp-cage is a 20-residue miniprotein, which is believed to be the fastest folder known so far. In this study, the folding free energy landscape of Trp-cage has been explored in explicit solvent by using an OPLSAA force field with periodic boundary condition. A highly parallel replica exchange molecular dynamics method is used for the conformation space sampling, with the help of a recently developed efficient molecular dynamics algorithm P3ME/RESPA (particle-particle particle-mesh Ewald/reference system propagator algorithm). A two-step folding mechanism is proposed that involves an intermediate state where two correctly formed partial hydrophobic cores are separated by an essential salt-bridge between residues Asp-9 and Arg-16 near the center of the peptide. This metastable intermediate state provides an explanation for the superfast folding process. The free energy landscape is found to be rugged at low temperatures, and then becomes smooth and funnel-like above 340 K. The lowest free energy structure at 300 K is only 1.50 Å C-RMSD (C-rms deviation) from the NMR structures. The simulated nuclear Overhauser effect pair distances are in excellent agreement with the raw NMR data. The temperature dependence of the Trp-cage population, however, is found to be significantly different from experiment, with a much higher melting transition temperature above 400 K (experimental 315 K), indicating that the current force fields, parameterized at room temperature, need to be improved to correctly predict the temperature dependence.

Trp-cage: Folding free energy landscape in explicit water

PubMed Central

Zhou, Ruhong

2003-01-01

Trp-cage is a 20-residue miniprotein, which is believed to be the fastest folder known so far. In this study, the folding free energy landscape of Trp-cage has been explored in explicit solvent by using an OPLSAA force field with periodic boundary condition. A highly parallel replica exchange molecular dynamics method is used for the conformation space sampling, with the help of a recently developed efficient molecular dynamics algorithm P3ME/RESPA (particle–particle particle–mesh Ewald/reference system propagator algorithm). A two-step folding mechanism is proposed that involves an intermediate state where two correctly formed partial hydrophobic cores are separated by an essential salt-bridge between residues Asp-9 and Arg-16 near the center of the peptide. This metastable intermediate state provides an explanation for the superfast folding process. The free energy landscape is found to be rugged at low temperatures, and then becomes smooth and funnel-like above 340 K. The lowest free energy structure at 300 K is only 1.50 Å Cα-RMSD (Cα-rms deviation) from the NMR structures. The simulated nuclear Overhauser effect pair distances are in excellent agreement with the raw NMR data. The temperature dependence of the Trp-cage population, however, is found to be significantly different from experiment, with a much higher melting transition temperature above 400 K (experimental 315 K), indicating that the current force fields, parameterized at room temperature, need to be improved to correctly predict the temperature dependence. PMID:14581616

Nuclear magnetic resonance studies of ancient buried wood-II. Observations on the origin of coal from lignite to bituminous coal

USGS Publications Warehouse

Hatcher, P.G.; Breger, I.A.; Szeverenyi, N.; Maciel, G.E.

1982-01-01

Coalified logs ranging in age from Late Pennsylvania to Miocene and in rank from lignite B to bituminous coal were analyzed by 13C nuclear magnetic resonance (NMR) utilizing the cross-polarization, magic-angle spinning technique, as well as by infrared spectroscopy. The results of this study indicate that at least three major stages of coalification can be observed as wood gradually undergoes transformation to bituminous coal. The first stage involves hydrolysis and loss of cellulose from wood with retention and differential concentration of the resistant lignin. The second stage involves conversion of the lignin residues directly to coalified wood of lignitic rank, during which the oxygen content of intermediate diagenetic products remains constant as the hydrogen content and the carbon content increases. These changes are thought to involve loss of methoxyl groups, water, and C3 side chains from the lignin. In the third major stage of coalification, the coalified wood increases in rank to subbituminous and bituminous coal; during this stage the oxygen content decreases, hydrogen remains constant, and the carbon content increases. These changes are thought to result from loss of soluble humic acids that are rich in oxygen and that are mobilized during compaction and dewatering. Relatively resistant resinous substances are differentially concentrated in the coal during this stage. The hypothesis that humic acids are formed as mobile by-products of the coalification of lignin and function only as vehicles for removal of oxygen represents a dramatic departure from commonly accepted views that they are relatively low-molecular-weight intermediates formed during the degradation of lignin that then condense to form high-molecular-weight coal structures. ?? 1982.

Exploring the Web : The Active Galaxy Population in the ORELSE Survey

NASA Astrophysics Data System (ADS)

Lubin, Lori

What are the physical processes that trigger starburst and nuclear activity in galaxies and drive galaxy evolution? Studies aimed at understanding this complex issue have largely focused on the cores of galaxy clusters or on field surveys, leaving underexplored intermediate-density regimes where rapid evolution occurs. As a result, we are conducting the ORELSE survey, a search for structure on scales > 10 Mpc around 18 clusters at 0.6 < z < 1.3. The survey covers 5 sq. deg., all targeted at high-density regions, making it comparable to field surveys such as DEEP2 and COSMOS. ORELSE is unmatched, with no other cluster survey having comparable breadth, depth, precision, and multi-band coverage. As such, ORELSE overcomes critical problems with previous high-redshift studies, including cosmic variance, restricted environmental ranges, sparse cluster samples, inconsistent star formation rate measures, and limited spectroscopy. From its initial spectral and photometric components, ORELSE already contains wellmeasured properties such as redshift, color, stellar mass, and star formation rate for a statistical sample of 7000 field+cluster galaxies. Because X-ray and mid-IR observations are crucial for a complete census of the active galaxy population, we propose to use the wealth of archival Chandra, Spitzer, and Herschel data in the ORELSE fields to map AGN and starburst galaxies over large scales. When complete, our sample will exceed by more than an order of magnitude the current samples of spectroscopically-confirmed active galaxies in high-redshift clusters and their environs. Combined with our numerical simulations plus galaxy formation models, we will provide a robust census of the active galaxy population in intermediate and high-density environments at z = 1, constrain the physical processes (e.g., merging, intracluster gas interactions, AGN feedback) responsible for triggering/quenching starburst and nuclear activity, and estimate their associated timescales.

Polyhydrido Copper Clusters: Synthetic Advances, Structural Diversity, and Nanocluster-to-Nanoparticle Conversion.

PubMed

Dhayal, Rajendra S; van Zyl, Werner E; Liu, C W

2016-01-19

Metal hydride clusters have historically been studied to unravel their aesthetically pleasing molecular structures and interesting properties, especially toward hydrogen related applications. Central to this work is the hydride ligand, H¯, the smallest closed-shell spherical anion known. Two new developments in polyhydrido nanocluster chemistry include the determination of heretofore unknown hydride coordination modes and novel structural constructs, and conversion from the molecular entities to rhombus-shaped copper nanoparticles (CuNPs). These advances, together with hydrogen evolution and catalysis, have provided both experimentalists and theorists with a rich scientific directive to further explore. The isolation of hexameric [{(Ph3P)CuH}6] (Stryker reagent) could be regarded as the springboard for the recent emergence of polyhydrido copper cluster chemistry due to its utilization in a variety of organic chemical transformations. The stability of clusters of various nuclearity was improved through phosphine, pyridine, and carbene type ligands. Our focus lies with the isolation of novel copper (poly)hydride clusters using mostly the phosphor-1,1-dithiolato type ligands. We found such chalcogen-stabilized clusters to be exceptionally air and moisture stable over a wide range of nuclearities (Cu7 to Cu32). In this Account, we (i) report on state-of-the-art copper hydride cluster chemistry, especially with regards to the diverse and novel structural types generally, and newly discovered hydride coordination modes in particular, (ii) demonstrate the indispensable power of neutron diffraction for the unambiguous assignment and location of hydride ligand(s) within a cluster, and (iii) prove unique transformations that can occur not only between well characterized high nuclearity clusters, but also how such clusters can transform to uniquely shaped nanoparticles of several nanometers in diameter through copper hydride reduction. The increase in the number of low- to high-nuclearity hydride clusters allows for different means by which they can be classified. We chose a classification based on the coordination mode of hydride ligand within the cluster. This includes copper clusters associated with bridging (μ2-H) and capping (μ3-H) hydride modes, followed by an interstitial (μ4-H) hydride mode that was introduced for the first time into octa- and hepta-nuclear copper clusters stabilized by dichalcogen-type ligands. This breakthrough provided a means to explore higher nuclearity polyhydrido nanoclusters, which contain both capping (μ3-H) and interstitial (μ(4-6)-H) hydrides. The presence of bidentate ligands having mixed S/P dative sites led to air- and moisture-stable copper hydride nanoclusters. The formation of rhombus-shaped nanoparticles (CuNPs) from copper polyhydrides in the presence of excess borohydrides suggests the presence of metal hydrides as intermediates during the formation of nanoparticles.

The future of U.S.-Russia nuclear arms control

NASA Astrophysics Data System (ADS)

Pifer, Steven

2017-11-01

Nuclear arms control has long made contributions to U.S.-Soviet and U.S.-Russian security, but the current regime is at risk. The 1987 Intermediate-range Nuclear Forces Treaty may be headed for collapse. Both the United States and Russia are modernizing their strategic forces, and the fate of the 2010 New Strategic Arms Reduction Treaty is unclear. In the unlikely case that the sides are prepared to go beyond New START, there are ways to address further reductions and related issues. A collapse of the arms control regime, on the other hand, would mean the end of constraints on U.S. and Russian nuclear forces, a significant loss of transparency, and potential costs to U.S. security.

Nuclear data for medical applications: An overview of present status and future needs

NASA Astrophysics Data System (ADS)

Syed, M. Qaim

2017-09-01

A brief overview of nuclear data required for medical applications is given. The major emphasis is on radionuclides for internal applications, both for diagnosis and therapy. The status of the presently available data is discussed and some of the emerging needs are outlined. Most of the needs are associated with the development of non-standard positron emitters and novel therapeutic radionuclides. Some new developments in application of radionuclides, e.g. theranostic approach, multimode imaging, radionanoparticles, etc. are described and the related nuclear data needs are discussed. The possible use of newer irradiation technologies for medical radionuclide production, e.g. intermediate energy charged-particle accelerators, high-power electron accelerators for photon production, and spallation neutron sources, will place heavy demands on nuclear data.

Indirect measurement of N-14 quadrupolar coupling for NH3 intercalated in potassium graphite

NASA Technical Reports Server (NTRS)

Tsang, T.; Fronko, R. M.; Resing, H. A.

1987-01-01

A method for indirect measurement of the nuclear quadrupolar coupling was developed and applied to NH3 molecules in the graphite intercalation compound K(NH3)4.3C24, which has a layered structure with alternating carbon and intercalant layers. Three triplets were observed in the H-1 NMR spectra of the compound. The value of the N-14 quadrupolar coupling constant of NH3 (3.7 MHz), determined indirectly from the H-1 NMR spectra, was intermediate between the gas value of 4.1 MHz and the solid-state value of 3.2 MHz. The method was also used to deduce the (H-1)-(H-1) and (N-14)-(H-1) dipolar interactions, the H-1 chemical shifts, and the molecular orientations and motions of NH3.

Chemistry of Amadori rearrangement products: analysis, synthesis, kinetics, reactions, and spectroscopic properties.

PubMed

Yaylayan, V A; Huyghues-Despointes, A

1994-01-01

The chemistry of the key intermediate in the Maillard reaction, the Amadori rearrangements product, is reviewed covering the areas of synthesis, chromatographic analyses, chemical and spectroscopic methods of characterization, reactions, and kinetics. Synthetic strategies involving free and protected sugars are described in detail with specific synthetic procedures. GC- and HPLC-based separations of Amadori products are discussed in relation to the type of columns employed and methods of detection. Applications of infrared (IR) and nuclear magnetic resonance (NMR) spectroscopy for structural elucidation of Amadori products are also reviewed. In addition, mass spectrometry of free, protected, and protein-bound Amadori products under different ionization conditions are presented. The mechanism of acid/base catalyzed thermal degradation reactions of Amadori compounds, as well as their kinetics of formation, are critically evaluated.

Technical Aspects Regarding the Management of Radioactive Waste from Decommissioning of Nuclear Facilities

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

Dragolici, F.; Turcanu, C. N.; Rotarescu, G.

2003-02-25

The proper application of the nuclear techniques and technologies in Romania started in 1957, once with the commissioning of the Research Reactor VVR-S from IFIN-HH-Magurele. During the last 45 years, appear thousands of nuclear application units with extremely diverse profiles (research, biology, medicine, education, agriculture, transport, all types of industry) which used different nuclear facilities containing radioactive sources and generating a great variety of radioactive waste during the decommissioning after the operation lifetime is accomplished. A new aspect appears by the planning of VVR-S Research Reactor decommissioning which will be a new source of radioactive waste generated by decontamination, disassemblingmore » and demolition activities. By construction and exploitation of the Radioactive Waste Treatment Plant (STDR)--Magurele and the National Repository for Low and Intermediate Radioactive Waste (DNDR)--Baita, Bihor county, in Romania was solved the management of radioactive wastes arising from operation and decommissioning of small nuclear facilities, being assured the protection of the people and environment. The present paper makes a review of the present technical status of the Romanian waste management facilities, especially raising on treatment capabilities of ''problem'' wastes such as Ra-266, Pu-238, Am-241 Co-60, Co-57, Sr-90, Cs-137 sealed sources from industrial, research and medical applications. Also, contain a preliminary estimation of quantities and types of wastes, which would result during the decommissioning project of the VVR-S Research Reactor from IFIN-HH giving attention to some special category of wastes like aluminum, graphite and equipment, components and structures that became radioactive through neutron activation. After analyzing the technical and scientific potential of STDR and DNDR to handle big amounts of wastes resulting from the decommissioning of VVR-S Research Reactor and small nuclear facilities, the necessity of up-gradation of these nuclear objectives before starting the decommissioning plan is revealed. A short presentation of the up-grading needs is also presented.« less

Theoretical model for the discrete flexoelectric effect and a description for the sequence of intermediate smectic phases with increasing periodicity.

PubMed

Emelyanenko, A V; Osipov, M A

2003-11-01

A general phenomenological description and a simple molecular model is proposed for the "discrete" flexoelectric effect in tilted smectic liquid crystal phases. This effect defines a polarization in a smectic layer induced by a difference of director orientations in the two smectic layers adjacent to it. It is shown that the "discrete" flexoelectric effect is determined by electrostatic dipole-quadrupole interaction between positionally correlated molecules located in adjacent smectic layers, while the corresponding dipole-dipole interaction is responsible for a coupling between polarization vectors in neighboring layers. It is shown that a simple phenomenological model of a ferrielectric smectic liquid crystal, which has recently been proposed in the literature, can be used to describe the whole sequence of intermediate chiral smectic C* phases with increasing periods, and to determine the nonplanar structure of each phase without additional assumptions. In this sequence the phases with three- and four-layer periodicities have the same structure, as observed in the experiment. The theory predicts also the structure of intermediate phases with longer periods that have not been studied experimentally so far. The structures of intermediate phases with periodicities of up to nine layers are presented together with the phase diagrams, and a relationship between molecular chirality and the three-dimensional structure of intermediate phases is discussed. It is considered also how the coupling between the spontaneous polarization determined by molecular chirality and the induced polarization determined by the discrete flexoelectric effect stabilizes the nonplanar structure of intermediate phases.

German Basic Course. Volume II, Lessons 16-25. Revised.

ERIC Educational Resources Information Center

Defense Language Inst., Monterey, CA.

This is the second volume of the intermediate phase of the German Basic Course. The objective of the intermediate phase is mastery of the structural elements of the German language. Accordingly, each lesson contains the following elements: (1) introduction of new structure through "structure perception drills"; (2) a basic dialog dealing with a…

Molecular structures and intramolecular dynamics of pentahalides

NASA Astrophysics Data System (ADS)

Ischenko, A. A.

2017-03-01

This paper reviews advances of modern gas electron diffraction (GED) method combined with high-resolution spectroscopy and quantum chemical calculations in studies of the impact of intramolecular dynamics in free molecules of pentahalides. Some recently developed approaches to the electron diffraction data interpretation, based on direct incorporation of the adiabatic potential energy surface parameters to the diffraction intensity are described. In this way, complementary data of different experimental and computational methods can be directly combined for solving problems of the molecular structure and its dynamics. The possibility to evaluate some important parameters of the adiabatic potential energy surface - barriers to pseudorotation and saddle point of intermediate configuration from diffraction intensities in solving the inverse GED problem is demonstrated on several examples. With increasing accuracy of the electron diffraction intensities and the development of the theoretical background of electron scattering and data interpretation, it has become possible to investigate complex nuclear dynamics in fluxional systems by the GED method. Results of other research groups are also included in the discussion.

Microwave Spectra and Structure of {H_2-CuF}: Overview of the Complexes of Hydrogen with Metal-Containing Diatomics

NASA Astrophysics Data System (ADS)

Grubbs, G. S. Grubbs, Ii; Frohman, Daniel J.; Yu, Zhenhong; Novick, Stewart E.

2013-06-01

We present here the FTMW spectra of the various isotopologues of the intermediate strength bound complex of dihydrogen with copper fluoride. The bond between the two moieties is surprisingly strong, the H-H forming the cross of the T with the Cu closest to H_2 in the C_{{2v}} structure. Laser ablation was used to produce both copper isotopologues of p-H_2-CuF, o-D_2-CuF, and HD-CuF whose J = 1 - 0 transitions were observed. Significant changes in the nuclear quadrupole coupling constants for the copper nucleus in H_2-CuF compared to that in uncomplexed CuF suggests bonding greater than that typical of van der Waals interactions. This talk will serve as the introduction to presentations at this meeting of other H_2 metal containing diatomics. D. J. Frohman, {G. S. Grubbs II}, Z. Yu, S. E. Novick, Inorg. Chem., 52, 816-822 (2013).

Constraining the astrophysical origin of the p-nuclei through nuclear physics and meteoritic data.

PubMed

Rauscher, T; Dauphas, N; Dillmann, I; Fröhlich, C; Fülöp, Zs; Gyürky, Gy

2013-06-01

A small number of naturally occurring, proton-rich nuclides (the p-nuclei) cannot be made in the s- and r-processes. Their origin is not well understood. Massive stars can produce p-nuclei through photodisintegration of pre-existing intermediate and heavy nuclei. This so-called γ-process requires high stellar plasma temperatures and occurs mainly in explosive O/Ne burning during a core-collapse supernova. Although the γ-process in massive stars has been successful in producing a large range of p-nuclei, significant deficiencies remain. An increasing number of processes and sites has been studied in recent years in search of viable alternatives replacing or supplementing the massive star models. A large number of unstable nuclei, however, with only theoretically predicted reaction rates are included in the reaction network and thus the nuclear input may also bear considerable uncertainties. The current status of astrophysical models, nuclear input and observational constraints is reviewed. After an overview of currently discussed models, the focus is on the possibility to better constrain those models through different means. Meteoritic data not only provide the actual isotopic abundances of the p-nuclei but can also put constraints on the possible contribution of proton-rich nucleosynthesis. The main part of the review focuses on the nuclear uncertainties involved in the determination of the astrophysical reaction rates required for the extended reaction networks used in nucleosynthesis studies. Experimental approaches are discussed together with their necessary connection to theory, which is especially pronounced for reactions with intermediate and heavy nuclei in explosive nuclear burning, even close to stability.

Dynamic Assembly of Brambleberry Mediates Nuclear Envelope Fusion during Early Development

PubMed Central

Abrams, Elliott W.; Zhang, Hong; Marlow, Florence L.; Kapp, Lee; Lu, Sumei; Mullins, Mary C.

2012-01-01

Summary To accommodate the large cells following zygote formation, early blastomeres employ modified cell divisions. Karyomeres are one such modification, a mitotic intermediate wherein individual chromatin masses are surrounded by nuclear envelope, which then fuse to form a single mononucleus. We identified brambleberry, a maternal-effect zebrafish mutant that disrupts karyomere fusion resulting in formation of multiple micronuclei. brambleberry is a previously unannotated gene homologous to Kar5p, which participates in nuclear fusion in yeast. We demonstrate that Brambleberry is required for pronuclear fusion following fertilization in zebrafish. As karyomeres form, Brambleberry localizes to the nuclear envelope with prominent puncta evident near karyomere-karyomere interfaces corresponding to membrane fusion sites. Our studies identify the first factor acting in karyomere fusion and suggest that specialized proteins are necessary for proper nuclear division in large dividing blastomeres. PMID:22863006

Rings in Evolved Stars: Fingerprints of Their Mass-Loss History

NASA Astrophysics Data System (ADS)

Ramos-Larios, Gerardo; Santamaria, Edgar; Sabin, Laurence; Guerrero, Martin; Marquez-Lugo, Alejandro

2015-08-01

The majority of intermediate mass evolved stars i.e. asymptotic giant branch (AGB) stars, post-AGB and pre-planetary nebulae (PPN) are well known for been characterized by external structures such as knots, arcs, ansae, jets, haloes, shells and even annular enhancements in intensity -features which are commonly referred to as rings. These are well described either as spherical bubbles of periodic isotropic nuclear mass pulsations (Balick, Wilson & Hajian 2001) or projections of spherical shells onto the plane of the sky by Kwok (2001).These interesting structures are part of the AGB wind, suggesting that this wind comes in a series of semi periodic lapses, indicating that the outflow has quasi-periodic oscillations.After an extensive analysis in the Hubble Space Telescope (HST) archives we found new ring-like structures in several evolved stars. Following the image analysis procedure described by Corradi et al. (2004), and using unsharp masking techniques it was possible to enhance the ring structures, and to obtain an effective removal of the underlying halo emission.Our new findings will help first to constrain the physical processes responsible for the rings creation and then to better understand the mass loss activity in these evolved stars.

NMR structural and kinetic assignment of fluoro-3H-naphthopyran photomerocyanines.

PubMed

Delbaere, S; Micheau, J C; Teral, Y; Bochu, C; Campredon, M; Vermeersch, G

2001-11-01

The kinetic and structural behavior of a photochromic compound, 3-(2-fluorophenyl)-3-phenyl-3H-naphtho[2,1-b]pyran (F-Py), was investigated using 1H and 19F nuclear magnetic resonance (NMR) spectroscopy. Upon irradiation, the four theoretically predicted photomerocyanines appear along with a fifth form X, whose final structure has not been elucidated. This last form and two of the photomerocyanines are thermally labile, whereas the other two do not show any signs of decay. The system has been analyzed by NMR spectroscopy. This led to the structural assignment of each photomerocyanine. The kinetics of the thermal bleaching were monitored by directly and separately measuring the concentrations of each species at regular time intervals using 19F NMR spectroscopy. We therefore propose a plausible reaction mechanism. On the basis of this mechanism, the mathematical treatment and the study of the effects of temperature led to the determination of the kinetic and thermodynamic parameters (rate coefficients, enthalpy and entropy of activation) of this photochromic system. The leading role of the labile intermediate X on the formation of trans-transoid-cis (TTC) and cis-transoid-cis (CTC) photomerocyanines is pointed out.

Fine Structure and Host-Virus Relationship of a Marine Bacterium and Its Bacteriophage

PubMed Central

Valentine, Artrice F.; Chapman, George B.

1966-01-01

Valentine, Artrice F. (Georgetown University, Washington, D.C.), and George B. Chapman. Fine structure and host-virus relationship of a marine bacterium and its bacteriophage. J. Bacteriol. 92:1535–1554. 1966.—The fine structure of a gram-negative marine bacterium, Cytophaga marinoflava sp. n., has been revealed by ultrathin sectioning and electron microscopy. Stages in the morphogenesis of the bacterial virus NCMB 385, which has been shown to be highly specific for this organism, were also demonstrated in bacterial cells fixed according to the Kellenberger technique. The bacterium possessed a cell wall, cytoplasmic membrane, and nuclear and cytoplasmic regions typical of bacterial cells. Both the cell wall and the cytoplasmic membrane showed a tripartite structure, i.e., each was composed of two dense layers separated by a low-density zone. Intracytoplasmic membrane systems were also observed, especially in dividing cells and in cells in which new viruses were being formed. As many as 18 hexagonally shaped, empty phage heads (membranes only) were observed in untreated, infected bacterial cells. Phage heads, intermediate in density to empty heads and fully condensed ones, possibly representing stages in the morphological development of the virus, were also seen. Images PMID:5924277

Chromophoric spin-labeled β-lactam antibiotics for ENDOR structural characterization of reaction intermediates of class A and class C β-lactamases

NASA Astrophysics Data System (ADS)

Mustafi, Devkumar; Hofer, Jennifer E.; Huang, Wanzhi; Palzkill, Timothy; Makinen, Marvin W.

2004-05-01

The chromophoric spin-label substrate 6- N-[3-(2,2,5,5-tetramethyl-1-oxypyrrolin-3-yl)-propen-2-oyl]penicillanic acid (SLPPEN) was synthesized by acylation of 6-aminopenicillanic acid with the acid chloride of 3-(2,2,5,5-tetramethyl-1-oxypyrrolinyl)-2-propenoic acid and characterized by physical methods. By application of angle-selected electron nuclear double resonance (ENDOR), we have determined the molecular structure of SLPPEN in solution. SLPPEN exhibited UV absorption properties that allowed accurate monitoring of the kinetics of its enzyme-catalyzed hydrolysis. The maximum value of the (substrate-product) difference extinction coefficient was 2824 M -1 cm -1 at 275 nm compared to 670 M -1 cm -1 at 232 nm for SLPEN [J. Am. Chem. Soc. 117 (1995) 6739]. For SLPPEN, the steady-state kinetic parameters kcat and kcat/ KM, determined under initial velocity conditions, were 637±36 s -1 and 13.8±1.4×10 6 M -1 s -1, respectively, for hydrolysis catalyzed by TEM-1 β-lactamase of E. coli, and 0.5±0.04 s -1 and 3.9±0.4×10 4 M -1 s -1 for hydrolysis catalyzed by the β-lactamase of Enterobacter cloacae P99. We have also observed "burst kinetics" for the hydrolysis of SLPPEN with P99 β-lactamase, indicative of formation of an acylenzyme reaction intermediate. In DMSO:H 2O (30:70, v:v) cryosolvent mixtures buffered to pH ∗ 7.0, the half-life of the acylenzyme intermediate formed with the P99 enzyme at -5 °C was ≥3 min, suitable for optical characterization. The observation of burst kinetics in the hydrolysis of SLPPEN catalyzed by P99 β-lactamase suggests that this chromophoric spin-labeled substrate is differentially sensitive to active site interactions underlying the cephalosporinase and penicillinase reactivity of this class C enzyme.

Electronic constant current and current pulse signal generator for nuclear instrumentation testing

DOEpatents

Brown, R.A.

1994-04-19

Circuitry is described for testing the ability of an intermediate range nuclear instrument to detect and measure a constant current and a periodic current pulse. The invention simulates the resistance and capacitance of the signal connection of a nuclear instrument ion chamber detector and interconnecting cable. An LED flasher/oscillator illuminates an LED at a periodic rate established by a timing capacitor and circuitry internal to the flasher/oscillator. When the LED is on, a periodic current pulse is applied to the instrument. When the LED is off, a constant current is applied. An inductor opposes battery current flow when the LED is on. 1 figures.

Electronic constant current and current pulse signal generator for nuclear instrumentation testing

DOEpatents

Brown, Roger A.

1994-01-01

Circuitry for testing the ability of an intermediate range nuclear instrut to detect and measure a constant current and a periodic current pulse. The invention simulates the resistance and capacitance of the signal connection of a nuclear instrument ion chamber detector and interconnecting cable. An LED flasher/oscillator illuminates an LED at a periodic rate established by a timing capacitor and circuitry internal to the flasher/oscillator. When the LED is on, a periodic current pulse is applied to the instrument. When the LED is off, a constant current is applied. An inductor opposes battery current flow when the LED is on.

Nuclear Physics Laboratory technical progress report, November 1, 1972-- November 1, 1973

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

None

1973-11-01

The experimental program was divided into the areas of nuclear physics (charged-particle experiments, gamma-ray experiments andd beta decay, neutron time-of-flight experiments, x-ray fluorescence analysis, other activities), intermediate enengy physics, and apparatus and facility development. The energy- loss spectrograph, rotating-beam neutron time-of-flight spectrometer, and cyclotron and the rearch done using these facilities are described. The theoretical program has concentrated on the effects of two-step processes in nuclear reactions. The trace element analysis program continued, and a neutron beam for cancer therapy is being developed. Lists of publications and personnel are also included. (RWR)

The DNA repair endonuclease XPG interacts directly and functionally with the WRN helicase defective in Werner syndrome

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

Trego, Kelly S.; Chernikova, Sophia B.; Davalos, Albert R.

XPG is a structure-specific endonuclease required for nucleotide excision repair (NER). XPG incision defects result in the cancer-prone syndrome xeroderma pigmentosum, whereas truncating mutations of XPG cause the severe postnatal progeroid developmental disorder Cockayne syndrome. We show that XPG interacts directly with WRN protein, which is defective in the premature aging disorder Werner syndrome, and that the two proteins undergo similar sub-nuclear redistribution in S-phase and co-localize in nuclear foci. The co-localization was observed in mid- to late-S-phase, when WRN moves from nucleoli to nuclear foci that have been shown to contain protein markers of both stalled replication forks andmore » telomeric proteins. We mapped the interaction between XPG and WRN to the C-terminal domains of each and show that interaction with the C-terminal domain of XPG strongly stimulates WRN helicase activity. WRN also possesses a competing DNA single-strand annealing activity that, combined with unwinding, has been shown to coordinate regression of model replication forks to form Holliday junction/chicken foot intermediate structures. We tested whether XPG stimulated WRN annealing activity and found that XPG itself has intrinsic strand annealing activity that requires the unstructured R- and C-terminal domains, but not the conserved catalytic core or endonuclease activity. Annealing by XPG is cooperative, rather than additive, with WRN annealing. Taken together, our results suggest a novel function for XPG in S-phase that is at least in part carried out coordinately with WRN, and which may contribute to the severity of the phenotypes that occur upon loss of XPG.« less

Measurement of Isobaric Analogue Resonances of 47Ar with the Active-Target Time Projection Chamber

NASA Astrophysics Data System (ADS)

Bradt, Joshua William

While the nuclear shell model accurately describes the structure of nuclei near stability, the structure of unstable, neutron-rich nuclei is still an area of active research. One region of interest is the set of nuclei near N=28. The shell model suggests that these nuclei should be approximately spherical due to the shell gap predicted by their magic number of neutrons; however, experiments have shown that the nuclei in this region rapidly become deformed as protons are removed from the spherical 48Ca. This makes 46Ar a particularly interesting system as it lies in a transition region between 48Ca and lighter isotones that are known to be deformed. An experiment was performed at the National Superconducting Cyclotron Laboratory (NSCL) to measure resonant proton scattering on 46Ar. The resonances observed in this reaction correspond to unbound levels in the 47K intermediate state nucleus which are isobaric analogues of states in the 47Ar nucleus. By measuring the spectroscopic factors of these states in 47Ar, we gain information about the single-particle structure of this system, which is directly related to the size of the N=28 shell gap. Four resonances were observed: one corresponding to the ground state in 47Ar, one corresponding its first excited 1/2- state, and two corresponding to 1/2+ states in either 47Ar or the intermediate state nucleus. However, only a limited amount of information about these states could be recovered due to the low experimental statistics and limited angular resolution caused by pileup rejection and the inability to accurately reconstruct the beam particle track. In addition to the nuclear physics motivations, this experiment served as the radioactive beam commissioning for the Active-Target Time Projection Chamber (AT-TPC). The AT-TPC is a new gas-filled charged particle detector built at the NSCL to measure low-energy radioactive beams from the ReA3 facility. Since the gas inside the detector serves as both the tracking medium and the scattering target, reactions are measured over a continuous range of energies with near-4π solid angle coverage. This experiment demonstrated that tracks recorded by the AT-TPC can be reconstructed to a good resolution, and it established the feasibility of performing similar experiments with this detector in the future.

Proceedings of Conference on Applications of Chemistry to Nuclear Weapons Effects (2nd). Held on 12-14 September 1972. Abstracts of Papers

DTIC Science & Technology

1974-12-23

16 Effects of turbulent entrainment and nonuniform mixing on fireball chemistry -------------------- 17 Entrainment by intermediate altitude...reaction rate models (*) ----------------------- 40 IV Nuclear bursts effects in the E- and F-regions ---------- 41 Shock enhanced LWIR at 151 from the C0...Regions CHAIRMAN: W. WHITAKER, AFWL 1525-1545 Shock Enhanced LWIR at 15p from the CO 2-N 2 T. McLaren System. Mount Auburn 1545-1600 CHECKMATE

Comparative analyses of spent nuclear fuel transport modal options: Transport options under existing site constraints

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

Brentlinger, L.A.; Hofmann, P.L.; Peterson, R.W.

1989-08-01

The movement of nuclear waste can be accomplished by various transport modal options involving different types of vehicles, transport casks, transport routes, and intermediate intermodal transfer facilities. A series of systems studies are required to evaluate modal/intermodal spent fuel transportation options in a consistent fashion. This report provides total life-cycle cost and life-cycle dose estimates for a series of transport modal options under existing site constraints. 14 refs., 7 figs., 28 tabs.

International Approaches for Nuclear Waste Disposal in Geological Formations: Report on Fifth Worldwide Review

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

Faybishenko, Boris; Birkholzer, Jens; Persoff, Peter

2016-08-01

An important issue for present and future generations is the final disposal of spent nuclear fuel. Over the past over forty years, the development of technologies to isolate both spent nuclear fuel (SNF) and other high-level nuclear waste (HLW) generated at nuclear power plants and from production of defense materials, and low- and intermediate-level nuclear waste (LILW) in underground rock and sediments has been found to be a challenging undertaking. Finding an appropriate solution for the disposal of nuclear waste is an important issue for protection of the environment and public health, and it is a prerequisite for the futuremore » of nuclear power. The purpose of a deep geological repository for nuclear waste is to provide to future generations, protection against any harmful release of radioactive material, even after the memory of the repository may have been lost, and regardless of the technical knowledge of future generations. The results of a wide variety of investigations on the development of technology for radioactive waste isolation from 19 countries were published in the First Worldwide Review in 1991 (Witherspoon, 1991). The results of investigations from 26 countries were published in the Second Worldwide Review in 1996 (Witherspoon, 1996). The results from 32 countries were summarized in the Third Worldwide Review in 2001 (Witherspoon and Bodvarsson, 2001). The last compilation had results from 24 countries assembled in the Fourth Worldwide Review (WWR) on radioactive waste isolation (Witherspoon and Bodvarsson, 2006). Since publication of the last report in 2006, radioactive waste disposal approaches have continued to evolve, and there have been major developments in a number of national geological disposal programs. Significant experience has been obtained both in preparing and reviewing cases for the operational and long-term safety of proposed and operating repositories. Disposal of radioactive waste is a complex issue, not only because of the nature of the waste, but also because of the detailed regulatory structure for dealing with radioactive waste, the variety of stakeholders involved, and (in some cases) the number of regulatory entities involved.« less

Microtubule minus end motors kinesin-14 and dynein drive nuclear congression in parallel pathways

PubMed Central

Scheffler, Kathleen; Minnes, Refael; Fraisier, Vincent; Paoletti, Anne

2015-01-01

Microtubules (MTs) and associated motors play a central role in nuclear migration, which is crucial for diverse biological functions including cell division, polarity, and sexual reproduction. In this paper, we report a dual mechanism underlying nuclear congression during fission yeast karyogamy upon mating of haploid cells. Using microfluidic chambers for long-term imaging, we captured the precise timing of nuclear congression and identified two minus end–directed motors operating in parallel in this process. Kinesin-14 Klp2 associated with MTs may cross-link and slide antiparallel MTs emanating from the two nuclei, whereas dynein accumulating at spindle pole bodies (SPBs) may pull MTs nucleated from the opposite SPB. Klp2-dependent nuclear congression proceeds at constant speed, whereas dynein accumulation results in an increase of nuclear velocity over time. Surprisingly, the light intermediate chain Dli1, but not dynactin, is required for this previously unknown function of dynein. We conclude that efficient nuclear congression depends on the cooperation of two minus end–directed motors. PMID:25869666

Structure of a low-population binding intermediate in protein-RNA recognition

PubMed Central

Bardaro, Michael F.; Aprile, Francesco A.; Varani, Gabriele; Vendruscolo, Michele

2016-01-01

The interaction of the HIV-1 protein transactivator of transcription (Tat) and its cognate transactivation response element (TAR) RNA transactivates viral transcription and represents a paradigm for the widespread occurrence of conformational rearrangements in protein-RNA recognition. Although the structures of free and bound forms of TAR are well characterized, the conformations of the intermediates in the binding process are still unknown. By determining the free energy landscape of the complex using NMR residual dipolar couplings in replica-averaged metadynamics simulations, we observe two low-population intermediates. We then rationally design two mutants, one in the protein and another in the RNA, that weaken specific nonnative interactions that stabilize one of the intermediates. By using surface plasmon resonance, we show that these mutations lower the release rate of Tat, as predicted. These results identify the structure of an intermediate for RNA-protein binding and illustrate a general strategy to achieve this goal with high resolution. PMID:27286828

The effect of illumination and electrode adjustment on the carrier behavior in special multilayer devices

NASA Astrophysics Data System (ADS)

Deng, Yanhong; Ou, Qingdong; Wang, Jinjiang; Zhang, Dengyu; Chen, Liezun; Li, Yanqing

2017-08-01

Intermediate connectors play an important role in semiconductor devices, especially in tandem devices. In this paper, four types of different intermediate connectors (e.g. Mg:Alq3/MoO3, MoO3, Mg:Alq3, and none) and two kinds of modified electrode materials (LiF and MoO3) integrated into the special multilayer devices are proposed, with the aim of studying the impact of light illumination and electrode adjustment on the carrier behavior of intermediate connectors through the current density-voltage characteristics, interfacial electronic structures, and capacitance-voltage characteristics. The results show that the illumination enhances the charge generation and separation in intermediate connectors, and further electrode interface modifications enhance the functionality of intermediate connectors. In addition, the device with an efficient intermediate connector structure shows a photoelectric effect, which paves the way for organic photovoltaic devices to realize optical-electrical integration transformation.

Structures of two intermediate phases between the B1 and B2 phases of PbS under high pressure

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

Li, Yanchun, E-mail: liyc@ihep.ac.cn, E-mail: liuj@ihep.ac.cn; Lin, Chuanlong; Li, Xiaodong

2014-12-15

The structural transitions of PbS were investigated at pressures up to 50 GPa using synchrotron powder and single crystal X-ray diffraction (XRD) methods in diamond anvil cells. We found two intermediate phases between the B1 phase under atmospheric pressure and the B2 phase at 21.1 GPa, which is different to previous reports. The structures of these two intermediate phases were indexed as B27 and B33, respectively. Their structural parameters were investigated using density functional theory (DFT) calculations. Our results provide a new insight into understanding the transition pathway between the B1 and B2 phases in PbS.

Conclusion.

ERIC Educational Resources Information Center

Johnston, Whittle

1990-01-01

Examines the foreign policy of the Reagan administration. Discusses the critics of the Reagan doctrine, focusing on the criticisms launched against his weapons' policies. Analyzes the policy course of the Intermediate Range Nuclear Forces (INF) Treaty, outlining goals of the administration during the INF negotiations. Contends that Reagan's…

How Does Your Protein Fold? Elucidating the Apomyoglobin Folding Pathway

PubMed Central

Dyson, H. Jane; Wright, Peter E.

2017-01-01

Conspectus Although each type of protein fold and in some cases individual proteins within a fold classification can have very different mechanisms of folding, the underlying biophysical and biochemical principles that operate to cause a linear polypeptide chain to fold into a globular structure must be the same. In an aqueous solution, the protein takes up the thermodynamically most stable structure, but the pathway along which the polypeptide proceeds in order to reach that structure is a function of the amino acid sequence, which must be the final determining factor, not only in shaping the final folded structure, but in dictating the folding pathway. A number of groups have focused on a single protein or group of proteins, to determine in detail the factors that influence the rate and mechanism of folding in a defined system, with the hope that hypothesis-driven experiments can elucidate the underlying principles governing the folding process. Our research group has focused on the folding of the globin family of proteins, and in particular on the monomeric protein apomyoglobin. Apomyoglobin (apoMb) folds relatively slowly (~2 seconds) via an ensemble of obligatory intermediates that form rapidly after the initiation of folding. The folding pathway can be dissected using rapid-mixing techniques, which can probe processes in the millisecond time range. Stopped-flow measurements detected by circular dichroism (CD) or fluorescence spectroscopy give information on the rates of folding events. Quench-flow experiments utilize the differential rates of hydrogen-deuterium exchange of amide protons protected in parts of the structure that are folded early; protection of amides can be detected by mass spectrometry or proton nuclear magnetic resonance spectroscopy (NMR). In addition, apoMb forms an intermediate at equilibrium at pH ~ 4, which is sufficiently stable for it to be structurally characterized by solution methods such as CD, fluorescence and NMR spectroscopies, and the conformational ensembles formed in the presence of denaturing agents and low pH can be characterized as models for the unfolded states of the protein. Newer NMR techniques such as measurement of residual dipolar couplings in the various partly folded states, and relaxation dispersion measurements to probe invisible states present at low concentrations, have contributed to providing a detailed picture of the apomyoglobin folding pathway. The research summarized in this review was aimed at characterizing and comparing the equilibrium and kinetic intermediates both structurally and dynamically, as well as delineating the complete folding pathway at a residue-specific level, in order to answer the question “What is it about the amino acid sequence that causes each molecule in the unfolded protein ensemble to start folding, and, once started, to proceed towards the formation of the correctly folded three-dimensional structure?” PMID:28032989

The Mammalian Cell Cycle Regulates Parvovirus Nuclear Capsid Assembly

PubMed Central

Riolobos, Laura; Domínguez, Carlos; Kann, Michael; Almendral, José M.

2015-01-01

It is unknown whether the mammalian cell cycle could impact the assembly of viruses maturing in the nucleus. We addressed this question using MVM, a reference member of the icosahedral ssDNA nuclear parvoviruses, which requires cell proliferation to infect by mechanisms partly understood. Constitutively expressed MVM capsid subunits (VPs) accumulated in the cytoplasm of mouse and human fibroblasts synchronized at G0, G1, and G1/S transition. Upon arrest release, VPs translocated to the nucleus as cells entered S phase, at efficiencies relying on cell origin and arrest method, and immediately assembled into capsids. In synchronously infected cells, the consecutive virus life cycle steps (gene expression, proteins nuclear translocation, capsid assembly, genome replication and encapsidation) proceeded tightly coupled to cell cycle progression from G0/G1 through S into G2 phase. However, a DNA synthesis stress caused by thymidine irreversibly disrupted virus life cycle, as VPs became increasingly retained in the cytoplasm hours post-stress, forming empty capsids in mouse fibroblasts, thereby impairing encapsidation of the nuclear viral DNA replicative intermediates. Synchronously infected cells subjected to density-arrest signals while traversing early S phase also blocked VPs transport, resulting in a similar misplaced cytoplasmic capsid assembly in mouse fibroblasts. In contrast, thymidine and density arrest signals deregulating virus assembly neither perturbed nuclear translocation of the NS1 protein nor viral genome replication occurring under S/G2 cycle arrest. An underlying mechanism of cell cycle control was identified in the nuclear translocation of phosphorylated VPs trimeric assembly intermediates, which accessed a non-conserved route distinct from the importin α2/β1 and transportin pathways. The exquisite cell cycle-dependence of parvovirus nuclear capsid assembly conforms a novel paradigm of time and functional coupling between cellular and virus life cycles. This junction may determine the characteristic parvovirus tropism for proliferative and cancer cells, and its disturbance could critically contribute to persistence in host tissues. PMID:26067441

Altered Expression of Retinal Molecular Markers in the Canine RPE65 Model of Leber Congenital Amaurosis

PubMed Central

Hernández, Maria; Pearce-Kelling, Susan E.; Rodriguez, F. David; Aguirre, Gustavo D.; Vecino, Elena

2010-01-01

Purpose. Leber congenital amaurosis (LCA) is a group of childhood-onset retinal diseases characterized by severe visual impairment or blindness. One form is caused by mutations in the RPE65 gene, which encodes the retinal pigment epithelium (RPE) isomerase. In this study, the retinal structure and expression of molecular markers for different retinal cell types were characterized, and differences between control and RPE65 mutant dogs during the temporal evolution of the disease were analyzed. Methods. Retinas from normal and mutant dogs of different ages were examined by immunofluorescence with a panel of 16 different antibodies. Results. Cones and rods were preserved in the mutant retinas, and the number of cones was normal. However, there was altered expression of cone arrestin and delocalization of rod opsin. The ON bipolar cells showed sprouting of the dendritic arbors toward the outer nuclear layer (ONL) and retraction of their axons in the inner nuclear layer (INL). A decreased expression of GABA, and an increased expression of intermediate filament glial markers was also found in the mutant retinas. These changes were more evident in the adult than the young mutant retinas. Conclusions. The structure of the retina is well preserved in the mutant retina, but several molecular changes take place in photoreceptors and in bipolar and amacrine cells. Some of these changes are structural, whereas others reflect a change in localization of the examined proteins. This study provides new information that can be applied to the interpretation of outcomes of retinal gene therapy in animal models and humans. PMID:20671290

High Temperature Stability of Dissimilar Metal Joints in Fission Surface Power Systems

NASA Technical Reports Server (NTRS)

Locci, Ivan E.; Nesbitt, James A.; Ritzert, Frank J.; Bowman, Cheryl L.

2007-01-01

Future generations of power systems for spacecraft and lunar surface systems will likely require a strong dependence on nuclear power. The design of a space nuclear power plant involves integrating together major subsystems with varying materia1 requirements. Refractory alloys are repeatedly considered for major structural components in space power reactor designs because refractory alloys retain their strength at higher temperatures than other classes of metals. The relatively higher mass and lower ductility of the refractory alloys make them less attractive for lower temperature subsystems in the power plant such as the power conversion system. The power conversion system would consist more likely of intermediate temperature Ni-based superalloys. One of many unanswered questions about the use of refractory alloys in a space power plant is how to transition from the use of the structural refractory alloy to more traditional structural alloys. Because deleterious phases can form when complex alloys are joined and operated at elevated temperatures, dissimilar material diffusion analyses of refractory alloys and superalloys are needed to inform designers about options of joint temperature and operational lifetime. Combinations of four superalloys and six refractory alloys were bonded and annealed at 1150 K and 1300 K to examine diffusional interactions in this study. Joints formed through hot pressing and hot isostatic pressing were compared. Results on newer alloys compared favorably to historical data. Diffusional stability is promising for some combinations of Mo-Re alloys and superalloys at 1150 K, but it appears that lower joint temperatures would be required for other refractory alloy couples.

Contingency Table Browser - prediction of early stage protein structure.

PubMed

Kalinowska, Barbara; Krzykalski, Artur; Roterman, Irena

2015-01-01

The Early Stage (ES) intermediate represents the starting structure in protein folding simulations based on the Fuzzy Oil Drop (FOD) model. The accuracy of FOD predictions is greatly dependent on the accuracy of the chosen intermediate. A suitable intermediate can be constructed using the sequence-structure relationship information contained in the so-called contingency table - this table expresses the likelihood of encountering various structural motifs for each tetrapeptide fragment in the amino acid sequence. The limited accuracy with which such structures could previously be predicted provided the motivation for a more indepth study of the contingency table itself. The Contingency Table Browser is a tool which can visualize, search and analyze the table. Our work presents possible applications of Contingency Table Browser, among them - analysis of specific protein sequences from the point of view of their structural ambiguity.

High-field EPR on membrane proteins - crossing the gap to NMR.

PubMed

Möbius, Klaus; Lubitz, Wolfgang; Savitsky, Anton

2013-11-01

In this review on advanced EPR spectroscopy, which addresses both the EPR and NMR communities, considerable emphasis is put on delineating the complementarity of NMR and EPR concerning the measurement of molecular interactions in large biomolecules. From these interactions, detailed information can be revealed on structure and dynamics of macromolecules embedded in solution- or solid-state environments. New developments in pulsed microwave and sweepable cryomagnet technology as well as ultrafast electronics for signal data handling and processing have pushed to new horizons the limits of EPR spectroscopy and its multifrequency extensions concerning the sensitivity of detection, the selectivity with respect to interactions, and the resolution in frequency and time domains. One of the most important advances has been the extension of EPR to high magnetic fields and microwave frequencies, very much in analogy to what happens in NMR. This is exemplified by referring to ongoing efforts for signal enhancement in both NMR and EPR double-resonance techniques by exploiting dynamic nuclear or electron spin polarization via unpaired electron spins and their electron-nuclear or electron-electron interactions. Signal and resolution enhancements are particularly spectacular for double-resonance techniques such as ENDOR and PELDOR at high magnetic fields. They provide greatly improved orientational selection for disordered samples that approaches single-crystal resolution at canonical g-tensor orientations - even for molecules with small g-anisotropies. Exchange of experience between the EPR and NMR communities allows for handling polarization and resolution improvement strategies in an optimal manner. Consequently, a dramatic improvement of EPR detection sensitivity could be achieved, even for short-lived paramagnetic reaction intermediates. Unique structural and dynamic information is thus revealed that can hardly be obtained by any other analytical techniques. Micromolar quantities of sample molecules have become sufficient to characterize stable and transient reaction intermediates of complex molecular systems - offering highly interesting applications for chemists, biochemists and molecular biologists. In three case studies, representative examples of advanced EPR spectroscopy are reviewed: (I) High-field PELDOR and ENDOR structure determination of cation-anion radical pairs in reaction centers from photosynthetic purple bacteria and cyanobacteria (Photosystem I); (II) High-field ENDOR and ELDOR-detected NMR spectroscopy on the oxygen-evolving complex of Photosystem II; and (III) High-field electron dipolar spectroscopy on nitroxide spin-labelled bacteriorhodopsin for structure-function studies. An extended conclusion with an outlook to further developments and applications is also presented. Copyright © 2013 Elsevier B.V. All rights reserved.

Quantification of the Spatial Organization of the Nuclear Lamina as a Tool for Cell Classification

PubMed Central

Righolt, Christiaan H.; Zatreanu, Diana A.; Raz, Vered

2013-01-01

The nuclear lamina is the structural scaffold of the nuclear envelope that plays multiple regulatory roles in chromatin organization and gene expression as well as a structural role in nuclear stability. The lamina proteins, also referred to as lamins, determine nuclear lamina organization and define the nuclear shape and the structural integrity of the cell nucleus. In addition, lamins are connected with both nuclear and cytoplasmic structures forming a dynamic cellular structure whose shape changes upon external and internal signals. When bound to the nuclear lamina, the lamins are mobile, have an impact on the nuclear envelop structure, and may induce changes in their regulatory functions. Changes in the nuclear lamina shape cause changes in cellular functions. A quantitative description of these structural changes could provide an unbiased description of changes in cellular function. In this review, we describe how changes in the nuclear lamina can be measured from three-dimensional images of lamins at the nuclear envelope, and we discuss how structural changes of the nuclear lamina can be used for cell classification. PMID:27335676

Quantification of the Spatial Organization of the Nuclear Lamina as a Tool for Cell Classification.

PubMed

Righolt, Christiaan H; Zatreanu, Diana A; Raz, Vered

2013-01-01

The nuclear lamina is the structural scaffold of the nuclear envelope that plays multiple regulatory roles in chromatin organization and gene expression as well as a structural role in nuclear stability. The lamina proteins, also referred to as lamins, determine nuclear lamina organization and define the nuclear shape and the structural integrity of the cell nucleus. In addition, lamins are connected with both nuclear and cytoplasmic structures forming a dynamic cellular structure whose shape changes upon external and internal signals. When bound to the nuclear lamina, the lamins are mobile, have an impact on the nuclear envelop structure, and may induce changes in their regulatory functions. Changes in the nuclear lamina shape cause changes in cellular functions. A quantitative description of these structural changes could provide an unbiased description of changes in cellular function. In this review, we describe how changes in the nuclear lamina can be measured from three-dimensional images of lamins at the nuclear envelope, and we discuss how structural changes of the nuclear lamina can be used for cell classification.

MurD ligase from E. coli: Tetrahedral intermediate formation study by hybrid quantum mechanical/molecular mechanical replica path method.

PubMed

Perdih, Andrej; Hodoscek, Milan; Solmajer, Tom

2009-02-15

MurD (UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase), a three-domain bacterial protein, catalyses a highly specific incorporation of D-glutamate to the cytoplasmic intermediate UDP-N-acetyl-muramoyl-L-alanine (UMA) utilizing ATP hydrolysis to ADP and P(i). This reaction is part of a biosynthetic path yielding bacterial peptidoglycan. On the basis of structural studies of MurD complexes, a stepwise catalytic mechanism was proposed that commences with a formation of the acyl-phosphate intermediate, followed by a nucleophilic attack of D-glutamate that, through the formation of a tetrahedral reaction intermediate and subsequent phosphate dissociation, affords the final product, UDP-N-acetyl-muramoyl-L-alanine-D-glutamate (UMAG). A hybrid quantum mechanical/molecular mechanical (QM/MM) molecular modeling approach was utilized, combining the B3LYP QM level of theory with empirical force field simulations to evaluate three possible reaction pathways leading to tetrahedral intermediate formation. Geometries of the starting structures based on crystallographic experimental data and tetrahedral intermediates were carefully examined together with a role of crucial amino acids and water molecules. The replica path method was used to generate the reaction pathways between the starting structures and the corresponding tetrahedral reaction intermediates, offering direct comparisons with a sequential kinetic mechanism and the available structural data for this enzyme. The acquired knowledge represents new and valuable information to assist in the ongoing efforts leading toward novel inhibitors of MurD as potential antibacterial drugs. (c) 2008 Wiley-Liss, Inc.

National Nuclear Data Center

Science.gov Websites

reaction data Sigma Retrieval & Plotting Nuclear structure & decay Data Nuclear Science References Experimental Unevaluated Nuclear Data List Evaluated Nuclear Structure Data File NNDC databases Ground and isomeric states properties Nuclear structure & decay data journal Nuclear reaction model code Tools and

Capturing a flavivirus pre-fusion intermediate.

PubMed

Kaufmann, Bärbel; Chipman, Paul R; Holdaway, Heather A; Johnson, Syd; Fremont, Daved H; Kuhn, Richard J; Diamond, Michael S; Rossmann, Michael G

2009-11-01

During cell entry of flaviviruses, low endosomal pH triggers the rearrangement of the viral surface glycoproteins to a fusion-active state that allows the release of the infectious RNA into the cytoplasm. In this work, West Nile virus was complexed with Fab fragments of the neutralizing mAb E16 and was subsequently exposed to low pH, trapping the virions in a pre-fusion intermediate state. The structure of the complex was studied by cryo-electron microscopy and provides the first structural glimpse of a flavivirus fusion intermediate near physiological conditions. A radial expansion of the outer protein layer of the virion was observed compared to the structure at pH 8. The resulting approximately 60 A-wide shell of low density between lipid bilayer and outer protein layer is likely traversed by the stem region of the E glycoprotein. By using antibody fragments, we have captured a structural intermediate of a virus that likely occurs during cell entry. The trapping of structural transition states by antibody fragments will be applicable for other processes in the flavivirus life cycle and delineating other cellular events that involve conformational rearrangements.

Rapid time-resolved diffraction studies of protein structures using synchrotron radiation

NASA Astrophysics Data System (ADS)

Bartunik, Hans D.; Bartunik, Lesley J.

1992-07-01

The crystal structure of intermediate states in biological reactions of proteins of multi-protein complexes may be studied by time-resolved X-ray diffraction techniques which make use of the high spectral brilliance, continuous wavelength distribution and pulsed time structure of synchrotron radiation. Laue diffraction methods provide a means of investigating intermediate structures with lifetimes in the millisecond time range at presently operational facilities. Third-generation storage rings which are under construction may permit one to reach a time resolution of one microsecond for non-cyclic and one nanosecond for cyclic reactions. The number of individual exposures required for exploring reciprocal space and hence the total time scale strongly depend on the lattice order that may be affected, e.g., by conformational changes. Time-resolved experiments require high population of a specific intermediate which has to be homogeneous over the crystal volume. A number of external excitation techniques have been developed including in situ liberation of active metabolites by laser pulse photolysis of photolabile inactive precursors. First applications to crystal structure analysis of catalytic intermediates of enzymes demonstrate the potential of time-resolved protein crystallography.

New proposal of mechanical reinforcement structures to annular REBaCuO bulk magnet for compact and cryogen-free NMR spectrometer

NASA Astrophysics Data System (ADS)

Fujishiro, H.; Takahashi, K.; Naito, T.; Yanagi, Y.; Itoh, Y.; Nakamura, T.

2018-07-01

We have proposed new reinforcement structures using an aluminum alloy ring to the annular REBaCuO bulks applicable to compact and cryogen-free 400 MHz (9.4 T) nuclear magnetic resonance (NMR) spectrometer using a numerical simulation of mechanical stress. The thermal compressive stress, σθcool, which was applied to the annular bulks during cooling due to the difference of thermal expansion coefficient between bulk and aluminum alloy, became fairly enhanced at the surface of the uppermost bulk for the new reinforcement structures, compared to the conventional reinforcement with the same height as the annular bulk, in which the compressive σθcool value was reduced. During field-cooled magnetization (FCM), the electromagnetic hoop stress, σθFCM, became the maximum at the innermost edge of the uppermost ring bulk at intermediate time step. The actual total hoop stress, σθ (= σθcool + σθFCM), due to both cooling and FCM processes was also analyzed and the new ring structures are fairly effective to reduce the σθ value and became lower than the fracture strength of the bulk. The new reinforcement structures have a possibility to avoid the fracture of the bulks and to realize a 400 MHz NMR spectrometer.

Radiation resistant PIDECα cell using photon intermediate direct energy conversion and a 210Po source.

PubMed

Weaver, Charles L; Schott, Robert J; Prelas, Mark A; Wisniewski, Denis A; Rothenberger, Jason B; Lukosi, Eric D; Oh, Kyuhak

2018-02-01

Radiation damage is a significant concern with both alphavoltaic and betavoltaic cells because their performance degrades, especially with high-energy - (>200keV) beta and alpha particles. Indirect excitation methods, such as the Photon Intermediate Direct Energy Conversion (PIDEC) framework, can protect the transducer from radiation. A nuclear battery using a 90 Sr beta source was constructed by the author's research group, which demonstrated the radiation resistance of a PIDEC cell driven by beta particles (PIDECβ cell). Use of alpha sources to drive nuclear batteries would appear to be much more attractive than beta sources due to higher potential power density. However, they are also subject to higher rates of radiation damage. This paper describes the successful incorporation of alpha particles into the PIDEC framework using the alpha emitter 210 Po to form a PIDECα cell. The PIDECα cell transducer was exposed to alpha particles for over one year without experiencing adverse effects from radiation damage. Copyright © 2017 Elsevier Ltd. All rights reserved.

Melter Feed Reactions at T ≤ 700°C for Nuclear Waste Vitrification

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

Xu, Kai; Hrma, Pavel R.; Rice, Jarrett A.

2015-07-23

Batch reactions and phase transitions in a nuclear waste feed heated at 5 K min-1 up to 600°C were investigated by optical microscopy, scanning electron microscopy with energy dispersive X-ray spectrometer, and X-ray diffraction. Quenched samples were leached in deionized water at room temperature and 80°C to extract soluble salts and early glass-forming melt, respectively. To determine the content and composition of leachable phases, the leachates were analyzed by the inductively-coupled plasma spectroscopy. By ~400°C, gibbsite and borax lost water and converted to amorphous and intermediate crystalline phases. Between 400°C and 600°C, the sodium borate early glass-forming melt reacted withmore » amorphous aluminum oxide and calcium oxide to form intermediate products containing Al and Ca. At ~600°C, half Na and B converted to the early glass-forming melt, and quartz began to dissolve in the melt.« less

Novel origin of lamin-derived cytoplasmic intermediate filaments in tardigrades

PubMed Central

Hering, Lars; Bouameur, Jamal-Eddine; Reichelt, Julian; Magin, Thomas M; Mayer, Georg

2016-01-01

Intermediate filament (IF) proteins, including nuclear lamins and cytoplasmic IF proteins, are essential cytoskeletal components of bilaterian cells. Despite their important role in protecting tissues against mechanical force, no cytoplasmic IF proteins have been convincingly identified in arthropods. Here we show that the ancestral cytoplasmic IF protein gene was lost in the entire panarthropod (onychophoran + tardigrade + arthropod) rather than arthropod lineage and that nuclear, lamin-derived proteins instead acquired new cytoplasmic roles at least three times independently in collembolans, copepods, and tardigrades. Transcriptomic and genomic data revealed three IF protein genes in the tardigrade Hypsibius dujardini, one of which (cytotardin) occurs exclusively in the cytoplasm of epidermal and foregut epithelia, where it forms belt-like filaments around each epithelial cell. These results suggest that a lamin derivative has been co-opted to enhance tissue stability in tardigrades, a function otherwise served by cytoplasmic IF proteins in all other bilaterians. DOI: http://dx.doi.org/10.7554/eLife.11117.001 PMID:26840051

Soviet campaign against INF (intermediate-range nuclear forces): strategy, tactics, means. Interim report

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

Alexiev, A.R.

1985-02-01

Beginning in 1979, the Soviet Union mounted a major effort to prevent the deployment of NATO's INF (intermediate-range nuclear forces), which was scheduled to begin in 1983. The campaign failed to achieve its main objective, but it remains an instructive example of the Soviet effort to manipulate domestic trends in Western countries. This Note attempts to provide some insight into Soviet tactics and operational style. It places the INF issue within the framework of Soviet security concepts, reviews Soviet efforts to influence decision-making elites in West Germany against INF and to exacerbate U.S.-European friction within NATO, and analyzes the methodsmore » used by the Soviets in their campaign to co-opt the West German peace movement. The author finds that the campaign waged by the Soviets demonstrated a remarkable organizational and political capability that enabled them and their allies to exploit large numbers of noncommunists in West Germany, and contribute to the growing polarization of West German politics.« less

Structural fingerprints and their evolution during oligomeric vs. oligomer-free amyloid fibril growth

PubMed Central

Foley, Joseph; Hill, Shannon E.; Miti, Tatiana; Mulaj, Mentor; Ciesla, Marissa; Robeel, Rhonda; Persichilli, Christopher; Raynes, Rachel; Westerheide, Sandy; Muschol, Martin

2013-01-01

Deposits of fibrils formed by disease-specific proteins are the molecular hallmark of such diverse human disorders as Alzheimer's disease, type II diabetes, or rheumatoid arthritis. Amyloid fibril formation by structurally and functionally unrelated proteins exhibits many generic characteristics, most prominently the cross β-sheet structure of their mature fibrils. At the same time, amyloid formation tends to proceed along one of two separate assembly pathways yielding either stiff monomeric filaments or globular oligomers and curvilinear protofibrils. Given the focus on oligomers as major toxic species, the very existence of an oligomer-free assembly pathway is significant. Little is known, though, about the structure of the various intermediates emerging along different pathways and whether the pathways converge towards a common or distinct fibril structures. Using infrared spectroscopy we probed the structural evolution of intermediates and late-stage fibrils formed during in vitro lysozyme amyloid assembly along an oligomeric and oligomer-free pathway. Infrared spectroscopy confirmed that both pathways produced amyloid-specific β-sheet peaks, but at pathway-specific wavenumbers. We further found that the amyloid-specific dye thioflavin T responded to all intermediates along either pathway. The relative amplitudes of thioflavin T fluorescence responses displayed pathway-specific differences and could be utilized for monitoring the structural evolution of intermediates. Pathway-specific structural features obtained from infrared spectroscopy and Thioflavin T responses were identical for fibrils grown at highly acidic or at physiological pH values and showed no discernible effects of protein hydrolysis. Our results suggest that late-stage fibrils formed along either pathway are amyloidogenic in nature, but have distinguishable structural fingerprints. These pathway-specific fingerprints emerge during the earliest aggregation events and persist throughout the entire cascade of aggregation intermediates formed along each pathway. PMID:24089713

Structural fingerprints and their evolution during oligomeric vs. oligomer-free amyloid fibril growth

NASA Astrophysics Data System (ADS)

Foley, Joseph; Hill, Shannon E.; Miti, Tatiana; Mulaj, Mentor; Ciesla, Marissa; Robeel, Rhonda; Persichilli, Christopher; Raynes, Rachel; Westerheide, Sandy; Muschol, Martin

2013-09-01

Deposits of fibrils formed by disease-specific proteins are the molecular hallmark of such diverse human disorders as Alzheimer's disease, type II diabetes, or rheumatoid arthritis. Amyloid fibril formation by structurally and functionally unrelated proteins exhibits many generic characteristics, most prominently the cross β-sheet structure of their mature fibrils. At the same time, amyloid formation tends to proceed along one of two separate assembly pathways yielding either stiff monomeric filaments or globular oligomers and curvilinear protofibrils. Given the focus on oligomers as major toxic species, the very existence of an oligomer-free assembly pathway is significant. Little is known, though, about the structure of the various intermediates emerging along different pathways and whether the pathways converge towards a common or distinct fibril structures. Using infrared spectroscopy we probed the structural evolution of intermediates and late-stage fibrils formed during in vitro lysozyme amyloid assembly along an oligomeric and oligomer-free pathway. Infrared spectroscopy confirmed that both pathways produced amyloid-specific β-sheet peaks, but at pathway-specific wavenumbers. We further found that the amyloid-specific dye thioflavin T responded to all intermediates along either pathway. The relative amplitudes of thioflavin T fluorescence responses displayed pathway-specific differences and could be utilized for monitoring the structural evolution of intermediates. Pathway-specific structural features obtained from infrared spectroscopy and Thioflavin T responses were identical for fibrils grown at highly acidic or at physiological pH values and showed no discernible effects of protein hydrolysis. Our results suggest that late-stage fibrils formed along either pathway are amyloidogenic in nature, but have distinguishable structural fingerprints. These pathway-specific fingerprints emerge during the earliest aggregation events and persist throughout the entire cascade of aggregation intermediates formed along each pathway.

Structural fingerprints and their evolution during oligomeric vs. oligomer-free amyloid fibril growth.

PubMed

Foley, Joseph; Hill, Shannon E; Miti, Tatiana; Mulaj, Mentor; Ciesla, Marissa; Robeel, Rhonda; Persichilli, Christopher; Raynes, Rachel; Westerheide, Sandy; Muschol, Martin

2013-09-28

Deposits of fibrils formed by disease-specific proteins are the molecular hallmark of such diverse human disorders as Alzheimer's disease, type II diabetes, or rheumatoid arthritis. Amyloid fibril formation by structurally and functionally unrelated proteins exhibits many generic characteristics, most prominently the cross β-sheet structure of their mature fibrils. At the same time, amyloid formation tends to proceed along one of two separate assembly pathways yielding either stiff monomeric filaments or globular oligomers and curvilinear protofibrils. Given the focus on oligomers as major toxic species, the very existence of an oligomer-free assembly pathway is significant. Little is known, though, about the structure of the various intermediates emerging along different pathways and whether the pathways converge towards a common or distinct fibril structures. Using infrared spectroscopy we probed the structural evolution of intermediates and late-stage fibrils formed during in vitro lysozyme amyloid assembly along an oligomeric and oligomer-free pathway. Infrared spectroscopy confirmed that both pathways produced amyloid-specific β-sheet peaks, but at pathway-specific wavenumbers. We further found that the amyloid-specific dye thioflavin T responded to all intermediates along either pathway. The relative amplitudes of thioflavin T fluorescence responses displayed pathway-specific differences and could be utilized for monitoring the structural evolution of intermediates. Pathway-specific structural features obtained from infrared spectroscopy and Thioflavin T responses were identical for fibrils grown at highly acidic or at physiological pH values and showed no discernible effects of protein hydrolysis. Our results suggest that late-stage fibrils formed along either pathway are amyloidogenic in nature, but have distinguishable structural fingerprints. These pathway-specific fingerprints emerge during the earliest aggregation events and persist throughout the entire cascade of aggregation intermediates formed along each pathway.

A simple polymeric model describes cell nuclear mechanical response

NASA Astrophysics Data System (ADS)

Banigan, Edward; Stephens, Andrew; Marko, John

The cell nucleus must continually resist inter- and intracellular mechanical forces, and proper mechanical response is essential to basic cell biological functions as diverse as migration, differentiation, and gene regulation. Experiments probing nuclear mechanics reveal that the nucleus stiffens under strain, leading to two characteristic regimes of force response. This behavior depends sensitively on the intermediate filament protein lamin A, which comprises the outer layer of the nucleus, and the properties of the chromatin interior. To understand these mechanics, we study a simulation model of a polymeric shell encapsulating a semiflexible polymer. This minimalistic model qualitatively captures the typical experimental nuclear force-extension relation and observed nuclear morphologies. Using a Flory-like theory, we explain the simulation results and mathematically estimate the force-extension relation. The model and experiments suggest that chromatin organization is a dominant contributor to nuclear mechanics, while the lamina protects cell nuclei from large deformations.

Dynamic assembly of brambleberry mediates nuclear envelope fusion during early development.

PubMed

Abrams, Elliott W; Zhang, Hong; Marlow, Florence L; Kapp, Lee; Lu, Sumei; Mullins, Mary C

2012-08-03

To accommodate the large cells following zygote formation, early blastomeres employ modified cell divisions. Karyomeres are one such modification, mitotic intermediates wherein individual chromatin masses are surrounded by nuclear envelope; the karyomeres then fuse to form a single mononucleus. We identified brambleberry, a maternal-effect zebrafish mutant that disrupts karyomere fusion, resulting in formation of multiple micronuclei. As karyomeres form, Brambleberry protein localizes to the nuclear envelope, with prominent puncta evident near karyomere-karyomere interfaces corresponding to membrane fusion sites. brambleberry corresponds to an unannotated gene with similarity to Kar5p, a protein that participates in nuclear fusion in yeast. We also demonstrate that Brambleberry is required for pronuclear fusion following fertilization in zebrafish. Our studies provide insight into the machinery required for karyomere fusion and suggest that specialized proteins are necessary for proper nuclear division in large dividing blastomeres. Copyright © 2012 Elsevier Inc. All rights reserved.

Archival and Dissemination of the U.S. and Canadian Experimental Nuclear Reaction Data (EXFOR Project)

NASA Astrophysics Data System (ADS)

Pritychenko, Boris; Hlavac, Stanislav; Schwerer, Otto; Zerkin, Viktor

2017-09-01

The Exchange Format (EXFOR) or experimental nuclear reaction database and the associated Web interface provide access to the wealth of low- and intermediate-energy nuclear reaction physics data. This resource includes numerical data sets and bibliographical information for more than 22,000 experiments since the beginning of nuclear science. Analysis of the experimental data sets, recovery and archiving will be discussed. Examples of the recent developments of the data renormalization, uploads and inverse reaction calculations for nuclear science and technology applications will be presented. The EXFOR database, updated monthly, provides an essential support for nuclear data evaluation, application development and research activities. It is publicly available at the National Nuclear Data Center website http://www.nndc.bnl.gov/exfor and the International Atomic Energy Agency mirror site http://www-nds.iaea.org/exfor. This work was sponsored in part by the Office of Nuclear Physics, Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-98CH10886 with Brookha ven Science Associates, LLC.

Hard-X-Ray-Induced Multistep Ultrafast Dissociation

NASA Astrophysics Data System (ADS)

Travnikova, Oksana; Marchenko, Tatiana; Goldsztejn, Gildas; Jänkälä, Kari; Sisourat, Nicolas; Carniato, Stéphane; Guillemin, Renaud; Journel, Loïc; Céolin, Denis; Püttner, Ralph; Iwayama, Hiroshi; Shigemasa, Eiji; Piancastelli, Maria Novella; Simon, Marc

2016-05-01

Creation of deep core holes with very short (τ ≤1 fs ) lifetimes triggers a chain of relaxation events leading to extensive nuclear dynamics on a few-femtosecond time scale. Here we demonstrate a general multistep ultrafast dissociation on an example of HCl following Cl 1 s →σ* excitation. Intermediate states with one or multiple holes in the shallower core electron shells are generated in the course of the decay cascades. The repulsive character and large gradients of the potential energy surfaces of these intermediates enable ultrafast fragmentation after the absorption of a hard x-ray photon.

Charge Dependence and Electric Quadrupole Effects on Single-Nucleon Removal in Relativistic and Intermediate Energy Nuclear Collisions

NASA Technical Reports Server (NTRS)

Norbury, John W.

1992-01-01

Single nucleon removal in relativistic and intermediate energy nucleus-nucleus collisions is studied using a generalization of Weizsacker-Williams theory that treats each electromagnetic multipole separately. Calculations are presented for electric dipole and quadrupole excitations and incorporate a realistic minimum impact parameter, Coulomb recoil corrections, and the uncertainties in the input photonuclear data. Discrepancies are discussed. The maximum quadrupole effect to be observed in future experiments is estimated and also an analysis of the charge dependence of the electromagnetic cross sections down to energies as low as 100 MeV/nucleon is made.

Charge dependence and electric quadrupole effects on single-nucleon removal in relativistic and intermediate energy nuclear collisions

NASA Technical Reports Server (NTRS)

Norbury, J. W.; Townsend, L. W. (Principal Investigator)

1990-01-01

Single-nucleon removal in relativistic and intermediate energy nucleus-nucleus collisions is studied using a generalization of Weizsacker-Williams theory that treats each electromagnetic multipole separately. Calculations are presented for electric dipole and quadrupole excitations and incorporate a realistic minimum impact parameter, Coulomb recoil corrections, and the uncertainties in the input photonuclear data. Discrepancies are discussed. The maximum quadrupole effect to be observed in future experiments is estimated and also an analysis of the charge dependence of the electromagnetic cross sections down to energies as low as 100 MeV/nucleon is made.

Evidence for close side-chain packing in an early protein folding intermediate previously assumed to be a molten globule

PubMed Central

Rosen, Laura E.; Connell, Katelyn B.; Marqusee, Susan

2014-01-01

The molten globule, a conformational ensemble with significant secondary structure but only loosely packed tertiary structure, has been suggested to be a ubiquitous intermediate in protein folding. However, it is difficult to assess the tertiary packing of transiently populated species to evaluate this hypothesis. Escherichia coli RNase H is known to populate an intermediate before the rate-limiting barrier to folding that has long been thought to be a molten globule. We investigated this hypothesis by making mimics of the intermediate that are the ground-state conformation at equilibrium, using two approaches: a truncation to generate a fragment mimic of the intermediate, and selective destabilization of the native state using point mutations. Spectroscopic characterization and the response of the mimics to further mutation are consistent with studies on the transient kinetic intermediate, indicating that they model the early intermediate. Both mimics fold cooperatively and exhibit NMR spectra indicative of a closely packed conformation, in contrast to the hypothesis of molten tertiary packing. This result is important for understanding the nature of the subsequent rate-limiting barrier to folding and has implications for the assumption that many other proteins populate molten globule folding intermediates. PMID:25258414

Evidence for close side-chain packing in an early protein folding intermediate previously assumed to be a molten globule.

PubMed

Rosen, Laura E; Connell, Katelyn B; Marqusee, Susan

2014-10-14

The molten globule, a conformational ensemble with significant secondary structure but only loosely packed tertiary structure, has been suggested to be a ubiquitous intermediate in protein folding. However, it is difficult to assess the tertiary packing of transiently populated species to evaluate this hypothesis. Escherichia coli RNase H is known to populate an intermediate before the rate-limiting barrier to folding that has long been thought to be a molten globule. We investigated this hypothesis by making mimics of the intermediate that are the ground-state conformation at equilibrium, using two approaches: a truncation to generate a fragment mimic of the intermediate, and selective destabilization of the native state using point mutations. Spectroscopic characterization and the response of the mimics to further mutation are consistent with studies on the transient kinetic intermediate, indicating that they model the early intermediate. Both mimics fold cooperatively and exhibit NMR spectra indicative of a closely packed conformation, in contrast to the hypothesis of molten tertiary packing. This result is important for understanding the nature of the subsequent rate-limiting barrier to folding and has implications for the assumption that many other proteins populate molten globule folding intermediates.

Direct Observation of Cooperative Protein Structural Dynamics of Homodimeric Hemoglobin from 100 ps to 10 ms with Pump-Probe X-ray Solution Scattering

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

Kim, Kyung Hwan; Muniyappan, Srinivasan; Oang, Key Young

2012-05-29

Proteins serve as molecular machines in performing their biological functions, but the detailed structural transitions are difficult to observe in their native aqueous environments in real time. For example, despite extensive studies, the solution-phase structures of the intermediates along the allosteric pathways for the transitions between the relaxed (R) and tense (T) forms have been elusive. In this work, we employed picosecond X-ray solution scattering and novel structural analysis to track the details of the structural dynamics of wild-type homodimeric hemoglobin (HbI) from the clam Scapharca inaequivalvis and its F97Y mutant over a wide time range from 100 ps tomore » 56.2 ms. From kinetic analysis of the measured time-resolved X-ray solution scattering data, we identified three structurally distinct intermediates (I 1, I 2, and I 3) and their kinetic pathways common for both the wild type and the mutant. The data revealed that the singly liganded and unliganded forms of each intermediate share the same structure, providing direct evidence that the ligand photolysis of only a single subunit induces the same structural change as the complete photolysis of both subunits does. In addition, by applying novel structural analysis to the scattering data, we elucidated the detailed structural changes in the protein, including changes in the heme-heme distance, the quaternary rotation angle of subunits, and interfacial water gain/loss. The earliest, R-like I 1 intermediate is generated within 100 ps and transforms to the R-like I 2 intermediate with a time constant of 3.2 ± 0.2 ns. Subsequently, the late, T-like I 3 intermediate is formed via subunit rotation, a decrease in the heme-heme distance, and substantial gain of interfacial water and exhibits ligation-dependent formation kinetics with time constants of 730 ± 120 ns for the fully photolyzed form and 5.6 ± 0.8 μs for the partially photolyzed form. For the mutant, the overall kinetics are accelerated, and the formation of the T-like I 3 intermediate involves interfacial water loss (instead of water entry) and lacks the contraction of the heme-heme distance, thus underscoring the dramatic effect of the F97Y mutation. The ability to keep track of the detailed movements of the protein in aqueous solution in real time provides new insights into the protein structural dynamics.« less

Migration of cochlear lateral wall cells.

PubMed

Dunaway, George; Mhaskar, Yashanad; Armour, Gary; Whitworth, Craig; Rybak, Leonard

2003-03-01

The role of apoptosis and proliferation in maintenance of cochlear lateral wall cells was examined. The methods employed for detection of apoptosis were the Hoechst fluorescence stain and TUNEL (TdT-mediated dUTP-biotin nick-end-labeling) assay, and proliferations were 5-bromo-2'-deoxyuridine (BrdU) incorporation and presence of the proliferating cell nuclear antigen. The incidence of apoptosis in the strial marginal cell was 50% greater (32.9+/-3.7%) than strial intermediate and basal cells but similar to spiral ligament cells. Although division of marginal strial cells was rarely detected, a significant number of proliferating cells in the remaining stria vascularis and spiral ligament were observed. These data implied that replacement of marginal cells arose elsewhere and could be followed by a BrdU-deoxythymidine pulse-chase study. At 2 h post injection, nuclear BrdU in marginal cells was not detected; however, by 24 h post injection, 20-25% of marginal cell nuclei were BrdU-positive. These observations are consistent with the hypothesis that marginal cells were replaced by underlying cells. Cell migration appears to be an important mechanism for preserving the function and structure of the stria vascularis.

Lamins at the crossroads of mechanosignaling

PubMed Central

Osmanagic-Myers, Selma; Dechat, Thomas

2015-01-01

The intermediate filament proteins, A- and B-type lamins, form the nuclear lamina scaffold adjacent to the inner nuclear membrane. B-type lamins confer elasticity, while A-type lamins lend viscosity and stiffness to nuclei. Lamins also contribute to chromatin regulation and various signaling pathways affecting gene expression. The mechanical roles of lamins and their functions in gene regulation are often viewed as independent activities, but recent findings suggest a highly cross-linked and interdependent regulation of these different functions, particularly in mechanosignaling. In this newly emerging concept, lamins act as a “mechanostat” that senses forces from outside and responds to tension by reinforcing the cytoskeleton and the extracellular matrix. A-type lamins, emerin, and the linker of the nucleoskeleton and cytoskeleton (LINC) complex directly transmit forces from the extracellular matrix into the nucleus. These mechanical forces lead to changes in the molecular structure, modification, and assembly state of A-type lamins. This in turn activates a tension-induced “inside-out signaling” through which the nucleus feeds back to the cytoskeleton and the extracellular matrix to balance outside and inside forces. These functions regulate differentiation and may be impaired in lamin-linked diseases, leading to cellular phenotypes, particularly in mechanical load-bearing tissues. PMID:25644599

New nuclear structure data beyond 136Sn

NASA Astrophysics Data System (ADS)

Lozeva, Radomira

2018-05-01

Exotic nuclei beyond the 132Sn double shell-closure are influenced by both the Sn superfluity and the evolving collectivity only few nucleons away. Toward even more neutron-rich nuclei, especially at intermediate mass number, the interplay between single-particle and collective particle-hole excitations competes. In some cases with the extreme addition of neutrons also other effects as the formation of neutron skin, stabilization as sub-shell gaps or orbital crossings may be expected. The knowledge of nuclear ingredients is especially interesting beyond 132Sn and little is known on how the excitation modes develop with the addition of both protons and neutrons and for example systematic prompt and decay studies can be such very sensitive probe. Recently, we have approached this region of nuclei in several experimental measurements following 238U projectile fission on 9Be and n-induced fission on 241Pu and 235U. Consistent data analysis allows to access various spins and excitation energies and provide new input to theory. Examples from these studies on several nuclei in the A 140 region were presented during the conference together with the possible interpretation of the new data. Here, we will illustrate one example on 136I using two complementary data sets.

Experiments in intermediate energy physics

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

Dehnhard, D.

Research in experimental nuclear physics was done from 1979 to 2002 primarily at intermediate energy facilities that provide pion, proton, and kaon beams. Particularly successful has been the work at the Los Alamos Meson Physics Facility (LAMPF) on unraveling the neutron and proton contributions to nuclear ground state and transition densities. This work was done on a wide variety of nuclei and with great detail on the carbon, oxygen, and helium isotopes. Some of the investigations involved the use of polarized targets which allowed the extraction of information on the spin-dependent part of the triangle-nucleon interaction. At the Indiana Universitymore » Cyclotron Facility (IUCF) we studied proton-induced charge exchange reactions with results of importance to astrophysics and the nuclear few-body problem. During the first few years, the analysis of heavy-ion nucleus scattering data that had been taken prior to 1979 was completed. During the last few years we created hypernuclei by use of a kaon beam at Brookhaven National Laboratory (BNL) and an electron beam at Jefferson Laboratory (JLab). The data taken at BNL for a study of the non-mesonic weak decay of the A particle in a nucleus are still under analysis by our collaborators. The work at JLab resulted in the best resolution hypernuclear spectra measured thus far with magnetic spectrometers.« less

Systems for the Intermodal Routing of Spent Nuclear Fuel

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

Peterson, Steven K; Liu, Cheng

The safe and secure movement of spent nuclear fuel from shutdown and active reactor facilities to intermediate or long term storage sites may, in some instances, require the use of several modes of transportation to accomplish the move. To that end, a fully operable multi-modal routing system is being developed within Oak Ridge National Laboratory s (ORNL) WebTRAGIS (Transportation Routing Analysis Geographic Information System). This study aims to provide an overview of multi-modal routing, the existing state of the TRAGIS networks, the source data needs, and the requirements for developing structural relationships between various modes to create a suitable systemmore » for modeling the transport of spent nuclear fuel via a multimodal network. Modern transportation systems are comprised of interconnected, yet separate, modal networks. Efficient transportation networks rely upon the smooth transfer of cargoes at junction points that serve as connectors between modes. A key logistical impediment to the shipment of spent nuclear fuel is the absence of identified or designated transfer locations between transport modes. Understanding the potential network impacts on intermodal transportation of spent nuclear fuel is vital for planning transportation routes from origin to destination. By identifying key locations where modes intersect, routing decisions can be made to prioritize cost savings, optimize transport times and minimize potential risks to the population and environment. In order to facilitate such a process, ORNL began the development of a base intermodal network and associated routing code. The network was developed using previous intermodal networks and information from publicly available data sources to construct a database of potential intermodal transfer locations with likely capability to handle spent nuclear fuel casks. The coding development focused on modifying the existing WebTRAGIS routing code to accommodate intermodal transfers and the selection of prioritization constraints and modifiers to determine route selection. The limitations of the current model and future directions for development are discussed, including the current state of information on possible intermodal transfer locations for spent fuel.« less

A study on the dependence of nuclear viscosity on temperature

NASA Astrophysics Data System (ADS)

Vardaci, E.; Di Nitto, A.; Nadtochy, P. N.; La Rana, G.; Cinausero, M.; Prete, G.; Gelli, N.; Ashaduzzaman, M.; Davide, F.; Pulcini, A.; Quero, D.; Kozulin, E. M.; Knyazheva, G. N.; Itkis, I. M.

2018-05-01

Nuclear viscosity is an irreplaceable ingredient of nuclear fission collective dynamical models. It drives the exchange of energy between the collective variables and the thermal bath of single particle degrees of freedom. Its dependence on the shape and temperature is a matter of controversy. By using systems of intermediate fissility we have demonstrated in a recent study that the viscosity parameters is larger for compact shapes, and decreases for larger deformations of the fissioning system, at variance with the conclusions of the statistical model modified to include empirically viscosity and time scales. In this contribution we propose an experimental scenario to highlight the possible dependence of the viscosity from the temperature.

Compensatory Evolution of Intrinsic Transcription Terminators in Bacillus Cereus

PubMed Central

Safina, Ksenia R.; Mironov, Andrey A.

2017-01-01

Many RNA molecules possess complicated secondary structure critical to their function. Mutations in double-helical regions of RNA may disrupt Watson–Crick (WC) interactions causing structure destabilization or even complete loss of function. Such disruption can be compensated by another mutation restoring base pairing, as has been shown for mRNA, rRNA and tRNA. Here, we investigate the evolution of intrinsic transcription terminators between closely related strains of Bacillus cereus. While the terminator structure is maintained by strong natural selection, as evidenced by the low frequency of disrupting mutations, we observe multiple instances of pairs of disrupting-compensating mutations in RNA structure stems. Such two-step switches between different WC pairs occur very fast, consistent with the low fitness conferred by the intermediate non-WC variant. Still, they are not instantaneous, and probably involve transient fixation of the intermediate variant. The GU wobble pair is the most frequent intermediate, and remains fixed longer than other intermediates, consistent with its less disruptive effect on the RNA structure. Double switches involving non-GU intermediates are more frequent at the ends of RNA stems, probably because they are associated with smaller fitness loss. Together, these results show that the fitness landscape of bacterial transcription terminators is rather rugged, but that the fitness valleys associated with unpaired stem nucleotides are rather shallow, facilitating evolution. PMID:28201729

Evolution of microstructure of Haynes 230 and Inconel 617 under mechanical testing at high temperatures

NASA Astrophysics Data System (ADS)

Hrutkay, Kyle

Haynes 230 and Inconel 617 are austenitic nickel based superalloys, which are candidate structural materials for next generation high temperature nuclear reactors. High temperature deformation behavior of Haynes 230 and Inconel 617 have been investigated at the microstructural level in order to gain a better understanding of mechanical properties. Tensile tests were performed at strain rates ranging from 10-3-10-5 s -1 at room temperature, 600 °C, 800 °C and 950 °C. Subsequent microstructural analysis, including Scanning Electron Microscopy, Transmission Electron Microscopy, Energy-Dispersive X-ray Spectroscopy, and X-Ray Diffraction were used to relate the microstructural evolution at high temperatures to that of room temperature samples. Grain sizes and precipitate morphologies were used to determine high temperature behavior and fracture mechanics. Serrated flow was observed at intermediate and high temperatures as a result of discontinuous slip and dynamic recrystallization. The amplitude of serration increased with a decrease in the strain rate and increase in the temperature. Dynamic strain ageing was responsible for serrations at intermediate temperatures by means of a locking and unlocking phenomenon between dislocations and solute atoms. Dynamic recrystallization nucleated by grain and twin bulging resulting in a refinement of grain size. Existing models found in the literature were discussed to explain both of these phenomena.

Structural Properties of Human IAPP Dimer in Membrane Environment Studied by All-Atom Molecular Dynamics Simulations.

PubMed

Liu, Na; Duan, Mojie; Yang, Minghui

2017-08-11

The aggregation of human islet amyloid polypeptide (hIAPP) can damage the membrane of the β-cells in the pancreatic islets and induce type 2 diabetes (T2D). Growing evidences indicated that the major toxic species are small oligomers of IAPP. Due to the fast aggregation nature, it is hard to characterize the structures of IAPP oligomers by experiments, especially in the complex membrane environment. On the other side, molecular dynamics simulation can provide atomic details of the structure and dynamics of the aggregation of IAPP. In this study, all-atom bias-exchange metadynamics (BE-Meta) and unbiased molecular dynamics simulations were employed to study the structural properties of IAPP dimer in the membranes environments. A number of intermediates, including α-helical states, β-sheet states, and fully disordered states, are identified. The formation of N-terminal β-sheet structure is prior to the C-terminal β-sheet structure towards the final fibril-like structures. The α-helical intermediates have lower propensity in the dimeric hIAPP and are off-pathway intermediates. The simulations also demonstrate that the β-sheet intermediates induce more perturbation on the membrane than the α-helical and disordered states and thus pose higher disruption ability.

Nuclear lamina remodelling and its implications for human disease.

PubMed

Chojnowski, Alexandre; Ong, Peh Fern; Dreesen, Oliver

2015-06-01

The intermediate filament A- and B-type lamins are key architectural components of the nuclear lamina, a proteinaceous meshwork that lies underneath the inner nuclear membrane. In the past decade, many different monogenic human diseases have been linked to mutations in various components of the nuclear lamina. Mutations in LMNA (encoding lamin A and C) cause a variety of human diseases, collectively called laminopathies. These include cardiomyopathies, muscular dystrophies, lipodystrophies and progeroid syndromes. In addition, elevated levels of lamin B1, attributable to genomic duplications of the LMNB1 locus, cause adult-onset autosomal dominant leukodystrophy. The molecular mechanism(s) enabling the mutations and perturbations of the nuclear lamina to give rise to such a wide variety of diseases that affect various tissues remains unclear. The composition of the nuclear lamina changes dynamically during development, between cell types and even within the same cell during differentiation and ageing. Here, we discuss the functional and cellular aspects of lamina remodelling and their implications for the tissue-specific nature of laminopathies.

Reactive intermediates in 4He nanodroplets: Infrared laser Stark spectroscopy of dihydroxycarbene

NASA Astrophysics Data System (ADS)

Broderick, Bernadette M.; McCaslin, Laura; Moradi, Christopher P.; Stanton, John F.; Douberly, Gary E.

2015-04-01

Singlet dihydroxycarbene ( HO C ̈ OH ) is produced via pyrolytic decomposition of oxalic acid, captured by helium nanodroplets, and probed with infrared laser Stark spectroscopy. Rovibrational bands in the OH stretch region are assigned to either trans,trans- or trans,cis-rotamers on the basis of symmetry type, nuclear spin statistical weights, and comparisons to electronic structure theory calculations. Stark spectroscopy provides the inertial components of the permanent electric dipole moments for these rotamers. The dipole components for trans, trans- and trans, cis-rotamers are (μa, μb) = (0.00, 0.68(6)) and (1.63(3), 1.50(5)), respectively. The infrared spectra lack evidence for the higher energy cis,cis-rotamer, which is consistent with a previously proposed pyrolytic decomposition mechanism of oxalic acid and computations of HO C ̈ OH torsional interconversion and tautomerization barriers.

Potential bile acid metabolites. XV. Synthesis of 4 beta-hydroxylated bile acids; unique bile acids in human fetal bile.

PubMed

Iida, T; Momose, T; Chang, F C; Goto, J; Nambara, T

1989-12-01

The 4 beta-hydroxylated derivatives of lithocholic, deoxycholic, chenodeoxycholic, and cholic acids were synthesized from their respective parent compounds. The principal reactions employed were 1) beta-face cis-dihydroxylation of delta 3 intermediates with osmium tetroxide-N-methylmorpholine N-oxide, 2) selective cathylation of vicinal 3 beta,4 beta-diols followed by oxidation of the resulting 4 beta-monocathylates, or direct selective oxidation at C-3 of 3 beta,4 beta-diols with pyridinium chlorochromate, and 3) stereoselective reduction of the 3-oxo compounds with tert-butylamine-borane complex. The results of analysis of the prepared 4 beta-hydroxylated bile acids with a diequatorial trans-glycol structure and their 3 beta-epimers by proton and carbon-13 nuclear magnetic resonance spectroscopies are briefly discussed along with the mass spectrometric properties.

Nonlinear acoustics experimental characterization of microstructure evolution in Inconel 617

NASA Astrophysics Data System (ADS)

Yao, Xiaochu; Liu, Yang; Lissenden, Cliff J.

2014-02-01

Inconel 617 is a candidate material for the intermediate heat exchanger in a very high temperature reactor for the next generation nuclear power plant. This application will require the material to withstand fatigue-ratcheting interaction at temperatures up to 950°C. Therefore nondestructive evaluation and structural health monitoring are important capabilities. Acoustic nonlinearity (which is quantified in terms of a material parameter, the acoustic nonlinearity parameter, β) has been proven to be sensitive to microstructural changes in material. This research develops a robust experimental procedure to track the evolution of damage precursors in laboratory tested Inconel 617 specimens using ultrasonic bulk waves. The results from the acoustic non-linear tests are compared with stereoscope surface damage results. Therefore, the relationship between acoustic nonlinearity and microstructural evaluation can be clearly demonstrated for the specimens tested.

Syntheses, structures and properties of polycarbosilanes formed directly by polymerization of Alkenylsilanes

NASA Technical Reports Server (NTRS)

Masnovi, John; Bu, Xin Y.; Beyene, Kassahun; Heimann, Paula; Kacik, Terrence; Andrist, A. Harry; Hurwitz, Frances I.

1993-01-01

Vinylsilane polymerizes to form predominantly a carbosilane polymer using dimethyltitanocene catalyst. This is in contrast to alkylsilanes, which afford polysilanes under the same conditions. The mechanism of polymerization of alkenylsilanes has been shown to be fundamentally different from that for the polymerization of alkylsilanes. The silyl substitute apparently activates a double bond to participate in a number of polymerization processes in this system, particularly hydrosilation. Isotopic labeling indicates the involvement of silametallocyclic intermediates, accompanied by extensive nuclear rearrangement. Polymers and copolymers derived from alkenylsilanes have relatively high char yields even for conditions which afford low molecular weight distributions. Formation of crystalline beta-SiC is optimum for a copolymer of an alkylsilane and an alkenylsilane having a silane/carbosilane backbone ratio of 85/15 and a C/Si ratio of 1.3/1.

ASME code considerations for the compact heat exchanger

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

Nestell, James; Sham, Sam

2015-08-31

The mission of the U.S. Department of Energy (DOE), Office of Nuclear Energy is to advance nuclear power in order to meet the nation's energy, environmental, and energy security needs. Advanced high temperature reactor systems such as sodium fast reactors and high and very high temperature gas-cooled reactors are being considered for the next generation of nuclear reactor plant designs. The coolants for these high temperature reactor systems include liquid sodium and helium gas. Supercritical carbon dioxide (sCO₂), a fluid at a temperature and pressure above the supercritical point of CO₂, is currently being investigated by DOE as a workingmore » fluid for a nuclear or fossil-heated recompression closed Brayton cycle energy conversion system that operates at 550°C (1022°F) at 200 bar (2900 psi). Higher operating temperatures are envisioned in future developments. All of these design concepts require a highly effective heat exchanger that transfers heat from the nuclear or chemical reactor to the chemical process fluid or the to the power cycle. In the nuclear designs described above, heat is transferred from the primary to the secondary loop via an intermediate heat exchanger (IHX) and then from the intermediate loop to either a working process or a power cycle via a secondary heat exchanger (SHX). The IHX is a component in the primary coolant loop which will be classified as "safety related." The intermediate loop will likely be classified as "not safety related but important to safety." These safety classifications have a direct bearing on heat exchanger design approaches for the IHX and SHX. The very high temperatures being considered for the VHTR will require the use of very high temperature alloys for the IHX and SHX. Material cost considerations alone will dictate that the IHX and SHX be highly effective; that is, provide high heat transfer area in a small volume. This feature must be accompanied by low pressure drop and mechanical reliability and robustness. Classic shell and tube designs will be large and costly, and may only be appropriate in steam generator service in the SHX where boiling inside the tubes occurs. For other energy conversion systems, all of these features can be met in a compact heat exchanger design. This report will examine some of the ASME Code issues that will need to be addressed to allow use of a Code-qualified compact heat exchanger in IHX or SHX nuclear service. Most effort will focus on the IHX, since the safety-related (Class A) design rules are more extensive than those for important-to-safety (Class B) or commercial rules that are relevant to the SHX.« less

Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics

PubMed Central

Granata, Daniele; Camilloni, Carlo; Vendruscolo, Michele; Laio, Alessandro

2013-01-01

The use of free-energy landscapes rationalizes a wide range of aspects of protein behavior by providing a clear illustration of the different states accessible to these molecules, as well as of their populations and pathways of interconversion. The determination of the free-energy landscapes of proteins by computational methods is, however, very challenging as it requires an extensive sampling of their conformational spaces. We describe here a technique to achieve this goal with relatively limited computational resources by incorporating nuclear magnetic resonance (NMR) chemical shifts as collective variables in metadynamics simulations. As in this approach the chemical shifts are not used as structural restraints, the resulting free-energy landscapes correspond to the force fields used in the simulations. We illustrate this approach in the case of the third Ig-binding domain of protein G from streptococcal bacteria (GB3). Our calculations reveal the existence of a folding intermediate of GB3 with nonnative structural elements. Furthermore, the availability of the free-energy landscape enables the folding mechanism of GB3 to be elucidated by analyzing the conformational ensembles corresponding to the native, intermediate, and unfolded states, as well as the transition states between them. Taken together, these results show that, by incorporating experimental data as collective variables in metadynamics simulations, it is possible to enhance the sampling efficiency by two or more orders of magnitude with respect to standard molecular dynamics simulations, and thus to estimate free-energy differences among the different states of a protein with a kBT accuracy by generating trajectories of just a few microseconds. PMID:23572592

Human beta-globin mRNAs that harbor a nonsense codon are degraded in murine erythroid tissues to intermediates lacking regions of exon I or exons I and II that have a cap-like structure at the 5' termini.

PubMed Central

Lim, S K; Maquat, L E

1992-01-01

Previous studies have demonstrated that nonsense codons within beta zero-thalassemic or in vitro-mutagenized human beta-globin transgenes result in the production of mRNAs that are degraded abnormally rapidly in the cytoplasm of murine erythroid cells. As a consequence, three RNA degradative intermediates are formed that lack sequences from either exon I or exons I and II. We show here that the intermediates, like the full-length mRNA from which they derive and the endogenous murine beta maj-globin mRNA, bind to the anticap monoclonal antibody H-20 in a way that is competed by the cap analogue m7G and eliminated by prior exposure to tobacco acid pyrophosphatase. Furthermore, the intermediates, like the two full-length mRNAs, are resistant to a 5'----3' exonuclease activity isolated from HeLa cell nuclei that degrades uncapped but not capped ribopolymers. Based on these observations, the intermediates appear to possess a structure that is indistinguishable from the cap at the 5' end of mRNA, i.e. a methylated nucleoside that is linked to the RNA by a 5'-5' phosphodiester bond. Detection of the intermediates during murine development was concomitant with detection of full-length thalassemic mRNA. Intermediate production appears to be influenced by RNA structure as indicated by the products that derive from a beta zero-thalassemic beta-globin transgene harboring a structural alteration (a 4 bp deletion) that was larger than any of those previously studied. Images PMID:1324170

Free Radical Imaging Using In Vivo Dynamic Nuclear Polarization-MRI.

PubMed

Utsumi, Hideo; Hyodo, Fuminori

2015-01-01

Redox reactions that generate free radical intermediates are essential to metabolic processes, and their intermediates can produce reactive oxygen species, which may promote diseases related to oxidative stress. The development of an in vivo electron spin resonance (ESR) spectrometer and its imaging enables us noninvasive and direct measurement of in vivo free radical reactions in living organisms. The dynamic nuclear polarization magnetic resonance imaging (DNP-MRI), also called PEDRI or OMRI, is also a new imaging method for observing free radical species in vivo. The spatiotemporal resolution of free radical imaging with DNP-MRI is comparable with that in MRI, and each of the radical species can be distinguished in the spectroscopic images by changing the frequency or magnetic field of ESR irradiation. Several kinds of stable nitroxyl radicals were used as spin probes to detect in vivo redox reactions. The signal decay of nitroxyl probes, which is determined with in vivo DNP-MRI, reflects the redox status under oxidative stress, and the signal decay is suppressed by prior administration of antioxidants. In addition, DNP-MRI can also visualize various intermediate free radicals from the intrinsic redox molecules. This noninvasive method, in vivo DNP-MRI, could become a useful tool for investigating the mechanism of oxidative injuries in animal disease models and the in vivo effects of antioxidant drugs. © 2015 Elsevier Inc. All rights reserved.

Use of 15N reverse gradient two-dimensional nuclear magnetic resonance spectroscopy to follow metabolic activity in Nicotiana plumbaginifolia cell-suspension cultures.

PubMed

Mesnard, F; Azaroual, N; Marty, D; Fliniaux, M A; Robins, R J; Vermeersch, G; Monti, J P

2000-02-01

Nitrogen metabolism was monitored in suspension cultured cells of Nicotiana plumbaginifolia Viv. using nuclear magnetic resonance (NMR) spectroscopy following the feeding of (15NH4)2SO4 and K15NO3. By using two-dimensional 15N-1H NMR with heteronuclear single-quantum-coherence spectroscopy and heteronuclear multiple-bond-coherence spectroscopy sequences, an enhanced resolution of the incorporation of 15N label into a range of compounds could be detected. Thus, in addition to the amino acids normally observed in one-dimensional 15N NMR (glutamine, aspartate, alanine), several other amino acids could be resolved, notably serine, glycine and proline. Furthermore, it was found that the peak normally assigned to the non-protein amino-acid gamma-aminobutyric acid in the one-dimensional 15N NMR spectrum was resolved into a several components. A peak of N-acetylated compounds was resolved, probably composed of the intermediates in arginine biosynthesis, N-acetylglutamate and N-acetylornithine and, possibly, the intermediate of putrescine degradation into gamma-aminobutyric acid, N-acetylputrescine. The occurrence of 15N-label in agmatine and the low detection of labelled putrescine indicate that crucial intermediates of the pathway from glutamate to polyamines and/or the tobacco alkaloids could be monitored. For the first time, labelling of the peptide glutathione and of the nucleotide uridine could be seen.

Enhanced picture of protein-folding intermediates using organic solvents in H/D exchange and quench-flow experiments

PubMed Central

Nishimura, Chiaki; Dyson, H. Jane; Wright, Peter E.

2005-01-01

Hydrogen/deuterium exchange followed by trapping of the labeled species in the aprotic solvent DMSO has been used to elucidate structure in both the burst-phase molten globule-folding intermediate of apomyoglobin and in an equilibrium intermediate that models the kinetic intermediate. Precise estimates can be made of exchange times in an interrupted exchange-out experiment at pH 4 followed by analysis in DMSO solution, giving extensive sequence-specific information about the structure of the equilibrium intermediate. In addition, the use of DMSO as a solvent for NMR measurements after quench-flow pH-pulse labeling experiments gives a greatly increased data set for the elucidation of the kinetic folding pathway. Interestingly, differences are observed in some regions of apomyoglobin between the equilibrium and kinetic intermediates. These differences are quantitative rather than qualitative; that is, the overall patterns of labeling and secondary structure formation remain similar between the two species. However, local differences are observed, which probably reflect the difference in the solution conditions for the equilibrium experiment (pH 4) vs. the kinetic experiment (pH 6) and the change in the status of the stabilizing hydrogen bond between the side chains of His-24 and His-119. PMID:15769860

Agarose Gel Electrophoresis Reveals Structural Fluidity of a Phage T3 DNA Packaging Intermediate

PubMed Central

Serwer, Philip; Wright, Elena T.

2012-01-01

We find a new aspect of DNA packaging-associated structural fluidity for phage T3 capsids. The procedure is (1) glutaraldehyde cross-linking of in vivo DNA packaging intermediates for stabilization of structure and then (2) determining of effective radius by two-dimensional agarose gel electrophoresis (2d-AGE). The intermediates are capsids with incompletely packaged DNA (ipDNA) and without an external DNA segment; these intermediates are called ipDNA-capsids. We initially increase production of ipDNA-capsids by raising NaCl concentration during in vivo DNA packaging. By 2d-AGE, we find a new state of contracted shell for some particles of one previously identified ipDNA-capsid. The contracted shell-state is found when ipDNA length/mature DNA length (F) is above 0.17, but not at lower F. Some contracted-shell ipDNA-capsids have the phage tail; others do not. The contracted-shell ipDNA-capsids are explained by premature DNA maturation cleavage that makes accessible a contracted-shell intermediate of a cycle of the T3 DNA packaging motor. The analysis of ipDNA-capsids, rather than intermediates with uncleaved DNA, provides a simplifying strategy for a complete biochemical analysis of in vivo DNA packaging. PMID:22222979

Structure of Mandelate Racemase with Bound Intermediate Analogues Benzohydroxamate and Cupferron†

PubMed Central

Lietzan, Adam D.; Nagar, Mitesh; Pellmann, Elise A.; Bourque, Jennifer R.; Bearne, Stephen L.; St Maurice, Martin

2012-01-01

Mandelate racemase (MR, EC 5.1.2.2) from Pseudomonas putida catalyzes the Mg2+-dependent interconversion of the enantiomers of mandelate, stabilizing the altered substrate in the transition state by 26 kcal/mol relative to the substrate in the ground state. To understand the origins of this binding discrimination, we solved the X-ray crystal structures of wild-type MR complexed with two analogues of the putative aci-carboxylate intermediate, benzohydroxamate and cupferron, to 2.2-Å resolution. Benzohydroxamate is shown to be a reasonable mimic of the transition state/intermediate since its binding affinity to 21 MR variants correlates well with changes in the free energy of transition state stabilization afforded by these variants. Both benzohydroxamate and cupferron chelate the active site divalent metal ion and are bound in a conformation with the phenyl ring coplanar with the hydroxamate and diazeniumdiolate moieties, respectively. Structural overlays of MR complexed with benzohydroxamate, cupferron, and the ground state analogue (S)-atrolacatate reveal that the para-carbon of the substrate phenyl ring moves by 0.8–1.2 Å between the ground state and intermediate state, consistent with the proposal that the phenyl ring moves during MR catalysis while the polar groups remain relatively fixed. Although the overall protein structure of MR with bound intermediate analogues is very similar to MR with bound (S)-atrolactate, the intermediate-Mg2+ distance shortens, suggesting a tighter complex with the catalytic Mg2+. In addition, Tyr 54 moves nearer to the phenyl ring of the bound intermediate analogues, contributing to an overall constriction of the active site cavity. However, site-directed mutagenesis experiments revealed that the role of Tyr 54 in MR catalysis is relatively minor, suggesting that alterations in enzyme structure that contribute to discrimination between the altered substrate in the transition state and the ground state by this proficient enzyme are extremely subtle. PMID:22264153

Passive cooling safety system for liquid metal cooled nuclear reactors

DOEpatents

Hunsbedt, Anstein; Boardman, Charles E.; Hui, Marvin M.; Berglund, Robert C.

1991-01-01

A liquid metal cooled nuclear reactor having a passive cooling system for removing residual heat resulting from fuel decay during reactor shutdown. The passive cooling system comprises a plurality of partitions surrounding the reactor vessel in spaced apart relation forming intermediate areas for circulating heat transferring fluid which remove and carry away heat from the reactor vessel. The passive cooling system includes a closed primary fluid circuit through the partitions surrounding the reactor vessel and a partially adjoining secondary open fluid circuit for carrying transferred heat out into the atmosphere.

Indirect passive cooling system for liquid metal cooled nuclear reactors

DOEpatents

Hunsbedt, Anstein; Boardman, Charles E.

1990-01-01

A liquid metal cooled nuclear reactor having a passive cooling system for removing residual heat resulting from fuel decay during reactor shutdown. The passive cooling system comprises a plurality of partitions surrounding the reactor vessel in spaced apart relation forming intermediate areas for circulating heat transferring fluid which remove and carry away heat from the reactor vessel. The passive cooling system includes a closed primary fluid circuit through the partitions surrounding the reactor vessel and a partially adjoining secondary open fluid circuit for carrying transferred heat out into the atmosphere.

Timing of first embryonic cleavage is a positive indicator of the in vitro developmental potential of porcine embryos derived from in vitro fertilization, somatic cell nuclear transfer and parthenogenesis.

PubMed

Isom, S Clay; Li, Rong Feng; Whitworth, Kristin M; Prather, Randall S

2012-03-01

Evidence in many species has suggested that those embryos that cleave earliest after fertilization are more developmentally competent than those that cleave relatively later after fertilization. Herein we document this phenomenon in porcine in vitro-fertilized (IVF), somatic cell nuclear transfer (SCNT), and parthenogenetic (PA) embryos. In vitro-matured pig oocytes were used to generate IVF, SCNT, and PA embryos. At 24 hr post-activation (or insemination; hpa/hpi), embryos were visually assessed, and cleaved embryos were moved into a new culture well. This process was repeated at 30 and 48 hpa/hpi. All embryos were allowed to develop 7 days in culture. For IVF embryos, 39.9%, 24.6%, and 10.5% of fast-, intermediate-, or slow-cleaving embryos, respectively, developed into blastocysts by day 7. For SCNT embryos, 31.8% of fast-, 5.7% of intermediate-, and 2.9% of late-cleaving embryos achieved the blastocyst stage of development. For PA embryos, the percentages of those cleaved embryos that developed to blastocyst were 59.3%, 36.7%, and 7.5% for early-, intermediate-, and late-cleaving embryos, respectively. Using RNA collected from early-, intermediate-, and late-cleaving embryos, real-time PCR was performed to assess the transcript levels of 14 different genes of widely varied function. The qPCR results suggest that maternal mRNA degradation may not proceed in an appropriate pattern in slow-cleaving embryos. These findings (1) confirm that, as observed in other species, earlier-cleaving porcine embryos are more successful at developing in culture than are slower-cleaving embryos, and (2) implicate mechanisms of maternal transcript destruction as potential determinants of oocyte/embryo quality. Copyright © 2011 Wiley Periodicals, Inc.

Implementation of the Brazilian National Repository - RBMN Project - 13008

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

Cassia Oliveira de Tello, Cledola

2013-07-01

Ionizing radiation in Brazil is used in electricity generation, medicine, industry, agriculture and for research and development purposes. All these activities can generate radioactive waste. At this point, in Brazil, the use of nuclear energy and radioisotopes justifies the construction of a national repository for radioactive wastes of low and intermediate-level. According to Federal Law No. 10308, Brazilian National Commission for Nuclear Energy (CNEN) is responsible for designing and constructing the intermediate and final storages for radioactive wastes. Additionally, a restriction on the construction of Angra 3 is that the repository is under construction until its operation start, attaining somemore » requirements of the Brazilian Environmental Regulator (IBAMA). Besides this NPP, in the National Energy Program is previewed the installation of four more plants, by 2030. In November 2008, CNEN launched the Project RBMN (Repository for Low and Intermediate-Level Radioactive Wastes), which aims at the implantation of a National Repository for disposal of low and intermediate-level of radiation wastes. This Project has some aspects that are unique in the Brazilian context, especially referring to the time between its construction and the end of its institutional period. This time is about 360 years, when the area will be released for unrestricted uses. It means that the Repository must be safe and secure for more than three hundred years, which is longer than half of the whole of Brazilian history. This aspect is very new for the Brazilian people, bringing a new dimension to public acceptance. Another point is this will be the first repository in South America, bringing a real challenge for the continent. The current status of the Project is summarized. (authors)« less

Thermal analysis of heat and power plant with high temperature reactor and intermediate steam cycle

NASA Astrophysics Data System (ADS)

Fic, Adam; Składzień, Jan; Gabriel, Michał

2015-03-01

Thermal analysis of a heat and power plant with a high temperature gas cooled nuclear reactor is presented. The main aim of the considered system is to supply a technological process with the heat at suitably high temperature level. The considered unit is also used to produce electricity. The high temperature helium cooled nuclear reactor is the primary heat source in the system, which consists of: the reactor cooling cycle, the steam cycle and the gas heat pump cycle. Helium used as a carrier in the first cycle (classic Brayton cycle), which includes the reactor, delivers heat in a steam generator to produce superheated steam with required parameters of the intermediate cycle. The intermediate cycle is provided to transport energy from the reactor installation to the process installation requiring a high temperature heat. The distance between reactor and the process installation is assumed short and negligable, or alternatively equal to 1 km in the analysis. The system is also equipped with a high temperature argon heat pump to obtain the temperature level of a heat carrier required by a high temperature process. Thus, the steam of the intermediate cycle supplies a lower heat exchanger of the heat pump, a process heat exchanger at the medium temperature level and a classical steam turbine system (Rankine cycle). The main purpose of the research was to evaluate the effectiveness of the system considered and to assess whether such a three cycle cogeneration system is reasonable. Multivariant calculations have been carried out employing the developed mathematical model. The results have been presented in a form of the energy efficiency and exergy efficiency of the system as a function of the temperature drop in the high temperature process heat exchanger and the reactor pressure.

Specific limb abnormalities induced by hydrogen peroxide in tadpoles of Indian jumping frog, Polypedates maculatus.

PubMed

Mahapatra, P K; Mohanty-Hejmadi, P; Chainy, G B

2001-11-01

Hydrogen peroxide (H2O2), one of the reactive oxygen intermediates (ROI) and a potential inducer of nuclear transcription factors induces consistent type of abnormal limb development (truncated with bent skeletal elements) in the tadpoles of Indian jumping frog, Polypedates maculatus.

ENGLISH FOR TODAY. BOOK FOUR, OUR CHANGING WORLD.

ERIC Educational Resources Information Center

SLAGER, WILLIAM R.; AND OTHERS

"OUR CHANGING WORLD," THE FOURTH BOOK IN THE "ENGLISH FOR TODAY" SERIES, CONTAINS 20 READINGS DEALING PRIMARILY WITH SCIENTIFIC DEVELOPMENTS IN THE SPACE AGE. DESIGNED FOR UPPER-INTERMEDIATE STUDENTS ON SECONDARY SCHOOL LEVEL, THE TOPICS RANGE FROM JET PLANES AND ROCKETS, SATELLITES AND NUCLEAR SUBMARINES TO COMPUTERS, SUPERMARKETS, AND MIRACLE…

Microtubule minus end motors kinesin-14 and dynein drive nuclear congression in parallel pathways.

PubMed

Scheffler, Kathleen; Minnes, Refael; Fraisier, Vincent; Paoletti, Anne; Tran, Phong T

2015-04-13

Microtubules (MTs) and associated motors play a central role in nuclear migration, which is crucial for diverse biological functions including cell division, polarity, and sexual reproduction. In this paper, we report a dual mechanism underlying nuclear congression during fission yeast karyogamy upon mating of haploid cells. Using microfluidic chambers for long-term imaging, we captured the precise timing of nuclear congression and identified two minus end-directed motors operating in parallel in this process. Kinesin-14 Klp2 associated with MTs may cross-link and slide antiparallel MTs emanating from the two nuclei, whereas dynein accumulating at spindle pole bodies (SPBs) may pull MTs nucleated from the opposite SPB. Klp2-dependent nuclear congression proceeds at constant speed, whereas dynein accumulation results in an increase of nuclear velocity over time. Surprisingly, the light intermediate chain Dli1, but not dynactin, is required for this previously unknown function of dynein. We conclude that efficient nuclear congression depends on the cooperation of two minus end-directed motors. © 2015 Scheffler et al.

Emerging structural insights into glycoprotein quality control coupled with N-glycan processing in the endoplasmic reticulum.

PubMed

Satoh, Tadashi; Yamaguchi, Takumi; Kato, Koichi

2015-01-30

In the endoplasmic reticulum (ER), the sugar chain is initially introduced onto newly synthesized proteins as a triantennary tetradecasaccharide (Glc3Man9GlcNAc2). The attached oligosaccharide chain is subjected to stepwise trimming by the actions of specific glucosidases and mannosidases. In these processes, the transiently expressed N-glycans, as processing intermediates, function as signals for the determination of glycoprotein fates, i.e., folding, transport, or degradation through interactions of a series of intracellular lectins. The monoglucosylated glycoforms are hallmarks of incompletely folded states of glycoproteins in this system, whereas the outer mannose trimming leads to ER-associated glycoprotein degradation. This review outlines the recently emerging evidence regarding the molecular and structural basis of this glycoprotein quality control system, which is regulated through dynamic interplay among intracellular lectins, glycosidases, and glycosyltransferase. Structural snapshots of carbohydrate-lectin interactions have been provided at the atomic level using X-ray crystallographic analyses. Conformational ensembles of uncomplexed triantennary high-mannose-type oligosaccharides have been characterized in a quantitative manner using molecular dynamics simulation in conjunction with nuclear magnetic resonance spectroscopy. These complementary views provide new insights into glycoprotein recognition in quality control coupled with N-glycan processing.

Structural intermediates and directionality of the swiveling motion of Pyruvate Phosphate Dikinase

NASA Astrophysics Data System (ADS)

Minges, Alexander; Ciupka, Daniel; Winkler, Christian; Höppner, Astrid; Gohlke, Holger; Groth, Georg

2017-03-01

Pyruvate phosphate dikinase (PPDK) is a vital enzyme in cellular energy metabolism catalyzing the ATP- and Pi-dependent formation of phosphoenolpyruvate from pyruvate in C4 -plants, but the reverse reaction forming ATP in bacteria and protozoa. The multi-domain enzyme is considered an efficient molecular machine that performs one of the largest single domain movements in proteins. However, a comprehensive understanding of the proposed swiveling domain motion has been limited by not knowing structural intermediates or molecular dynamics of the catalytic process. Here, we present crystal structures of PPDKs from Flaveria, a model genus for studying the evolution of C4 -enzymes from phylogenetic ancestors. These structures resolve yet unknown conformational intermediates and provide the first detailed view on the large conformational transitions of the protein in the catalytic cycle. Independently performed unrestrained MD simulations and configurational free energy calculations also identified these intermediates. In all, our experimental and computational data reveal strict coupling of the CD swiveling motion to the conformational state of the NBD. Moreover, structural asymmetries and nucleotide binding states in the PPDK dimer support an alternate binding change mechanism for this intriguing bioenergetic enzyme.

Identification and characterization of the intermediate phase in hybrid organic-inorganic MAPbI3 perovskite.

PubMed

Guo, Xin; McCleese, Christopher; Kolodziej, Charles; Samia, Anna C S; Zhao, Yixin; Burda, Clemens

2016-03-07

Perovskite films were prepared using single step solution deposition at different annealing temperatures and annealing times. The crystal structure, phases and grain size were investigated with XRD, XPS and SEM/EDX. The prepared films show a typical orientation of tetragonal perovskite phase and a gradual transition at room temperature from the yellow intermediate phase to the black perovskite phase. Films with high purity were obtained by sintering at 100 °C. In addition, the chemical composition and crystal structure of intermediate phase were investigated in detail. FTIR, UV-vis and NMR spectra revealed the occurance of DMF complexes. Interestingly, the intermediate phase could be transformed to the black perovskite phase upon X-ray irradiation. In addition, the recovery of the aged perovskite films from a yellow intermediate phase back to the black perovskite was shown to be viable via heating and X-ray irradiation.

Characterization of a transient +2 sulfur oxidation state intermediate from the oxidation of aqueous sulfide

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

Vairavmurthy, M.A.; Zhou, Weiqing

1995-04-01

The oxidation H{sub 2}S to sulfate involves a net transfer of eight electrons and occurs through the formation of several partially oxidized intermediates with oxidation states ranging from {minus}1 to +5. Known intermediates include elemental sulfur (oxidation state 0), polysulfides (outer sulfur: {minus}1, inner sulfur: 0), sulfite (+4) and thiosulfate (outer sulfur: {minus}1, inner sulfur: +5). A noticeable gap in this series of intermediates is that of a +2 sulfur oxidation state oxoacid/oxoanion species, which was never detected experimentally. Here, we present evidence of the transient existence of +2 oxidation state intermediate in the Ni(II)-catalyzed oxidation of aqueous sulfide. X-raymore » absorption near-edge structure (XANES) spectroscopy and Fourier-transform-infrared (FT-IR) spectroscopy were used to characterize this species; they suggest that it has a sulfoxylate ion (SO{sub 2}{sup 2{minus}}) structure.« less

The Mechanism of Viral Replication. Structure of Replication Complexes of Encephalomyocarditis Virus

PubMed Central

Thach, Sigrid S.; Dobbertin, Darrell; Lawrence, Charles; Golini, Fred; Thach, Robert E.

1974-01-01

The structure of the purified replicative intermediate of encephalomyocarditis virus was determined by electron microscopy. Approximately 80% of the replicative intermediate complexes were characterized by a filament of double-stranded RNA of widely variable length, which had a “bush” of single-stranded RNA at one end. In many examples one or more additional single-stranded bushes were appended internally to the double-stranded RNA filament. These results support the view that before deproteinization, replicative intermediate contains little if any double-stranded RNA. Images PMID:4366773

Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds

PubMed Central

Popolan-Vaida, Denisia M.; Chen, Bingjie; Moshammer, Kai; Mohamed, Samah Y.; Wang, Heng; Sioud, Salim; Raji, Misjudeen A.; Kohse-Höinghaus, Katharina; Hansen, Nils; Dagaut, Philippe; Leone, Stephen R.

2017-01-01

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability of liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500–600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound’s molecular structure (n-alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. Finally, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels. PMID:29183984

Combined PDF and Rietveld studies of ADORable zeolites and the disordered intermediate IPC-1P.

PubMed

Morris, Samuel A; Wheatley, Paul S; Položij, Miroslav; Nachtigall, Petr; Eliášová, Pavla; Čejka, Jiří; Lucas, Tim C; Hriljac, Joseph A; Pinar, Ana B; Morris, Russell E

2016-09-28

The disordered intermediate of the ADORable zeolite UTL has been structurally confirmed using the pair distribution function (PDF) technique. The intermediate, IPC-1P, is a disordered layered compound formed by the hydrolysis of UTL in 0.1 M hydrochloric acid solution. Its structure is unsolvable by traditional X-ray diffraction techniques. The PDF technique was first benchmarked against high-quality synchrotron Rietveld refinements of IPC-2 (OKO) and IPC-4 (PCR) - two end products of IPC-1P condensation that share very similar structural features. An IPC-1P starting model derived from density functional theory was used for the PDF refinement, which yielded a final fit of Rw = 18% and a geometrically reasonable structure. This confirms the layers do stay intact throughout the ADOR process and shows PDF is a viable technique for layered zeolite structure determination.

Nuclear Data Networks

Science.gov Websites

calibrations. NSDD The international network of Nuclear Structure and Decay Data evaluators Group of and updating of nuclear structure data contained in Evaluated Nuclear Structure Data File (ENSDF

Structure and dynamics of human vimentin intermediate filament dimer and tetramer in explicit and implicit solvent models.

PubMed

Qin, Zhao; Buehler, Markus J

2011-01-01

Intermediate filaments, in addition to microtubules and microfilaments, are one of the three major components of the cytoskeleton in eukaryotic cells, and play an important role in mechanotransduction as well as in providing mechanical stability to cells at large stretch. The molecular structures, mechanical and dynamical properties of the intermediate filament basic building blocks, the dimer and the tetramer, however, have remained elusive due to persistent experimental challenges owing to the large size and fibrillar geometry of this protein. We have recently reported an atomistic-level model of the human vimentin dimer and tetramer, obtained through a bottom-up approach based on structural optimization via molecular simulation based on an implicit solvent model (Qin et al. in PLoS ONE 2009 4(10):e7294, 9). Here we present extensive simulations and structural analyses of the model based on ultra large-scale atomistic-level simulations in an explicit solvent model, with system sizes exceeding 500,000 atoms and simulations carried out at 20 ns time-scales. We report a detailed comparison of the structural and dynamical behavior of this large biomolecular model with implicit and explicit solvent models. Our simulations confirm the stability of the molecular model and provide insight into the dynamical properties of the dimer and tetramer. Specifically, our simulations reveal a heterogeneous distribution of the bending stiffness along the molecular axis with the formation of rather soft and highly flexible hinge-like regions defined by non-alpha-helical linker domains. We report a comparison of Ramachandran maps and the solvent accessible surface area between implicit and explicit solvent models, and compute the persistence length of the dimer and tetramer structure of vimentin intermediate filaments for various subdomains of the protein. Our simulations provide detailed insight into the dynamical properties of the vimentin dimer and tetramer intermediate filament building blocks, which may guide the development of novel coarse-grained models of intermediate filaments, and could also help in understanding assembly mechanisms.

Crystal structure and magnetic properties of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' containing residual {alpha}-Fe prepared by low-temperature ammonia nitridation

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

Yamashita, S.; Masubuchi, Y.; Nakazawa, Y.

2012-10-15

Slight enhancement of saturation magnetization to 219 A m{sup 2} kg{sup -1} was observed from 199 A m{sup 2} kg{sup -1} for the original {alpha}-Fe on the intermediate nitrided mixture of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' with residual {alpha}-Fe among the low temperature ammonia nitridation products under 5 T magnetic field at room temperature. The value changed not linearly against the yield as had been expected. Crystal structure refinement indicated that the phase similar to {alpha} Prime Prime -Fe{sub 16}N{sub 2} had deviations on its lattice constants and positional parameters, compared to previously reported values for {alpha} Prime Primemore » -Fe{sub 16}N{sub 2}. Spin-polarized total energy calculations were performed using the projector-augmented wave method as implemented in the Vienna ab-initio simulation package (VASP) to calculate magnetic moment on the refined crystal structure of the intermediate '{alpha} Prime Prime -Fe{sub 16}N{sub 2}'. The calculations supported the observed magnetization enhancement in the intermediate nitridation product. - Graphical abstract: Crystal structural parameters slightly change in the intermediate nitrided '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' from those in {alpha} Prime Prime -Fe{sub 16}N{sub 2} to show the magnetization maxima in the mixture of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' and the residual {alpha}-F. Highlights: Black-Right-Pointing-Pointer Larger magnetization was observed than the value of Fe{sub 16}N{sub 2} on its intermediate nitrided mixture with residual {alpha}-Fe. Black-Right-Pointing-Pointer The enhancement was related to the crystal structural deviation from Fe{sub 16}N{sub 2} on the intermediate nitride. Black-Right-Pointing-Pointer It was supported by spin-polarized total energy calculation using the deviated structure.« less

A thiamin-bound, pre-decarboxylation reaction intermediate analogue in the pyruvate dehydrogenase E1 subunit induces large scale disorder-to-order transformations in the enzyme and reveals novel structural features in the covalently bound adduct.

PubMed

Arjunan, Palaniappa; Sax, Martin; Brunskill, Andrew; Chandrasekhar, Krishnamoorthy; Nemeria, Natalia; Zhang, Sheng; Jordan, Frank; Furey, William

2006-06-02

The crystal structure of the E1 component from the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDHc) has been determined with phosphonolactylthiamin diphosphate (PLThDP) in its active site. PLThDP serves as a structural and electrostatic analogue of the natural intermediate alpha-lactylthiamin diphosphate (LThDP), in which the carboxylate from the natural substrate pyruvate is replaced by a phosphonate group. This represents the first example of an experimentally determined, three-dimensional structure of a thiamin diphosphate (ThDP)-dependent enzyme containing a covalently bound, pre-decarboxylation reaction intermediate analogue and should serve as a model for the corresponding intermediates in other ThDP-dependent decarboxylases. Regarding the PDHc-specific reaction, the presence of PLThDP induces large scale conformational changes in the enzyme. In conjunction with the E1-PLThDP and E1-ThDP structures, analysis of a H407A E1-PLThDP variant structure shows that an interaction between His-407 and PLThDP is essential for stabilization of two loop regions in the active site that are otherwise disordered in the absence of intermediate analogue. This ordering completes formation of the active site and creates a new ordered surface likely involved in interactions with the lipoyl domains of E2s within the PDHc complex. The tetrahedral intermediate analogue is tightly held in the active site through direct hydrogen bonds to residues His-407, Tyr-599, and His-640 and reveals a new, enzyme-induced, strain-related feature that appears to aid in the decarboxylation process. This feature is almost certainly present in all ThDP-dependent decarboxylases; thus its inclusion in our understanding of general thiamin catalysis is important.

LeMMINGs - I. The eMERLIN legacy survey of nearby galaxies. 1.5-GHz parsec-scale radio structures and cores

NASA Astrophysics Data System (ADS)

Baldi, R. D.; Williams, D. R. A.; McHardy, I. M.; Beswick, R. J.; Argo, M. K.; Dullo, B. T.; Knapen, J. H.; Brinks, E.; Muxlow, T. W. B.; Aalto, S.; Alberdi, A.; Bendo, G. J.; Corbel, S.; Evans, R.; Fenech, D. M.; Green, D. A.; Klöckner, H.-R.; Körding, E.; Kharb, P.; Maccarone, T. J.; Martí-Vidal, I.; Mundell, C. G.; Panessa, F.; Peck, A. B.; Pérez-Torres, M. A.; Saikia, D. J.; Saikia, P.; Shankar, F.; Spencer, R. E.; Stevens, I. R.; Uttley, P.; Westcott, J.

2018-05-01

We present the first data release of high-resolution (≤0.2 arcsec) 1.5-GHz radio images of 103 nearby galaxies from the Palomar sample, observed with the eMERLIN array, as part of the LeMMINGs survey. This sample includes galaxies which are active (low-ionization nuclear emission-line regions [LINER] and Seyfert) and quiescent (H II galaxies and absorption line galaxies, ALGs), which are reclassified based upon revised emission-line diagrams. We detect radio emission ≳0.2 mJy for 47/103 galaxies (22/34 for LINERS, 4/4 for Seyferts, 16/51 for H II galaxies, and 5/14 for ALGs) with radio sizes typically of ≲100 pc. We identify the radio core position within the radio structures for 41 sources. Half of the sample shows jetted morphologies. The remaining half shows single radio cores or complex morphologies. LINERs show radio structures more core-brightened than Seyferts. Radio luminosities of the sample range from 1032 to 1040 erg s-1: LINERs and H II galaxies show the highest and lowest radio powers, respectively, while ALGs and Seyferts have intermediate luminosities. We find that radio core luminosities correlate with black hole (BH) mass down to ˜107 M⊙, but a break emerges at lower masses. Using [O III] line luminosity as a proxy for the accretion luminosity, active nuclei and jetted H II galaxies follow an optical Fundamental Plane of BH activity, suggesting a common disc-jet relationship. In conclusion, LINER nuclei are the scaled-down version of FR I radio galaxies; Seyferts show less collimated jets; H II galaxies may host weak active BHs and/or nuclear star-forming cores; and recurrent BH activity may account for ALG properties.

Femtosecond coherent nuclear dynamics of excited tetraphenylethylene: Ultrafast transient absorption and ultrafast Raman loss spectroscopic studies

NASA Astrophysics Data System (ADS)

Kayal, Surajit; Roy, Khokan; Umapathy, Siva

2018-01-01

Ultrafast torsional dynamics plays an important role in the photoinduced excited state dynamics. Tetraphenylethylene (TPE), a model system for the molecular motor, executes interesting torsional dynamics upon photoexcitation. The photoreaction of TPE involves ultrafast internal conversion via a nearly planar intermediate state (relaxed state) that further leads to a twisted zwitterionic state. Here, we report the photoinduced structural dynamics of excited TPE during the course of photoisomerization in the condensed phase by ultrafast Raman loss (URLS) and femtosecond transient absorption (TA) spectroscopy. TA measurements on the S1 state reveal step-wise population relaxation from the Franck-Condon (FC) state → relaxed state → twisted state, while the URLS study provides insights on the vibrational dynamics during the course of the reaction. The TA spectral dynamics and vibrational Raman amplitudes within 1 ps reveal vibrational wave packet propagating from the FC state to the relaxed state. Fourier transformation of this oscillation leads to a ˜130 cm-1 low-frequency phenyl torsional mode. Two vibrational marker bands, Cet=Cet stretching (˜1512 cm-1) and Cph=Cph stretching (˜1584 cm-1) modes, appear immediately after photoexcitation in the URLS spectra. The initial red-shift of the Cph=Cph stretching mode with a time constant of ˜400 fs (in butyronitrile) is assigned to the rate of planarization of excited TPE. In addition, the Cet=Cet stretching mode shows initial blue-shift within 1 ps followed by frequency red-shift, suggesting that on the sub-picosecond time scale, structural relaxation is dominated by phenyl torsion rather than the central Cet=Cet twist. Furthermore, the effect of the solvent on the structural dynamics is discussed in the context of ultrafast nuclear dynamics and solute-solvent coupling.

Femtosecond coherent nuclear dynamics of excited tetraphenylethylene: Ultrafast transient absorption and ultrafast Raman loss spectroscopic studies.

PubMed

Kayal, Surajit; Roy, Khokan; Umapathy, Siva

2018-01-14

Ultrafast torsional dynamics plays an important role in the photoinduced excited state dynamics. Tetraphenylethylene (TPE), a model system for the molecular motor, executes interesting torsional dynamics upon photoexcitation. The photoreaction of TPE involves ultrafast internal conversion via a nearly planar intermediate state (relaxed state) that further leads to a twisted zwitterionic state. Here, we report the photoinduced structural dynamics of excited TPE during the course of photoisomerization in the condensed phase by ultrafast Raman loss (URLS) and femtosecond transient absorption (TA) spectroscopy. TA measurements on the S 1 state reveal step-wise population relaxation from the Franck-Condon (FC) state → relaxed state → twisted state, while the URLS study provides insights on the vibrational dynamics during the course of the reaction. The TA spectral dynamics and vibrational Raman amplitudes within 1 ps reveal vibrational wave packet propagating from the FC state to the relaxed state. Fourier transformation of this oscillation leads to a ∼130 cm -1 low-frequency phenyl torsional mode. Two vibrational marker bands, C et =C et stretching (∼1512 cm -1 ) and C ph =C ph stretching (∼1584 cm -1 ) modes, appear immediately after photoexcitation in the URLS spectra. The initial red-shift of the C ph =C ph stretching mode with a time constant of ∼400 fs (in butyronitrile) is assigned to the rate of planarization of excited TPE. In addition, the C et =C et stretching mode shows initial blue-shift within 1 ps followed by frequency red-shift, suggesting that on the sub-picosecond time scale, structural relaxation is dominated by phenyl torsion rather than the central C et =C et twist. Furthermore, the effect of the solvent on the structural dynamics is discussed in the context of ultrafast nuclear dynamics and solute-solvent coupling.

Conceptual-level workflow modeling of scientific experiments using NMR as a case study

PubMed Central

Verdi, Kacy K; Ellis, Heidi JC; Gryk, Michael R

2007-01-01

Background Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human reasoning are required. Workflows for experiments also highlight transitions among experimental phases, allowing intermediate results to be verified and supporting the proper handling of semantic mismatches and different file formats among the various tools used in the scientific process. Thus, scientific workflows are important for the modeling and subsequent capture of bioinformatics-related data. While much research has been conducted on the implementation of scientific workflows, the initial process of actually designing and generating the workflow at the conceptual level has received little consideration. Results We propose a structured process to capture scientific workflows at the conceptual level that allows workflows to be documented efficiently, results in concise models of the workflow and more-correct workflow implementations, and provides insight into the scientific process itself. The approach uses three modeling techniques to model the structural, data flow, and control flow aspects of the workflow. The domain of biomolecular structure determination using Nuclear Magnetic Resonance spectroscopy is used to demonstrate the process. Specifically, we show the application of the approach to capture the workflow for the process of conducting biomolecular analysis using Nuclear Magnetic Resonance (NMR) spectroscopy. Conclusion Using the approach, we were able to accurately document, in a short amount of time, numerous steps in the process of conducting an experiment using NMR spectroscopy. The resulting models are correct and precise, as outside validation of the models identified only minor omissions in the models. In addition, the models provide an accurate visual description of the control flow for conducting biomolecular analysis using NMR spectroscopy experiment. PMID:17263870

Selective alterations of the host cell architecture upon infection with parvovirus minute virus of mice

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

Nueesch, Juerg P.F.; Lachmann, Sylvie; Rommelaere, Jean

During a productive infection, the prototype strain of parvovirus minute virus of mice (MVMp) induces dramatic morphological alterations to the fibroblast host cell A9, resulting in cell lysis and progeny virus release. In order to understand the mechanisms underlying these changes, we characterized the fate of various cytoskeletal filaments and investigated the nuclear/cytoplasmic compartmentalization of infected cells. While most pronounced effects could be seen on micro- and intermediate filaments, manifest in dramatic rearrangements and degradation of filamentous (F-)actin and vimentin structures, only little impact could be seen on microtubules or the nuclear envelope during the entire monitored time of infection.more » To further analyze the disruption of the cytoskeletal structures, we investigated the viral impact on selective regulatory pathways. Thereby, we found a correlation between microtubule stability and MVM-induced phosphorylation of {alpha}/{beta} tubulin. In contrast, disassembly of actin filaments late in infection could be traced back to the disregulation of two F-actin associated proteins gelsolin and Wiscott-Aldrich Syndrome Protein (WASP). Thereby, an increase in the amount of gelsolin, an F-actin severing protein was observed during infection, accounting for the disruption of stress fibers upon infection. Concomitantly, the actin polymerization activity also diminished due to a loss of WASP, the activator protein of the actin polymerization machinery the Arp2/3 complex. No effects could be seen in amount and distribution of other F-actin regulatory factors such as cortactin, cofilin, and profilin. In summary, the selective attack of MVM towards distinct host cell cytoskeletal structures argues for a regulatory feature during infection, rather than a collapse of the host cell as a mere side effect of virus production.« less

Conceptual-level workflow modeling of scientific experiments using NMR as a case study.

PubMed

Verdi, Kacy K; Ellis, Heidi Jc; Gryk, Michael R

2007-01-30

Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human reasoning are required. Workflows for experiments also highlight transitions among experimental phases, allowing intermediate results to be verified and supporting the proper handling of semantic mismatches and different file formats among the various tools used in the scientific process. Thus, scientific workflows are important for the modeling and subsequent capture of bioinformatics-related data. While much research has been conducted on the implementation of scientific workflows, the initial process of actually designing and generating the workflow at the conceptual level has received little consideration. We propose a structured process to capture scientific workflows at the conceptual level that allows workflows to be documented efficiently, results in concise models of the workflow and more-correct workflow implementations, and provides insight into the scientific process itself. The approach uses three modeling techniques to model the structural, data flow, and control flow aspects of the workflow. The domain of biomolecular structure determination using Nuclear Magnetic Resonance spectroscopy is used to demonstrate the process. Specifically, we show the application of the approach to capture the workflow for the process of conducting biomolecular analysis using Nuclear Magnetic Resonance (NMR) spectroscopy. Using the approach, we were able to accurately document, in a short amount of time, numerous steps in the process of conducting an experiment using NMR spectroscopy. The resulting models are correct and precise, as outside validation of the models identified only minor omissions in the models. In addition, the models provide an accurate visual description of the control flow for conducting biomolecular analysis using NMR spectroscopy experiment.

VizieR Online Data Catalog: Intermediate-luminosity X-ray objects catalog (Colbert+, 2002)

NASA Astrophysics Data System (ADS)

Colbert, E. J. M.; Ptak, A. F.

2002-11-01

ROSAT, and now Chandra, X-ray images allow studies of extranuclear X-ray point sources in galaxies other than our own. X-ray observations of normal galaxies with ROSAT and Chandra have revealed that off-nuclear, compact, intermediate-luminosity (LX[2-10keV]>=1039erg/s) X-ray objects (IXOs, a.k.a. ULXs [ultraluminous X-ray sources]) are quite common. Here we present a catalog and finding charts for 87 IXOs in 54 galaxies, derived from all of the ROSAT HRI imaging data for galaxies with cz<=5000km/s from the Third Reference Catalog of Bright Galaxies. (2 data files).

VizieR Online Data Catalog: NuGrid stellar data set I. Yields from H to Bi (Pignatari+, 2016)

NASA Astrophysics Data System (ADS)

Pignatari, M.; Herwig, F.; Hirschi, R.; Bennett, M.; Rockefeller, G.; Fryer, C.; Timmes, F. X.; Ritter, C.; Heger, A.; Jones, S.; Battino, U.; Dotter, A.; Trappitsch, R.; Diehl, S.; Frischknecht, U.; Hungerford, A.; Magkotsios, G.; Travaglio, C.; Young, P.

2016-10-01

We provide a set of stellar evolution and nucleosynthesis calculations that applies established physics assumptions simultaneously to low- and intermediate-mass and massive star models. Our goal is to provide an internally consistent and comprehensive nuclear production and yield database for applications in areas such as presolar grain studies. Our non-rotating models assume convective boundary mixing (CBM) where it has been adopted before. We include 8 (12) initial masses for Z=0.01 (0.02). Models are followed either until the end of the asymptotic giant branch phase or the end of Si burning, complemented by simple analytic core-collapse supernova (SN) models with two options for fallback and shock velocities. The explosions show which pre-SN yields will most strongly be effected by the explosive nucleosynthesis. We discuss how these two explosion parameters impact the light elements and the s and p process. For low- and intermediate-mass models, our stellar yields from H to Bi include the effect of CBM at the He-intershell boundaries and the stellar evolution feedback of the mixing process that produces the 13C pocket. All post-processing nucleosynthesis calculations use the same nuclear reaction rate network and nuclear physics input. We provide a discussion of the nuclear production across the entire mass range organized by element group. The entirety of our stellar nucleosynthesis profile and time evolution output are available electronically, and tools to explore the data on the NuGrid VOspace hosted by the Canadian Astronomical Data Centre are introduced. (12 data files).

NuGrid Stellar Data Set. I.Stellar Yields from H to Bi for Stars with Metallicities Z = 0.02 and Z = 0.01

NASA Astrophysics Data System (ADS)

Pignatari, M.; Herwig, F.; Hirschi, R.; Bennett, M.; Rockefeller, G.; Fryer, C.; Timmes, F. X.; Ritter, C.; Heger, A.; Jones, S.; Battino, U.; Dotter, A.; Trappitsch, R.; Diehl, S.; Frischknecht, U.; Hungerford, A.; Magkotsios, G.; Travaglio, C.; Young, P.

2016-08-01

We provide a set of stellar evolution and nucleosynthesis calculations that applies established physics assumptions simultaneously to low- and intermediate-mass and massive star models. Our goal is to provide an internally consistent and comprehensive nuclear production and yield database for applications in areas such as presolar grain studies. Our non-rotating models assume convective boundary mixing (CBM) where it has been adopted before. We include 8 (12) initial masses for Z = 0.01 (0.02). Models are followed either until the end of the asymptotic giant branch phase or the end of Si burning, complemented by simple analytic core-collapse supernova (SN) models with two options for fallback and shock velocities. The explosions show which pre-SN yields will most strongly be effected by the explosive nucleosynthesis. We discuss how these two explosion parameters impact the light elements and the s and p process. For low- and intermediate-mass models, our stellar yields from H to Bi include the effect of CBM at the He-intershell boundaries and the stellar evolution feedback of the mixing process that produces the {}13{{C}} pocket. All post-processing nucleosynthesis calculations use the same nuclear reaction rate network and nuclear physics input. We provide a discussion of the nuclear production across the entire mass range organized by element group. The entirety of our stellar nucleosynthesis profile and time evolution output are available electronically, and tools to explore the data on the NuGrid VOspace hosted by the Canadian Astronomical Data Centre are introduced.

Physical particularities of nuclear reactors using heavy moderators of neutrons

NASA Astrophysics Data System (ADS)

Kulikov, G. G.; Shmelev, A. N.

2016-12-01

In nuclear reactors, thermal neutron spectra are formed using moderators with small atomic weights. For fast reactors, inserting such moderators in the core may create problems since they efficiently decelerate the neutrons. In order to form an intermediate neutron spectrum, it is preferable to employ neutron moderators with sufficiently large atomic weights, using 233U as a fissile nuclide and 232Th and 231Pa as fertile ones. The aim of the work is to investigate the properties of heavy neutron moderators and to assess their advantages. The analysis employs the JENDL-4.0 nuclear data library and the SCALE program package for simulating the variation of fuel composition caused by irradiation in the reactor. The following main results are obtained. By using heavy moderators with small neutron moderation steps, one is able to (1) increase the rate of resonance capture, so that the amount of fertile material in the fuel may be reduced while maintaining the breeding factor of the core; (2) use the vacant space for improving the fuel-element properties by adding inert, strong, and thermally conductive materials and by implementing dispersive fuel elements in which the fissile material is self-replenished and neutron multiplication remains stable during the process of fuel burnup; and (3) employ mixtures of different fertile materials with resonance capture cross sections in order to increase the resonance-lattice density and the probability of resonance neutron capture leading to formation of fissile material. The general conclusion is that, by forming an intermediate neutron spectrum with heavy neutron moderators, one can use the fuel more efficiently and improve nuclear safety.

Effects of the impurity-host interactions on the nonradiative processes in ZnS:Cr

NASA Astrophysics Data System (ADS)

Tablero, C.

2010-11-01

There is a great deal of controversy about whether the behavior of an intermediate band in the gap of semiconductors is similar or not to the deep-gap levels. It can have significant consequences, for example, on the nonradiative recombination. In order to analyze the behavior of an intermediate band, we have considered the effect of the inward and outward displacements corresponding to breathing and longitudinal modes of Cr-doped ZnS and on the charge density for different processes involved in the nonradiative recombination using first-principles. This metal-doped zinc chalcogenide has a partially filled band within the host semiconductor gap. In contrast to the properties exhibited by deep-gap levels in other systems, we find small variations in the equilibrium configurations, forces, and electronic density around the Cr when the nonradiative recombination mechanisms modify the intermediate band charge. The charge density around the impurity is equilibrated in response to the perturbations in the equilibrium nuclear configuration and the charge of the intermediate band. The equilibration follows a Le Chatelier principle through the modification of the contribution from the impurity to the intermediate band and to the valence band. The intermediate band introduced by Cr in ZnS for the concentrations analyzed makes the electronic capture difficult and later multiphonon emission in the charge-transfer processes, in accordance with experimental results.

Glenn T. Seaborg and heavy ion nuclear science

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

Loveland, W.

1992-04-01

Radiochemistry has played a limited but important role in the study of nucleus-nucleus collisions. Many of the important radiochemical studies have taken place in Seaborg's laboratory or in the laboratories of others who have spent time in Berkeley working with Glenn T. Seaborg. I will discuss studies of low energy deep inelastic reactions with special emphasis on charge equilibration, studies of the properties of heavy residues in intermediate energy nuclear collisions and studies of target fragmentation in relativistic and ultrarelativistic reactions. The emphasis will be on the unique information afforded by radiochemistry and the physical insight derived from radiochemical studies.more » Future roles of radiochemistry in heavy ion nuclear science also will be discussed.« less

Glenn T. Seaborg and heavy ion nuclear science

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

Loveland, W.

1992-04-01

Radiochemistry has played a limited but important role in the study of nucleus-nucleus collisions. Many of the important radiochemical studies have taken place in Seaborg`s laboratory or in the laboratories of others who have spent time in Berkeley working with Glenn T. Seaborg. I will discuss studies of low energy deep inelastic reactions with special emphasis on charge equilibration, studies of the properties of heavy residues in intermediate energy nuclear collisions and studies of target fragmentation in relativistic and ultrarelativistic reactions. The emphasis will be on the unique information afforded by radiochemistry and the physical insight derived from radiochemical studies.more » Future roles of radiochemistry in heavy ion nuclear science also will be discussed.« less

Qualitative analysis of the stability of the oxazine ring of various benzoxazine and pyridooxazine derivatives with proton nuclear magnetic resonance spectroscopy.

PubMed

Moloney, G P; Craik, D J; Iskander, M N

1992-07-01

A series of 3,4-dihydro-1,3-benzoxazine and 3,4-dihydro-1,3-pyridooxazine derivatives was synthesized, and the hydrolysis of the derivatives was studied with proton nuclear magnetic resonance spectroscopy. The oxazine derivatives underwent various degrees of hydrolysis when H2O was added to dimethyl sulfoxide solutions of the compounds. The rates and extents of decomposition of the oxazine ring systems depended on the electronic effects of substituents within the molecules. Examination of the proton nuclear magnetic resonance spectra that were generated during decomposition of the oxazines and trends in stability of the oxazine derivatives suggest the formation of an intermediate in the hydrolysis mechanism.

The Intermediate Neutrino Program

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

Adams, C.; Alonso, J. R.; Ankowski, A. M.

2017-04-03

The US neutrino community gathered at the Workshop on the Intermediate Neutrino Program (WINP) at Brookhaven National Laboratory February 4-6, 2015 to explore opportunities in neutrino physics over the next five to ten years. Scientists from particle, astroparticle and nuclear physics participated in the workshop. The workshop examined promising opportunities for neutrino physics in the intermediate term, including possible new small to mid-scale experiments, US contributions to large experiments, upgrades to existing experiments, R&D plans and theory. The workshop was organized into two sets of parallel working group sessions, divided by physics topics and technology. Physics working groups covered topicsmore » on Sterile Neutrinos, Neutrino Mixing, Neutrino Interactions, Neutrino Properties and Astrophysical Neutrinos. Technology sessions were organized into Theory, Short-Baseline Accelerator Neutrinos, Reactor Neutrinos, Detector R&D and Source, Cyclotron and Meson Decay at Rest sessions.This report summarizes discussion and conclusions from the workshop.« less

Intermediate phases in some rare earth-ruthenium systems

NASA Technical Reports Server (NTRS)

Sharifrazi, P.; Raman, A.; Mohanty, R. C.

1984-01-01

The phase equilibria and crystal structures of intermediate phases were investigated in eight representative RE-Ru systems using powder X-ray diffraction and metallographic techniques. The Fe3C, Mn5C2 and Er5Ru3 structures occur in all but the Ce-Ru systems. Phases analogous to Er5Ru3 possess an unknown crystal structure similar to Er5Rh3(I). MgCu2 and MgZn2 type Laves phases are encountered in the light rare earth and heavy rare earth systems, respectively, and RERu2 phases, where RE = Nd and Sm, possess both the Laves phase structures. An intermediate phase, NdRu, with an unknown structure, occurs only in the Nd-Ru system. A bcc structure with 40 atoms per unit cell is encountered in the phases Er3Ru2 and Y3Ru2. The behavior of cerium in Ce-Ru alloys is unique in that four unidentified structures, not encountered in other RE-Ru systems, have been encountered. Also a phase designated as Ce3Ru is found with the Th7Fe3 type structure.

The shape of the cosmic X-ray background: nuclear starburst discs and the redshift evolution of AGN obscuration

NASA Astrophysics Data System (ADS)

Gohil, R.; Ballantyne, D. R.

2018-04-01

A significant number of active galactic nuclei (AGNs) are observed to be hidden behind dust and gas. The distribution of material around AGNs plays an important role in modelling the cosmic X-ray background (CXB), especially the fraction of type 2 AGNs (f2). One of the possible explanations for obscuration in Seyfert galaxies at intermediate redshifts is dusty starburst discs. We compute the two-dimensional (2D) hydrostatic structure of 768 nuclear starburst discs (NSDs) under various physical conditions and also the distribution of column density along the line of sight (NH) associated with these discs. Then the NH distribution is evolved with redshift by using the redshift-dependent distribution function of input parameters. Parameter f2 shows a strong positive evolution up to z = 2, but only a weak level of enhancement at higher z. The Compton-thin and Compton-thick AGN fractions associated with these starburst regions increase ∝ (1 + z)δ, where δ is estimated to be 1.12 and 1.45, respectively. The reflection parameter Rf associated with column density NH ≥ 1023.5 cm-2 extends from 0.13 at z = 0 to 0.58 at z = 4. A CXB model employing this evolving NH distribution indicates that more compact (Rout < 120 pc) NSDs provide a better fit to the CXB. In addition to `Seyfert-like' AGNs obscured by nuclear starbursts, we predict that 40-60 per cent of quasars must be Compton-thick to produce a peak of the CXB spectrum within the observational uncertainty. The predicted total number counts of AGNs in 8-24 keV bands are in fair agreement with observations from the Nuclear Spectroscopic Telescope Array (NuSTAR).

Novel Insights into the Role of Neurospora crassa NDUFAF2, an Evolutionarily Conserved Mitochondrial Complex I Assembly Factor

PubMed Central

Pereira, Bruno; Videira, Arnaldo

2013-01-01

Complex I deficiency is commonly associated with mitochondrial oxidative phosphorylation diseases. Mutations in nuclear genes encoding structural subunits or assembly factors of complex I have been increasingly identified as the cause of the diseases. One such factor, NDUFAF2, is a paralog of the NDUFA12 structural subunit of the enzyme, but the mechanism by which it exerts its function remains unknown. Herein, we demonstrate that the Neurospora crassa NDUFAF2 homologue, the 13.4L protein, is a late assembly factor that associates with complex I assembly intermediates containing the membrane arm and the connecting part but lacking the N module of the enzyme. Furthermore, we provide evidence that dissociation of the assembly factor is dependent on the incorporation of the putative regulatory module composed of the subunits of 13.4 (NDUFA12), 18.4 (NDUFS6), and 21 (NDUFS4) kDa. Our results demonstrate that the 13.4L protein is a complex I assembly factor functionally conserved from fungi to mammals. PMID:23648483

Effects of relativity of RTEX in collisions of U sup q+ with light targets

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

Chen, Mau Hsiung.

1990-11-07

We have calculated the resonant transfer and excitation cross sections in collisions of U{sup q+} (q = 82, 89, 90) ion with H{sub 2}, He and C in impulse approximation using the multi-configuration Dirac-Fock method. The calculations were carried out in intermediate coupling with configuration interaction. The quantum electrodynamic and finite nuclear size corrections were included in the calculations of transition energies. The Auger rates were calculated including the contributions from Coulomb as well as the transverse Breit interactions. For U{sup 89+} and U{sup 90+}, effects of relatively not only shift the peak positions but also change the peak structure.more » The total dielectronic recombination strength has been found to increase by 50% due to the effects of relativity. The present theoretical RTEX cross sections for U{sup 90+} in hydrogen agree well with experiment. For U{sup 82+}, Breit interaction had been found to have little effect on the RTEX cross sections involving L-shell excitation. However, the spin-orbit interaction can still make significant change in the peak structure. 24 refs., 4 figs.« less

Coal liquefaction process streams characterization and evaluation: Analysis of Black Thunder coal and liquefaction products from HRI Bench Unit Run CC-15

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

Pugmire, R.J.; Solum, M.S.

This study was designed to apply {sup 13}C-nuclear magnetic resonance (NMR) spectrometry to the analysis of direct coal liquefaction process-stream materials. {sup 13}C-NMR was shown to have a high potential for application to direct coal liquefaction-derived samples in Phase II of this program. In this Phase III project, {sup 13}C-NMR was applied to a set of samples derived from the HRI Inc. bench-scale liquefaction Run CC-15. The samples include the feed coal, net products and intermediate streams from three operating periods of the run. High-resolution {sup 13}C-NMR data were obtained for the liquid samples and solid-state CP/MAS {sup 13}C-NMR datamore » were obtained for the coal and filter-cake samples. The {sup 1}C-NMR technique is used to derive a set of twelve carbon structural parameters for each sample (CONSOL Table A). Average molecular structural descriptors can then be derived from these parameters (CONSOL Table B).« less

Halo structure of 8B determined from intermediate energy proton elastic scattering in inverse kinematics

NASA Astrophysics Data System (ADS)

Korolev, G. A.; Dobrovolsky, A. V.; Inglessi, A. G.; Alkhazov, G. D.; Egelhof, P.; Estradé, A.; Dillmann, I.; Farinon, F.; Geissel, H.; Ilieva, S.; Ke, Y.; Khanzadeev, A. V.; Kiselev, O. A.; Kurcewicz, J.; Le, X. C.; Litvinov, Yu. A.; Petrov, G. E.; Prochazka, A.; Scheidenberger, C.; Sergeev, L. O.; Simon, H.; Takechi, M.; Tang, S.; Volkov, V.; Vorobyov, A. A.; Weick, H.; Yatsoura, V. I.

2018-05-01

The absolute differential cross section for small-angle proton elastic scattering on the proton-rich 8B nucleus has been measured in inverse kinematics for the first time. The experiment was performed using a secondary radioactive beam with an energy of 0.7 GeV/u at GSI, Darmstadt. The active target, namely hydrogen-filled time projection ionization chamber IKAR, was used to measure the energy, angle and vertex point of the recoil protons. The scattering angle of the projectiles was simultaneously determined by the tracking detectors. The measured differential cross section is analyzed on the basis of the Glauber multiple scattering theory using phenomenological nuclear-density distributions with two free parameters. The radial density distribution deduced for 8B exhibits a halo structure with the root-mean-square (rms) matter radius Rm = 2.58 (6) fm and the rms halo radius Rh = 4.24 (25) fm. The results on 8B are compared to those on the mirror nucleus 8Li investigated earlier by the same method. A comparison is also made with previous experimental results and theoretical predictions for both nuclei.

The role of intermediate filaments in maintaining integrity and function of intestinal epithelial cells after massive bowel resection in a rat.

PubMed

Sukhotnik, I; Shahar, Y Ben; Pollak, Y; Dorfman, T; Shefer, H Kreizman; Assi, Z E; Mor-Vaknin, N; Coran, A G

2018-02-01

Intermediate filaments (IFs) are a part of the cytoskeleton that extend throughout the cytoplasm of all cells and function in the maintenance of cell-shape by bearing tension and serving as structural components of the nuclear lamina. In normal intestine, IFs provide a tissue-specific three-dimensional scaffolding with unique context-dependent organizational features. The purpose of this study was to evaluate the role of IFs during intestinal adaptation in a rat model of short bowel syndrome (SBS). Male rats were divided into two groups: Sham rats underwent bowel transection and SBS rats underwent a 75% bowel resection. Parameters of intestinal adaptation, enterocyte proliferation and apoptosis were determined 2 weeks after operation. Illumina's Digital Gene Expression (DGE) analysis was used to determine the cytoskeleton-related gene expression profiling. IF-related genes and protein expression were determined using real-time PCR, Western blotting and immunohistochemistry. Massive small bowel resection resulted in a significant increase in enterocyte proliferation and concomitant increase in cell apoptosis. From the total number of 20,000 probes, 16 cytoskeleton-related genes were investigated. Between these genes, only myosin and tubulin levels were upregulated in SBS compared to sham animals. Between IF-related genes, desmin, vimentin and lamin levels were down-regulated and keratin and neurofilament remain unchanged. The levels of TGF-β, vimentin and desmin gene and protein were down-regulated in resected rats (vs sham animals). Two weeks following massive bowel resection in rats, the accelerated cell turnover was accompanied by a stimulated microfilaments and microtubules, and by inhibited intermediate filaments. Resistance to cell compression rather that maintenance of cell-shape by bearing tension are responsible for contraction, motility and postmitotic cell separation in a late stage of intestinal adaptation.

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

Dunn, Darrell; Poinssot, Christophe; Begg, Bruce

Management of nuclear waste remains an important international topic that includes reprocessing of commercial nuclear fuel, waste-form design and development, storage and disposal packaging, the process of repository site selection, system design, and performance assessment. Requirements to manage and dispose of materials from the production of nuclear weapons, and the renewed interest in nuclear power, in particular through the Generation IV Forum and the Advanced Fuel Cycle Initiative, can be expected to increase the need for scientific advances in waste management. A broad range of scientific and engineering disciplines is necessary to provide safe and effective solutions and address complexmore » issues. This volume offers an interdisciplinary perspective on materials-related issues associated with nuclear waste management programs. Invited and contributed papers cover a wide range of topics including studies on: spent fuel; performance assessment and models; waste forms for low- and intermediate-level waste; ceramic and glass waste forms for plutonium and high-level waste; radionuclides; containers and engineered barriers; disposal environments and site characteristics; and partitioning and transmutation.« less

Nuclear design of a vapor core reactor for space nuclear propulsion

NASA Astrophysics Data System (ADS)

Dugan, Edward T.; Watanabe, Yoichi; Kuras, Stephen A.; Maya, Isaac; Diaz, Nils J.

1993-01-01

Neutronic analysis methodology and results are presented for the nuclear design of a vapor core reactor for space nuclear propulsion. The Nuclear Vapor Thermal Reactor (NVTR) Rocket Engine uses modified NERVA geometry and systems which the solid fuel replaced by uranium tetrafluoride vapor. The NVTR is an intermediate term gas core thermal rocket engine with specific impulse in the range of 1000-1200 seconds; a thrust of 75,000 lbs for a hydrogen flow rate of 30 kg/s; average core exit temperatures of 3100 K to 3400 K; and reactor thermal powers of 1400 to 1800 MW. Initial calculations were performed on epithermal NVTRs using ZrC fuel elements. Studies are now directed at thermal NVTRs that use fuel elements made of C-C composite. The large ZrC-moderated reactors resulted in thrust-to-weight ratios of only 1 to 2; the compact C-C composite systems yield thrust-to-weight ratios of 3 to 5.

ADHESION AND POLLUTION PARTICLE-INDUCED OXIDANT GENERATION IS NEITHER NECESSARY NOR SUFFICIENT FOR CYTOKINE INDUCTION IN HUMAN ALVEOLAR MACROPHAGES

EPA Science Inventory

Adhesion of human monocytes (MOs) results in the rapid transcriptional activation of cytokine genes that are dependent on nuclear factor (NF)-kappaB. Several pathways leading to activation of NF-kappaB have been described, including those involving reactive oxygen intermediates (...

78 FR 28005 - System Energy Resources, Inc.; Grand Gulf Nuclear Station; Order Approving Direct and Indirect...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-13

... Operations, Inc. (EOI), requested on behalf of itself, SERI, and their parent companies (together, the...) will remain as the ultimate parent company, but a new intermediate company, Entergy Utilities Holdings, LLC, a Delaware limited liability company, will be created, which will be the direct parent company of...

The North Atlantic Treaty Organization at 40.

ERIC Educational Resources Information Center

Baker, John A.

1989-01-01

Surveys the history of the North Atlantic Treaty Organization's (NATO) on the 40th anniversary of the signing of the Treaty. Highlights milestones in the Organization's history of dealing with the Soviet Union, from containment to the Intermediate-Range Nuclear Forces Treaty. Discusses needs, tasks, and challenges that NATO faces in the 1990s.…

Intermediate-range Nuclear Forces (INF) negotiations and treaty: An historical case study. Master's thesis

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

Wussler, D.E.

1989-09-01

This thesis performs detailed analysis of the Intermediate Range Nuclear Forces (INF) negotiations and treaty and compares them with those of the two Strategic Arms Limitations Talks (SALT). The study's objectives were: describe SALT and INF negotiations and the contents of the treaties; analyze US and Soviet goals and strategies during the INF negotiations; determine which goals were or were not attained by both sides, and ascertain reasons for this; and delineate arms control progress and prospects since INF Treaty ratification. The study found that the two SALT treaties did impose ceilings in certain areas of strategic weapons but didmore » not curtail the arms race. Treaty verification methods were criticized as being lax. The US achieved the major goal of ridding Europe of the Soviet SS-20 missile. It had to deploy missiles of its own to make the USSR realize the seriousness of its resolve. The US had total support from NATO in achieving this goal. However, with INF gone, the European conventional forces imbalance looms larger, and the West is fighting to obtain asymmetric conventional cuts.« less

Solution state nuclear magnetic resonance spectroscopy for biological metabolism and pathway intermediate analysis.

PubMed

Nealon, Gareth L; Howard, Mark J

2016-12-15

Using nuclear magnetic resonance (NMR) spectroscopy in the study of metabolism has been immensely popular in medical- and health-related research but has yet to be widely applied to more fundamental biological problems. This review provides some NMR background relevant to metabolism, describes why 1 H NMR spectra are complex as well as introducing relevant terminology and definitions. The applications and practical considerations of NMR metabolic profiling and 13 C NMR-based flux analyses are discussed together with the elegant 'enzyme trap' approach for identifying novel metabolic pathway intermediates. The importance of sample preparation and data analysis are also described and explained with reference to data precision and multivariate analysis to introduce researchers unfamiliar with NMR and metabolism to consider this technique for their research interests. Finally, a brief glance into the future suggests NMR-based metabolism has room to expand in the 21st century through new isotope labels, and NMR technologies and methodologies. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

MOON for neutrino-less {beta}{beta} decays and {beta}{beta} nuclear matrix elements

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

Ejiri, H.

2009-11-09

The MOON project aims at spectroscopic 0v{beta}{beta} studies with the v-mass sensitivity of 100-30 meV by measuring two beta rays from {sup 100}Mo and/or {sup 82}Se. The detector is a compact super-module of multi-layer PL scintillator plates. R and D works made by the pro to-type MOON-1 and the small PL plate show the possible energy resolution of around {sigma}{approx}2.2%, as required for the mass sensitivity. Nuclear matrix elements M{sup 2v} for 2v{beta}{beta} are shown to be given by the sum {sigma}{sub L}M{sub k} of the 2v{beta}{beta} matrix elements M{sub k} through intermediate quasi-particle states in the Fermi-surface, where Mimore » is obtained experimentally by using the GT(J{sup {pi}} = 1{sup +}) matrix elements of M{sub i}(k) and M{sub f}(k) for the successive single-{beta} transitions through the k-th intermediate state.« less

Public health activities for mitigation of radiation exposures and risk communication challenges after the Fukushima nuclear accident

PubMed Central

Shimura, Tsutomu; Yamaguchi, Ichiro; Terada, Hiroshi; Robert Svendsen, Erik; Kunugita, Naoki

2015-01-01

Herein we summarize the public health actions taken to mitigate exposure of the public to radiation after the Fukushima accident that occurred on 11 March 2011 in order to record valuable lessons learned for disaster preparedness. Evacuations from the radiation-affected areas and control of the distribution of various food products contributed to the reduction of external and internal radiation exposure resulting from the Fukushima incident. However, risk communication is also an important issue during the emergency response effort and subsequent phases of dealiing with a nuclear disaster. To assist with their healing process, sound, reliable scientific information should continue to be disseminated to the radiation-affected communities via two-way communication. We will describe the essential public health actions following a nuclear disaster for the early, intermediate and late phases that will be useful for radiological preparedness planning in response to other nuclear or radiological disasters. PMID:25862700

Pegram Nuclear Physics Laboratories Progress Report for January 1969 through December 1969 to the United States Atomic Energy Commission

DTIC Science & Technology

1969-12-01

1 +1 4J. Lr) x 0 ra4 -4 Lr) C1 U4)) -I Cd Cd -1 ~ 0 r-4 Nn 0 >- C N u ~~~) +1 +1 +1 ct w +1 a) 0O u 4.-44- L"A ~ - r-5- a) Ln Ln) o +1 +1 +1 + 10 b4... 10 - 10 -7 seconds). These isomers have been observed and so were intermediate structures in the sub-threshold fission of 2 37Np, 2 34U etc., which...bo- Un n C4 1 . 0) 1.4 M) V4-1 aj ) t.) Eq 0 9d ’-4 ;:a. 0 U co 4- d H. 4) a) ,q a) 41 u 4J -rq a) ) .p4 (D 0 ’-4 o 0 D U)29. 10 1 1 Neutron TOF

Ruptured pericardial perivascular epithelioid cell tumor (PEComa) leading to sudden death: an autopsy case report and review of the literature.

PubMed

Zhang, Lingxin; Carpenter, Danielle; Dehner, Louis P

2016-01-01

A 30-year-old man with past medical history of atrial fibrillation/flutter passed away after presenting with sudden-onset cardiac dysfunction. The postmortem examination revealed cardiac tamponade secondary to rupture of a 7.2-cm pericardial perivascular epithelioid cell tumor (PEComa). The tumor grossly appeared to arise from the transverse pericardial sinus and focally penetrated the epicardium of the right atrium. Microscopically, it was composed of predominately spindle cells with low nuclear grade, no pleomorphism, or readily apparent mitoses. Immunohistochemistry revealed cytoplasmic reactivity for HMB-45, desmin, and smooth muscle actin. Electron microscopic findings were characterized by melanosome-like structures intermixed with intermediate filaments and abundant stacked endoplasmic reticulum. The present case is unique among previously reported pericardial/myocardial PEComas as a first example resulting in unexpected cardiac tamponade and sudden cardiac death. Copyright © 2016 Elsevier Inc. All rights reserved.

Synthesis and biological activity of the novel indanedione anticoagulant rodenticides containing fluorine

PubMed Central

Chen, Feng; Liu, Liping; Bai, Zengguo; Zhang, Tianhua; Zhao, Keke

2017-01-01

ABSTRACT Here, 3 fluorinated intermediates of drug were synthesized: (M1), (M2), (M3). Three new anticoagulant rodenticides were designed which were based on 4-hydroxycoumarin or 1,3-indandione, added acute toxicity groups containing fluorine. The structures of synthesized compounds were analyzed and proved by FT-IR spectroscopy and 1H nuclear magnetic resonance (1H-NMR). The compounds were also evaluated for their anticoagulant and acute biologic activity. In addition, both the acute orally toxicity and the feeding indexes of R1 and R2 were tested. The result of the experiment proved that the new synthesis of 1, 3 - indan diketone for maternal new anticoagulant rodenticide can replace the current 4 - hydroxyl coumarin as the mother of the second generation anticoagulant rodenticide and 1, 3 - indan diketone for maternal new anticoagulant rodenticides will have a good development prospect. PMID:27759485

Synthesis and biological activity of the novel indanedione anticoagulant rodenticides containing fluorine.

PubMed

Chen, Feng; Liu, Liping; Bai, Zengguo; Zhang, Tianhua; Zhao, Keke

2017-01-02

Here, 3 fluorinated intermediates of drug were synthesized: (M1), (M2), (M3). Three new anticoagulant rodenticides were designed which were based on 4-hydroxycoumarin or 1,3-indandione, added acute toxicity groups containing fluorine. The structures of synthesized compounds were analyzed and proved by FT-IR spectroscopy and 1 H nuclear magnetic resonance ( 1 H-NMR). The compounds were also evaluated for their anticoagulant and acute biologic activity. In addition, both the acute orally toxicity and the feeding indexes of R 1 and R 2 were tested. The result of the experiment proved that the new synthesis of 1, 3 - indan diketone for maternal new anticoagulant rodenticide can replace the current 4 - hydroxyl coumarin as the mother of the second generation anticoagulant rodenticide and 1, 3 - indan diketone for maternal new anticoagulant rodenticides will have a good development prospect.

The Assembly Pathway of Mitochondrial Respiratory Chain Complex I.

PubMed

Guerrero-Castillo, Sergio; Baertling, Fabian; Kownatzki, Daniel; Wessels, Hans J; Arnold, Susanne; Brandt, Ulrich; Nijtmans, Leo

2017-01-10

Mitochondrial complex I is the largest integral membrane enzyme of the respiratory chain and consists of 44 different subunits encoded in the mitochondrial and nuclear genome. Its biosynthesis is a highly complicated and multifaceted process involving at least 14 additional assembly factors. How these subunits assemble into a functional complex I and where the assembly factors come into play is largely unknown. Here, we applied a dynamic complexome profiling approach to elucidate the assembly of human mitochondrial complex I and its further incorporation into respiratory chain supercomplexes. We delineate the stepwise incorporation of all but one subunit into a series of distinct assembly intermediates and their association with known and putative assembly factors, which had not been implicated in this process before. The resulting detailed and comprehensive model of complex I assembly is fully consistent with recent structural data and the remarkable modular architecture of this multiprotein complex. Copyright © 2017 Elsevier Inc. All rights reserved.

Development of a New 47-Group Library for the CASL Neutronics Simulators

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

Kim, Kang Seog; Williams, Mark L; Wiarda, Dorothea

The CASL core simulator MPACT is under development for the neutronics and thermal-hydraulics coupled simulation for the pressurized light water reactors. The key characteristics of the MPACT code include a subgroup method for resonance self-shielding, and a whole core solver with a 1D/2D synthesis method. The ORNL AMPX/SCALE code packages have been significantly improved to support various intermediate resonance self-shielding approximations such as the subgroup and embedded self-shielding methods. New 47-group AMPX and MPACT libraries based on ENDF/B-VII.0 have been generated for the CASL core simulator MPACT of which group structure comes from the HELIOS library. The new 47-group MPACTmore » library includes all nuclear data required for static and transient core simulations. This study discusses a detailed procedure to generate the 47-group AMPX and MPACT libraries and benchmark results for the VERA progression problems.« less

Irc3 is a mitochondrial DNA branch migration enzyme

PubMed Central

Gaidutšik, Ilja; Sedman, Tiina; Sillamaa, Sirelin; Sedman, Juhan

2016-01-01

Integrity of mitochondrial DNA (mtDNA) is essential for cellular energy metabolism. In the budding yeast Saccharomyces cerevisiae, a large number of nuclear genes influence the stability of mitochondrial genome; however, most corresponding gene products act indirectly and the actual molecular mechanisms of mtDNA inheritance remain poorly characterized. Recently, we found that a Superfamily II helicase Irc3 is required for the maintenance of mitochondrial genome integrity. Here we show that Irc3 is a mitochondrial DNA branch migration enzyme. Irc3 modulates mtDNA metabolic intermediates by preferential binding and unwinding Holliday junctions and replication fork structures. Furthermore, we demonstrate that the loss of Irc3 can be complemented with mitochondrially targeted RecG of Escherichia coli. We suggest that Irc3 could support the stability of mtDNA by stimulating fork regression and branch migration or by inhibiting the formation of irregular branched molecules. PMID:27194389

Reactive intermediates in 4He nanodroplets: Infrared laser Stark spectroscopy of dihydroxycarbene

DOE PAGES

Broderick, Bernadette M.; McCaslin, Laura; Moradi, Christopher P.; ...

2015-04-14

Singlet dihydroxycarbene (HOmore » $$\\ddot C$$OH) is produced via pyrolytic decomposition of oxalic acid, captured by helium nanodroplets, and probed with infrared laser Stark spectroscopy. Rovibrational bands in the OH stretch region are assigned to either trans, trans-or trans, cis-rotamers on the basis of symmetry type, nuclear spin statistical weights, and comparisons to electronic structure theory calculations. Stark spectroscopy provides the inertial components of the permanent electric dipole moments for these rotamers. The dipole components for trans, trans-and trans, cis-rotamers are (μ a, μ b) = (0.00,0.68(6)) and (1.63(3), 1.50(5)), respectively. The infrared spectra lack evidence for the higher energy cis,cis-rotamer, which is consistent with a previously proposed pyrolytic decomposition mechanism of oxalic acid and computations of HO$$\\ddot C$$OH torsional interconversion and tautomerization barriers.« less

Epigenetic silencing of a foreign gene in nuclear transformants of Chlamydomonas.

PubMed Central

Cerutti, H; Johnson, A M; Gillham, N W; Boynton, J E

1997-01-01

The unstable expression of introduced genes poses a serious problem for the application of transgenic technology in plants. In transformants of the unicellular green alga Chlamydomonas reinhardtii, expression of a eubacterial aadA gene, conferring spectinomycin resistance, is transcriptionally suppressed by a reversible epigenetic mechanism(s). Variations in the size and frequency of colonies surviving on different concentrations of spectinomycin as well as the levels of transcriptional activity of the introduced transgene(s) suggest the existence of intermediate expression states in genetically identical cells. Gene silencing does not correlate with methylation of the integrated DNA and does not involve large alterations in its chromatin structure, as revealed by digestion with restriction endonucleases and DNase I. Transgene repression is enhanced by lower temperatures, similar to position effect variegation in Drosophila. By analogy to epigenetic phenomena in several eukaryotes, our results suggest a possible role for (hetero)chromatic chromosomal domains in transcriptional inactivation. PMID:9212467

[Studies of the morphology of the thyroid gland and thyroid hormone levels in the blood of rats in experiments on "Kosmos-1667" and "Kosmos-1887"].

PubMed

Plakhuta-Plakutina, G I; Kabitskiĭ, E N; Dmitrieva, N P; Amirkhanian, E A

1990-01-01

Using histological, electron microscopic, and biochemical (measurement of total thyroxine, free thyroxine and triiodothyronine in plasma) method, thyroid glands of 17 male rats of the Wistar SPF strain flown for 7 days on Cosmos-1667 and for 13 days on Cosmos-1887 were investigated. It was found that a longer exposure to space flight effects (for 13 days) led to a thyroid activity decline (significant reduction of thyrocyte size and nuclear area, accumulation of colloid drops in the cytoplasm, decrease of iodinated thyroglobulins in the colloid, etc.) together with a substantial decrease of T4 and T3 in plasma. The above structural and functional changes in the thyroid gland and hormonal status are characteristic of a moderate stress-reaction and reflect variations of the early and intermediate stages of adaptation to microgravity during 7- and 13-day space flights.

Time-resolved distance determination by tryptophan fluorescence quenching: probing intermediates in membrane protein folding.

PubMed

Kleinschmidt, J H; Tamm, L K

1999-04-20

The mechanism of insertion and folding of an integral membrane protein has been investigated with the beta-barrel forming outer membrane protein A (OmpA) of Escherichia coli. This work describes a new approach to this problem by combining structural information obtained from tryptophan fluorescence quenching at different depths in the lipid bilayer with the kinetics of the refolding process. Experiments carried out over a temperature range between 2 and 40 degrees C allowed us to detect, trap, and characterize previously unidentified folding intermediates on the pathway of OmpA insertion and folding into lipid bilayers. Three membrane-bound intermediates were found in which the average distances of the Trps were 14-16, 10-11, and 0-5 A, respectively, from the bilayer center. The first folding intermediate is stable at 2 degrees C for at least 1 h. A second intermediate has been isolated at temperatures between 7 and 20 degrees C. The Trps move 4-5 A closer to the center of the bilayer at this stage. Subsequently, in an intermediate that is observable at 26-28 degrees C, the Trps move another 5-10 A closer to the center of the bilayer. The final (native) structure is observed at higher temperatures of refolding. In this structure, the Trps are located on average about 9-10 A from the bilayer center. Monitoring the evolution of Trp fluorescence quenching by a set of brominated lipids during refolding at various temperatures therefore allowed us to identify and characterize intermediate states in the folding process of an integral membrane protein.

Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds.

PubMed

Wang, Zhandong; Popolan-Vaida, Denisia M; Chen, Bingjie; Moshammer, Kai; Mohamed, Samah Y; Wang, Heng; Sioud, Salim; Raji, Misjudeen A; Kohse-Höinghaus, Katharina; Hansen, Nils; Dagaut, Philippe; Leone, Stephen R; Sarathy, S Mani

2017-12-12

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability of liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500-600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound's molecular structure ( n -alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. Finally, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels. Copyright © 2017 the Author(s). Published by PNAS.

Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds

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

Wang, Zhandong; Popolan-Vaida, Denisia M.; Chen, Bingjie

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability ofmore » liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500–600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound’s molecular structure (n-alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. In conclusion, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels.« less

Unraveling the structure and chemical mechanisms of highly oxygenated intermediates in oxidation of organic compounds

DOE PAGES

Wang, Zhandong; Popolan-Vaida, Denisia M.; Chen, Bingjie; ...

2017-11-28

Decades of research on the autooxidation of organic compounds have provided fundamental and practical insights into these processes; however, the structure of many key autooxidation intermediates and the reactions leading to their formation still remain unclear. This work provides additional experimental evidence that highly oxygenated intermediates with one or more hydroperoxy groups are prevalent in the autooxidation of various oxygenated (e.g., alcohol, aldehyde, keto compounds, ether, and ester) and nonoxygenated (e.g., normal alkane, branched alkane, and cycloalkane) organic compounds. These findings improve our understanding of autooxidation reaction mechanisms that are routinely used to predict fuel ignition and oxidative stability ofmore » liquid hydrocarbons, while also providing insights relevant to the formation mechanisms of tropospheric aerosol building blocks. The direct observation of highly oxygenated intermediates for the autooxidation of alkanes at 500–600 K builds upon prior observations made in atmospheric conditions for the autooxidation of terpenes and other unsaturated hydrocarbons; it shows that highly oxygenated intermediates are stable at conditions above room temperature. These results further reveal that highly oxygenated intermediates are not only accessible by chemical activation but also by thermal activation. Theoretical calculations on H-atom migration reactions are presented to rationalize the relationship between the organic compound’s molecular structure (n-alkane, branched alkane, and cycloalkane) and its propensity to produce highly oxygenated intermediates via extensive autooxidation of hydroperoxyalkylperoxy radicals. In conclusion, detailed chemical kinetic simulations demonstrate the influence of these additional reaction pathways on the ignition of practical fuels.« less

Quantum Chemical Mass Spectrometry: Verification and Extension of the Mobile Proton Model for Histidine

NASA Astrophysics Data System (ADS)

Cautereels, Julie; Blockhuys, Frank

2017-06-01

The quantum chemical mass spectrometry for materials science (QCMS2) method is used to verify the proposed mechanism for proton transfer - the Mobile Proton Model (MPM) - by histidine for ten XHS tripeptides, based on quantum chemical calculations at the DFT/B3LYP/6-311+G* level of theory. The fragmentations of the different intermediate structures in the MPM mechanism are studied within the QCMS2 framework, and the energetics of the proposed mechanism itself and those of the fragmentations of the intermediate structures are compared, leading to the computational confirmation of the MPM. In addition, the calculations suggest that the mechanism should be extended from considering only the formation of five-membered ring intermediates to include larger-ring intermediates. [Figure not available: see fulltext.

Peroxo and Oxo Intermediates in Mononuclear Non-heme Iron Enzymes and Related Active Sites

PubMed Central

Wong, Shaun D.; Liu, Lei V.; Decker, Andrea; Chow, Marina S.

2009-01-01

Summary FeIII–OOH and FeIV=O intermediates have now been documented in a number of non-heme iron active sites. In this Opinion we use spectroscopy combined with electronic structure calculations to define the frontier molecular orbitals (FMOs) of these species and their contributions to reactivity. For the low-spin FeIII–OOH species in activated bleomycin we show that the reactivity of this non-heme iron intermediate is very different from that of the analogous Compound 0 of cytochrome P450. For FeIV=O S = 1 model species we experimentally define the electronic structure and its contribution to reactivity, and computationally evaluate how this would change for the FeIV=O S = 2 intermediates found in non-heme iron enzymes. PMID:19278895

α versus non-α cluster decays of the excited compound nucleus *124Ce using various formulations of the nuclear proximity potential

NASA Astrophysics Data System (ADS)

Kaur, Arshdeep; Chopra, Sahila; Gupta, Raj K.

2015-06-01

The earlier study of *124Ce formed in the 32S+92Mo reaction at an above barrier beam energy of 150 MeV, using the pocket formula of Blocki et al. for the nuclear proximity potential in the dynamical cluster-decay model (DCM), is extended to the use of other nuclear interaction potentials derived from the Skyrme energy density functional (SEDF) based on the semiclassical extended Thomas Fermi (ETF) approach under the frozen density approximation. The Skyrme forces used are the old SII, SIII, SIV, SKa, SkM, and SLy4 and new GSkI and KDE0(v1), given for both normal and isospin-rich nuclei. It is found that the α -nucleus structure, over the non-α nucleus structure, is preferred for only two Skyrme forces, the SIII and KDE0(v1). An extended intermediate mass fragments (IMFs) window, along with the new decay region of heavy mass fragments (HMFs) and the near-symmetric and symmetric fission fragments which, on adding the complementary heavy fragments, corresponds to (A /2 )±12 mass region of the fusion-fission (ff) process, are predicted by considering cross sections of orders observed in the experiment under study. For the predicted (total) fusion cross section, the survival probability Psurv of the compound nucleus (CN) against fission is shown to be very small because of the very large predicted ff component. On the other hand, the CN formation probability PCN is found to be nearly equal to 1, and hence the decay under study is a pure CN decay for all the nuclear potentials considered, since the estimated noncompound nucleus (nCN) content is almost negligible. We have also applied the extended-Wong model of Gupta and collaborators, and find that the ℓmax values and total fusion cross sections are of the same order as for the DCM. Thus, the extended-Wong model, which describes only the total fusion cross section in terms of the barrier characteristics of the entrance channel nuclei, could be useful for initial experimental studies to be fully treated using the DCM for all the observed decay products.

Alpha-Helical Protein Networks Are Self-Protective and Flaw-Tolerant

PubMed Central

Ackbarow, Theodor; Sen, Dipanjan; Thaulow, Christian; Buehler, Markus J.

2009-01-01

Alpha-helix based protein networks as they appear in intermediate filaments in the cell’s cytoskeleton and the nuclear membrane robustly withstand large deformation of up to several hundred percent strain, despite the presence of structural imperfections or flaws. This performance is not achieved by most synthetic materials, which typically fail at much smaller deformation and show a great sensitivity to the existence of structural flaws. Here we report a series of molecular dynamics simulations with a simple coarse-grained multi-scale model of alpha-helical protein domains, explaining the structural and mechanistic basis for this observed behavior. We find that the characteristic properties of alpha-helix based protein networks are due to the particular nanomechanical properties of their protein constituents, enabling the formation of large dissipative yield regions around structural flaws, effectively protecting the protein network against catastrophic failure. We show that the key for these self protecting properties is a geometric transformation of the crack shape that significantly reduces the stress concentration at corners. Specifically, our analysis demonstrates that the failure strain of alpha-helix based protein networks is insensitive to the presence of structural flaws in the protein network, only marginally affecting their overall strength. Our findings may help to explain the ability of cells to undergo large deformation without catastrophic failure while providing significant mechanical resistance. PMID:19547709

The impact of intermediate care services on job satisfaction, skills and career development opportunities.

PubMed

Nancarrow, Susan

2007-07-01

The purpose of this study was to examine, in depth, the impact of intermediate care services on staff job satisfaction, skills development and career development opportunities. Recruitment and retention difficulties present a major barrier to the effective delivery of intermediate care services in the UK. The limited existing literature is contradictory, but points to the possibility of staff deskilling and suggests that intermediate care is poorly understood and may be seen by other practitioners as being of lower status than hospital work. These factors have the potential to reduce staff morale and limit the possibilities of recruiting staff. The research is based on interviews with 26 staff from case studies of two intermediate care services in South Yorkshire. Participants reported high levels of job satisfaction, which was because of the enabling philosophy of care, increased autonomy, the setting of care and the actual teams within which the workers were employed. For most disciplines, intermediate care facilitated the application of existing skills in a different way; enhancing some skills, while restricting the use of others. Barriers to career development opportunities were attributed to the relative recency of intermediate care services, small size of the services and lack of clear career structures. Career development opportunities in intermediate care could be improved through staff rotations through acute, community and intermediate care to increase their awareness of the roles of intermediate care staff. The non-hierarchical management structures limits management career development opportunities, instead, there is a need to enhance professional growth opportunities through the use of consultant posts and specialization within intermediate care. This study provides insight into the impact of an increasingly popular model of care on the roles and job satisfaction of workers and highlights the importance of this learning for recruitment and retention of staff.

Characterization of reaction intermediate aggregates in aniline oxidative polymerization at low proton concentration.

PubMed

Ding, Zhongfen; Sanchez, Timothy; Labouriau, Andrea; Iyer, Srinivas; Larson, Toti; Currier, Robert; Zhao, Yusheng; Yang, Dali

2010-08-19

Aggregates of reaction intermediates form during the early stages of aniline oxidative polymerization whenever the initial mole ratio of proton concentration to aniline monomer concentration is low ([H(+)](0)/[An](0)

Structure based aggregation studies reveal the presence of helix-rich intermediate during α-Synuclein aggregation

PubMed Central

Ghosh, Dhiman; Singh, Pradeep K.; Sahay, Shruti; Jha, Narendra Nath; Jacob, Reeba S.; Sen, Shamik; Kumar, Ashutosh; Riek, Roland; Maji, Samir K.

2015-01-01

Mechanistic understanding of nucleation dependent polymerization by α-synuclein (α-Syn) into toxic oligomers and amyloids is important for the drug development against Parkinson's disease. However the structural and morphological characterization during nucleation and subsequent fibrillation process of α-Syn is not clearly understood. Using a variety of complementary biophysical techniques monitoring entire pathway of nine different synucleins, we found that transition of unstructured conformation into β-sheet rich fibril formation involves helix-rich intermediates. These intermediates are common for all aggregating synucleins, contain high solvent-exposed hydrophobic surfaces, are cytotoxic to SHSY-5Y cells and accelerate α-Syn aggregation efficiently. A multidimensional NMR study characterizing the intermediate accompanied with site-specific fluorescence study suggests that the N-terminal and central portions mainly participate in the helix-rich intermediate formation while the C-terminus remained in an extended conformation. However, significant conformational transitions occur at the middle and at the C-terminus during helix to β-sheet transition as evident from Trp fluorescence study. Since partial helix-rich intermediates were also observed for other amyloidogenic proteins such as Aβ and IAPP, we hypothesize that this class of intermediates may be one of the important intermediates for amyloid formation pathway by many natively unstructured protein/peptides and represent a potential target for drug development against amyloid diseases. PMID:25784353

First Search for the EMC Effect and Nuclear Shadowing in Neutrino Nucleus Deep Inelastic Scattering at MINERvA

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

Mousseau, Joel A.

2015-01-01

Decades of research in electron-nucleus deep inelastic scattering (DIS) have provided a clear picture of nuclear physics at high momentum transfer. While these effects have been clearly demonstrated by experiment, the theoretical explanation of their origin in some kinematic regions has been lacking. Particularly, the effects in the intermediate regions of Bjorken-x, anti-shadowing and the EMC effect have no universally accepted quantum mechanical explanation. In addition, these effects have not been measured systematically with neutrino-nucleus deep inelastic scattering, due to experiments lacking multiple heavy targets.

The cytoplasmic mRNA degradation factor Pat1 is required for rRNA processing

PubMed Central

Muppavarapu, Mridula; Huch, Susanne; Nissan, Tracy

2016-01-01

ABSTRACT Pat1 is a key cytoplasmic mRNA degradation factor, the loss of which severely increases mRNA half-lives. Several recent studies have shown that Pat1 can enter the nucleus and can shuttle between the nucleus and the cytoplasm. As a result, many nuclear roles have been proposed for Pat1. In this study, we analyzed four previously suggested nuclear roles of Pat1 and show that Pat1 is not required for efficient pre-mRNA splicing or pre-mRNA decay in yeast. However, lack of Pat1 results in accumulation of pre-rRNA processing intermediates. Intriguingly, we identified a novel genetic relationship between Pat1 and the rRNA decay machinery, specifically the exosome and the TRAMP complex. While the pre-rRNA processing intermediates that accumulate in the pat1 deletion mutant are, at least to some extent, recognized as aberrant by the rRNA degradation machinery, it is unlikely that these accumulations are the cause of their synthetic sick relationship. Here, we show that the dysregulation of the levels of mRNAs related to ribosome biogenesis could be the cause of the accumulation of the pre-rRNA processing intermediates. Although our results support a role for Pat1 in transcription, they nevertheless suggest that the primary cause of the dysregulated mRNA levels is most likely due to Pat1's role in mRNA decapping and mRNA degradation. PMID:26918764

The cytoplasmic mRNA degradation factor Pat1 is required for rRNA processing.

PubMed

Muppavarapu, Mridula; Huch, Susanne; Nissan, Tracy

2016-01-01

Pat1 is a key cytoplasmic mRNA degradation factor, the loss of which severely increases mRNA half-lives. Several recent studies have shown that Pat1 can enter the nucleus and can shuttle between the nucleus and the cytoplasm. As a result, many nuclear roles have been proposed for Pat1. In this study, we analyzed four previously suggested nuclear roles of Pat1 and show that Pat1 is not required for efficient pre-mRNA splicing or pre-mRNA decay in yeast. However, lack of Pat1 results in accumulation of pre-rRNA processing intermediates. Intriguingly, we identified a novel genetic relationship between Pat1 and the rRNA decay machinery, specifically the exosome and the TRAMP complex. While the pre-rRNA processing intermediates that accumulate in the pat1 deletion mutant are, at least to some extent, recognized as aberrant by the rRNA degradation machinery, it is unlikely that these accumulations are the cause of their synthetic sick relationship. Here, we show that the dysregulation of the levels of mRNAs related to ribosome biogenesis could be the cause of the accumulation of the pre-rRNA processing intermediates. Although our results support a role for Pat1 in transcription, they nevertheless suggest that the primary cause of the dysregulated mRNA levels is most likely due to Pat1's role in mRNA decapping and mRNA degradation.

Considerations of the Differences between Bedded and Domal Salt Pertaining to Disposal of Heat-Generating Nuclear Waste

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

Hansen, Francis D.; Kuhlman, Kristopher L.; Sobolik, Steven R.

Salt formations hold promise for eternal removal of nuclear waste from our biosphere. Germany and the United States have ample salt formations for this purpose, ranging from flat-bedded formations to geologically mature dome structures. As both nations revisit nuclear waste disposal options, the choice between bedded, domal, or intermediate pillow formations is once again a contemporary issue. For decades, favorable attributes of salt as a disposal medium have been extoled and evaluated, carefully and thoroughly. Yet, a sense of discovery continues as science and engineering interrogate naturally heterogeneous systems. Salt formations are impermeable to fluids. Excavation-induced fractures heal as sealmore » systems are placed or natural closure progresses toward equilibrium. Engineering required for nuclear waste disposal gains from mining and storage industries, as humans have been mining salt for millennia. This great intellectual warehouse has been honed and distilled, but not perfected, for all nuances of nuclear waste disposal. Nonetheless, nations are able and have already produced suitable license applications for radioactive waste disposal in salt. A remaining conundrum is site location. Salt formations provide isolation and geotechnical barriers reestablish impermeability after waste is placed in the geology. Between excavation and closure, physical, mechanical, thermal, chemical, and hydrological processes ensue. Positive attributes for isolation in salt have many commonalities independent of the geologic setting. In some cases, specific details of the environment will affect the disposal concept and thereby define interaction of features, events and processes, while simultaneously influencing scenario development. Here we identify and discuss high-level differences and similarities of bedded and domal salt formations. Positive geologic and engineering attributes for disposal purposes are more common among salt formations than are significant differences. Developing models, testing material, characterizing processes, and analyzing performance all have overlapping application regardless of the salt formation of interest.« less

Considerations of the Differences between Bedded and Domal Salt Pertaining to Disposal of Heat-Generating Nuclear Waste

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

Hansen, Francis D.; Kuhlman, Kristopher L.; Sobolik, Steven R.

Salt formations hold promise for eternal removal of nuclear waste from our biosphere. Germany and the United States have ample salt formations for this purpose, ranging from flat-bedded formations to geologically mature dome structures. As both nations revisit nuclear waste disposal options, the choice between bedded, domal, or intermediate pillow formations is once again a contemporary issue. For decades, favorable attributes of salt as a disposal medium have been extoled and evaluated, carefully and thoroughly. Yet, a sense of discovery continues as science and engineering interrogate naturally heterogeneous systems. Salt formations are impermeable to fluids. Excavation-induced fractures heal as sealmore » systems are placed or natural closure progresses toward equilibrium. Engineering required for nuclear waste disposal gains from mining and storage industries, as humans have been mining salt for millennia. This great intellectual warehouse has been honed and distilled, but not perfected, for all nuances of nuclear waste disposal. Nonetheless, nations are able and have already produced suitable license applications for radioactive waste disposal in salt. A remaining conundrum is site location. Salt formations provide isolation, and geotechnical barriers reestablish impermeability after waste is placed in the geology. Between excavation and closure, physical, mechanical, thermal, chemical, and hydrological processes ensue. Positive attributes for isolation in salt have many commonalities independent of the geologic setting. In some cases, specific details of the environment will affect the disposal concept and thereby define interaction of features, events and processes, while simultaneously influencing scenario development. Here we identify and discuss high-level differences and similarities of bedded and domal salt formations. Positive geologic and engineering attributes for disposal purposes are more common among salt formations than are significant differences. Developing models, testing material, characterizing processes, and analyzing performance all have overlapping application regardless of the salt formation of interest.« less

Structural analysis of kinetic folding intermediates for a TIM barrel protein, indole-3-glycerol phosphate synthase, by hydrogen exchange mass spectrometry and Gō-model simulation

PubMed Central

Gu, Zhenyu; Rao, Maithreyi K.; Forsyth, William R.

2009-01-01

The structures of partially-folded states appearing during the folding of a (βα)8 TIM barrel protein, the indole-3-glycerol phosphate synthase from S. solfataricus (sIGPS), was assessed by hydrogen exchange mass spectrometry (HX-MS) and Gō-model simulations. HX-MS analysis of the peptic peptides derived from the pulse-labeled product of the sub-millisecond folding reaction from the urea-denatured state revealed strong protection in the (βα)4 region, modest protection in the neighboring (βα)1–3 and (βα)5β6 segments and no significant protection in the remaining N- and C-terminal segments. These results demonstrate that this species is not a collapsed form of the unfolded state under native-favoring conditions nor is it the native state formed via fast-track folding. However, the striking contrast of these results with the strong protection observed in the (βα)2–5β6 region after 5 s of folding demonstrates that these species represent kinetically-distinct folding intermediates that are not identical as previously thought. A re-examination of the kinetic folding mechanism by chevron analysis of fluorescence data confirmed distinct roles for these two species: the burst-phase intermediate is predicted to be a misfolded, off-pathway intermediate while the subsequent 5 s intermediate corresponds to an on-pathway equilibrium intermediate. Comparison with the predictions using a Cα Gō-model simulation of the kinetic folding reaction for sIGPS shows good agreement with the core of structure offering protection against exchange in the on-pathway intermediate(s). Because the native-centric Gō-model simulations do not explicitly include sequence-specific information, the simulation results support the hypothesis that the topology of TIM barrel proteins is a primary determinant of the folding free energy surface for the productive folding reaction. The early misfolding reaction must involve aspects of non-native structure not detected by the Gō-model simulation. PMID:17942114

The Effects of Focused/Unfocused Audio-Appended Reading Tasks on Intermediate Female EFL Learners' Written Accuracy

ERIC Educational Resources Information Center

Alavinia, Parviz; Shafaei, Ali; Salimi, Asghar

2018-01-01

The current research study was conducted to examine the impacts of focused and unfocused audio-appended reading tasks on female EFL learners' acquisition of a rule-bound structure (passive voice) and a non-rule-bound structure (prepositions). The participants of this study involved ninety intermediate female English learners. They were assigned…

Folding thermodynamics of pseudoknotted chain conformations

PubMed Central

Kopeikin, Zoia; Chen, Shi-Jie

2008-01-01

We develop a statistical mechanical framework for the folding thermodynamics of pseudoknotted structures. As applications of the theory, we investigate the folding stability and the free energy landscapes for both the thermal and the mechanical unfolding of pseudoknotted chains. For the mechanical unfolding process, we predict the force-extension curves, from which we can obtain the information about structural transitions in the unfolding process. In general, a pseudoknotted structure unfolds through multiple structural transitions. The interplay between the helix stems and the loops plays an important role in the folding stability of pseudoknots. For instance, variations in loop sizes can lead to the destabilization of some intermediate states and change the (equilibrium) folding pathways (e.g., two helix stems unfold either cooperatively or sequentially). In both thermal and mechanical unfolding, depending on the nucleotide sequence, misfolded intermediate states can emerge in the folding process. In addition, thermal and mechanical unfoldings often have different (equilibrium) pathways. For example, for certain sequences, the misfolded intermediates, which generally have longer tails, can fold, unfold, and refold again in the pulling process, which means that these intermediates can switch between two different average end-end extensions. PMID:16674261

Serial Femtosecond Crystallography and Ultrafast Absorption Spectroscopy of the Photoswitchable Fluorescent Protein IrisFP.

PubMed

Colletier, Jacques-Philippe; Sliwa, Michel; Gallat, François-Xavier; Sugahara, Michihiro; Guillon, Virginia; Schirò, Giorgio; Coquelle, Nicolas; Woodhouse, Joyce; Roux, Laure; Gotthard, Guillaume; Royant, Antoine; Uriarte, Lucas Martinez; Ruckebusch, Cyril; Joti, Yasumasa; Byrdin, Martin; Mizohata, Eiichi; Nango, Eriko; Tanaka, Tomoyuki; Tono, Kensuke; Yabashi, Makina; Adam, Virgile; Cammarata, Marco; Schlichting, Ilme; Bourgeois, Dominique; Weik, Martin

2016-03-03

Reversibly photoswitchable fluorescent proteins find growing applications in cell biology, yet mechanistic details, in particular on the ultrafast photochemical time scale, remain unknown. We employed time-resolved pump-probe absorption spectroscopy on the reversibly photoswitchable fluorescent protein IrisFP in solution to study photoswitching from the nonfluorescent (off) to the fluorescent (on) state. Evidence is provided for the existence of several intermediate states on the pico- and microsecond time scales that are attributed to chromophore isomerization and proton transfer, respectively. Kinetic modeling favors a sequential mechanism with the existence of two excited state intermediates with lifetimes of 2 and 15 ps, the second of which controls the photoswitching quantum yield. In order to support that IrisFP is suited for time-resolved experiments aiming at a structural characterization of these ps intermediates, we used serial femtosecond crystallography at an X-ray free electron laser and solved the structure of IrisFP in its on state. Sample consumption was minimized by embedding crystals in mineral grease, in which they remain photoswitchable. Our spectroscopic and structural results pave the way for time-resolved serial femtosecond crystallography aiming at characterizing the structure of ultrafast intermediates in reversibly photoswitchable fluorescent proteins.

Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair.

PubMed

Zhang, Yuchen; Alsop, Richard J; Soomro, Asfia; Yang, Fei-Chi; Rheinstädter, Maikel C

2015-01-01

The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3-90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers.

Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair

PubMed Central

Zhang, Yuchen; Alsop, Richard J.; Soomro, Asfia; Yang, Fei-Chi

2015-01-01

The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3–90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers. PMID:26557428

Crystal structure of group II intron domain 1 reveals a template for RNA assembly

DOE PAGES

Zhao, Chen; Rajashankar, Kanagalaghatta R.; Marcia, Marco; ...

2015-10-26

Although the importance of large noncoding RNAs is increasingly appreciated, our understanding of their structures and architectural dynamics remains limited. In particular, we know little about RNA folding intermediates and how they facilitate the productive assembly of RNA tertiary structures. In this paper, we report the crystal structure of an obligate intermediate that is required during the earliest stages of group II intron folding. Composed of domain 1 from the Oceanobacillus iheyensis group II intron (266 nucleotides), this intermediate retains native-like features but adopts a compact conformation in which the active site cleft is closed. Transition between this closed andmore » the open (native) conformation is achieved through discrete rotations of hinge motifs in two regions of the molecule. Finally, the open state is then stabilized by sequential docking of downstream intron domains, suggesting a 'first come, first folded' strategy that may represent a generalizable pathway for assembly of large RNA and ribonucleoprotein structures.« less

Effects of gramicidin-A on the adsorption of phospholipids to the air–water interface

PubMed Central

Biswas, Samares C.; Rananavare, Shankar B.; Hall, Stephen B.

2012-01-01

Prior studies suggest that the hydrophobic surfactant proteins, SP-B and SP-C, promote adsorption of the lipids in pulmonary surfactant to an air–water interface by stabilizing a negatively curved rate-limiting structure that is intermediate between bilayer vesicles and the surface film. This model predicts that other peptides capable of stabilizing negative curvature should also promote lipid adsorption. Previous reports have shown that under appropriate conditions, gramicidin-A (GrA) induces dioleoyl phosphatidylcholine (DOPC), but not dimyristoyl phosphatidylcholine (DMPC), to form the negatively curved hexagonal-II (HII) phase. The studies reported here determined if GrA would produce the same effects on adsorption of DMPC and DOPC that the hydrophobic surfactant proteins have on the surfactant lipids. Small angle X-ray scattering and 31P-nuclear magnetic resonance confirmed that at the particular conditions used to study adsorption, GrA induced DOPC to form the HII phase, but DMPC remained lamellar. Measurements of surface tension showed that GrA in vesicles produced a general increase in the rate of adsorption for both phospholipids. When restricted to the interface, however, in preexisting films, GrA with DOPC, but not with DMPC, replicated the ability of the surfactant proteins to promote adsorption of vesicles containing only the lipids. The correlation between the structural and functional effects of GrA with the two phospholipids, and the similar effects on adsorption of GrA with DOPC and the hydrophobic surfactant proteins with the surfactant lipids fit with the model in which SP-B and SP-C facilitate adsorption by stabilizing a rate-limiting intermediate with negative curvature. PMID:16242116

Unique fluorophores in the dimeric archaeal histones hMfB and hPyA1 reveal the impact of nonnative structure in a monomeric kinetic intermediate

PubMed Central

Stump, Matthew R.; Gloss, Lisa M.

2008-01-01

Homodimeric archaeal histones and heterodimeric eukaryotic histones share a conserved structure but fold through different kinetic mechanisms, with a correlation between faster folding/association rates and the population of kinetic intermediates. Wild-type hMfB (from Methanothermus fervidus) has no intrinsic fluorophores; Met35, which is Tyr in hyperthermophilic archaeal histones such as hPyA1 (from Pyrococcus strain GB-3A), was mutated to Tyr and Trp. Two Tyr-to-Trp mutants of hPyA1 were also characterized. All fluorophores were introduced into the long, central α-helix of the histone fold. Far-UV circular dichroism (CD) indicated that the fluorophores did not significantly alter the helical content of the histones. The equilibrium unfolding transitions of the histone variants were two-state, reversible processes, with ΔG°(H2O) values within 1 kcal/mol of the wild-type dimers. The hPyA1 Trp variants fold by two-state kinetic mechanisms like wild-type hPyA1, but with increased folding and unfolding rates, suggesting that the mutated residues (Tyr-32 and Tyr-36) contribute to transition state structure. Like wild-type hMfB, M35Y and M35W hMfB fold by a three-state mechanism, with a stopped-flow CD burst-phase monomeric intermediate. The M35 mutants populate monomeric intermediates with increased secondary structure and stability but exhibit decreased folding rates; this suggests that nonnative interactions occur from burial of the hydrophobic Tyr and Trp residues in this kinetic intermediate. These results implicate the long central helix as a key component of the structure in the kinetic monomeric intermediates of hMfB as well as the dimerization transition state in the folding of hPyA1. PMID:18096639

Spring/dimple instrument tube restraint

DOEpatents

DeMario, Edmund E.; Lawson, Charles N.

1993-01-01

A nuclear fuel assembly for a pressurized water nuclear reactor has a spring and dimple structure formed in a non-radioactive insert tube placed in the top of a sensor receiving instrumentation tube thimble disposed in the fuel assembly and attached at a top nozzle, a bottom nozzle, and intermediate grids. The instrumentation tube thimble is open at the top, where the sensor or its connection extends through the cooling water for coupling to a sensor signal processor. The spring and dimple insert tube is mounted within the instrumentation tube thimble and extends downwardly adjacent the top. The springs and dimples restrain the sensor and its connections against lateral displacement causing impact with the instrumentation tube thimble due to the strong axial flow of cooling water. The instrumentation tube has a stainless steel outer sleeve and a zirconium alloy inner sleeve below the insert tube adjacent the top. The insert tube is relatively non-radioactivated inconel alloy. The opposed springs and dimples are formed on diametrically opposite inner walls of the insert tube, the springs being formed as spaced axial cuts in the insert tube, with a web of the insert tube between the cuts bowed radially inwardly for forming the spring, and the dimples being formed as radially inward protrusions opposed to the springs.

Spring/dimple instrument tube restraint

DOEpatents

DeMario, E.E.; Lawson, C.N.

1993-11-23

A nuclear fuel assembly for a pressurized water nuclear reactor has a spring and dimple structure formed in a non-radioactive insert tube placed in the top of a sensor receiving instrumentation tube thimble disposed in the fuel assembly and attached at a top nozzle, a bottom nozzle, and intermediate grids. The instrumentation tube thimble is open at the top, where the sensor or its connection extends through the cooling water for coupling to a sensor signal processor. The spring and dimple insert tube is mounted within the instrumentation tube thimble and extends downwardly adjacent the top. The springs and dimples restrain the sensor and its connections against lateral displacement causing impact with the instrumentation tube thimble due to the strong axial flow of cooling water. The instrumentation tube has a stainless steel outer sleeve and a zirconium alloy inner sleeve below the insert tube adjacent the top. The insert tube is relatively non-radioactivated inconel alloy. The opposed springs and dimples are formed on diametrically opposite inner walls of the insert tube, the springs being formed as spaced axial cuts in the insert tube, with a web of the insert tube between the cuts bowed radially inwardly for forming the spring, and the dimples being formed as radially inward protrusions opposed to the springs. 7 figures.

Integrated head package cable carrier for a nuclear power plant

DOEpatents

Meuschke, Robert E.; Trombola, Daniel M.

1995-01-01

A cabling arrangement is provided for a nuclear reactor located within a containment. Structure inside the containment is characterized by a wall having a near side surrounding the reactor vessel defining a cavity, an operating deck outside the cavity, a sub-space below the deck and on a far side of the wall spaced from the near side, and an operating area above the deck. The arrangement includes a movable frame supporting a plurality of cables extending through the frame, each connectable at a first end to a head package on the reactor vessel and each having a second end located in the sub-space. The frame is movable, with the cables, between a first position during normal operation of the reactor when the cables are connected to the head package, located outside the sub-space proximate the head package, and a second position during refueling when the cables are disconnected from the head package, located in the sub-space. In a preferred embodiment, the frame straddles the top of the wall in a substantially horizontal orientation in the first position, pivots about an end distal from the head package to a substantially vertically oriented intermediate position, and is guided, while remaining about vertically oriented, along a track in the sub-space to the second position.

Comparing results of X-ray diffraction, µ-Raman spectroscopy and neutron diffraction when identifying chemical phases in seized nuclear material, during a comparative nuclear forensics exercise.

PubMed

Rondahl, Stina Holmgren; Pointurier, Fabien; Ahlinder, Linnea; Ramebäck, Henrik; Marie, Olivier; Ravat, Brice; Delaunay, François; Young, Emma; Blagojevic, Ned; Hester, James R; Thorogood, Gordon; Nelwamondo, Aubrey N; Ntsoane, Tshepo P; Roberts, Sarah K; Holliday, Kiel S

2018-01-01

This work presents the results for identification of chemical phases obtained by several laboratories as a part of an international nuclear forensic round-robin exercise. In this work powder X-ray diffraction (p-XRD) is regarded as the reference technique. Neutron diffraction produced a superior high-angle diffraction pattern relative to p-XRD. Requiring only small amounts of sample, µ-Raman spectroscopy was used for the first time in this context as a potentially complementary technique to p-XRD. The chemical phases were identified as pure UO 2 in two materials, and as a mixture of UO 2 , U 3 O 8 and an intermediate species U 3 O 7 in the third material.

Design and Implementation of an International Training Program on Repository Development and Management

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

Vugrin, K.W.; Twitchell, Ch.A.

2008-07-01

Korea Hydro and Nuclear Power Co., Ltd. (KHNP) is an electric company in the Republic of Korea with twenty operational nuclear power plants and eight additional units that are either planned or currently under construction. Regulations require that KHNP manage the radioactive waste generated by their nuclear power plants. In the course of planning low, intermediate, and high level waste storage facilities, KHNP sought interaction with an acknowledged expert in the field of radioactive waste management and, consequently, contacted Sandia National Laboratories (SNL). KHNP has contracted with SNL to provide a year long training program on repository science. This papermore » discusses the design of the curriculum, specific plans for execution of the training program, and recommendations for smooth implementation of international training programs. (authors)« less

Role for Tyrosine Phosphorylation of A-kinase Anchoring Protein 8 (AKAP8) in Its Dissociation from Chromatin and the Nuclear Matrix.

PubMed

Kubota, Sho; Morii, Mariko; Yuki, Ryuzaburo; Yamaguchi, Noritaka; Yamaguchi, Hiromi; Aoyama, Kazumasa; Kuga, Takahisa; Tomonaga, Takeshi; Yamaguchi, Naoto

2015-04-24

Protein-tyrosine phosphorylation regulates a wide variety of cellular processes at the plasma membrane. Recently, we showed that nuclear tyrosine kinases induce global nuclear structure changes, which we called chromatin structural changes. However, the mechanisms are not fully understood. In this study we identify protein kinase A anchoring protein 8 (AKAP8/AKAP95), which associates with chromatin and the nuclear matrix, as a nuclear tyrosine-phosphorylated protein. Tyrosine phosphorylation of AKAP8 is induced by several tyrosine kinases, such as Src, Fyn, and c-Abl but not Syk. Nucleus-targeted Lyn and c-Src strongly dissociate AKAP8 from chromatin and the nuclear matrix in a kinase activity-dependent manner. The levels of tyrosine phosphorylation of AKAP8 are decreased by substitution of multiple tyrosine residues on AKAP8 into phenylalanine. Importantly, the phenylalanine mutations of AKAP8 inhibit its dissociation from nuclear structures, suggesting that the association/dissociation of AKAP8 with/from nuclear structures is regulated by its tyrosine phosphorylation. Furthermore, the phenylalanine mutations of AKAP8 suppress the levels of nuclear tyrosine kinase-induced chromatin structural changes. In contrast, AKAP8 knockdown increases the levels of chromatin structural changes. Intriguingly, stimulation with hydrogen peroxide induces chromatin structural changes accompanied by the dissociation of AKAP8 from nuclear structures. These results suggest that AKAP8 is involved in the regulation of chromatin structural changes through nuclear tyrosine phosphorylation. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Kinetic advantage of controlled intermediate nuclear fusion

NASA Astrophysics Data System (ADS)

Guo, Xiaoming

2012-09-01

The dominated process of controlled fusion is to let nuclei gain enough kinetic energy to overcome Coulomb barrier. As a result, a fusion scheme can consider two factors in its design: to increase kinetic energy of nuclei and to alter the Coulomb barrier. Cold Fusion and Hot fusion are all one-factor schemes while Intermediate Fusion is a twofactors scheme. This made CINF kinetically superior. Cold Fusion reduces deuteron-deuteron distance, addressing Coulomb barrier, and Hot Fusion heat up plasma into extreme high temperature, addressing kinetic energy. Without enough kinetic energy made Cold Fusion skeptical. Extreme high temperature made Hot Fusion very difficult to engineer. Because CIFN addresses both factors, CIFN is a more promising technique to be industrialized.

Co-ordination of the International Network of Nuclear Structure and Decay Data Evaluators; Summary Report of an IAEA Technical Meeting

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

Abriola, D.; Tuli, J.

The IAEA Nuclear Data Section convened the 18th meeting of the International Network of Nuclear Structure and Decay Data Evaluators at the IAEA Headquarters, Vienna, 23 to 27 March 2009. This meeting was attended by 22 scientists from 14 Member States, plus IAEA staff, concerned with the compilation, evaluation and dissemination of nuclear structure and decay data. A summary of the meeting, recommendations/conclusions, data centre reports, and various proposals considered, modified and agreed by the participants are contained within this document. The International Network of Nuclear Structure and Decay Data (NSDD) Evaluators holds biennial meetings under the auspices of themore » IAEA, and consists of evaluation groups and data service centres in several countries. This network has the objective of providing up-to-date nuclear structure and decay data for all known nuclides by evaluating all existing experimental data. Data resulting from this international evaluation collaboration is included in the Evaluated Nuclear Structure Data File (ENSDF) and published in the journals Nuclear Physics A and Nuclear Data Sheets (NDS).« less

Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments.

PubMed

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0-2.2 M) than the formation of the native state (0-1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7-2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin.

Nuclear Structure in China 2010

NASA Astrophysics Data System (ADS)

Bai, Hong-Bo; Meng, Jie; Zhao, En-Guang; Zhou, Shan-Gui

2011-08-01

Personal view on nuclear physics research / Jie Meng -- High-spin level structures in [symbol]Zr / X. P. Cao ... [et al.] -- Constraining the symmetry energy from the neutron skin thickness of tin isotopes / Lie-Wen Chen ... [et al.] -- Wobbling rotation in atomic nuclei / Y. S. Chen and Zao-Chun Gao -- The mixing of scalar mesons and the possible nonstrange dibaryons / L. R. Dai ... [et al.] -- Net baryon productions and gluon saturation in the SPS, RHIC and LHC energy regions / Sheng-Qin Feng -- Production of heavy isotopes with collisions between two actinide nuclides / Z. Q. Feng ... [et al.] -- The projected configuration interaction method / Zao-Chun Gao and Yong-Shou Chen -- Applications of Nilsson mean-field plus extended pairing model to rare-earth nuclei / Xin Guan ... [et al.] -- Complex scaling method and the resonant states / Jian-You Guo ... [et al.] -- Probing the equation of state by deep sub-barrier fusion reactions / Hong-Jun Hao and Jun-Long Tian -- Doublet structure study in A[symbol]105 mass region / C. Y. He ... [et al.] -- Rotational bands in transfermium nuclei / X. T. He -- Shape coexistence and shape evolution [symbol]Yb / H. Hua ... [et al.] -- Multistep shell model method in the complex energy plane / R. J. Liotta -- The evolution of protoneutron stars with kaon condensate / Ang Li -- High spin structures in the [symbol]Lu nucleus / Li Cong-Bo ... [et al.] -- Nuclear stopping and equation of state / QingFeng Li and Ying Yuan -- Covariant description of the low-lying states in neutron-deficient Kr isotopes / Z. X. Li ... [et al.] -- Isospin corrections for superallowed [symbol] transitions / HaoZhao Liang ... [et al.] -- The positive-parity band structures in [symbol]Ag / C. Liu ... [et al.] -- New band structures in odd-odd [symbol]I and [symbol]I / Liu GongYe ... [et al.] -- The sd-pair shell model and interacting boson model / Yan-An Luo ... [et al.] -- Cross-section distributions of fragments in the calcium isotopes projectile fragmentation at the intermediate energy / C. W. Ma ... [et al.].Systematic study of spin assignment and dynamic moment of inertia of high-j intruder band in [symbol]In / K. Y. Ma ... [et al.] -- Signals of diproton emission from the three-body breakup channel of [symbol]Al and [symbol]Mg / Ma Yu-Gang ... [et al.] -- Uncertainties of Th/Eu and Th/Hf chronometers from nucleus masses / Z. M. Niu ... [et al.] -- The chiral doublet bands with [symbol] configuration in A[symbol]100 mass region / B. Qi ... [et al.] -- [symbol] formation probabilities in nuclei and pairing collectivity / Chong Qi -- A theoretical prospective on triggered gamma emission from [symbol]Hf[symbol] isomer / ShuiFa Shen ... [et al.] -- Study of nuclear giant resonances using a Fermi-liquid method / Bao-Xi Sun -- Rotational bands in doubly odd [symbol]Sb / D. P. Sun ... [et al.] -- The study of the neutron N=90 nuclei / W. X. Teng ... [et al.] -- Dynamical modes and mechanisms in ternary reaction of [symbol]Au+[symbol]Au / Jun-Long Tian ... [et al.] -- Dynamical study of X(3872) as a D[symbol] molecular state / B. Wang ... [et al.] -- Super-heavy stability island with a semi-empirical nuclear mass formula / N. Wang ... [et al.] -- Pseudospin partner bands in [symbol]Sb / S. Y. Wang ... [et al.] -- Study of elastic resonance scattering at CIAE / Y. B. Wang ... [et al.] -- Systematic study of survival probability of excited superheavy nuclei / C. J. Xia ... [et al.] -- Angular momentum projection of the Nilsson mean-field plus nearest-orbit pairing interaction model / Ming-Xia Xie ... [et al.] -- Possible shape coexistence for [symbol]Sm in a reflection-asymmetric relativistic mean-field approach / W. Zhang ... [et al.] -- Nuclear pairing reduction due to rotation and blocking / Zhen-Hua Zhang -- Nucleon pair approximation of the shell model: a review and perspective / Y. M. Zhao ... [et al.] -- Band structures in doubly odd [symbol]I / Y. Zheng ... [et al.] -- Lifetimes of high spin states in [symbol]Ag / Y. Zheng ... [et al.] -- Effect of tensor interaction on the shell structure of superheavy nuclei / Xian-Rong Zhou ... [et al.].

Gas turbine engine adapted for use in combination with an apparatus for separating a portion of oxygen from compressed air

DOEpatents

Bland, Robert J [Oviedo, FL; Horazak, Dennis A [Orlando, FL

2012-03-06

A gas turbine engine is provided comprising an outer shell, a compressor assembly, at least one combustor assembly, a turbine assembly and duct structure. The outer shell includes a compressor section, a combustor section, an intermediate section and a turbine section. The intermediate section includes at least one first opening and at least one second opening. The compressor assembly is located in the compressor section to define with the compressor section a compressor apparatus to compress air. The at least one combustor assembly is coupled to the combustor section to define with the combustor section a combustor apparatus. The turbine assembly is located in the turbine section to define with the turbine section a turbine apparatus. The duct structure is coupled to the intermediate section to receive at least a portion of the compressed air from the compressor apparatus through the at least one first opening in the intermediate section, pass the compressed air to an apparatus for separating a portion of oxygen from the compressed air to produced vitiated compressed air and return the vitiated compressed air to the intermediate section via the at least one second opening in the intermediate section.

Russian-American Security Cooperation After St. Petersburg: Challenges and Opportunities

DTIC Science & Technology

2007-04-01

appears to have prompted several Russian inquiries as to how Wash- ington would react if Moscow withdrew from the 1987 Intermediate-Range Nuclear Forces...Arms Control Today, Vol. 36, No. 2, March 2006, pp. 37-38. 74. Peter Eisler , “U.S., Russia Break Impasse on Plan to Keep Arms From Rogue Users,” USA

Physical particularities of nuclear reactors using heavy moderators of neutrons

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

Kulikov, G. G., E-mail: ggkulikov@mephi.ru; Shmelev, A. N.

2016-12-15

In nuclear reactors, thermal neutron spectra are formed using moderators with small atomic weights. For fast reactors, inserting such moderators in the core may create problems since they efficiently decelerate the neutrons. In order to form an intermediate neutron spectrum, it is preferable to employ neutron moderators with sufficiently large atomic weights, using {sup 233}U as a fissile nuclide and {sup 232}Th and {sup 231}Pa as fertile ones. The aim of the work is to investigate the properties of heavy neutron moderators and to assess their advantages. The analysis employs the JENDL-4.0 nuclear data library and the SCALE program packagemore » for simulating the variation of fuel composition caused by irradiation in the reactor. The following main results are obtained. By using heavy moderators with small neutron moderation steps, one is able to (1) increase the rate of resonance capture, so that the amount of fertile material in the fuel may be reduced while maintaining the breeding factor of the core; (2) use the vacant space for improving the fuel-element properties by adding inert, strong, and thermally conductive materials and by implementing dispersive fuel elements in which the fissile material is self-replenished and neutron multiplication remains stable during the process of fuel burnup; and (3) employ mixtures of different fertile materials with resonance capture cross sections in order to increase the resonance-lattice density and the probability of resonance neutron capture leading to formation of fissile material. The general conclusion is that, by forming an intermediate neutron spectrum with heavy neutron moderators, one can use the fuel more efficiently and improve nuclear safety.« less

Commercial nuclear power 1990

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

Not Available

1990-09-28

This report presents the status at the end of 1989 and the outlook for commercial nuclear capacity and generation for all countries in the world with free market economies (FME). The report provides documentation of the US nuclear capacity and generation projections through 2030. The long-term projections of US nuclear capacity and generation are provided to the US Department of Energy's (DOE) Office of Civilian Radioactive Waste Management (OCRWM) for use in estimating nuclear waste fund revenues and to aid in planning the disposal of nuclear waste. These projections also support the Energy Information Administration's annual report, Domestic Uranium Miningmore » and Milling Industry: Viability Assessment, and are provided to the Organization for Economic Cooperation and Development. The foreign nuclear capacity projections are used by the DOE uranium enrichment program in assessing potential markets for future enrichment contracts. The two major sections of this report discuss US and foreign commercial nuclear power. The US section (Chapters 2 and 3) deals with (1) the status of nuclear power as of the end of 1989; (2) projections of nuclear capacity and generation at 5-year intervals from 1990 through 2030; and (3) a discussion of institutional and technical issues that affect nuclear power. The nuclear capacity projections are discussed in terms of two projection periods: the intermediate term through 2010 and the long term through 2030. A No New Orders case is presented for each of the projection periods, as well as Lower Reference and Upper Reference cases. 5 figs., 30 tabs.« less

Trapped in imidazole: how to accumulate multiple photoelectrons on a black-absorbing ruthenium complex.

PubMed

Zedler, Linda; Kupfer, Stephan; de Moraes, Inês Rabelo; Wächtler, Maria; Beckert, Rainer; Schmitt, Michael; Popp, Jürgen; Rau, Sven; Dietzek, Benjamin

2014-03-24

Ruthenium dyes incorporating a 4H-imidazole chromophore as a ligand exhibit a spectrally broad absorption in the UV/Vis region. Furthermore, they show the ability to store two electrons within the 4H-imidazole ligand. These features render them promising molecular systems, for example, as inter- or intramolecular electron relays. To optimize the structures with respect to their electron-storage capability, it is crucial to understand the impact of structural changes accompanying photoinduced charge transfer in the electronic intermediates of multistep electron-transfer processes. The photophysical properties of these (reactive) intermediates might impact the function of the molecular systems quite substantially. However, the spectroscopic study of short-lived intermediates in stepwise multielectron-transfer processes is experimentally challenging. To this end, this contribution reports on the electrochemical generation of anions identical to intermediate structures and their spectroscopic characterization by in situ resonance Raman and UV/Vis spectroelectrochemistry and computational methods. Thereby, an efficient two-electron pathway to the 4H-imidazole electron-accepting ligand is identified. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Intermediates and the folding of proteins L and G

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

Brown, Scott; Head-Gordon, Teresa

We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G that are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted {beta}-1 and {beta}-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contactsmore » involving the third {beta}-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment.« less

Intermediates and the folding of proteins L and G

PubMed Central

Brown, Scott; Head-Gordon, Teresa

2004-01-01

We use a minimalist protein model, in combination with a sequence design strategy, to determine differences in primary structure for proteins L and G, which are responsible for the two proteins folding through distinctly different folding mechanisms. We find that the folding of proteins L and G are consistent with a nucleation-condensation mechanism, each of which is described as helix-assisted β-1 and β-2 hairpin formation, respectively. We determine that the model for protein G exhibits an early intermediate that precedes the rate-limiting barrier of folding, and which draws together misaligned secondary structure elements that are stabilized by hydrophobic core contacts involving the third β-strand, and presages the later transition state in which the correct strand alignment of these same secondary structure elements is restored. Finally, the validity of the targeted intermediate ensemble for protein G was analyzed by fitting the kinetic data to a two-step first-order reversible reaction, proving that protein G folding involves an on-pathway early intermediate, and should be populated and therefore observable by experiment. PMID:15044729

Structural analysis of vimentin and keratin intermediate filaments by cryo-electron tomography.

PubMed

Norlén, Lars; Masich, Sergej; Goldie, Kenneth N; Hoenger, Andreas

2007-06-10

Intermediate filaments are a large and structurally diverse group of cellular filaments that are classified into five different groups. They are referred to as intermediate filaments (IFs) because they are intermediate in diameter between the two other cytoskeletal filament systems that is filamentous actin and microtubules. The basic building block of IFs is a predominantly alpha-helical rod with variable length globular N- and C-terminal domains. On the ultra-structural level there are two major differences between IFs and microtubules or actin filaments: IFs are non-polar, and they do not exhibit large globular domains. IF molecules associate via a coiled-coil interaction into dimers and higher oligomers. Structural investigations into the molecular building plan of IFs have been performed with a variety of biophysical and imaging methods such as negative staining and metal-shadowing electron microscopy (EM), mass determination by scanning transmission EM, X-ray crystallography on fragments of the IF stalk and low-angle X-ray scattering. The actual packing of IF dimers into a long filament varies between the different families. Typically the dimers form so called protofibrils that further assemble into a filament. Here we introduce new cryo-imaging methods for structural investigations of IFs in vitro and in vivo, i.e., cryo-electron microscopy and cryo-electron tomography, as well as associated techniques such as the preparation and handling of vitrified sections of cellular specimens.

The intron 1 of HPV 16 has a suboptimal branch point at a guanosine.

PubMed

De la Rosa-Rios, Marco Antonio; Martínez-Salazar, Martha; Martínez-Garcia, Martha; González-Bonilla, César; Villegas-Sepúlveda, Nicolás

2006-06-01

The branch point sequence (BPS) of intron 1 of the HPV-16 was determined via RT-PCR in a cell free system, using lariat intermediates obtained by in vitro splicing reactions. We used synthetic E6/E7 transcripts and HeLa nuclear protein extracts to obtain the splicing intermediates. Then, a divergent oligonucleotide primer set, pairing on the lariat RNA that encompassed the 2'-5' phosphodiester bond formed between the 5' end of the intron and the BPS, was used for cDNA synthesis and PCR amplification. Subsequent RT-PCR assays revealed four splicing intermediates, made up of a major intermediary corresponding to the BPS and four cryptic branched sequences. Only intermediates bound at the 5' end of the intron are probably the authentic branch point sequence, and all of them branch at guanosine 328 instead of the typical adenosine. Unusually, the BPS of intron 1 of HPV-16 is a suboptimal sequence (AGUGAGU) that differs from the eukaryotic consensus BPS, which correlates with the splicing profile observed for early transcripts of HPV-16 in tumors and tumor derived cell lines. The implications of this unusual branch point sequence for splicing of the HPV-16 pre-mRNA are discussed.

Structural, biological and biophysical properties of glycated and glycoxidized phosphatidylethanolamines

PubMed Central

Annibal, Andrea; Riemer, Thomas; Jovanovic, Olga; Westphal, Dennis; Griesser, Eva; Pohl, Elena E.; Schiller, Jürgen; Hoffmann, Ralf; Fedorova, Maria

2018-01-01

Glycation and glycoxidation of proteins and peptides have been intensively studied and are considered as reliable diagnostic biomarkers of hyperglycemia and early stages of type II diabetes. However, glucose can also react with primary amino groups present in other cellular components, such as aminophospholipids (aminoPLs). Although it is proposed that glycated aminoPLs can induce many cellular responses and contribute to the development and progression of diabetes, the routes of their formation and their biological roles are only partially revealed. The same is true for the influence of glucose-derived modifications on the biophysical properties of PLs. Here we studied structural, signaling, and biophysical properties of glycated and glycoxidized phosphatidylethanolamines (PEs). By combining high resolution mass spectrometry and nuclear magnetic resonance spectroscopy it was possible to deduce the structures of several intermediates indicating an oxidative cleavage of the Amadori product yielding glycoxidized PEs including advanced glycation end products, such as carboxyethyl- and carboxymethyl-ethanolamines. The pro-oxidative role of glycated PEs was demonstrated and further associated with several cellular responses including activation of NFκB signaling pathways. Label free proteomics indicated significant alterations in proteins regulating cellular metabolisms. Finally, the biophysical properties of PL membranes changed significantly upon PE glycation, such as melting temperature (Tm), membrane surface charge, and ion transport across the phospholipid bilayer. PMID:27012418

Thermal decomposition of ammonium hexachloroosmate.

PubMed

Asanova, T I; Kantor, I; Asanov, I P; Korenev, S V; Yusenko, K V

2016-12-07

Structural changes of (NH 4 ) 2 [OsCl 6 ] occurring during thermal decomposition in a reduction atmosphere have been studied in situ using combined energy-dispersive X-ray absorption spectroscopy (ED-XAFS) and powder X-ray diffraction (PXRD). According to PXRD, (NH 4 ) 2 [OsCl 6 ] transforms directly to metallic Os without the formation of any crystalline intermediates but through a plateau where no reactions occur. XANES and EXAFS data by means of Multivariate Curve Resolution (MCR) analysis show that thermal decomposition occurs with the formation of an amorphous intermediate {OsCl 4 } x with a possible polymeric structure. Being revealed for the first time the intermediate was subjected to determine the local atomic structure around osmium. The thermal decomposition of hexachloroosmate is much more complex and occurs within a minimum two-step process, which has never been observed before.

Immunohistochemistry of choriocarcinoma: an aid in differential diagnosis and in elucidating pathogenesis.

PubMed

Mao, Tsui-Lien; Kurman, Robert J; Huang, Chao-Cheng; Lin, Ming-Chieh; Shih, Ie-Ming

2007-11-01

Choriocarcinoma is traditionally described as being composed of cytotrophoblast and syncytiotrophoblast. Microscopically, these 2 types of cells are intimately associated with each other, forming a characteristic biphasic plexiform pattern, however, the nature of these 2 types of trophoblastic cells is not well understood. In this study, we used immunohistochemistry for several trophoblastic markers to analyze the trophoblastic subpopulations in 36 gestational choriocarcinomas. Eighty-one specimens including placenta, complete mole, placental site nodule, epithelioid trophoblastic tumor, and placental site trophoblastic tumor were analyzed. The antibodies included Mel-CAM, HLA-G, MUC-4, and beta-catenin. A semiquantitative assessment of positive cells and the cellular localization of these markers were recorded. We found diffuse strong membranous and cytoplasmic staining for MUC-4 in mononucleate cells in all 36 cases (100%) and a similar pattern of localization in 28 cases (78%) for HLA-G. This distribution was similar to that in normal placentas, where MUC-4 and HLA-G are expressed in the trophoblastic cells of the trophoblastic columns and implantation site. In choriocarcinoma, mononucleate trophoblastic cells showed moderate immunoreactivity for Mel-CAM, a specific marker for implantation site intermediate trophoblast, in 78% of the cases. The MUC-4, HLA-G, and Mel-CAM-positive trophoblastic cells were larger than cytotrophoblastic cells, with more abundant cytoplasm, consistent with the morphology of intermediate trophoblast. In contrast, 31% of the choriocarcinomas contained a very small proportion (<5%) of mononucleate trophoblastic cells compatible with cytotrophoblast that was positive for nuclear beta-catenin, a cytotrophoblast-associated marker. These results suggest that choriocarcinoma is composed predominantly of a mixture of syncytiotrophoblast and intermediate trophoblast with only a small proportion of cytotrophoblast. The presence of nuclear beta-catenin staining in the cytotrophoblast of choriocarcinoma is consistent with the view that choriocarcinoma develops from transformed cytotrophoblastic cells which are presumably the cancer stem cells that differentiate into either intermediate trophoblast or syncytiotrophoblast.

Intermediate Traces and Intermediate Learners: Evidence for the Use of Intermediate Structure during Sentence Processing in Second Language French

ERIC Educational Resources Information Center

Miller, A. Kate

2015-01-01

This study reports on a sentence processing experiment in second language (L2) French that looks for evidence of trace reactivation at clause edge and in the canonical object position in indirect object cleft sentences with complex embedding and cyclic movement. Reaction time (RT) asymmetries were examined among low (n = 20) and high (n = 20)…

The organization and contribution of helicases to RNA splicing.

PubMed

De, Inessa; Schmitzová, Jana; Pena, Vladimir

2016-01-01

Splicing is an essential step of gene expression. It occurs in two consecutive chemical reactions catalyzed by a large protein-RNA complex named the spliceosome. Assembled on the pre-mRNA substrate from five small nuclear proteins, the spliceosome acts as a protein-controlled ribozyme to catalyze the two reactions and finally dissociates into its components, which are re-used for a new round of splicing. Upon following this cyclic pathway, the spliceosome undergoes numerous intermediate stages that differ in composition as well as in their internal RNA-RNA and RNA-protein contacts. The driving forces and control mechanisms of these remodeling processes are provided by specific molecular motors called RNA helicases. While eight spliceosomal helicases are present in all organisms, higher eukaryotes contain five additional ones potentially required to drive a more intricate splicing pathway and link it to an RNA metabolism of increasing complexity. Spliceosomal helicases exhibit a notable structural diversity in their accessory domains and overall architecture, in accordance with the diversity of their task-specific functions. This review summarizes structure-function knowledge about all spliceosomal helicases, including the latter five, which traditionally are treated separately from the conserved ones. The implications of the structural characteristics of helicases for their functions, as well as for their structural communication within the multi-subunits environment of the spliceosome, are pointed out. © 2016 Wiley Periodicals, Inc.

Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

NASA Astrophysics Data System (ADS)

Knott, Michael; Best, Robert B.

2014-05-01

Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an "induced fit" or "conformational selection" mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD.

The Unfolding and Refolding Reactions of Triosephosphate Isomerase from Trypanosoma Cruzi Follow Similar Pathways. Guanidinium Hydrochloride Studies

NASA Astrophysics Data System (ADS)

Vázquez-Contreras, Edgar; Pérez Hernández, Gerardo; Sánchez-Rebollar, Brenda Guadalupe; Chánez-Cárdenas, María Elena

2005-04-01

The unfolding and refolding reactions of Trypanosoma cruzi triosephosphate isomerase (TcTIM) was studied under equilibrium conditions at increasing guanidinium hydrochloride concentrations. The changes in activity intrinsic fluorescence and far-ultraviolet circular dichroism as a function of denaturant were used as a quaternary, tertiary and secondary structural probes respectively. The change in extrinsic ANS fluorescence intensity was also investigated. The results show that the transition between the homodimeric native enzyme to the unfolded monomers (unfolding), and its inverse reaction (refolding) are described by similar pathways and two equilibrium intermediates were detected in both reactions. The mild denaturant concentrations intermediate is active and contains significant amount of secondary and tertiary structures. The medium denaturant concentrations intermediate is inactive and able to bind the fluorescent dye. This intermediates are maybe related with those observed in the denaturation pattern of TIMs from other species; the results are discussed in this context.

Nuclear reactor sealing system

DOEpatents

McEdwards, James A.

1983-01-01

A liquid metal-cooled nuclear reactor sealing system. The nuclear reactor includes a vessel sealed at its upper end by a closure head. The closure head comprises at least two components, one of which is rotatable; and the two components define an annulus therebetween. The sealing system includes at least a first and second inflatable seal disposed in series in an upper portion of the annulus. The system further includes a dip seal extending into a body of insulation located adjacent a bottom portion of the closure head. The dip seal comprises a trough formed by a lower portion of one of the components, and a seal blade pendently supported from the other component and extending downwardly into the trough. A body of liquid metal is contained in the trough which submerges a portion of the seal blade. The seal blade is provided with at least one aperture located above the body of liquid metal for providing fluid communication between the annulus intermediate the dip seal and the inflatable seals, and a body of cover gas located inside the vessel. There also is provided means for introducing a purge gas into the annulus intermediate the inflatable seals and the seal blade. The purge gas is introduced in an amount sufficient to substantially reduce diffusion of radioactive cover gas or sodium vapor up to the inflatable seals. The purge gas mixes with the cover gas in the reactor vessel where it can be withdrawn from the vessel for treatment and recycle to the vessel.

Belief Structures of Students For and Against the Nuclear Freeze.

ERIC Educational Resources Information Center

Tankard, James W., Jr.

An investigation of college students' belief structures underlying their support or non-support of a nuclear freeze revealed a three-dimensional structure for beliefs in the areas of nuclear weapons and national defense. A questionnaire containing 25 belief statements concerning national defense and nuclear weapons and 4 media use questions was…

Nuclear Data Sheets page at the NNDC

Science.gov Websites

Data Sheets is a journal primarily devoted to the publication of evaluated nuclear structure and decay ; neutron, proton, alpha, cluster and cluster emission; fission. Nuclear structure and decay data are basis. The ENSDF database is the source for the nuclear structure and decay articles, which deal with a

Capillary electrophoretic study of dibasic acids of different structures: Relation to separation of oxidative intermediates in remediation

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

Yu, Z.; Cocke, D.L.

Dicarboxylic acids are important in environmental chemistry because they are intermediates in oxidative processes involved in natural remediation and waste management processes such as oxidative detoxification and advanced oxidation. Capillary electrophoresis (CE), a promising technique for separating and analyzing these intermediates, has been used to examine a series of dibasic acids of different structures and conformations. This series includes malonic acid, succinic acid, glutaric acid, adipic acid, pimelic acid, maleic acid, fumaric acid, phthalic acid, and trans, trans-muconic acid. The CE parameters as well as structural variations (molecular structure and molecular isomers, buffer composition, pH, applied voltage, injection mode, current,more » temperature, and detection wavelength) that affect the separations and analytical results have been examined in this study. Those factors that affect the separation have been delineated. Among these parameters, the pH has been found to be the most important, which affects the double-layer of the capillary wall, the electro-osmotic flow and analyte mobility. The optimum pH for separating these dibasic acids, as well as the other parameters are discussed in detail and related to the development of methods for analyzing oxidation intermediates in oxidative waste management procedures.« less

Characterization of folding intermediates during urea-induced denaturation of human carbonic anhydrase II.

PubMed

Wahiduzzaman; Dar, Mohammad Aasif; Haque, Md Anzarul; Idrees, Danish; Hassan, Md Imtaiyaz; Islam, Asimul; Ahmad, Faizan

2017-02-01

Knowledge of folding/unfolding pathway is fundamental basis to study protein structure and stability. Human carbonic anhydrase II (HCAII) is a ∼29kDa, β-sheet dominated monomeric protein of 259 amino acid residues. In the present study, the urea-induced denaturation of HCAII was carried out which was a tri-phasic process, i.e., N (native) ↔ X I ↔ X II ↔ D (denatured) with stable intermediates X I and X II populated around 2 and 4M urea, respectively. The far-UV CD was used to characterize the intermediate states (X I and X II ) for secondary structural content, near-UV CD for tertiary structure, dynamic light scattering for hydrodynamic radius and ANS fluorescence spectroscopy for the presence of exposed hydrophobic patches. Based on these experiments, we concluded that urea-induced X I state has characteristics of molten globule state while X II state bears characteristics features of pre-molten globule state. Characterization of the intermediates on the folding pathway will contribute to a deeper understanding of the structure-function relationship of HCAII. Furthermore, this system may provide an excellent model to study urea stress and the strategies adopted by the organisms to combat such a stress. Copyright © 2016 Elsevier B.V. All rights reserved.

Final technical report

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

Loveland, Walter David

2016-08-27

This report describes the research carried out under this grant for the period from 1997 to 2014. This work has been previously described in annual progress reports and renewal applications. As a result of this project, ~100 papers were published in open refereed journals and 107 invited talks were given by the PI. The research subjects covered by this project included the synthesis and characterization of super-heavy nuclei, the critical study of the reaction mechanisms used in these synthesis reactions, the mechanism(s) of intermediate energy and relativistic nuclear collisions, the study of reactions induced by radioactive nuclear beams, and generalmore » properties of the heaviest elements.« less

Recovery of transplutonium elements from nuclear reactor waste

DOEpatents

Campbell, David O.; Buxton, Samuel R.

1977-05-24

A method of separating actinide values from nitric acid waste solutions resulting from reprocessing of irradiated nuclear fuels comprises oxalate precipitation of the major portion of actinide and lanthanide values to provide a trivalent fraction suitable for subsequent actinide/lanthanide partition, exchange of actinide and lanthanide values in the supernate onto a suitable cation exchange resin to provide an intermediate-lived raffinate waste stream substantially free of actinides, and elution of the actinide values from the exchange resin. The eluate is then used to dissolve the trivalent oxalate fraction prior to actinide/lanthanide partition or may be combined with the reprocessing waste stream and recycled.

Effects of Long- and Intermediate-Wavelength Nonuniformities on Hot-Spot Energetics of Hydrodynamic Equivalent Targets

NASA Astrophysics Data System (ADS)

Bose, A.; Betti, R.; Woo, K. M.; Christopherson, A. R.; Shvarts, D.

2015-11-01

The impact of intermediate- and low-mode nonuniformities on the performance of inertial confinement fusion (ICF) implosions is investigated by a detailed study of hot-spot energetics. It is found that low- (1 ~ 2) and intermediate-mode (1 >= 10) asymmetries affect the hot-spot hydrodynamics in very different ways. It is observed that for low-mode asymmetries, the fusion yield decreases because of a significant reduction in hot-spot pressure while the neutron-averaged hot-spot volume remains comparable to that of unperturbed (clean) simulations. On the other hand, implosions with moderate-amplitude, intermediate-wavelength modes, which are amplified by the Rayleigh-Taylor instability (RTI), exhibit a fusion-yield degradation primarily caused by a reduction in the burn volume without significant degradation of the pressure. For very large amplitudes, the intermediate modes show a ``secondary piston effect,'' where the converging RTI spikes compress a much smaller volume, allowing for a secondary conversion of the shell's kinetic energy to internal energy at a central region. Understanding the effects of nonuniformities on the hot-spot energetics provides valuable insight in determining the causes of performance degradation in current ICF experiments. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944 and DE-FC02-04ER54789 (Fusion Science Center).

Tight coupling between nucleus and cell migration through the perinuclear actin cap

PubMed Central

Kim, Dong-Hwee; Cho, Sangkyun; Wirtz, Denis

2014-01-01

ABSTRACT Although eukaryotic cells are known to alternate between ‘advancing’ episodes of fast and persistent movement and ‘hesitation’ episodes of low speed and low persistence, the molecular mechanism that controls the dynamic changes in morphology, speed and persistence of eukaryotic migratory cells remains unclear. Here, we show that the movement of the interphase nucleus during random cell migration switches intermittently between two distinct modes – rotation and translocation – that follow with high fidelity the sequential rounded and elongated morphologies of the nucleus and cell body, respectively. Nuclear rotation and translocation mediate the stop-and-go motion of the cell through the dynamic formation and dissolution, respectively, of the contractile perinuclear actin cap, which is dynamically coupled to the nuclear lamina and the nuclear envelope through LINC complexes. A persistent cell movement and nuclear translocation driven by the actin cap are halted following the disruption of the actin cap, which in turn allows the cell to repolarize for its next persistent move owing to nuclear rotation mediated by cytoplasmic dynein light intermediate chain 2. PMID:24639463

Examination of key intermediates in the catalytic cycle of aspartate-beta-semialdehyde dehydrogenase from a gram-positive infectious bacteria.

PubMed

Faehnle, Christopher R; Le Coq, Johanne; Liu, Xuying; Viola, Ronald E

2006-10-13

Aspartate-beta-semialdehyde dehydrogenase (ASADH) catalyzes a critical branch point transformation in amino acid bio-synthesis. The products of the aspartate pathway are essential in microorganisms, and this entire pathway is absent in mammals, making this enzyme an attractive target for antibiotic development. The first structure of an ASADH from a Gram-positive bacterium, Streptococcus pneumoniae, has now been determined. The overall structure of the apoenzyme has a similar fold to those of the Gram-negative and archaeal ASADHs but contains some interesting structural variations that can be exploited for inhibitor design. Binding of the coenzyme NADP, as well as a truncated nucleotide analogue, into an alternative conformation from that observed in Gram-negative ASADHs causes an enzyme domain closure that precedes catalysis. The covalent acyl-enzyme intermediate was trapped by soaking the substrate into crystals of the coenzyme complex, and the structure of this elusive intermediate provides detailed insights into the catalytic mechanism.

Keeping the LINC: the importance of nucleocytoskeletal coupling in intracellular force transmission and cellular function.

PubMed

Lombardi, Maria L; Lammerding, Jan

2011-12-01

Providing a stable physical connection between the nucleus and the cytoskeleton is essential for a wide range of cellular functions and it could also participate in mechanosensing by transmitting intra- and extra-cellular mechanical stimuli via the cytoskeleton to the nucleus. Nesprins and SUN proteins, located at the nuclear envelope, form the LINC (linker of nucleoskeleton and cytoskeleton) complex that connects the nucleus to the cytoskeleton; underlying nuclear lamins contribute to anchoring LINC complex components at the nuclear envelope. Disruption of the LINC complex or loss of lamins can result in disturbed perinuclear actin and intermediate filament networks and causes severe functional defects, including impaired nuclear positioning, cell polarization and cell motility. Recent studies have identified the LINC complex as the major force-transmitting element at the nuclear envelope and suggest that many of the aforementioned defects can be attributed to disturbed force transmission between the nucleus and the cytoskeleton. Thus mutations in nesprins, SUN proteins or lamins, which have been linked to muscular dystrophies and cardiomyopathies, may weaken or completely eliminate LINC complex function at the nuclear envelope and result in impaired intracellular force transmission, thereby disrupting critical cellular functions.

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.

Application of MCR-ALS to reveal intermediate conformations in the thermally induced α-β transition of poly-L-lysine monitored by FT-IR spectroscopy

NASA Astrophysics Data System (ADS)

Alcaráz, Mirta R.; Schwaighofer, Andreas; Goicoechea, Héctor; Lendl, Bernhard

2017-10-01

Temperature-induced conformational transitions of poly-L-lysine were monitored with Fourier-transform infrared (FT-IR) spectroscopy between 10 °C and 70 °C. Chemometric analysis of dynamic IR spectra was performed by multivariate curve analysis-alternating least squares (MCR-ALS) of the amide I‧ and amide II‧ spectral region. With this approach, the pure spectral and concentration profiles of the conformational transition were obtained. Beside the initial α-helical, the intermediate random coil/extended helices and the final β-sheet structure, an additional intermediate PLL conformation was identified and attributed to a transient β-sheet structure.

Comparing results of X-ray diffraction, µ-Raman spectroscopy and neutron diffraction when identifying chemical phases in seized nuclear material, during a comparative nuclear forensics exercise

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

Rondahl, Stina Holmgren; Pointurier, Fabien; Ahlinder, Linnea

This work presents the results for identification of chemical phases obtained by several laboratories as a part of an international nuclear forensic round-robin exercise. In this work powder X-ray diffraction (p-XRD) is regarded as the reference technique. Neutron diffraction produced a superior high-angle diffraction pattern relative to p-XRD. Requiring only small amounts of sample, µ-Raman spectroscopy was used for the first time in this context as a potentially complementary technique to p-XRD. The chemical phases were identified as pure UO 2 in two materials, and as a mixture of UO 2, U 3O 8 and an intermediate species U 3Omore » 7 in the third material.« less

Comparing results of X-ray diffraction, µ-Raman spectroscopy and neutron diffraction when identifying chemical phases in seized nuclear material, during a comparative nuclear forensics exercise

DOE PAGES

Rondahl, Stina Holmgren; Pointurier, Fabien; Ahlinder, Linnea; ...

2018-01-24

This work presents the results for identification of chemical phases obtained by several laboratories as a part of an international nuclear forensic round-robin exercise. In this work powder X-ray diffraction (p-XRD) is regarded as the reference technique. Neutron diffraction produced a superior high-angle diffraction pattern relative to p-XRD. Requiring only small amounts of sample, µ-Raman spectroscopy was used for the first time in this context as a potentially complementary technique to p-XRD. The chemical phases were identified as pure UO 2 in two materials, and as a mixture of UO 2, U 3O 8 and an intermediate species U 3Omore » 7 in the third material.« less

Nuclear spin relaxation of methane in solid xenon

NASA Astrophysics Data System (ADS)

Sugimoto, Takeru; Arakawa, Ichiro; Yamakawa, Koichiro

2018-03-01

Nuclear spin relaxation of methane in solid xenon has been studied by infrared spectroscopy. From the analysis of the temporal changes of the rovibrational peaks, the rates of the nuclear spin relaxation of I = 2 ← 1 correlated to the rotational relaxation of J = 0 ← 1 were obtained at temperatures of 5.1-11.5 K. On the basis of the temperature dependence of the relaxation rate, the activation energy of the indirect two-phonon process was determined to be 50 ± 6 K, which is in good agreement with the rotational transition energies of J = 2 ← 1 and J = 3 ← 1. Taking into account this result and the spin degeneracy, we argue that the lowest J = 3 level in which the I = 1 and I = 2 states are degenerate acts as the intermediate point of the indirect process.

Charged particle induced delayed X-rays (DEX) for the analysis of intermediate and heavy elements

NASA Astrophysics Data System (ADS)

Pillay, A. E.; Erasmus, C. S.; Andeweg, A. H.; Sellschop, J. P. F.; Annegarn, H. J.; Dunn, J.

1988-12-01

The emission of K X-rays from proton-rich and metastable radionuclides, following proton activation of the stable isotopes of the elements of interest, has not been widely used as a means of analysis. The thrust of this paper proposes a nuclear technique using delayed X-rays for the analysis of low concentrations of intermediate and heavy elements. The method is similar to the delayed gamma-ray technique. Proton bombardment induces mainly (p, n) reactions whereas the delayed X-rays originate largely from e --capture and isomeric transition. Samples of rare earth and platinum group elements (PGE), in the form of compacted powders, were irradiated with an 11 MeV proton beam and delayed X-rays detected with a 100 mm 2 Ge detector. Single element spectra for a range of rare earths and PGEs are presented. Analytical conditions are demonstrated for Pd in the range 0.1-5%. Spectra from actual geological samples of a PGE ore, preconcentrated by fire-assay, and monazite are presented. All six platinum group elements are visible and interference-free in a single spectrum, a marked advance on other nuclear techniques for these elements, including PIXE and neutron activation analysis (NAA).

Contributed Review: Nuclear magnetic resonance core analysis at 0.3 T

NASA Astrophysics Data System (ADS)

Mitchell, Jonathan; Fordham, Edmund J.

2014-11-01

Nuclear magnetic resonance (NMR) provides a powerful toolbox for petrophysical characterization of reservoir core plugs and fluids in the laboratory. Previously, there has been considerable focus on low field magnet technology for well log calibration. Now there is renewed interest in the study of reservoir samples using stronger magnets to complement these standard NMR measurements. Here, the capabilities of an imaging magnet with a field strength of 0.3 T (corresponding to 12.9 MHz for proton) are reviewed in the context of reservoir core analysis. Quantitative estimates of porosity (saturation) and pore size distributions are obtained under favorable conditions (e.g., in carbonates), with the added advantage of multidimensional imaging, detection of lower gyromagnetic ratio nuclei, and short probe recovery times that make the system suitable for shale studies. Intermediate field instruments provide quantitative porosity maps of rock plugs that cannot be obtained using high field medical scanners due to the field-dependent susceptibility contrast in the porous medium. Example data are presented that highlight the potential applications of an intermediate field imaging instrument as a complement to low field instruments in core analysis and for materials science studies in general.

Exploring hypothetical learning progressions for the chemistry of nitrogen and nuclear processes

NASA Astrophysics Data System (ADS)

Henry, Deborah McKern

Chemistry is a bridge that connects a number of scientific disciplines. High school students should be able to determine whether scientific information is accurate, how chemistry applies to daily life, and the mechanism by which systems operate (NRC, 2012). This research focuses on describing hypothetical learning progressions for student understanding of the chemical reactions of nitrogen and nuclear processes and examines whether there is consistency in scientific reasoning between these two distinct conceptual areas. The constant comparative method was used to analyze the written products of students including homework, formative and summative tests, laboratory notebooks, reflective journals, written presentations, and discussion board contributions via Edmodo (an online program). The ten participants were 15 and 16 year old students enrolled in a general high school chemistry course. Instruction took place over a ten week period. The learning progression levels ranged from 0 to 4 and were described as missing, novice, intermediate, proficient, and expert. The results were compared to the standards set by the NRC with a lower anchor (expectations for grade 8) and upper anchor (expectations for grade 12). The results indicate that, on average, students were able to reach an intermediate level of understanding for these concepts.

Corrosion susceptibility of steel drums containing cemented intermediate level nuclear wastes

NASA Astrophysics Data System (ADS)

Duffó, Gustavo S.; Farina, Silvia B.; Schulz, Fátima M.; Marotta, Francesca

2010-10-01

Cementation processes are used as immobilization techniques for low or intermediate level radioactive waste for economical and safety reasons and for being a simple operation. In particular, ion-exchange resins commonly used for purification of radioactive liquid waste from nuclear reactors are immobilized before being stored to improve the leach resistance of the waste matrix and to maintain mechanical stability. Combustible solid radioactive waste can be incinerated and the resulting ashes can also be immobilized before storage. The immobilized resins and ashes are then contained in steel drums that may undergo corrosion depending on the presence of certain contaminants. The work described in this paper was aimed at evaluating the corrosion susceptibility of steel drums in contact with cemented ion-exchange resins and incineration ashes containing different concentrations of aggressive species (mostly chloride and sulphate ions). A special type of specimen was designed to simulate the cemented waste in the drum. The evolution of the corrosion potential and the corrosion current density of the steel, as well as the electrical resistivity of the matrix were monitored over a time period of 1 year. The results show the deleterious effect of chloride on the expected lifespan of the waste containers.

Nuclear Structure Aspects in Nuclear Astrophysics

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

Smith, Michael Scott

2006-12-01

Nuclear Astrophysics as a broad and diverse field of study can be viewed as a magnifier of the impact of microscopic processes on the evolution of macroscopic events. One of the primary goals in Nuclear Astrophysics is the understanding of the nucleosynthesis processes that take place in the cosmos and the simulation of the correlated stellar and explosive burning scenarios. These simulations are strongly dependent on the input from Nuclear Physics which sets the time scale for all stellar dynamic processes--from giga-years of stellar evolution to milliseconds of stellar explosions--and provides the basis for most of the signatures that wemore » have for the interpretation of these events--from stellar luminosities, elemental and isotopic abundances to neutrino flux from distant supernovae. The Nuclear Physics input comes through nuclear structure, low energy reaction rates, nuclear masses, and decay rates. There is a common perception that low energy reaction rates are the most important component of the required nuclear physics input; however, in this article we take a broader approach and present an overview of the close correlation between various nuclear structure aspects and their impact on nuclear astrophysics. We discuss the interplay between the weak and the strong forces on stellar time scales due to the limitations they provide for the evolution of slow and rapid burning processes. The effects of shell structure in nuclei on stellar burning processes as well as the impact of clustering in nuclei is outlined. Furthermore we illustrate the effects of the various nuclear structure aspects on the major nucleosynthesis processes that have been identified in the last few decades. We summarize and provide a coherent overview of the impact of all aspects of nuclear structure on nuclear astrophysics.« less

Atomic physics constraints on the X boson

NASA Astrophysics Data System (ADS)

Jentschura, Ulrich D.; Nándori, István

2018-04-01

Recently, a peak in the light fermion pair spectrum at invariant q2≈(16.7MeV ) 2 has been observed in the bombardment of 7Li by protons. This peak has been interpreted in terms of a protophobic interaction of fermions with a gauge boson (X boson) of invariant mass ≈16.7 MeV which couples mainly to neutrons. High-precision atomic physics experiments aimed at observing the protophobic interaction need to separate the X boson effect from the nuclear-size effect, which is a problem because of the short range of the interaction (11.8 fm), which is commensurate with a "nuclear halo." Here we analyze the X boson in terms of its consequences for both electronic atoms as well as muonic hydrogen and deuterium. We find that the most promising atomic systems where the X boson has an appreciable effect, distinguishable from a finite-nuclear-size effect, are muonic atoms of low and intermediate nuclear charge numbers.

Altering lamina assembly reveals lamina-dependent and -independent functions for A-type lamins.

PubMed

Zwerger, Monika; Roschitzki-Voser, Heidi; Zbinden, Reto; Denais, Celine; Herrmann, Harald; Lammerding, Jan; Grütter, Markus G; Medalia, Ohad

2015-10-01

Lamins are intermediate filament proteins that form a fibrous meshwork, called the nuclear lamina, between the inner nuclear membrane and peripheral heterochromatin of metazoan cells. The assembly and incorporation of lamin A/C into the lamina, as well as their various functions, are still not well understood. Here, we employed designed ankyrin repeat proteins (DARPins) as new experimental tools for lamin research. We screened for DARPins that specifically bound to lamin A/C, and interfered with lamin assembly in vitro and with incorporation of lamin A/C into the native lamina in living cells. The selected DARPins inhibited lamin assembly and delocalized A-type lamins to the nucleoplasm without modifying lamin expression levels or the amino acid sequence. Using these lamin binders, we demonstrate the importance of proper integration of lamin A/C into the lamina for nuclear mechanical properties and nuclear envelope integrity. Finally, our study provides evidence for cell-type-specific differences in lamin functions. © 2015. Published by The Company of Biologists Ltd.

Altering lamina assembly reveals lamina-dependent and -independent functions for A-type lamins

PubMed Central

Zwerger, Monika; Roschitzki-Voser, Heidi; Zbinden, Reto; Denais, Celine; Herrmann, Harald; Lammerding, Jan; Grütter, Markus G.; Medalia, Ohad

2015-01-01

ABSTRACT Lamins are intermediate filament proteins that form a fibrous meshwork, called the nuclear lamina, between the inner nuclear membrane and peripheral heterochromatin of metazoan cells. The assembly and incorporation of lamin A/C into the lamina, as well as their various functions, are still not well understood. Here, we employed designed ankyrin repeat proteins (DARPins) as new experimental tools for lamin research. We screened for DARPins that specifically bound to lamin A/C, and interfered with lamin assembly in vitro and with incorporation of lamin A/C into the native lamina in living cells. The selected DARPins inhibited lamin assembly and delocalized A-type lamins to the nucleoplasm without modifying lamin expression levels or the amino acid sequence. Using these lamin binders, we demonstrate the importance of proper integration of lamin A/C into the lamina for nuclear mechanical properties and nuclear envelope integrity. Finally, our study provides evidence for cell-type-specific differences in lamin functions. PMID:26275827

IER-297 CED-2: Final Design for Thermal/Epithermal eXperiments with Jemima Plates with Polyethylene and Hafnium

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

Nelson, A. J.; Percher, C. M.; Zywiec, W. J.

This report presents the final design (CED-2) for IER-297, and focuses on 15 critical configurations using highly enriched uranium (HEU) Jemima plates moderated by polyethylene with and without hafnium diluent. The goal of the U.S. Nuclear Criticality Safety Program’s Thermal/Epithermal eXperiments (TEX) is to design and conduct new critical experiments to address high priority nuclear data needs from the nuclear criticality safety and nuclear data communities, with special emphasis on intermediate energy (0.625 eV – 100 keV) assemblies that can be easily modified to include various high priority diluent materials. The TEX (IER 184) CED-1 Report [1], completed in 2012,more » demonstrated the feasibility of meeting the TEX goals with two existing NCSP fissile assets, plutonium Zero Power Physics Reactor (ZPPR) plates and highly enriched uranium (HEU) Jemima plates. The first set of TEX experiments will focus on using the plutonium ZPPR plates with polyethylene moderator and tantalum diluents.« less

Meiotic Nuclear Oscillations Are Necessary to Avoid Excessive Chromosome Associations.

PubMed

Chacón, Mariola R; Delivani, Petrina; Tolić, Iva M

2016-11-01

Pairing of homologous chromosomes is a crucial step in meiosis, which in fission yeast depends on nuclear oscillations. However, how nuclear oscillations help pairing is unknown. Here, we show that homologous loci typically pair when the spindle pole body is at the cell pole and the nucleus is elongated, whereas they unpair when the spindle pole body is in the cell center and the nucleus is round. Inhibition of oscillations demonstrated that movement is required for initial pairing and that prolonged association of loci leads to mis-segregation. The double-strand break marker Rec25 accumulates in elongated nuclei, indicating that prolonged chromosome stretching triggers recombinatory pathways leading to mis-segregation. Mis-segregation is rescued by overexpression of the Holliday junction resolvase Mus81, suggesting that prolonged pairing results in irresolvable recombination intermediates. We conclude that nuclear oscillations exhibit a dual role, promoting initial pairing and restricting the time of chromosome associations to ensure proper segregation. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Protein vivisection reveals elusive intermediates in folding

PubMed Central

Zheng, Zhongzhou; Sosnick, Tobin R.

2010-01-01

Although most folding intermediates escape detection, their characterization is crucial to the elucidation of folding mechanisms. Here we outline a powerful strategy to populate partially unfolded intermediates: A buried aliphatic residue is substituted with a charged residue (e.g., Leu→Glu−) to destabilize and unfold a specific region of the protein. We apply this strategy to Ubiquitin, reversibly trapping a folding intermediate in which the β5 strand is unfolded. The intermediate refolds to a native-like structure upon charge neutralization under mildly acidic conditions. Characterization of the trapped intermediate using NMR and hydrogen exchange methods identifies a second folding intermediate and reveals the order and free energies of the two major folding events on the native side of the rate-limiting step. This general strategy may be combined with other methods and have broad applications in the study of protein folding and other reactions that require trapping of high energy states. PMID:20144618

Superasymmetric fission of heavy nuclei induced by intermediate-energy protons

NASA Astrophysics Data System (ADS)

Deppman, A.; Andrade-II, E.; Guimarães, V.; Karapetyan, G. S.; Tavares, O. A. P.; Balabekyan, A. R.; Demekhina, N. A.; Adam, J.; Garcia, F.; Katovsky, K.

2013-12-01

In this work we present the results for the investigation of intermediate-mass fragment (IMF) production with the proton-induced reaction at 660 MeV on 238U and 237Np target. The data were obtained with the LNR Phasotron U-400M Cyclotron at Joint Institute for Nuclear Research (JINR), Dubna, Russia. A total of 93 isotopes, in the mass range of 30

Two-potential approach for electron-molecular collisions at intermediate and high energies - Application to e-N2 scatterings

NASA Technical Reports Server (NTRS)

Choi, B. H.; Poe, R. T.; Sun, J. C.; Shan, Y.

1979-01-01

A general theoretical approach is proposed for the calculation of elastic, vibrational, and rotational transitions for electron-molecule scattering at intermediate and high-electron-impact energies. In this formulation, contributions to the scattering process come from the incoherent sum of two dominant potentials: a short-range shielded nuclear Coulomb potential from individual atomic centers, and a permanent/induced long-range potential. Application to e-N2 scattering from 50-500 eV incident electron energies has yielded good agreement with absolutely calibrated experiments. Comparisons with other theoretical approaches are made. The physical picture as well as the general features of electron-molecule scattering process are discussed within the framework of the two-potential approach.

Visualizing the molecular sociology at the HeLa cell nuclear periphery.

PubMed

Mahamid, Julia; Pfeffer, Stefan; Schaffer, Miroslava; Villa, Elizabeth; Danev, Radostin; Cuellar, Luis Kuhn; Förster, Friedrich; Hyman, Anthony A; Plitzko, Jürgen M; Baumeister, Wolfgang

2016-02-26

The molecular organization of eukaryotic nuclear volumes remains largely unexplored. Here we combined recent developments in cryo-electron tomography (cryo-ET) to produce three-dimensional snapshots of the HeLa cell nuclear periphery. Subtomogram averaging and classification of ribosomes revealed the native structure and organization of the cytoplasmic translation machinery. Analysis of a large dynamic structure-the nuclear pore complex-revealed variations detectable at the level of individual complexes. Cryo-ET was used to visualize previously elusive structures, such as nucleosome chains and the filaments of the nuclear lamina, in situ. Elucidation of the lamina structure provides insight into its contribution to metazoan nuclear stiffness. Copyright © 2016, American Association for the Advancement of Science.

The controversial nuclear matrix: a balanced point of view.

PubMed

Martelli, A M; Falcieri, E; Zweyer, M; Bortul, R; Tabellini, G; Cappellini, A; Cocco, L; Manzoli, L

2002-10-01

The nuclear matrix is defined as the residual framework after the removal of the nuclear envelope, chromatin, and soluble components by sequential extractions. According to several investigators the nuclear matrix provides the structural basis for intranuclear order. However, the existence itself and the nature of this structure is still uncertain. Although the techniques used for the visualization of the nuclear matrix have improved over the years, it is still unclear to what extent the isolated nuclear matrix corresponds to an in vivo existing structure. Therefore, considerable skepticism continues to surround the nuclear matrix fraction as an accurate representation of the situation in living cells. Here, we summarize the experimental evidence in favor of, or against, the presence of a diffuse nucleoskeleton as a facilitating organizational nonchromatin structure of the nucleus.

Intermediate states and structure evolution in the free-falling process of the dislocation in graphene

NASA Astrophysics Data System (ADS)

Wang, Shaofeng; Yao, Yin; Bai, Jianhui; Wang, Rui

2017-04-01

This paper investigated the intermediate states and the structure evolution of the dislocation in graphene when it falls freely from the saddle point of the energy landscape. The O-type dislocation, an unstable equilibrium structure located at the saddle point, is obtained from the lattice theory of the dislocation structure and improved by the ab initio calculation to take the buckling into account. Intermediate states along the kinetics path in the falling process are obtained from the ab initio simulation. Once the dislocation falls from the saddle point to the energy valley, this O-type dislocation transforms into the stable structure that is referred to as the B-type dislocation, and in the meantime, it moves a distance that equals half a Burgers vector. The structure evolution and the energy variation in the free-falling process are revealed explicitly. It is observed that rather than smooth change, a platform manifests itself in the energy curve. The unusual behaviour in the energy curve is mainly originated from symmetry breaking and bond formation in the dislocation core. The results can provide deep insight in the mechanism of the brittle feature of covalent materials.

Structure and mechanical behavior of bird beaks

NASA Astrophysics Data System (ADS)

Seki, Yasuaki

The structure and mechanical behavior of Toco toucan (Ramphastos toco) and Wreathed hornbill (Rhyticeros undulatus) beaks were examined. The structure of Toco toucan and Wreathed hornbill beak was found to be a sandwich composite with an exterior of keratin and a fibrous bony network of closed cells made of trabeculae. A distinctive feature of the hornbill beak is its casque formed from cornified keratin layers. The casque is believed to have an acoustic function due to the complex internal structure. The toucan and hornbill beaks have a hollow region that extends from proximal to mid-section. The rhamphotheca is comprised of super-posed polygonal scales (45 mum diameter and 1 mum thickness) fixed by some organic adhesive. The branched intermediate filaments embedded in keratin matrix were discovered by transmission electron microscopy (TEM). The diameter of intermediate laments was ~10 nm. The orientation of intermediate filaments was examined with TEM tomography and the branched filaments were homogeneously distributed. The closed-cell foam is comprised of the fibrous structure of bony struts with an edge connectivity of three or four and the cells are sealed off by the thin membranes. The volumetric structure of bird beak foam was reproduced by computed tomography for finite element modeling.

The physical chemistry of Criegee intermediates in the gas phase

DOE PAGES

Osborn, David L.; Taatjes, Craig A.

2015-07-24

Here, carbonyl oxides, also known as Criegee intermediates, are key intermediates in both gas phase ozonolysis of unsaturated hydrocarbons in the troposphere and solution phase organic synthesis via ozonolysis. Although the study of Criegee intermediates in both arenas has a long history, direct studies in the gas phase have only recently become possible through new methods of generating stabilised Criegee intermediates in sufficient quantities. This advance has catalysed a large number of new experimental and theoretical investigations of Criegee intermediate chemistry. In this article we review the physical chemistry of Criegee intermediates, focusing on their molecular structure, spectroscopy, unimolecular andmore » bimolecular reactions. These recent results have overturned conclusions from some previous studies, while confirming others, and have clarified areas of investigation that will be critical targets for future studies. In addition to expanding our fundamental understanding of Criegee intermediates, the rapidly expanding knowledge base will support increasingly predictive models of their impacts on society.« less

Super-Planckian Thermophotovoltaics Without Vacuum Gaps

NASA Astrophysics Data System (ADS)

Mirmoosa, M. S.; Biehs, S.-A.; Simovski, C. R.

2017-11-01

We introduce the concept of a thermophotovoltaic system whose emitter is separated from the photovoltaic cell by an intermediate thick slab of gallium arsenide. Owing to the engineered structure of the emitter (a multilayer structure of negative- and positive-ɛ layers) together with a high refractiveindex and transparency of the intermediate slab, we achieve a super-Planckian and frequency-selective spectrum of radiative heat transfer which is desirable for the efficient performance of thermophotovoltaic systems.

Folding of the RNA Recognition Motif (RRM) Domains of the Amyotrophic Lateral Sclerosis (ALS)-linked Protein TDP-43 Reveals an Intermediate State*

PubMed Central

Mackness, Brian C.; Tran, Meme T.; McClain, Shannan P.; Matthews, C. Robert; Zitzewitz, Jill A.

2014-01-01

Pathological alteration of TDP-43 (TAR DNA-binding protein-43), a protein involved in various RNA-mediated processes, is a hallmark feature of the neurodegenerative diseases amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Fragments of TDP-43, composed of the second RNA recognition motif (RRM2) and the disordered C terminus, have been observed in cytoplasmic inclusions in sporadic amyotrophic lateral sclerosis cases, suggesting that conformational changes involving RRM2 together with the disordered C terminus play a role in aggregation and toxicity. The biophysical data collected by CD and fluorescence spectroscopies reveal a three-state equilibrium unfolding model for RRM2, with a partially folded intermediate state that is not observed in RRM1. Strikingly, a portion of RRM2 beginning at position 208, which mimics a cleavage site observed in patient tissues, increases the population of this intermediate state. Mutually stabilizing interactions between the domains in the tethered RRM1 and RRM2 construct reduce the population of the intermediate state and enhance DNA/RNA binding. Despite the high sequence homology of the two domains, a network of large hydrophobic residues in RRM2 provides a possible explanation for the increased stability of RRM2 compared with RRM1. The cluster analysis suggests that the intermediate state may play a functional role by enhancing access to the nuclear export signal contained within its sequence. The intermediate state may also serve as a molecular hazard linking productive folding and function with pathological misfolding and aggregation that may contribute to disease. PMID:24497641

The evolution of intermediate castration virulence and ant coexistence in a spatially structured environment.

PubMed

Szilágyi, András; Scheuring, István; Edwards, David P; Orivel, Jerome; Yu, Douglas W

2009-12-01

Theory suggests that spatial structuring should select for intermediate levels of virulence in parasites, but empirical tests are rare and have never been conducted with castration (sterilizing) parasites. To test this theory in a natural landscape, we construct a spatially explicit model of the symbiosis between the ant-plant Cordia nodosa and its two, protecting ant symbionts, Allomerus and Azteca. Allomerus is also a castration parasite, preventing fruiting to increase colony fecundity. Limiting the dispersal of Allomerus and host plant selects for intermediate castration virulence. Increasing the frequency of the mutualist, Azteca, selects for higher castration virulence in Allomerus, because seeds from Azteca-inhabited plants are a public good that Allomerus exploits. These results are consistent with field observations and, to our knowledge, provide the first empirical evidence supporting the hypothesis that spatial structure can reduce castration virulence and the first such evidence in a natural landscape for either mortality or castration virulence.

Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes.

PubMed

Lin, Milo M; Meinhold, Lars; Shorokhov, Dmitry; Zewail, Ahmed H

2008-08-07

A 2D free-energy landscape model is presented to describe the (un)folding transition of DNA/RNA hairpins, together with molecular dynamics simulations and experimental findings. The dependence of the (un)folding transition on the stem sequence and the loop length is shown in the enthalpic and entropic contributions to the free energy. Intermediate structures are well defined by the two coordinates of the landscape during (un)zipping. Both the free-energy landscape model and the extensive molecular dynamics simulations totaling over 10 mus predict the existence of temperature-dependent kinetic intermediate states during hairpin (un)zipping and provide the theoretical description of recent ultrafast temperature-jump studies which indicate that hairpin (un)zipping is, in general, not a two-state process. The model allows for lucid prediction of the collapsed state(s) in simple 2D space and we term it the kinetic intermediate structure (KIS) model.

A Springloaded Metal-Ligand Mesocate Allows Access to Trapped Intermediates of Self-Assembly.

PubMed

Bogie, Paul M; Holloway, Lauren R; Lyon, Yana; Onishi, Nicole C; Beran, Gregory J O; Julian, Ryan R; Hooley, Richard J

2018-04-02

A strained, "springloaded" Fe 2 L 3 iminopyridine mesocate shows highly variable reactivity upon postassembly reaction with competitive diamines. The strained assembly is reactive toward transimination in minutes at ambient temperature and allows observation of kinetically trapped intermediates in the self-assembly pathway. When diamines are used that can only form less favored cage products upon full equilibration, trapped ML 3 fragments with pendant, "hanging" NH 2 groups are selectively formed instead. Slight variations in diamine structure have large effects on the product outcome: less rigid diamines convert the mesocate to more favored self-assembled cage complexes under mild conditions and allow observation of heterocomplex intermediates in the displacement pathway. The mesocate allows control of equilibrium processes and direction of product outcomes via small, iterative changes in added subcomponent structure and provides a method of accessing metal-ligand cage structures not normally observed in multicomponent Fe-iminopyridine self-assembly.

Interrogating viral capsid assembly with ion mobility-mass spectrometry

NASA Astrophysics Data System (ADS)

Uetrecht, Charlotte; Barbu, Ioana M.; Shoemaker, Glen K.; van Duijn, Esther; Heck, Albert J. R.

2011-02-01

Most proteins fulfil their function as part of large protein complexes. Surprisingly, little is known about the pathways and regulation of protein assembly. Several viral coat proteins can spontaneously assemble into capsids in vitro with morphologies identical to the native virion and thus resemble ideal model systems for studying protein complex formation. Even for these systems, the mechanism for self-assembly is still poorly understood, although it is generally thought that smaller oligomeric structures form key intermediates. This assembly nucleus and larger viral assembly intermediates are typically low abundant and difficult to monitor. Here, we characterised small oligomers of Hepatitis B virus (HBV) and norovirus under equilibrium conditions using native ion mobility mass spectrometry. This data in conjunction with computational modelling enabled us to elucidate structural features of these oligomers. Instead of more globular shapes, the intermediates exhibit sheet-like structures suggesting that they are assembly competent. We propose pathways for the formation of both capsids.

Moving Cell Boundaries Drive Nuclear Shaping during Cell Spreading.

PubMed

Li, Yuan; Lovett, David; Zhang, Qiao; Neelam, Srujana; Kuchibhotla, Ram Anirudh; Zhu, Ruijun; Gundersen, Gregg G; Lele, Tanmay P; Dickinson, Richard B

2015-08-18

The nucleus has a smooth, regular appearance in normal cells, and its shape is greatly altered in human pathologies. Yet, how the cell establishes nuclear shape is not well understood. We imaged the dynamics of nuclear shaping in NIH3T3 fibroblasts. Nuclei translated toward the substratum and began flattening during the early stages of cell spreading. Initially, nuclear height and width correlated with the degree of cell spreading, but over time, reached steady-state values even as the cell continued to spread. Actomyosin activity, actomyosin bundles, microtubules, and intermediate filaments, as well as the LINC complex, were all dispensable for nuclear flattening as long as the cell could spread. Inhibition of actin polymerization as well as myosin light chain kinase with the drug ML7 limited both the initial spreading of cells and flattening of nuclei, and for well-spread cells, inhibition of myosin-II ATPase with the drug blebbistatin decreased cell spreading with associated nuclear rounding. Together, these results show that cell spreading is necessary and sufficient to drive nuclear flattening under a wide range of conditions, including in the presence or absence of myosin activity. To explain this observation, we propose a computational model for nuclear and cell mechanics that shows how frictional transmission of stress from the moving cell boundaries to the nuclear surface shapes the nucleus during early cell spreading. Our results point to a surprisingly simple mechanical system in cells for establishing nuclear shapes. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Moving Cell Boundaries Drive Nuclear Shaping during Cell Spreading

PubMed Central

Li, Yuan; Lovett, David; Zhang, Qiao; Neelam, Srujana; Kuchibhotla, Ram Anirudh; Zhu, Ruijun; Gundersen, Gregg G.; Lele, Tanmay P.; Dickinson, Richard B.

2015-01-01

The nucleus has a smooth, regular appearance in normal cells, and its shape is greatly altered in human pathologies. Yet, how the cell establishes nuclear shape is not well understood. We imaged the dynamics of nuclear shaping in NIH3T3 fibroblasts. Nuclei translated toward the substratum and began flattening during the early stages of cell spreading. Initially, nuclear height and width correlated with the degree of cell spreading, but over time, reached steady-state values even as the cell continued to spread. Actomyosin activity, actomyosin bundles, microtubules, and intermediate filaments, as well as the LINC complex, were all dispensable for nuclear flattening as long as the cell could spread. Inhibition of actin polymerization as well as myosin light chain kinase with the drug ML7 limited both the initial spreading of cells and flattening of nuclei, and for well-spread cells, inhibition of myosin-II ATPase with the drug blebbistatin decreased cell spreading with associated nuclear rounding. Together, these results show that cell spreading is necessary and sufficient to drive nuclear flattening under a wide range of conditions, including in the presence or absence of myosin activity. To explain this observation, we propose a computational model for nuclear and cell mechanics that shows how frictional transmission of stress from the moving cell boundaries to the nuclear surface shapes the nucleus during early cell spreading. Our results point to a surprisingly simple mechanical system in cells for establishing nuclear shapes. PMID:26287620

Solid-State Nuclear Magnetic Resonance Investigation of the Structural Topology and Lipid Interactions of a Viral Fusion Protein Chimera Containing the Fusion Peptide and Transmembrane Domain.

PubMed

Yao, Hongwei; Lee, Myungwoon; Liao, Shu-Yu; Hong, Mei

2016-12-13

The fusion peptide (FP) and transmembrane domain (TMD) of viral fusion proteins play important roles during virus-cell membrane fusion, by inducing membrane curvature and transient dehydration. The structure of the water-soluble ectodomain of viral fusion proteins has been extensively studied crystallographically, but the structures of the FP and TMD bound to phospholipid membranes are not well understood. We recently investigated the conformations and lipid interactions of the separate FP and TMD peptides of parainfluenza virus 5 (PIV5) fusion protein F using solid-state nuclear magnetic resonance. These studies provide structural information about the two domains when they are spatially well separated in the fusion process. To investigate how these two domains are structured relative to each other in the postfusion state, when the ectodomain forms a six-helix bundle that is thought to force the FP and TMD together in the membrane, we have now expressed and purified a chimera of the FP and TMD, connected by a Gly-Lys linker, and measured the chemical shifts and interdomain contacts of the protein in several lipid membranes. The FP-TMD chimera exhibits α-helical chemical shifts in all the membranes examined and does not cause strong curvature of lamellar membranes or membranes with negative spontaneous curvature. These properties differ qualitatively from those of the separate peptides, indicating that the FP and TMD interact with each other in the lipid membrane. However, no 13 C- 13 C cross peaks are observed in two-dimensional correlation spectra, suggesting that the two helices are not tightly associated. These results suggest that the ectodomain six-helix bundle does not propagate into the membrane to the two hydrophobic termini. However, the loosely associated FP and TMD helices are found to generate significant negative Gaussian curvature to membranes that possess spontaneous positive curvature, consistent with the notion that the FP-TMD assembly may facilitate the transition of the membrane from hemifusion intermediates to the fusion pore.

Resonance-Raman spectro-electrochemistry of intermediates in molecular artificial photosynthesis of bimetallic complexes.

PubMed

Zedler, Linda; Guthmuller, Julien; Rabelo de Moraes, Inês; Kupfer, Stephan; Krieck, Sven; Schmitt, Michael; Popp, Jürgen; Rau, Sven; Dietzek, Benjamin

2014-05-25

The sequential order of photoinduced charge transfer processes and accompanying structure changes were analyzed by UV-vis and resonance-Raman spectroscopy of intermediates of a Ru(ii) based photocatalytic hydrogen evolving system obtained by electrochemical reduction.

Magnetic Ordering of Erbium and Uranium NICKEL(2) SILICON(2) by Neutron Scattering

NASA Astrophysics Data System (ADS)

Lin, Hong

The magnetic ordering has been studied in UNi _2Si_2 and erbium single crystals by elastic neutron scattering. Abundant results are given regarding the magnetic structure, magnetic phase transitions, and the effect of a magnetic field on these properties. Three ordered phases are observed in UNi _2Si_2. They have been determined to be an incommensurate longitudinal spin density wave with a magnetic wave vector around q = 0.74c ^* in the high temperature phase, a simple body-centred antiferromagnet in the intermediate temperature phase, and a square wave in the low temperature phase. This square wave can be viewed equivalently as a longitudinal spin density wave with q = 2/3c ^* superimposed on a ferromagnetic component. Hysteresis and sample dependence are observed in the low-temperature phase transition. The two lower temperature phase transitions are both first order. The transition to paramagnetism is second order with a critical exponent beta = 0.35 +/- 0.03. When a magnetic field is applied along the c axis, the intermediate temperature phase is destabilised and disappears above a field of 3.5T. Although there is no new phase induced by the field, there exists a reentrant point where the three ordered phases can coexist. Erbium has three distinct ordered phases: the cone phase at low temperatures, the c-axis modulated (CAM) phase at higher temperatures, and the intermediate phase with moments modulated both along c and perpendicular to c. Within these phases the modulation of the moments may lock in to the lattice. The observed weak harmonics of the wave vector q in the basal plane for the cone phase and the q = 1/4c^* structure in the intermediate phase can be explained by a basal-plane spin slip model. The effect of magnetic field along the c axis on the magnetic structure is to stabilise the cone phase and to destabilise the intermediate phase. A new lock-in structure with q = 1/4c^* in the cone phase is induced by fields above 1.8T. The presence of the field also stabilises the lock-in structure with q = 2/7c^* in both the intermediate and the CAM phases.

Modular heat exchanger

DOEpatents

Giardina, A.R.

1981-03-03

A shell and tube heat exchanger is described having a plurality of individually removable tube bundle modules. A lattice of structural steel forming rectangular openings therein is placed at each end of a cylindrical shell. Longitudinal structural members are placed in the shell between corners of the rectangular openings situated on opposite ends of the shell. Intermediate support members interconnect the longitudinal supports so as to increase the longitudinal supports rigidity. Rectangular parallelepiped tube bundle modules occupy the space defined by the longitudinal supports and end supports and each include a rectangular tube sheet situated on each end of a plurality of tubes extending there through, a plurality of rectangular tube supports located between the tube sheets, and a tube bundle module stiffening structure disposed about the bundle's periphery and being attached to the tube sheets and tube supports. The corners of each tube bundle module have longitudinal framework members which are mateable with and supported by the longitudinal support members. Intermediate support members constitute several lattices, each of which is situated in a plane between the end support members. The intermediate support members constituting the several lattices extend horizontally and vertically between longitudinal supports of adjacent tube module voids. An alternative embodiment for intermediate support members constitute a series of structural plates situated at the corners of the module voids and having recesses therein for receiving the respective longitudinal support members adjacent thereto, protrusions separating the recesses, and a plurality of struts situated between protrusions of adjacent structural plates. 12 figs.

Modular heat exchanger

DOEpatents

Giardina, Angelo R. [Marple Township, Delaware County, PA

1981-03-03

A shell and tube heat exchanger having a plurality of individually removable tube bundle modules. A lattice of structural steel forming rectangular openings therein is placed at each end of a cylindrical shell. Longitudinal structural members are placed in the shell between corners of the rectangular openings situated on opposite ends of the shell. Intermediate support members interconnect the longitudinal supports so as to increase the longitudinal supports rigidity. Rectangular parallelpiped tube bundle moldules occupy the space defined by the longitudinal supports and end supports and each include a rectangular tube sheet situated on each end of a plurality of tubes extending therethrough, a plurality of rectangular tube supports located between the tube sheets, and a tube bundle module stiffening structure disposed about the bundle's periphery and being attached to the tube sheets and tube supports. The corners of each tube bundle module have longitudinal framework members which are mateable with and supported by the longitudinal support members. Intermediate support members constitute several lattice, each of which is situate d in a plane between the end support members. The intermediate support members constituting the several lattice extend horizontally and vertically between longitudinal supports of adjacent tube module voids. An alternative embodiment for intermediate support members constitute a series of structural plates situated at the corners of the module voids and having recesses therein for receiving the respective longitudinal support members adjacent thereto, protrusions separating the recesses, and a plurality of struts situated between protrusions of adjacent structural plates.

Common structural features of toxic intermediates from α-synuclein and GroES fibrillogenesis detected using cryogenic coherent X-ray diffraction imaging.

PubMed

Kameda, Hiroshi; Usugi, Sayaka; Kobayashi, Mana; Fukui, Naoya; Lee, Seki; Hongo, Kunihiro; Mizobata, Tomohiro; Sekiguchi, Yuki; Masaki, Yu; Kobayashi, Amane; Oroguchi, Tomotaka; Nakasako, Masayoshi; Takayama, Yuki; Yamamoto, Masaki; Kawata, Yasushi

2017-01-01

The aggregation and deposition of α-synuclein (αSyn) in neuronal cells is correlated to pathogenesis of Parkinson's disease. Although the mechanism of αSyn aggregation and fibril formation has been studied extensively, the structural hallmarks that are directly responsible for toxicity toward cells are still under debate. Here, we have compared the structural characteristics of the toxic intermediate molecular species of αSyn and similar toxic species of another protein, GroES, using coherent X-ray diffraction analysis. Using coherent X-ray free electron laser pulses of SACLA, we analysed αSyn and GroES fibril intermediate species and characterized various aggregate structures. Unlike previous studies where an annular oligomeric form of αSyn was identified, particle reconstruction from scattering traces suggested that the specific forms of the toxic particles were varied, with the sizes of the particles falling within a specific range. We did however discover a common structural feature in both αSyn and GroES samples; the edges of the detected particles were nearly parallel and produced a characteristic diffraction pattern in the diffraction experiments. The presence of parallel-edged particles in toxic intermediates of αSyn and GroES fibrillogenesis pointed towards a plausible common molecular interface that leads to the formation of mature fibrils. © The Authors 2016. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

High-Rate Charging Induced Intermediate Phases and Structural Changes of Layer-Structured Cathode for Lithium-Ion Batteries

DOE PAGES

Zhou, Yong-Ning; Yue, Ji-Li; Hu, Enyuan; ...

2016-08-08

Using fast time-resolved in situ X-ray diffraction, charge-rate dependent phase transition processes of layer structured cathode material LiNi 1/3Mn 1/3Co 1/3O 2 for lithium-ion batteries are studied. During first charge, intermediate phases emerge at high rates of 10C, 30C, and 60C, but not at low rates of 0.1C and 1C. These intermediate phases can be continuously observed during relaxation after the charging current is switched off. After half-way charging at high rate, sample studied by scanning transmission electron microscopy shows Li-rich and Li-poor phases' coexistence with tetrahedral occupation of Li in Li-poor phase. Also, the high rate induced overpotential ismore » thought to be the driving force for the formation of this intermediate Li-poor phase. The in situ quick X-ray absorption results show that the oxidation of Ni accelerates with increasing charging rate and the Ni 4+ state can be reached at the end of charge with 30C rate. Finally, these results give new insights in the understanding of the layered cathodes during high-rate charging.« less

Evidence for a Shared Mechanism in the Formation of Urea-Induced Kinetic and Equilibrium Intermediates of Horse Apomyoglobin from Ultrarapid Mixing Experiments

PubMed Central

Mizukami, Takuya; Abe, Yukiko; Maki, Kosuke

2015-01-01

In this study, the equivalence of the kinetic mechanisms of the formation of urea-induced kinetic folding intermediates and non-native equilibrium states was investigated in apomyoglobin. Despite having similar structural properties, equilibrium and kinetic intermediates accumulate under different conditions and via different mechanisms, and it remains unknown whether their formation involves shared or distinct kinetic mechanisms. To investigate the potential mechanisms of formation, the refolding and unfolding kinetics of horse apomyoglobin were measured by continuous- and stopped-flow fluorescence over a time range from approximately 100 μs to 10 s, along with equilibrium unfolding transitions, as a function of urea concentration at pH 6.0 and 8°C. The formation of a kinetic intermediate was observed over a wider range of urea concentrations (0–2.2 M) than the formation of the native state (0–1.6 M). Additionally, the kinetic intermediate remained populated as the predominant equilibrium state under conditions where the native and unfolded states were unstable (at ~0.7–2 M urea). A continuous shift from the kinetic to the equilibrium intermediate was observed as urea concentrations increased from 0 M to ~2 M, which indicates that these states share a common kinetic folding mechanism. This finding supports the conclusion that these intermediates are equivalent. Our results in turn suggest that the regions of the protein that resist denaturant perturbations form during the earlier stages of folding, which further supports the structural equivalence of transient and equilibrium intermediates. An additional folding intermediate accumulated within ~140 μs of refolding and an unfolding intermediate accumulated in <1 ms of unfolding. Finally, by using quantitative modeling, we showed that a five-state sequential scheme appropriately describes the folding mechanism of horse apomyoglobin. PMID:26244984

A Metal Bump Bonding Method Using Ag Nanoparticles as Intermediate Layer

NASA Astrophysics Data System (ADS)

Fu, Weixin; Nimura, Masatsugu; Kasahara, Takashi; Mimatsu, Hayata; Okada, Akiko; Shoji, Shuichi; Ishizuka, Shugo; Mizuno, Jun

2015-11-01

The future development of low-temperature and low-pressure bonding technology is necessary for fine-pitch bump application. We propose a bump structure using Ag nanoparticles as an intermediate layer coated on a fine-pitch Cu pillar bump. The intermediate layer is prepared using an efficient and cost-saving squeegee-coating method followed by a 100°C baking process. This bump structure can be easily flattened before the bonding process, and the low-temperature sinterability of the nanoparticles is retained. The bonding experiment was successfully performed at 250°C and 39.8 MPa and the bonding strength was comparable to that achieved via other bonding technology utilizing metal particles or porous material as bump materials.

The nuclear matrix prepared by amine modification

PubMed Central

Wan, Katherine M.; Nickerson, Jeffrey A.; Krockmalnic, Gabriela; Penman, Sheldon

1999-01-01

The nucleus is spatially ordered by attachments to a nonchromatin nuclear structure, the nuclear matrix. The nuclear matrix and chromatin are intimately connected and integrated structures, and so a major technical challenge in nuclear matrix research has been to remove chromatin while retaining a native nuclear matrix. Most methods for removing chromatin require first a nuclease digestion and then a salt extraction to remove cut chromatin. We have hypothesized that cut chromatin is held in place by charge interactions involving nucleosomal amino groups. We have tested this hypothesis by chemically modifying amino groups after nuclease digestion. By using this protocol, chromatin could be effectively removed at physiological ionic strength. We compared the ultrastructure and composition of this nuclear matrix preparation with the traditional high-salt nuclear matrix and with the third nuclear matrix preparation that we have developed from which chromatin is removed after extensive crosslinking. All three matrix preparations reveal internal nuclear matrix structures that are built on a network of branched filaments of about 10 nm diameter. That such different chromatin-removal protocols reveal similar principles of nuclear matrix construction increases our confidence that we are observing important architectural elements of the native structure in the living cell. PMID:9927671

Unfolding Kinetics of β-Lactoglobulin Induced by Surfactant and Denaturant: A Stopped-Flow/Fluorescence Study

PubMed Central

Viseu, Maria Isabel; Melo, Eduardo P.; Carvalho, Teresa Isabel; Correia, Raquel F.; Costa, Sílvia M. B.

2007-01-01

The β→α transition of β-lactoglobulin, a globular protein abundant in the milk of several mammals, is investigated in this work. This transition, induced by the cationic surfactant dodecyltrimethylammonium chloride (DTAC), is accompanied by partial unfolding of the protein. In this work, unfolding of bovine β-lactoglobulin in DTAC is compared with its unfolding induced by the chemical denaturant guanidine hydrochloride (GnHCl). The final protein states attained in the two media have quite different secondary structure: in DTAC the α-helical content increases, leading to the so-called α-state; in GnHCl the amount of ordered secondary-structure decreases, resulting in a random coil-rich final state (denatured, or D, state). To obtain information on both mechanistic routes, in DTAC and GnHCl, and to characterize intermediates, the kinetics of unfolding were investigated in the two media. Equilibrium and kinetic data show the partial accumulation of an on-pathway intermediate in each unfolding route: in DTAC, an intermediate (I1) with mostly native secondary structure but loose tertiary structure appears between the native (β) and α-states; in GnHCl, another intermediate (I2) appears between states β and D. Kinetic rate constants follow a linear Chevron-plot representation in GnHCl, but show a more complex mechanism in DTAC, which acts like a stronger binding species. PMID:17693475

Electron-nuclear corellations for photoinduced dynamics in molecular dimers

NASA Astrophysics Data System (ADS)

Kilin, Dmitri S.; Pereversev, Yuryi V.; Prezhdo, Oleg V.

2003-03-01

Ultrafast photoinduced dynamics of electronic excitation in molecular dimers is drastically affected by dynamic reorganization of of inter- and intra- molecular nuclear configuration modelled by quantized nuclear degree of freedom [1]. The dynamics of the electronic population and nuclear coherence is analyzed with help of both numerical solution of the chain of coupled differential equations for mean coordinate, population inversion, electronic-vibrational correlation etc.[2] and by propagating the Gaussian wavepackets in relevant adiabatic potentials. Intriguing results were obtained in the approximation of small energy difference and small change of nuclear equilibrium configuration for excited electronic states. In the limiting case of resonance between electronic states energy difference and frequency of the nuclear mode these results have been justified by comparison to exactly solvable Jaynes-Cummings model. It has been found that the photoinduced processes in dimer are arranged according to their time scales:(i) fast scale of nuclear motion,(ii) intermediate scale of dynamical redistribution of electronic population between excited states as well as growth and dynamics of electronic -nuclear correlation,(iii) slow scale of electronic population approaching to the quasiequilibrium distribution, decay of electronic-nuclear correlation, and diminishing the amplitude of mean coordinate oscillations, accompanied by essential growth of the nuclear coordinate dispersion associated with the overall nuclear wavepacket width. Demonstrated quantum-relaxational features of photoinduced vibronic dinamical processess in molecular dimers are obtained by simple method, applicable to large biological systems with many degrees of freedom. [1] J. A. Cina, D. S. Kilin, T. S. Humble, J. Chem. Phys. (2003) in press. [2] O. V. Prezhdo, J. Chem. Phys. 117, 2995 (2002).

Gradient COUP-TFI Expression Is Required for Functional Organization of the Hippocampal Septo-Temporal Longitudinal Axis.

PubMed

Flore, Gemma; Di Ruberto, Giuseppina; Parisot, Joséphine; Sannino, Sara; Russo, Fabio; Illingworth, Elizabeth A; Studer, Michèle; De Leonibus, Elvira

2017-02-01

The hippocampus (HP), a medial cortical structure, is subdivided into a distinct dorsal (septal) and ventral (temporal) portion, which is separated by an intermediate region lying on a longitudinal curvature. While the dorsal portion is more dedicated to spatial navigation and memory, the most ventral part processes emotional information. Genetic factors expressed in gradient during development seem to control the size and correct positioning of the HP along its longitudinal axis; however, their roles in regulating differential growth and in supporting its anatomical and functional dissociation remain unexplored. Here, we challenge the in vivo function of the nuclear receptor COUP-TFI (chicken ovalbumin upstream promoter transcription factor 1) in controlling the hippocampal, anatomical, and functional properties along its longitudinal axis. Loss of cortical COUP-TFI function results in a dysmorphic HP with altered shape, volume, and connectivity, particularly in its dorsal and intermediate regions. Notably, topographic inputs from the entorhinal cortex are strongly impaired in the dorsal portion of COUP-TFI mutants. These severe morphological changes are associated with selective spatial learning and memory impairment. These findings identify a novel transcriptional regulator required in the functional organization along the hippocampal septo-temporal axis supporting a genetic basis of the hippocampal volumetric growth with its final shape, circuit, and type of memory function. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A search for the production of direct leptons in nucleon-nucleus and nucleus-nucleus collisions. [Intermediate Energy Nuclear Physics Group, Dept. of Physics and Astronomy, Louisiana State Univ. , Baton Rouge

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

Kirk, P.N.

1992-12-15

Activities included contributions to the AMY Collaboration, the transverse energy detector, the Di-Lepton Spectrometer, with emphasis on the single-lepton experiment. Elastic and inelastic scattering differential cross sections and total cross sections are shown for [pi][sup +] and [pi][sup [minus

Key Planning Factors for Recovery from a Chemical Warfare Agent Incident

DTIC Science & Technology

2012-07-01

confusion and degradation of public trust. Such consequences were brought to light for the U.S. during the Fukushima Daiichi nuclear power plant...appendices follow : the first describing the relationships among the National Disaster Recovery Framework Recovery Support Functions, the National...phases of action following a disaster incident— short-, intermediate-, and long-term—that can overlap, sometimes considerably. As shown in Figure 2

Enhancing BWR proliferation resistance fuel with minor actinides

NASA Astrophysics Data System (ADS)

Chang, Gray S.

2009-03-01

To reduce spent fuel for storage and enhance the proliferation resistance for the intermediate-term, there are two major approaches (a) increase the discharged spent fuel burnup in the advanced light water reactor- LWR (Gen-III Plus), which not only can reduce the spent fuel for storage, but also increase the 238Pu isotopes ratio to enhance the proliferation resistance, and (b) use of transuranic nuclides ( 237Np and 241Am) in the high burnup fuel, which can drastically increase the proliferation resistance isotope ratio of 238Pu/Pu. For future advanced nuclear systems, minor actinides (MA) are viewed more as a resource to be recycled, and transmuted to less hazardous and possibly more useful forms, rather than simply disposed of as a waste stream in an expensive repository facility. As a result, MAs play a much larger part in the design of advanced systems and fuel cycles, not only as additional sources of useful energy, but also as direct contributors to the reactivity control of the systems into which they are incorporated. In the study, a typical boiling water reactor (BWR) fuel unit lattice cell model with UO 2 fuel pins will be used to investigate the effectiveness of minor actinide reduction approach (MARA) for enhancing proliferation resistance and improving the fuel cycle performance in the intermediate-term goal for future nuclear energy systems. To account for the water coolant density variation from the bottom (0.76 g/cm 3) to the top (0.35 g/cm 3) of the core, the axial coolant channel and fuel pin were divided to 24 nodes. The MA transmutation characteristics at different elevations were compared and their impact on neutronics criticality discussed. The concept of MARA, which involves the use of transuranic nuclides ( 237Np and/or 241Am), significantly increases the 238Pu/Pu ratio for proliferation resistance, as well as serves as a burnable absorber to hold-down the initial excess reactivity. It is believed that MARA can play an important role in atoms for peace and the intermediate-term of nuclear energy reconnaissance.

Integrative structure and functional anatomy of a nuclear pore complex

NASA Astrophysics Data System (ADS)

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D.; Hogan, Joanna A.; Upla, Paula; Chemmama, Ilan E.; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S.; Wang, Junjie; Williams, Rosemary; Unruh, Jay R.; Greenberg, Charles H.; Jacobs, Erica Y.; Yu, Zhiheng; de La Cruz, M. Jason; Mironska, Roxana; Stokes, David L.; Aitchison, John D.; Jarrold, Martin F.; Gerton, Jennifer L.; Ludtke, Steven J.; Akey, Christopher W.; Chait, Brian T.; Sali, Andrej; Rout, Michael P.

2018-03-01

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

Integrative structure and functional anatomy of a nuclear pore complex.

PubMed

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D; Hogan, Joanna A; Upla, Paula; Chemmama, Ilan E; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S; Wang, Junjie; Williams, Rosemary; Unruh, Jay R; Greenberg, Charles H; Jacobs, Erica Y; Yu, Zhiheng; de la Cruz, M Jason; Mironska, Roxana; Stokes, David L; Aitchison, John D; Jarrold, Martin F; Gerton, Jennifer L; Ludtke, Steven J; Akey, Christopher W; Chait, Brian T; Sali, Andrej; Rout, Michael P

2018-03-22

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

Condensins exert force on chromatin-nuclear envelope tethers to mediate nucleoplasmic reticulum formation in Drosophila melanogaster.

PubMed

Bozler, Julianna; Nguyen, Huy Q; Rogers, Gregory C; Bosco, Giovanni

2014-12-30

Although the nuclear envelope is known primarily for its role as a boundary between the nucleus and cytoplasm in eukaryotes, it plays a vital and dynamic role in many cellular processes. Studies of nuclear structure have revealed tissue-specific changes in nuclear envelope architecture, suggesting that its three-dimensional structure contributes to its functionality. Despite the importance of the nuclear envelope, the factors that regulate and maintain nuclear envelope shape remain largely unexplored. The nuclear envelope makes extensive and dynamic interactions with the underlying chromatin. Given this inexorable link between chromatin and the nuclear envelope, it is possible that local and global chromatin organization reciprocally impact nuclear envelope form and function. In this study, we use Drosophila salivary glands to show that the three-dimensional structure of the nuclear envelope can be altered with condensin II-mediated chromatin condensation. Both naturally occurring and engineered chromatin-envelope interactions are sufficient to allow chromatin compaction forces to drive distortions of the nuclear envelope. Weakening of the nuclear lamina further enhanced envelope remodeling, suggesting that envelope structure is capable of counterbalancing chromatin compaction forces. Our experiments reveal that the nucleoplasmic reticulum is born of the nuclear envelope and remains dynamic in that they can be reabsorbed into the nuclear envelope. We propose a model where inner nuclear envelope-chromatin tethers allow interphase chromosome movements to change nuclear envelope morphology. Therefore, interphase chromatin compaction may be a normal mechanism that reorganizes nuclear architecture, while under pathological conditions, such as laminopathies, compaction forces may contribute to defects in nuclear morphology. Copyright © 2015 Bozler et al.

Condensins Exert Force on Chromatin-Nuclear Envelope Tethers to Mediate Nucleoplasmic Reticulum Formation in Drosophila melanogaster

PubMed Central

Bozler, Julianna; Nguyen, Huy Q.; Rogers, Gregory C.; Bosco, Giovanni

2014-01-01

Although the nuclear envelope is known primarily for its role as a boundary between the nucleus and cytoplasm in eukaryotes, it plays a vital and dynamic role in many cellular processes. Studies of nuclear structure have revealed tissue-specific changes in nuclear envelope architecture, suggesting that its three-dimensional structure contributes to its functionality. Despite the importance of the nuclear envelope, the factors that regulate and maintain nuclear envelope shape remain largely unexplored. The nuclear envelope makes extensive and dynamic interactions with the underlying chromatin. Given this inexorable link between chromatin and the nuclear envelope, it is possible that local and global chromatin organization reciprocally impact nuclear envelope form and function. In this study, we use Drosophila salivary glands to show that the three-dimensional structure of the nuclear envelope can be altered with condensin II-mediated chromatin condensation. Both naturally occurring and engineered chromatin-envelope interactions are sufficient to allow chromatin compaction forces to drive distortions of the nuclear envelope. Weakening of the nuclear lamina further enhanced envelope remodeling, suggesting that envelope structure is capable of counterbalancing chromatin compaction forces. Our experiments reveal that the nucleoplasmic reticulum is born of the nuclear envelope and remains dynamic in that they can be reabsorbed into the nuclear envelope. We propose a model where inner nuclear envelope-chromatin tethers allow interphase chromosome movements to change nuclear envelope morphology. Therefore, interphase chromatin compaction may be a normal mechanism that reorganizes nuclear architecture, while under pathological conditions, such as laminopathies, compaction forces may contribute to defects in nuclear morphology. PMID:25552604

Transient intermediates are populated in the folding pathways of single-domain two-state folding protein L

NASA Astrophysics Data System (ADS)

Maity, Hiranmay; Reddy, Govardhan

2018-04-01

Small single-domain globular proteins, which are believed to be dominantly two-state folders, played an important role in elucidating various aspects of the protein folding mechanism. However, recent single molecule fluorescence resonance energy transfer experiments [H. Y. Aviram et al. J. Chem. Phys. 148, 123303 (2018)] on a single-domain two-state folding protein L showed evidence for the population of an intermediate state and it was suggested that in this state, a β-hairpin present near the C-terminal of the native protein state is unfolded. We performed molecular dynamics simulations using a coarse-grained self-organized-polymer model with side chains to study the folding pathways of protein L. In agreement with the experiments, an intermediate is populated in the simulation folding pathways where the C-terminal β-hairpin detaches from the rest of the protein structure. The lifetime of this intermediate structure increased with the decrease in temperature. In low temperature conditions, we also observed a second intermediate state, which is globular with a significant fraction of the native-like tertiary contacts satisfying the features of a dry molten globule.

Direct Structural and Chemical Characterization of the Photolytic Intermediates of Methylcobalamin Using Time-Resolved X-ray Absorption Spectroscopy

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

Subramanian, Ganesh; Zhang, Xiaoyi; Kodis, Gerdenis

Cobalt-carbon bond cleavage is crucial to most natural and synthetic applications of the cobalamin class of compounds, and here we present the first direct electronic and geometric structural characteristics of intermediates formed following photoexcitation of methylcobalamin (MeCbl) using time-resolved X-ray absorption spectroscopy (XAS). We catch transients corresponding to two intermediates, in the hundreds of picoseconds and a few microseconds. Highlights of the picosecond intermediate, which is reduced in comparison to the ground state, are elongation of the upper axial Co-C bond and relaxation of the corrin ring. This is not so with the recombining photocleaved products captured at a fewmore » microseconds, where the Co-C bond almost (yet not entirely) reverts to its ground state configuration and a substantially elongated lower axial Co-NIm bond is observed. The reduced cobalt site here confirms formation of methyl radical as the photoproduct.« less

Ratio of shear viscosity to entropy density in multifragmentation of Au + Au

NASA Astrophysics Data System (ADS)

Zhou, C. L.; Ma, Y. G.; Fang, D. Q.; Li, S. X.; Zhang, G. Q.

2012-06-01

The ratio of the shear viscosity (η) to entropy density (s) for the intermediate energy heavy-ion collisions has been calculated by using the Green-Kubo method in the framework of the quantum molecular dynamics model. The theoretical curve of η/s as a function of the incident energy for the head-on Au + Au collisions displays that a minimum region of η/s has been approached at higher incident energies, where the minimum η/s value is about 7 times Kovtun-Son-Starinets (KSS) bound (1/4π). We argue that the onset of minimum η/s region at higher incident energies corresponds to the nuclear liquid gas phase transition in nuclear multifragmentation.

Thomas Graham, Jr.: Preparing for the 1995 NPT Conference

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

NONE

1994-07-01

With attention increasingly focused on the critical nuclear Non-Proliferation Treaty (NPT) extension and review conference beginning in April 1995, Thomas Graham, Jr. plays a key role in negotiations to gain indefinite treaty extension during voting at the conference. He has been Arms Control and Disarmament Agency (ACDA) general counsel since 1983, served as acting director from January to November 1992 and since November 23, 1992, has been acting deputy director. Among other assignments, he served as legal advisor to the US SALT II delegation and senior ACDA representative to the US Intermediate-Range Nuclear Forces delegation in 1981-82. He was interviewedmore » May 26 by Jack Mendelsohn and Jon B. Wolfsthal.« less

Chiral symmetry and the nucleon-nucleon interaction

DOE PAGES

Machleidt, Ruprecht

2016-04-20

We review how nuclear forces emerge from low-energy quantum chromodynamics (QCD) via chiral effective field theory (EFT). During the past two decades, this approach has evolved into a powerful tool to derive nuclear two- and many-body forces in a systematic and model-independent way. We then focus on the nucleon-nucleon (NN) interaction and show in detail how, governed by chiral symmetry, the long- and intermediate-range of the NN potential builds up order by order. We proceed up to sixth order in small momenta, where convergence is achieved. Lastly, the final result allows for a full assessment of the validity of themore » chiral EFT approach to the NN interaction.« less