Local epigenetic reprograming induced by G-quadruplex ligands

PubMed Central

Recolin, Bénédicte; Campbell, Beth C.; Maiter, Ahmed; Sale, Julian E.; Balasubramanian, Shankar

2017-01-01

DNA and histone modifications regulate transcriptional activity and thus represent valuable targets to reprogram the activity of genes. Current epigenetic therapies target the machinery that regulates these modifications, leading to global transcriptional reprogramming with the potential for extensive undesired effects. Epigenetic information can also be modified as a consequence of disrupting processive DNA replication. Here we demonstrate that impeding replication by small molecule-mediated stabilisation of G-quadruplex nucleic acid secondary structures triggers local epigenetic plasticity. We report the use of the BU-1 locus of chicken DT40 cells to screen for small molecules able to induce G-quadruplex-dependent transcriptional reprogramming. Further characterisation of the top hit compound revealed its ability to induce a dose-dependent inactivation of BU-1 expression in two steps, first loss of H3K4me3 and subsequently DNA cytosine methylation, changes that were heritable across cell divisions even after the compound was removed. Targeting DNA secondary structures thus represents a potentially new approach for locus-specific epigenetic reprogramming. PMID:29064488

Local epigenetic reprogramming induced by G-quadruplex ligands

NASA Astrophysics Data System (ADS)

Guilbaud, Guillaume; Murat, Pierre; Recolin, Bénédicte; Campbell, Beth C.; Maiter, Ahmed; Sale, Julian E.; Balasubramanian, Shankar

2017-11-01

DNA and histone modifications regulate transcriptional activity and thus represent valuable targets to reprogram the activity of genes. Current epigenetic therapies target the machinery that regulates these modifications, leading to global transcriptional reprogramming with the potential for extensive undesired effects. Epigenetic information can also be modified as a consequence of disrupting processive DNA replication. Here, we demonstrate that impeding replication by small-molecule-mediated stabilization of G-quadruplex nucleic acid secondary structures triggers local epigenetic plasticity. We report the use of the BU-1 locus of chicken DT40 cells to screen for small molecules able to induce G-quadruplex-dependent transcriptional reprogramming. Further characterization of the top hit compound revealed its ability to induce a dose-dependent inactivation of BU-1 expression in two steps: the loss of H3K4me3 and then subsequent DNA cytosine methylation, changes that were heritable across cell divisions even after the compound was removed. Targeting DNA secondary structures thus represents a potentially new approach for locus-specific epigenetic reprogramming.

Macromolecular ab initio phasing enforcing secondary and tertiary structure.

PubMed

Millán, Claudia; Sammito, Massimo; Usón, Isabel

2015-01-01

Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors' approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a 'still-life', but some are correct enough for density modification and main-chain tracing to reveal the protein's true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases.

Interactive graphical computer-aided design system

NASA Technical Reports Server (NTRS)

Edge, T. M.

1975-01-01

System is used for design, layout, and modification of large-scale-integrated (LSI) metal-oxide semiconductor (MOS) arrays. System is structured around small computer which provides real-time support for graphics storage display unit with keyboard, slave display unit, hard copy unit, and graphics tablet for designer/computer interface.

Plasma Modification of Graphite Fibers and Its Effect on Composite Properties.

DTIC Science & Technology

1983-08-01

liquids have been difficult to measure with adequate accuracy. As a result, critical surface energy data are not readily available. A flotation method...tension of the fiber surface. However, the fiber density must always exceed the density of the flotation liquid. Although this is a very useful...technioue, it is inanplicable to graphite fiber due to its irregular surface structure, small filament diameter and small difference in density with flotation

Evidence for the implication of the histone code in building the genome structure.

PubMed

Prakash, Kirti; Fournier, David

2018-02-01

Histones are punctuated with small chemical modifications that alter their interaction with DNA. One attractive hypothesis stipulates that certain combinations of these histone modifications may function, alone or together, as a part of a predictive histone code to provide ground rules for chromatin folding. We consider four features that relate histone modifications to chromatin folding: charge neutralisation, molecular specificity, robustness and evolvability. Next, we present evidence for the association among different histone modifications at various levels of chromatin organisation and show how these relationships relate to function such as transcription, replication and cell division. Finally, we propose a model where the histone code can set critical checkpoints for chromatin to fold reversibly between different orders of the organisation in response to a biological stimulus. Copyright © 2017 Elsevier B.V. All rights reserved.

Inorganic–organic hybrid materials through post-synthesis modification: Impact of the treatment with azides on the mesopore structure

PubMed Central

Keppeler, Miriam; Holzbock, Jürgen; Akbarzadeh, Johanna; Peterlik, Herwig

2011-01-01

Summary Hybrid, hierarchically organized, monolithic silica gels, comprising periodically arranged mesopores and a cellular macroscopic network, have been prepared through a co-condensation reaction of tetrakis(2-hydroxyethyl)orthosilicate with chloromethyl-trimethoxysilane or 3-(chloropropyl)-triethoxysilane. Subsequent conversion of the chloro groups into azido groups, by nucleophilic substitution with NaN3 in N,N-dimethylformamide, was conducted upon preservation of the monolithic structure. However, treatment with NaN3 had a strong influence on the structure in the mesoporous regime, with changes such as an increase of mesopore diameter, pore volume and lattice constants, as well as a concomitant decrease of the pore wall thickness, as confirmed by small angle X-ray scattering, transmission electron microscopy, and nitrogen sorption analysis. Similar effects were observed for unmodified silica gels by simple ageing in azide-containing media, whether a relatively small or a sterically demanding counter ion (Na+ or (H3C)4N+) was used. The structural modification did not seem to depend greatly on whether an organic aprotic solvent (N,N-dimethylformamide, 1,1,3,3-tetramethylurea, 1,3-dimethyl-2-imidazolidinone) or a protic solvent that can form hydrogen bonds, such as water, was used. PMID:22003454

Synthesis and application of pyridine-based ambipolar hosts: control of charge balance in organic light emitting devices (OLEDs) by chemical structure modification

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

Koech, Phillip K.; Polikarpov, Evgueni; Rainbolt, James E.

2010-11-05

Pyridine-based host materials were synthesized via Grignard metathesis of bromopyridines to provide the required organometallic reagent. The isomeric hosts (4-(9H-carbazol-9-yl)phenyl)(phenyl)(pyridin-3-yl)phosphine oxide (HM-A4), (5-(9H-carbazol-9-yl)pyridin-2-yl)diphenylphosphine oxide (HM-A5), and (5-(diphenylamino)pyridin-2-yl)diphenylphosphine oxide (HM-A6), (4-(diphenylamino)phenyl)(phenyl)(pyridin-3-yl)phosphine oxide (HM-A8) have similar frontier orbital energies. Organic light emitting devices (OLEDs) fabricated using the series of the host materials demonstrate that small structural modification of the host results in significant change in charge transporting ability.

Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes.

PubMed

Gaspin, C; Cavaillé, J; Erauso, G; Bachellerie, J P

2000-04-07

Ribose methylation is a prevalent type of nucleotide modification in rRNA. Eukaryotic rRNAs display a complex pattern of ribose methylations, amounting to 55 in yeast Saccharomyces cerevisiae and about 100 in vertebrates. Ribose methylations of eukaryotic rRNAs are each guided by a cognate small RNA, belonging to the family of box C/D antisense snoRNAs, through transient formation of a specific base-pairing at the rRNA modification site. In prokaryotes, the pattern of rRNA ribose methylations has been fully characterized in a single species so far, Escherichia coli, which contains only four ribose methylated rRNA nucleotides. However, the hyperthermophile archaeon Sulfolobus solfataricus contains, like eukaryotes, a large number of (yet unmapped) rRNA ribose methylations and homologs of eukaryotic box C/D small nucleolar ribonuclear proteins have been identified in archaeal genomes. We have therefore searched archaeal genomes for potential homologs of eukaryotic methylation guide small nucleolar RNAs, by combining searches for structured motifs with homology searches. We have identified a family of 46 small RNAs, conserved in the genomes of three hyperthermophile Pyrococcus species, which we have experimentally characterized in Pyrococcus abyssi. The Pyrococcus small RNAs, the first reported homologs of methylation guide small nucleolar RNAs in organisms devoid of a nucleus, appear as a paradigm of minimalist box C/D antisense RNAs. They differ from their eukaryotic homologs by their outstanding structural homogeneity, extended consensus box motifs and the quasi-systematic presence of two (instead of one) rRNA antisense elements. Remarkably, for each small RNA the two antisense elements always match rRNA sequences close to each other in rRNA structure, suggesting an important role in rRNA folding. Only a few of the predicted P. abyssi rRNA ribose methylations have been detected so far. Further analysis of these archaeal small RNAs could provide new insights into the origin and functions of methylation guide small nucleolar RNAs and illuminate the still elusive role of rRNA ribose methylations. Copyright 2000 Academic Press.

Ship-in-a-bottle catalysts

DOEpatents

Haw, James F.; Song, Weiguo

2006-07-18

In accordance with the present invention there is provided a novel catalyst system in which the catalytic structure is tailormade at the nanometer scale using the invention's novel ship-in-a-bottle synthesis techniques. The invention describes modified forms of solid catalysts for use in heterogeneous catalysis that have a microporous structure defined by nanocages. Examples include zeolites, SAPOs, and analogous materials that have the controlled pore dimensions and hydrothermal stability required for many industrial processes. The invention provides for modification of these catalysts using reagents that are small enough to pass through the windows used to access the cages. The small reagents are then reacted to form larger molecules in the cages.

Electron-deuteron DIS with spectator tagging at EIC: Development of theoretical framework

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

Cosyn, Wim B.; Guzey, Vadim A.; Sargsian, Misak M.

2016-03-01

An Electron-Ion Collider (EIC) would enable next-generation measurements of deep-inelastic scattering (DIS) on the deuteron with detection of a forward-moving nucleon (p, n) and measurement of its recoil momentum ("spectator tagging''). Such experiments offer full control of the nuclear configuration during the high-energy process and can be used for precision studies of the neutron's partonic structure and its spin dependence, nuclear modifications of partonic structure, and nuclear shadowing at small x. We review the theoretical description of spectator tagging at EIC energies (light-front nuclear structure, on-shell extrapolation in the recoil nucleon momentum, final-state interactions, diffractive effects at small x) andmore » report about on-going developments.« less

Application of the CRISPR/Cas9 gene editing technique to research on functional genomes of parasites.

PubMed

Cui, Yubao; Yu, Lili

2016-12-01

The clustered regularly-interspaced short palindromic repeats (CRISPR) structural family functions as an acquired immune system in prokaryotes. Gene editing techniques have co-opted CRISPR and the associated Cas nucleases to allow for the precise genetic modification of human cells, zebrafish, mice, and other eukaryotes. Indeed, this approach has been used to induce a variety of modifications including directed insertion/deletion (InDel) of bases, gene knock-in, introduction of mutations in both alleles of a target gene, and deletion of small DNA fragments. Thus, CRISPR technology offers a precise molecular tool for directed genome modification with a range of potential applications; further, its high mutation efficiency, simple process, and low cost provide additional advantages over prior editing techniques. This paper will provide an overview of the basic structure and function of the CRISPR gene editing system as well as current and potential applications to research on parasites. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Functional Interplay between Small Non-Coding RNAs and RNA Modification in the Brain.

PubMed

Leighton, Laura J; Bredy, Timothy W

2018-06-07

Small non-coding RNAs are essential for transcription, translation and gene regulation in all cell types, but are particularly important in neurons, with known roles in neurodevelopment, neuroplasticity and neurological disease. Many small non-coding RNAs are directly involved in the post-transcriptional modification of other RNA species, while others are themselves substrates for modification, or are functionally modulated by modification of their target RNAs. In this review, we explore the known and potential functions of several distinct classes of small non-coding RNAs in the mammalian brain, focusing on the newly recognised interplay between the epitranscriptome and the activity of small RNAs. We discuss the potential for this relationship to influence the spatial and temporal dynamics of gene activation in the brain, and predict that further research in the field of epitranscriptomics will identify interactions between small RNAs and RNA modifications which are essential for higher order brain functions such as learning and memory.

Numerical modelling to assess maintenance strategy management options for a small tidal inlet

NASA Astrophysics Data System (ADS)

Shaeri, Saeed; Tomlinson, Rodger; Etemad-Shahidi, Amir; Strauss, Darrell

2017-03-01

Small tidal inlets are found to be more sensitive to anthropogenic alteration than their larger counterparts. Such alterations, although typically supported by technical design reports, sometimes require amendments or modification. One of the most suitable tools to conduct the necessary studies in this regard is numerical modelling, since the behaviour of the inlet system in response to proposed remedial actions, can easily be identified. In this paper, various alternative proposals are investigated to determine the most practical and viable option to mitigate the need for ongoing maintenance at a typical small, jettied tidal inlet. The main tool to investigate the alternatives is the hydro-sedimentological modelling of the inlet system, which was performed using the Delft3D software package. The proposed alternative entrance modifications were based upon structural alterations of the inlet system (such as a jetty extension or submerged weir) and non-structural scenarios (such as a change of the time of the dredging campaign or the deposition location of the dredged material). It was concluded that whilst a detailed study is inevitable in order to achieve a comprehensive design plan, based upon the results of this study the construction of a submerged weir at the entrance channel can satisfy the needs of most of the stakeholders, with justifiable costs over a longer period.

Earth Viewing Applications Laboratory (EVAL). Dedicated payload, standard test rack payload, sensor modifications

NASA Technical Reports Server (NTRS)

1976-01-01

The preliminary analysis of strawman earth-viewing shuttle sortie payloads begun with the partial spacelab payload was analyzed. The payloads analyzed represent the two extremes of shuttle sortie application payloads: a full shuttle sortie payload dedicated to earth-viewing applications, and a small structure payload which can fly on a space available basis with another primary shuttle payload such as a free flying satellite. The intent of the dedicated mission analysis was to configure an ambitious, but feasible, payload; which, while rich in scientific return, would also stress the system and reveal any deficiences or problem areas in mission planning, support equipment, and operations. Conversely, the intent of the small structure payload was to demonstrate the ease with which a small, simple, flexible payload can be accommodated on shuttle flights.

Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries

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

Pröpper, Kevin; Instituto de Biologia Molecular de Barcelona; Meindl, Kathrin

2014-06-01

The structure solution of DNA-binding protein structures and complexes based on the combination of location of DNA-binding protein motif fragments with density modification in a multi-solution frame is described. Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite themore » fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.« less

Structural modification in the formation of starch - silver nanocomposites

NASA Astrophysics Data System (ADS)

Begum, S. N. Suraiya; Aswal, V. K.; Ramasamy, Radha Perumal

2016-05-01

Polymer based nanocomposites have gained wide applications in field of battery technology. Starch is a naturally occurring polysaccharide with sustainable properties such as biodegradable, non toxic, excellent film forming capacity and it also act as reducing agent for the metal nanoparticles. In our research various concentration of silver nitrate (AgNO3) was added to the starch solution and films were obtained using solution casting method. Surface electron microscope (SEM) of the films shows modifications depending upon the concentration of AgNO3. Small angle neutron scattering (SANS) analysis showed that addition of silver nitrate modifies the starch to disc like structures and with increasing the AgNO3 concentration leads to the formation of fractals. This research could benefit battery technology where solid polymer membranes using starch is used.

Proximity-activated nanoparticles: in vitro performance of specific structural modification by enzymatic cleavage

PubMed Central

Adam Smith, R; Sewell, Sarah L; Giorgio, Todd D

2008-01-01

The development and in vitro performance of a modular nanoscale system capable of specific structural modification by enzymatic activity is described in this work. Due to its small physical size and adaptable characteristics, this system has the potential for utilization in targeted delivery systems and biosensing. Nanoparticle probes were synthesized containing two distinct fluorescent species including a quantum dot base particle and fluorescently labeled cleavable peptide substrate. Activity of these probes was monitored by gel electrophoresis with quantitative cleavage measurements made by fluorometric analysis. The model proximity-activated nanoparticles studied here exhibit significant susceptibility to cleavage by matrix metalloprotease-7 (MMP-7) at physiologically relevant concentrations, with nearly complete cleavage of available substrate molecules after 24 hours. This response is specific to MMP-7 enzyme activity, as cleavage is completely inhibited with the addition of EDTA. Utilization of enzyme-specific modification is a sensitive approach with broad applications for targeted therapeutics and biosensing. The versatility of this nanoparticle system is highlighted in its modular design, as it has the capability to integrate characteristics for detection, biosensing, targeting, and payload delivery into a single, multifunctional nanoparticle structure. PMID:18488420

Not just gene expression: 3D implications of chromatin modifications during sexual plant reproduction.

PubMed

Dukowic-Schulze, Stefanie; Liu, Chang; Chen, Changbin

2018-01-01

DNA methylation and histone modifications are epigenetic changes on a DNA molecule that alter the three-dimensional (3D) structure locally as well as globally, impacting chromatin looping and packaging on a larger scale. Epigenetic marks thus inform higher-order chromosome organization and placement in the nucleus. Conventional epigenetic marks are joined by chromatin modifiers like cohesins, condensins and membrane-anchoring complexes to support particularly 3D chromosome organization. The most popular consequences of epigenetic modifications are gene expression changes, but chromatin modifications have implications beyond this, particularly in actively dividing cells and during sexual reproduction. In this opinion paper, we will focus on epigenetic mechanisms and chromatin modifications during meiosis as part of plant sexual reproduction where 3D management of chromosomes and re-organization of chromatin are defining features and prime tasks in reproductive cells, not limited to modulating gene expression. Meiotic chromosome organization, pairing and synapsis of homologous chromosomes as well as distribution of meiotic double-strand breaks and resulting crossovers are presumably highly influenced by epigenetic mechanisms. Special mobile small RNAs have been described in anthers, where these so-called phasiRNAs seem to direct DNA methylation in meiotic cells. Intriguingly, many of the mentioned developmental processes make use of epigenetic changes and small RNAs in a manner other than gene expression changes. Widening our approaches and opening our mind to thinking three-dimensionally regarding epigenetics in plant development holds high promise for new discoveries and could give us a boost for further knowledge.

Profiling protein function with small molecule microarrays

PubMed Central

Winssinger, Nicolas; Ficarro, Scott; Schultz, Peter G.; Harris, Jennifer L.

2002-01-01

The regulation of protein function through posttranslational modification, local environment, and protein–protein interaction is critical to cellular function. The ability to analyze on a genome-wide scale protein functional activity rather than changes in protein abundance or structure would provide important new insights into complex biological processes. Herein, we report the application of a spatially addressable small molecule microarray to an activity-based profile of proteases in crude cell lysates. The potential of this small molecule-based profiling technology is demonstrated by the detection of caspase activation upon induction of apoptosis, characterization of the activated caspase, and inhibition of the caspase-executed apoptotic phenotype using the small molecule inhibitor identified in the microarray-based profile. PMID:12167675

Characterization of ion-induced radiation effects in nuclear materials using synchrotron x-ray techniques

DOE PAGES

Lang, Maik; Tracy, Cameron L.; Palomares, Raul I.; ...

2015-05-01

Recent efforts to characterize the nanoscale structural and chemical modifications induced by energetic ion irradiation in nuclear materials have greatly benefited from the application of synchrotron-based x-ray diffraction (XRD) and x-ray absorption spectroscopy (XAS) techniques. Key to the study of actinide-bearing materials has been the use of small sample volumes, which are particularly advantageous, as the small quantities minimize the level of radiation exposure at the ion-beam and synchrotron user facility. This approach utilizes energetic heavy ions (energy range: 100 MeV–3 GeV) that pass completely through the sample thickness and deposit an almost constant energy per unit length along theirmore » trajectory. High energy x-rays (25–65 keV) from intense synchrotron light sources are then used in transmission geometry to analyze ion-induced structural and chemical modifications throughout the ion tracks. We describe in detail the experimental approach for utilizing synchrotron radiation (SR) to study the radiation response of a range of nuclear materials (e.g., ThO 2 and Gd 2Ti xZr 2–xO 7). Also addressed is the use of high-pressure techniques, such as the heatable diamond anvil cell, as a new means to expose irradiated materials to well-controlled high-temperature (up to 1000 °C) and/or high-pressure (up to 50 GPa) conditions. Furthermore, this is particularly useful for characterizing the annealing kinetics of irradiation-induced material modifications.« less

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

Aden, Bethany; Kite, Camille M.; Hopkins, Benjamin W.

Designing thin films or surface scaffolds with an appropriate display of chemical functionality is useful for biomedical applications, sensing platforms, adhesives, and barrier coatings. Relationships between the structural characteristics of model thin films based on reactive poly(2-vinyl-4,4-dimethyl azlactone) (PVDMA) brushes and the amount and distribution of primary amines used to chemically functionalize these layers in situ are quantitatively detailed via neutron reflectometry and compared with results from ellipsometry. After functionalization, the PVDMA brush thickness increases as a result of the primary amines reacting with the azlactone rings. Both techniques show that the extent of functionalization by small-molecule amines depends onmore » the size of the amine, the grafting density of brush chains, and their molecular weight. However, constrained analysis of neutron reflectivity data predicated on that technique’s sensitivity to isotopic substitution and its ability to resolve structure at the nanoscale shows that the extent of functionalization is not accurately represented by the average extent of functionalization determined from ellipsometric thickness: reactive modification is not uniform, even in modestly dense brushes, except when the penetrant is small. In addition, there appears to be a loss of PVDMA chains during functionalization, attributed to chain scission resulting from additional stretching brought about by functionalization. In conclusion, these findings provide unprecedented insight into the alteration of surface properties by reactive modification and broadly support efforts to produce tailored surfaces in which properties such as friction, colloidal stability, adhesion, wettability, and biocompatibility can be modulated in situ by chemical modification.« less

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

Aden, Bethany; Kite, Camille M.; Hopkins, Benjamin W.

Designing thin films or surface scaffolds with an appropriate display of chemical functionality is useful for biomedical applications, sensing platforms, adhesives, and barrier coatings. Relationships between the structural characteristics of model thin films based on reactive poly(2-vinyl-4,4-dimethylazlactone) (PVDMA) brushes and the amount and distribution of primary amines used to chemically functionalize the layer in situ are quantitatively detailed via neutron reflectometry and compared with results from ellipsometry. After functionalization, the PVDMA brush thickness increases as a result of the primary amines reacting with the azlactone rings. Both techniques show that the extent of functionalization by small-molecule amines depends on themore » size of the amine, the grafting density of brush chains and their molecular weight. However, constrained analysis of neutron reflectivity data predicated on that technique’s sensitivity to isotopic substitution and its ability to resolve structure at the nanoscale, shows that the extent of functionalization is not accurately represented by the average extent of functionalization determined from ellipsometric thickness: reactive modification is not uniform, even in modestly dense brushes, except when the penetrant is small. Additionally, there appears to be a loss of PVDMA chains during functionalization, attributed to chain scission resulting from additional stretching brought about by functionalization. These findings provide unprecedented insight into the alteration of surface properties by reactive modification and broadly support efforts to produce tailored surfaces in which properties such as friction, colloidal stability, adhesion, wettability, and biocompatibility can be modulated in situ by chemical modification.« less

Synchrotron x-ray modification of nanoparticle superlattice formation

NASA Astrophysics Data System (ADS)

Lu, Chenguang; Akey, Austin J.; Herman, Irving P.

2012-09-01

The synchrotron x-ray radiation used to perform small angle x-ray scattering (SAXS) during the formation of three-dimensional nanoparticle superlattices by drop casting nanoparticle solutions affects the structure and the local crystalline order of the resulting films. The domain size decreases due to the real-time SAXS analysis during drying and more macroscopic changes are visible to the eye.

Reducing Unsteady Loads on a Piggyback Miniature Submarine

NASA Technical Reports Server (NTRS)

Lin, John

2009-01-01

A small, simple fixture has been found to be highly effective in reducing destructive unsteady hydrodynamic loads on a miniature submarine that is attached in piggyback fashion to the top of a larger, nuclear-powered, host submarine. The fixture, denoted compact ramp, can be installed with minimal structural modification, and the use of it does not entail any change in submarine operations.

Regulation of alternative splicing by local histone modifications: potential roles for RNA-guided mechanisms

PubMed Central

Zhou, Hua-Lin; Luo, Guangbin; Wise, Jo Ann; Lou, Hua

2014-01-01

The molecular mechanisms through which alternative splicing and histone modifications regulate gene expression are now understood in considerable detail. Here, we discuss recent studies that connect these two previously separate avenues of investigation, beginning with the unexpected discoveries that nucleosomes are preferentially positioned over exons and DNA methylation and certain histone modifications also show exonic enrichment. These findings have profound implications linking chromatin structure, histone modification and splicing regulation. Complementary single gene studies provided insight into the mechanisms through which DNA methylation and histones modifications modulate alternative splicing patterns. Here, we review an emerging theme resulting from these studies: RNA-guided mechanisms integrating chromatin modification and splicing. Several groundbreaking papers reported that small noncoding RNAs affect alternative exon usage by targeting histone methyltransferase complexes to form localized facultative heterochromatin. More recent studies provided evidence that pre-messenger RNA itself can serve as a guide to enable precise alternative splicing regulation via local recruitment of histone-modifying enzymes, and emerging evidence points to a similar role for long noncoding RNAs. An exciting challenge for the future is to understand the impact of local modulation of transcription elongation rates on the dynamic interplay between histone modifications, alternative splicing and other processes occurring on chromatin. PMID:24081581

Oligomerization of the protein tau in the Alzheimer's disease

NASA Astrophysics Data System (ADS)

Larini, Luca

The Alzheimer's disease is characterized by the formation of protein aggregates both within and outside of the brain's cells, the neurons. Within the neurons, the aggregation of the microtubule associated protein tau leads to the destruction of the microtubules in the axon of the neuron. Tau is extremely flexible and is classified as an intrinsically disordered protein due to its low propensity to form secondary structure. Tau promotes tubulin assembly into microtubules, which are an essential component of the cytoskeleton of the axon. The microtubule binding region of tau consists of 4 pseudo-repeats that are critical for aggregation as well. In this study, we focus on the aggregation propensity of different segments of the microtubule binding region as well as post-translational modifications that can alter tau dynamics and structure. We have performed replica exchange molecular dynamics simulations to characterize the ensemble of conformations of the monomer and small oligomers as well as how these structures are stabilized or destabilized by mutations and post-translational modifications.

Reversal of the asymmetry in a cylindrical coaxial capacitively coupled Ar/Cl 2 plasma

DOE PAGES

Upadhyay, Janardan; Im, Do; Popović, Svetozar; ...

2015-10-08

The reduction of the asymmetry in the plasma sheath voltages of a cylindrical coaxial capacitively coupled plasma is crucial for efficient surface modification of the inner surfaces of concave three-dimensional structures, including superconducting radio frequency cavities. One critical asymmetry effect is the negative dc self-bias, formed across the inner electrode plasma sheath due to its lower surface area compared to the outer electrode. The effect on the self-bias potential with the surface enhancement by geometric modification on the inner electrode structure is studied. The shapes of the inner electrodes are chosen as cylindrical tube, large and small pitch bellows, andmore » disc-loaded corrugated structure (DLCS). The dc self-bias measurements for all these shapes were taken at different process parameters in Ar/Cl 2 discharge. Lastly, the reversal of the negative dc self-bias potential to become positive for a DLCS inner electrode was observed and the best etch rate is achieved due to the reduction in plasma asymmetry.« less

pH-driven colloidal transformations based on the vasoactive drug nicergoline.

PubMed

Salentinig, Stefan; Tangso, Kristian J; Hawley, Adrian; Boyd, Ben J

2014-12-16

The structure of colloidal self-assembled drug delivery systems can be influenced by intermolecular interactions between drug and amphiphilic molecules, and is important to understand in the context of designing improved delivery systems. Controlling these structures can enable controlled or targeted release systems for poorly water-soluble drugs. Here we present the interaction of the hydrophobic vasoactive drug nicergoline with the internal structure of nanostructured emulsion particles based on the monoglyceride-water system. Addition of this drug leads to modification of the internal bicontinuous cubic structure to generate highly pH-responsive systems. The colloidal structures were characterized with small-angle X-ray scattering and visualized using cryogenic transmission electron microscopy. Reversible transformations to inverse micelles at high pH, vesicles at low pH, and the modification of the spacing of the bicontinuous cubic structure at intermediate pH were observed, and enabled the in situ determination of an apparent pKa for the drug in this system--a difficult task using solution-based approaches. The characterization of this phase behavior is also highly interesting for the design of pH-responsive controlled release systems for poorly water-soluble drug molecules.

Evidence of ion intercalation mediated band structure modification and opto-ionic coupling in lithium niobite

NASA Astrophysics Data System (ADS)

Shank, Joshua C.; Tellekamp, M. Brooks; Doolittle, W. Alan

2015-01-01

The theoretically suggested band structure of the novel p-type semiconductor lithium niobite (LiNbO2), the direct coupling of photons to ion motion, and optically induced band structure modifications are investigated by temperature dependent photoluminescence. LiNbO2 has previously been used as a memristor material but is shown here to be useful as a sensor owing to the electrical, optical, and chemical ease of lithium removal and insertion. Despite the high concentration of vacancies present in lithium niobite due to the intentional removal of lithium atoms, strong photoluminescence spectra are observed even at room temperature that experimentally confirm the suggested band structure implying transitions from a flat conduction band to a degenerate valence band. Removal of small amounts of lithium significantly modifies the photoluminescence spectra including additional larger than stoichiometric-band gap features. Sufficient removal of lithium results in the elimination of the photoluminescence response supporting the predicted transition from a direct to indirect band gap semiconductor. In addition, non-thermal coupling between the incident laser and lithium ions is observed and results in modulation of the electrical impedance.

Recent Progress in Monolithic Silica Columns for High-Speed and High-Selectivity Separations.

PubMed

Ikegami, Tohru; Tanaka, Nobuo

2016-06-12

Monolithic silica columns have greater (through-pore size)/(skeleton size) ratios than particulate columns and fixed support structures in a column for chemical modification, resulting in high-efficiency columns and stationary phases. This review looks at how the size range of monolithic silica columns has been expanded, how high-efficiency monolithic silica columns have been realized, and how various methods of silica surface functionalization, leading to selective stationary phases, have been developed on monolithic silica supports, and provides information on the current status of these columns. Also discussed are the practical aspects of monolithic silica columns, including how their versatility can be improved by the preparation of small-sized structural features (sub-micron) and columns (1 mm ID or smaller) and by optimizing reaction conditions for in situ chemical modification with various restrictions, with an emphasis on recent research results for both topics.

Extracellular Matrix and Redox Signaling in Cellular Responses to Stress.

PubMed

Roberts, David D

2017-10-20

Cells in multicellular organisms communicate extensively with neighboring cells and distant organs using a variety of secreted proteins and small molecules. Cells also reside in a structural extracellular matrix (ECM), and changes in its composition, mechanical properties, and post-translational modifications provide additional layers of communication. This Forum addresses emerging mechanisms by which redox signaling controls and is controlled by changes in the ECM, focusing on the roles of matricellular proteins. These proteins engage specific cell surface signaling receptors, integrins, and proteoglycans to regulate the biosynthesis and catabolism of redox signaling molecules and the activation of their signal transducers. These signaling pathways, in turn, regulate the composition of ECM and its function. Covalent post-translational modifications of ECM by redox molecules further regulate its structure and function. Recent studies of acute injuries and chronic disease have identified important pathophysiological roles for this cross-talk and new therapeutic opportunities. Antioxid. Redox Signal. 27, 771-773.

Small Artery Elastin Distribution and Architecture-Focus on Three Dimensional Organization.

PubMed

Hill, Michael A; Nourian, Zahra; Ho, I-Lin; Clifford, Philip S; Martinez-Lemus, Luis; Meininger, Gerald A

2016-11-01

The distribution of ECM proteins within the walls of resistance vessels is complex both in variety of proteins and structural arrangement. In particular, elastin exists as discrete fibers varying in orientation across the adventitia and media as well as often resembling a sheet-like structure in the case of the IEL. Adding to the complexity is the tissue heterogeneity that exists in these structural arrangements. For example, small intracranial cerebral arteries lack adventitial elastin while similar sized arteries from skeletal muscle and intestinal mesentery exhibit a complex adventitial network of elastin fibers. With regard to the IEL, several vascular beds exhibit an elastin sheet with punctate holes/fenestrae while in others the IEL is discontinuous and fibrous in appearance. Importantly, these structural patterns likely sub-serve specific functional properties, including mechanosensing, control of external forces, mechanical properties of the vascular wall, cellular positioning, and communication between cells. Of further significance, these processes are altered in vascular disorders such as hypertension and diabetes mellitus where there is modification of ECM. This brief report focuses on the three-dimensional wall structure of small arteries and considers possible implications with regard to mechanosensing under physiological and pathophysiological conditions. © 2016 John Wiley & Sons Ltd.

Effects of Harbor Modification on Crescent City, California's Tsunami Vulnerability

NASA Astrophysics Data System (ADS)

Dengler, Lori; Uslu, Burak

2011-06-01

More damaging tsunamis have impacted Crescent City, California in historic times than any other location on the West Coast of the USA. Crescent City's harbor has undergone significant modification since the early 20th century, including construction of several breakwaters, dredging, and a 200 × 300 m2 small boat basin. In 2006, a M w 8.3 earthquake in the Kuril Islands generated a moderate Pacific-wide tsunami. Crescent City recorded the highest amplitudes of any tide gauge in the Pacific and was the only location to experience structural damage. Strong currents damaged docks and boats within the small boat basin, causing more than US 20 million in damage and replacement costs. We examine how modifications to Crescent City's harbor may have affected its vulnerability to moderate tsunamis such as the 2006 event. A bathymetric grid of the basin was constructed based on US Army Corps of Engineers soundings in 1964 and 1965 before the construction of the small boat basin. The method of splitting tsunamis was used to estimate tsunami water heights and current velocities at several locations in the harbor using both the 1964-1965 grid and the 2006 bathymetric grid for the 2006 Kuril event and a similar-sized source along the Sanriku coast of Japan. Model velocity outputs are compared for the two different bathymetries at the tide gauge location and at six additional computational sites in the harbor. The largest difference between the two grids is at the small boat basin entrance, where the 2006 bathymetry produces currents over three times the strength of the currents produced by the 1965 bathymetry. Peak currents from a Sanriku event are comparable to those produced by the 2006 event, and within the boat basin may have been higher. The modifications of the harbor, and in particular the addition of the small boat basin, appear to have contributed to the high current velocities and resulting damage in 2006 and help to explain why the 1933 M w 8.4-8.7 Sanriku tsunami caused no damage at Crescent City.

Fatigue Analyses Under Constant- and Variable-Amplitude Loading Using Small-Crack Theory

NASA Technical Reports Server (NTRS)

Newman, J. C., Jr.; Phillips, E. P.; Everett, R. A., Jr.

1999-01-01

Studies on the growth of small cracks have led to the observation that fatigue life of many engineering materials is primarily "crack growth" from micro-structural features, such as inclusion particles, voids, slip-bands or from manufacturing defects. This paper reviews the capabilities of a plasticity-induced crack-closure model to predict fatigue lives of metallic materials using "small-crack theory" under various loading conditions. Constraint factors, to account for three-dimensional effects, were selected to correlate large-crack growth rate data as a function of the effective stress-intensity factor range (delta-Keff) under constant-amplitude loading. Modifications to the delta-Keff-rate relations in the near-threshold regime were needed to fit measured small-crack growth rate behavior. The model was then used to calculate small-and large-crack growth rates, and to predict total fatigue lives, for notched and un-notched specimens under constant-amplitude and spectrum loading. Fatigue lives were predicted using crack-growth relations and micro-structural features like those that initiated cracks in the fatigue specimens for most of the materials analyzed. Results from the tests and analyses agreed well.

Structure and function of small heat shock/alpha-crystallin proteins: established concepts and emerging ideas.

PubMed

MacRae, T H

2000-06-01

Small heat shock/alpha-crystallin proteins are defined by conserved sequence of approximately 90 amino acid residues, termed the alpha-crystallin domain, which is bounded by variable amino- and carboxy-terminal extensions. These proteins form oligomers, most of uncertain quaternary structure, and oligomerization is prerequisite to their function as molecular chaperones. Sequence modelling and physical analyses show that the secondary structure of small heat shock/alpha-crystallin proteins is predominately beta-pleated sheet. Crystallography, site-directed spin-labelling and yeast two-hybrid selection demonstrate regions of secondary structure within the alpha-crystallin domain that interact during oligomer assembly, a process also dependent on the amino terminus. Oligomers are dynamic, exhibiting subunit exchange and organizational plasticity, perhaps leading to functional diversity. Exposure of hydrophobic residues by structural modification facilitates chaperoning where denaturing proteins in the molten globule state associate with oligomers. The flexible carboxy-terminal extension contributes to chaperone activity by enhancing the solubility of small heat shock/alpha-crystallin proteins. Site-directed mutagenesis has yielded proteins where the effect of the change on structure and function depends upon the residue modified, the organism under study and the analytical techniques used. Most revealing, substitution of a conserved arginine residue within the alpha-crystallin domain has a major impact on quaternary structure and chaperone action probably through realignment of beta-sheets. These mutations are linked to inherited diseases. Oligomer size is regulated by a stress-responsive cascade including MAPKAP kinase 2/3 and p38. Phosphorylation of small heat shock/alpha-crystallin proteins has important consequences within stressed cells, especially for microfilaments.

Synthesis and Characterization of a New Modification of the Quasi-Low-Dimensional Compound KMo 4O 6

NASA Astrophysics Data System (ADS)

Ramanujachary, K. V.; Greenblatt, D. M.; Jones, E. B.; McCarroll, W. H.

1993-01-01

Prismatic single crystals, up to 3 mm in length, of a third modification of KMo4O6 have been prepared by electrolysis of a melt with a high ratio of K2MoO4 to MoO3. Single-crystal X-ray diffraction analysis shows that the structure conforms more closely than the other two modifications to that reported originally for NaMo4O6. When current is passed parallel to the tetragonal c axis (i.e., parallel to the trans-edge-sharing chains of Mo6 octahedra) the compound displays metallic conductivity down to 100 K, where a broad transition to semiconducting behavior occurs. If the current is passed perpendicular to the c axis the conductivity is approximately a factor of 5 lower. Magnetic susceptibility measurements on a randomly oriented collection of crystals showed Pauli paramagnetic behavior with a small Curie tail at low temperatures.

Modifications of the Mesoscopic Structure of Cellulose in Paper Degradation

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

Missori, Mauro; Bicchieri, Marina; Mondelli, Claudia

2006-12-08

Paper is the main component of a huge quantity of cultural heritage. It is primarily composed of cellulose that undergoes significant degradation with the passage of time. By using small angle neutron scattering (SANS), we investigated cellulose's supramolecular structure, which allows access to degradation agents, in ancient and modern samples. For the first time, SANS data were interpreted in terms of water-filled pores, with their sizes increasing from 1.61 nm up to 1.97 nm in natural and artificially aged papers. The protective effect of gelatine sizing was also observed.

Modifications of the Mesoscopic Structure of Cellulose in Paper Degradation

NASA Astrophysics Data System (ADS)

Missori, Mauro; Mondelli, Claudia; de Spirito, Marco; Castellano, Carlo; Bicchieri, Marina; Schweins, Ralf; Arcovito, Giuseppe; Papi, Massimiliano; Castellano, Agostina Congiu

2006-12-01

Paper is the main component of a huge quantity of cultural heritage. It is primarily composed of cellulose that undergoes significant degradation with the passage of time. By using small angle neutron scattering (SANS), we investigated cellulose’s supramolecular structure, which allows access to degradation agents, in ancient and modern samples. For the first time, SANS data were interpreted in terms of water-filled pores, with their sizes increasing from 1.61 nm up to 1.97 nm in natural and artificially aged papers. The protective effect of gelatine sizing was also observed.

Assessing Chemical Transformation of Reactive, Interfacial Thin Films Made of End-Tethered Poly(2-vinyl-4,4-dimethyl azlactone) (PVDMA) Chains

DOE PAGES

Aden, Bethany; Kite, Camille M.; Hopkins, Benjamin W.; ...

2017-01-24

Designing thin films or surface scaffolds with an appropriate display of chemical functionality is useful for biomedical applications, sensing platforms, adhesives, and barrier coatings. Relationships between the structural characteristics of model thin films based on reactive poly(2-vinyl-4,4-dimethyl azlactone) (PVDMA) brushes and the amount and distribution of primary amines used to chemically functionalize these layers in situ are quantitatively detailed via neutron reflectometry and compared with results from ellipsometry. After functionalization, the PVDMA brush thickness increases as a result of the primary amines reacting with the azlactone rings. Both techniques show that the extent of functionalization by small-molecule amines depends onmore » the size of the amine, the grafting density of brush chains, and their molecular weight. However, constrained analysis of neutron reflectivity data predicated on that technique’s sensitivity to isotopic substitution and its ability to resolve structure at the nanoscale shows that the extent of functionalization is not accurately represented by the average extent of functionalization determined from ellipsometric thickness: reactive modification is not uniform, even in modestly dense brushes, except when the penetrant is small. In addition, there appears to be a loss of PVDMA chains during functionalization, attributed to chain scission resulting from additional stretching brought about by functionalization. In conclusion, these findings provide unprecedented insight into the alteration of surface properties by reactive modification and broadly support efforts to produce tailored surfaces in which properties such as friction, colloidal stability, adhesion, wettability, and biocompatibility can be modulated in situ by chemical modification.« less

Effect of thermal modification on rheological properties of polyethylene blends

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

Siriprumpoonthum, Monchai; Nobukawa, Shogo; Yamaguchi, Masayuki, E-mail: m-yama@jaist.ac.jp

2014-03-15

We examined the effects of thermal modification under flow field on the rheological properties of linear low-density polyethylene (LLDPE) with high molecular weight, low-density polyethylene (LDPE), and their blends, without thermal stabilizer. Although structural changes during processing are not detected by size extrusion chromatography or nuclear magnetic resonance spectroscopy, linear viscoelastic properties changed greatly, especially for the LLDPE. A cross-linking reaction took place, leading to, presumably, star-shaped long-chain branches. Consequently, the modified LLDPE, having high zero-shear viscosity, became a thermorheologically complex melt. Moreover, it should be noted that the drawdown force, defined as the uniaxial elongational force at a constantmore » draw ratio, was significantly enhanced for the blends. Enhancement of elongational viscosity was also detected. The drawdown force and elongational viscosity are marked for the thermally modified blend as compared with those for the blend of thermally modified pure components. Intermolecular cross-linking reactions between LDPE and LLDPE, yielding polymers with more than two branch points per chain, result in marked strain-hardening in the elongational viscosity behavior even at small strain. The recovery curve of the oscillatory modulus after the shear modification is further evidence of a branched structure.« less

Ball with hair: modular functionalization of highly stable G-quadruplex DNA nano-scaffolds through N2-guanine modification

PubMed Central

Lech, Christopher Jacques

2017-01-01

Abstract Functionalized nanoparticles have seen valuable applications, particularly in the delivery of therapeutic and diagnostic agents in biological systems. However, the manufacturing of such nano-scale systems with the consistency required for biological application can be challenging, as variation in size and shape have large influences in nanoparticle behavior in vivo. We report on the development of a versatile nano-scaffold based on the modular functionalization of a DNA G-quadruplex. DNA sequences are functionalized in a modular fashion using well-established phosphoramidite chemical synthesis with nucleotides containing modification of the amino (N2) position of the guanine base. In physiological conditions, these sequences fold into well-defined G-quadruplex structures. The resulting DNA nano-scaffolds are thermally stable, consistent in size, and functionalized in a manner that allows for control over the density and relative orientation of functional chemistries on the nano-scaffold surface. Various chemistries including small modifications (N2-methyl-guanine), bulky aromatic modifications (N2-benzyl-guanine), and long chain-like modifications (N2-6-amino-hexyl-guanine) are tested and are found to be generally compatible with G-quadruplex formation. Furthermore, these modifications stabilize the G-quadruplex scaffold by 2.0–13.3 °C per modification in the melting temperature, with concurrent modifications producing extremely stable nano-scaffolds. We demonstrate the potential of this approach by functionalizing nano-scaffolds for use within the biotin–avidin conjugation approach. PMID:28499037

Surface modification of amorphous substrates by disulfide derivatives: A photo-assisted route to direct functionalization of chalcogenide glasses

NASA Astrophysics Data System (ADS)

Amalric, Julien; Marchand-Brynaert, Jacqueline

2011-12-01

A novel route for chalcogenide glass surface modification is disclosed. The formation of an organic monolayer from disulfide derivatives is studied on two different glasses of formula GexAsySez by water contact angle measurement, X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy in attenuated total reflection mode (FTIR-ATR). The potential anchoring group is the disulfide functionality. Since thioctic acid derivatives absorb around 335 nm, an irradiation step is included, in order to favor S-S disruption. Three types of disulfide compounds are grafted onto small glass breaks for contact angle and XPS analyses. The results show effective changes of surface state. According to contact angle measurement, the deposited organic layer functionalized by a small polyethylene glycol chain leads to a more hydrophilic surface, long alkyl chain or a perfluorinated carbon chain leads to a more hydrophobic surface. XPS shows the presence at the surface of an organic layer with sulfur and ethylene oxide chains, or augmentation of organic carbons or fluorine and Csbnd F bonds. The photo-assisted grafting of the disulfides onto an ATR prism made of chalcogenide glass shows that this surface modification process does not affect infrared transparency, despite UV treatment, and accurate structural analysis can be performed.

Repetitive sequences and epigenetic modification: inseparable partners play important roles in the evolution of plant sex chromosomes.

PubMed

Li, Shu-Fen; Zhang, Guo-Jun; Yuan, Jin-Hong; Deng, Chuan-Liang; Gao, Wu-Jun

2016-05-01

The present review discusses the roles of repetitive sequences played in plant sex chromosome evolution, and highlights epigenetic modification as potential mechanism of repetitive sequences involved in sex chromosome evolution. Sex determination in plants is mostly based on sex chromosomes. Classic theory proposes that sex chromosomes evolve from a specific pair of autosomes with emergence of a sex-determining gene(s). Subsequently, the newly formed sex chromosomes stop recombination in a small region around the sex-determining locus, and over time, the non-recombining region expands to almost all parts of the sex chromosomes. Accumulation of repetitive sequences, mostly transposable elements and tandem repeats, is a conspicuous feature of the non-recombining region of the Y chromosome, even in primitive one. Repetitive sequences may play multiple roles in sex chromosome evolution, such as triggering heterochromatization and causing recombination suppression, leading to structural and morphological differentiation of sex chromosomes, and promoting Y chromosome degeneration and X chromosome dosage compensation. In this article, we review the current status of this field, and based on preliminary evidence, we posit that repetitive sequences are involved in sex chromosome evolution probably via epigenetic modification, such as DNA and histone methylation, with small interfering RNAs as the mediator.

Derivatizing weak polyelectrolytes--solution properties, self-aggregation, and association with anionic surfaces of hydrophobically modified poly(ethylene imine).

PubMed

Griffiths, Peter C; Paul, Alison; Fallis, Ian A; Wellappili, Champa; Murphy, Damien M; Jenkins, Robert; Waters, Sarah J; Nilmini, Renuka; Heenan, Richard K; King, Stephen M

2007-10-15

The physical properties of weak polyelectrolytes may be tailored via hydrophobic modification to exhibit useful properties under appropriate pH and ionic strength conditions as a consequence of the often inherently competing effects of electrostatics and hydrophobicity. Pulsed-gradient spin-echo NMR (PGSE-NMR), electron paramagnetic resonance (EPR), small-angle neutron scattering (SANS) surface tension, fluorescence, and pH titration have been used to examine the solution conformation and aggregation behavior of a series of hydrophobically modified hyperbranched poly(ethylene imine) (PEI) polymers in aqueous solution, and their interaction with sodium dodecylsulfate (SDS). PGSE-NMR gave a particularly insightful picture of the apparent molecular weight distribution. The presence of the hydrophobes led to a lower effective charge on the polymer at any given pH, compared to the (parent) nonmodified samples. Analysis of the SANS data showed that the propensity to form highly elliptical or rod-like aggregates at higher pHs, reflecting both the changes in protonation behavior induced by the hydrophobic modification and an hydrophobic interaction, but that these structures were disrupted with decreasing pH (increasing charge). The parent samples were not surface active yet the hydrophobically modified samples show pronounced surface activity and the presence of small hydrophobic domains. The surface activity increased with an increase in the degree of modification. On addition of SDS, the onset of the formation of polymer/surfactant complexes was insensitive to the degree of modification with the resultant PEI/SDS complexes resembling the size and shape of simple SDS micelles. Indeed, the presence of the SDS effectively nullifies the effects of the hydrophobe. Hydrophobic modification is therefore a viable option to tailor pH dependent properties, whose effects may be removed by the presence of surfactant.

Targeting RNA structure in SMN2 reverses spinal muscular atrophy molecular phenotypes.

PubMed

Garcia-Lopez, Amparo; Tessaro, Francesca; Jonker, Hendrik R A; Wacker, Anna; Richter, Christian; Comte, Arnaud; Berntenis, Nikolaos; Schmucki, Roland; Hatje, Klas; Petermann, Olivier; Chiriano, Gianpaolo; Perozzo, Remo; Sciarra, Daniel; Konieczny, Piotr; Faustino, Ignacio; Fournet, Guy; Orozco, Modesto; Artero, Ruben; Metzger, Friedrich; Ebeling, Martin; Goekjian, Peter; Joseph, Benoît; Schwalbe, Harald; Scapozza, Leonardo

2018-05-23

Modification of SMN2 exon 7 (E7) splicing is a validated therapeutic strategy against spinal muscular atrophy (SMA). However, a target-based approach to identify small-molecule E7 splicing modifiers has not been attempted, which could reveal novel therapies with improved mechanistic insight. Here, we chose as a target the stem-loop RNA structure TSL2, which overlaps with the 5' splicing site of E7. A small-molecule TSL2-binding compound, homocarbonyltopsentin (PK4C9), was identified that increases E7 splicing to therapeutic levels and rescues downstream molecular alterations in SMA cells. High-resolution NMR combined with molecular modelling revealed that PK4C9 binds to pentaloop conformations of TSL2 and promotes a shift to triloop conformations that display enhanced E7 splicing. Collectively, our study validates TSL2 as a target for small-molecule drug discovery in SMA, identifies a novel mechanism of action for an E7 splicing modifier, and sets a precedent for other splicing-mediated diseases where RNA structure could be similarly targeted.

Parametric Study of Amorphous High-Entropy Alloys formation from two New Perspectives: Atomic Radius Modification and Crystalline Structure of Alloying Elements

NASA Astrophysics Data System (ADS)

Hu, Q.; Guo, S.; Wang, J. M.; Yan, Y. H.; Chen, S. S.; Lu, D. P.; Liu, K. M.; Zou, J. Z.; Zeng, X. R.

2017-01-01

Chemical and topological parameters have been widely used for predicting the phase selection in high-entropy alloys (HEAs). Nevertheless, previous studies could be faulted due to the small number of available data points, the negligence of kinetic effects, and the insensitivity to small compositional changes. Here in this work, 92 TiZrHfM, TiZrHfMM, TiZrHfMMM (M = Fe, Cr, V, Nb, Al, Ag, Cu, Ni) HEAs were prepared by melt spinning, to build a reliable and sufficiently large material database to inspect the robustness of previously established parameters. Modification of atomic radii by considering the change of local electronic environment in alloys, was critically found out to be superior in distinguishing the formation of amorphous and crystalline alloys, when compared to using atomic radii of pure elements in topological parameters. Moreover, crystal structures of alloying element were found to play an important role in the amorphous phase formation, which was then attributed to how alloying hexagonal-close-packed elements and face-centered-cubic or body-centered-cubic elements can affect the mixing enthalpy. Findings from this work not only provide parametric studies for HEAs with new and important perspectives, but also reveal possibly a hidden connection among some important concepts in various fields.

Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species.

PubMed

Lui, Lauren M; Uzilov, Andrew V; Bernick, David L; Corredor, Andrea; Lowe, Todd M; Dennis, Patrick P

2018-05-16

Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2'-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genus Pyrobaculum, particularly rich in C/D box sRNA genes. Using high-throughput small RNA sequencing, specialized computational searches and comparative genomics, we analyzed 526 Pyrobaculum C/D box sRNAs, organizing them into 110 families based on synteny and conservation of guide sequences which determine methylation targets. We examined gene duplications and rearrangements, including one family that has expanded in a pattern similar to retrotransposed repetitive elements in eukaryotes. New training data and inclusion of kink-turn secondary structural features enabled creation of an improved search model. Our analyses provide the most comprehensive, dynamic view of C/D box sRNA evolutionary history within a genus, in terms of modification function, feature plasticity, and gene mobility.

Biopharmaceuticals from plants: a multitude of options for posttranslational modifications.

PubMed

Warzecha, Heribert

2008-01-01

In 1982 the first recombinant therapeutic, human insulin, was introduced into the market and started a new branch of pharmaceutical development, manufacture, and therapy options. To date, more than 130 recombinant protein therapeutics have been approved by the US Food and Drug Administration (FDA) and many more are being developed world wide. With the increasing number of protein therapeutics the number of potential production organisms is also expanding, and posttranslational modification of proteins has become a topic of special focus. One major difference between small-molecule drugs and protein therapeutics is that the latter are reliant on a host organism for their production and this can have a large influence on the final structure and can ultimately affect the pharmacokinetics, immunogenicity, and the function of the protein depending on the production process. Plants can be efficiently used as production systems for recombinant proteins thereby offering a variety of options for transgene targeting and modification. This review is intended to give an overview about the potential of plants to serve as a production system for therapeutic and prophylactic biopharmaceuticals with respect to posttranslational modifications.

ATR-IR study of skin components: Lipids, proteins and water. Part I: Temperature effect

NASA Astrophysics Data System (ADS)

Olsztyńska-Janus, S.; Pietruszka, A.; Kiełbowicz, Z.; Czarnecki, M. A.

2018-01-01

In this work we report the studies of the effect of temperature on skin components, such as lipids, proteins and water. Modifications of lipids structure induced by increasing temperature (from 20 to 90 °C) have been studied using ATR-IR (Attenuated Total Reflectance Infrared) spectroscopy, which is a powerful tool for characterization of the molecular structure and properties of tissues, such as skin. Due to the small depth of penetration (0.6-5.6 μm), ATR-IR spectroscopy probes only the outermost layer of the skin, i.e. the stratum corneum (SC). The assignment of main spectral features of skin components allows for the determination of phase transitions from the temperature dependencies of band intensities [e.g. νas(CH2) and νs(CH2)]. The phase transitions were determined by using two methods: the first one was based on the first derivative of the Boltzmann function and the second one employed tangent lines of sigmoidal, aforementioned dependencies. The phase transitions in lipids were correlated with modifications of the structure of water and proteins.

Structure-Based Design of a Small Molecule CD4-Antagonist with Broad Spectrum Anti-HIV-1 Activity

DOE PAGES

Curreli, Francesca; Kwon, Young Do; Zhang, Hongtao; ...

2015-08-24

Earlier we reported the discovery and design of NBD-556 and their analogs which demonstrated their potential as HIV-1 entry inhibitors. However, progress in developing these inhibitors has been stymied by their CD4-agonist properties, an unfavorable trait for use as drug. Here in this paper, we demonstrate the successful conversion of a full CD4-agonist (NBD-556) through a partial CD4-agonist (NBD-09027), to a full CD4-antagonist (NBD-11021) by structure-based modification of the critical oxalamide midregion, previously thought to be intolerant of modification. NBD-11021 showed unprecedented neutralization breath for this class of inhibitors, with pan-neutralization against a panel of 56 Env-pseudotyped HIV-1 representing diversemore » subtypes of clinical isolates (IC 50 as low as 270 nM). The cocrystal structure of NBD-11021 complexed to a monomeric HIV-1 gp120 core revealed its detail binding characteristics. The study is expected to provide a framework for further development of NBD series as HIV-1 entry inhibitors for clinical application against AIDS.« less

Synthetic Biological Approaches to Natural Product Biosynthesis

PubMed Central

Winter, Jaclyn M; Tang, Yi

2012-01-01

Small molecules produced in Nature continue to be an inspiration for the development of new therapeutic agents. These natural products possess exquisite chemical diversity, which gives rise to their wide range of biological activities. In their host organism, natural products are assembled and modified by dedicated biosynthetic pathways that Nature has meticulously developed. Often times, the complex structures or chemical modifications instated by these pathways are difficult to replicate using traditional synthetic methods. An alternative approach for creating or enhancing the structural variation of natural products is through combinatorial biosynthesis. By rationally reprogramming and manipulating the biosynthetic machinery responsible for their production, unnatural metabolites that were otherwise inaccessible can be obtained. Additionally, new chemical structures can be synthesized or derivatized by developing the enzymes that carry out these complicated chemical reactions into biocatalysts. In this review, we will discuss a variety of combinatorial biosynthetic strategies, their technical challenges, and highlight some recent (since 2007) examples of rationally designed unnatural metabolites, as well as platforms that have been established for the production and modification of clinically important pharmaceutical compounds. PMID:22221832

Structure-Based Design of a Small Molecule CD4-Antagonist with Broad Spectrum Anti-HIV-1 Activity

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

Curreli, Francesca; Kwon, Young Do; Zhang, Hongtao

Earlier we reported the discovery and design of NBD-556 and their analogs which demonstrated their potential as HIV-1 entry inhibitors. However, progress in developing these inhibitors has been stymied by their CD4-agonist properties, an unfavorable trait for use as drug. Here in this paper, we demonstrate the successful conversion of a full CD4-agonist (NBD-556) through a partial CD4-agonist (NBD-09027), to a full CD4-antagonist (NBD-11021) by structure-based modification of the critical oxalamide midregion, previously thought to be intolerant of modification. NBD-11021 showed unprecedented neutralization breath for this class of inhibitors, with pan-neutralization against a panel of 56 Env-pseudotyped HIV-1 representing diversemore » subtypes of clinical isolates (IC 50 as low as 270 nM). The cocrystal structure of NBD-11021 complexed to a monomeric HIV-1 gp120 core revealed its detail binding characteristics. The study is expected to provide a framework for further development of NBD series as HIV-1 entry inhibitors for clinical application against AIDS.« less

Supramolecular Architectures and Mimics of Complex Natural Folds Derived from Rationally Designed alpha-Helical Protein Structures

NASA Astrophysics Data System (ADS)

Tavenor, Nathan Albert

Protein-based supramolecular polymers (SMPs) are a class of biomaterials which draw inspiration from and expand upon the many examples of complex protein quaternary structures observed in nature: collagen, microtubules, viral capsids, etc. Designing synthetic supramolecular protein scaffolds both increases our understanding of natural superstructures and allows for the creation of novel materials. Similar to small-molecule SMPs, protein-based SMPs form due to self-assembly driven by intermolecular interactions between monomers, and monomer structure determines the properties of the overall material. Using protein-based monomers takes advantage of the self-assembly and highly specific molecular recognition properties encodable in polypeptide sequences to rationally design SMP architectures. The central hypothesis underlying our work is that alpha-helical coiled coils, a well-studied protein quaternary folding motif, are well-suited to SMP design through the addition of synthetic linkers at solvent-exposed sites. Through small changes in the structures of the cross-links and/or peptide sequence, we have been able to control both the nanoscale organization and the macroscopic properties of the SMPs. Changes to the linker and hydrophobic core of the peptide can be used to control polymer rigidity, stability, and dimensionality. The gaps in knowledge that this thesis sought to fill on this project were 1) the relationship between the molecular structure of the cross-linked polypeptides and the macroscopic properties of the SMPs and 2) a means of creating materials exhibiting multi-dimensional net or framework topologies. Separate from the above efforts on supramolecular architectures was work on improving backbone modification strategies for an alpha-helix in the context of a complex protein tertiary fold. Earlier work in our lab had successfully incorporated unnatural building blocks into every major secondary structure (beta-sheet, alpha-helix, loops and beta-turns) of a small protein with a tertiary fold. Although the tertiary fold of the native sequence was mimicked by the resulting artificial protein, the thermodynamic stability was greatly compromised. Most of this energetic penalty derived from the modifications present in the alpha-helix. The contribution within this thesis was direct comparison of several alpha-helical design strategies and establishment of the thermodynamic consequences of each.

On small beams with large topological charge: II. Photons, electrons and gravitational waves

NASA Astrophysics Data System (ADS)

Krenn, Mario; Zeilinger, Anton

2018-06-01

Beams of light with a large topological charge significantly change their spatial structure when they are focused strongly. Physically, it can be explained by an emerging electromagnetic field component in the direction of propagation, which is neglected in the simplified scalar wave picture in optics. Here we ask: is this a specific photonic behavior, or can similar phenomena also be predicted for other species of particles? We show that the same modification of the spatial structure exists for relativistic electrons as well as for focused gravitational waves. However, this is for different physical reasons: for electrons, which are described by the Dirac equation, the spatial structure changes due to a spin–orbit coupling in the relativistic regime. In gravitational waves described with linearized general relativity, the curvature of space–time between the transverse and propagation direction leads to the modification of the spatial structure. Thus, this universal phenomenon exists for both massive and massless elementary particles with spin 1/2, 1 and 2. It would be very interesting whether other types of particles such as composite systems (neutrons or C60) or neutrinos show a similar behavior and how this phenomenon can be explained in a unified physical way.

Efficient reanalysis of structures by a direct modification method. [local stiffness modifications of large structures

NASA Technical Reports Server (NTRS)

Raibstein, A. I.; Kalev, I.; Pipano, A.

1976-01-01

A procedure for the local stiffness modifications of large structures is described. It enables structural modifications without an a priori definition of the changes in the original structure and without loss of efficiency due to multiple loading conditions. The solution procedure, implemented in NASTRAN, involved the decomposed stiffness matrix and the displacement vectors of the original structure. It solves the modified structure exactly, irrespective of the magnitude of the stiffness changes. In order to investigate the efficiency of the present procedure and to test its applicability within a design environment, several real and large structures were solved. The results of the efficiency studies indicate that the break-even point of the procedure varies between 8% and 60% stiffness modifications, depending upon the structure's characteristics and the options employed.

Role of Polymorphism and Thin-Film Morphology in Organic Semiconductors Processed by Solution Shearing

PubMed Central

2018-01-01

Organic semiconductors (OSCs) are promising materials for cost-effective production of electronic devices because they can be processed from solution employing high-throughput techniques. However, small-molecule OSCs are prone to structural modifications because of the presence of weak van der Waals intermolecular interactions. Hence, controlling the crystallization in these materials is pivotal to achieve high device reproducibility. In this perspective article, we focus on controlling polymorphism and morphology in small-molecule organic semiconducting thin films deposited by solution-shearing techniques compatible with roll-to-roll systems. Special attention is paid to the influence that the different experimental deposition parameters can have on thin films. Further, the main characterization techniques for thin-film structures are reviewed, highlighting the in situ characterization tools that can provide crucial insights into the crystallization mechanisms. PMID:29503976

Modifications in small nuclear RNAs and their roles in spliceosome assembly and function.

PubMed

Bohnsack, Markus T; Sloan, Katherine E

2018-06-01

Modifications in cellular RNAs have emerged as key regulators of all aspects of gene expression, including pre-mRNA splicing. During spliceosome assembly and function, the small nuclear RNAs (snRNAs) form numerous dynamic RNA-RNA and RNA-protein interactions, which are required for spliceosome assembly, correct positioning of the spliceosome on substrate pre-mRNAs and catalysis. The human snRNAs contain several base methylations as well as a myriad of pseudouridines and 2'-O-methylated nucleotides, which are largely introduced by small Cajal body-specific-RNPs. Modified nucleotides typically cluster in functionally important regions of the snRNAs, suggesting that their presence could optimise the interactions of snRNAs with each other or with pre-mRNAs, or may affect the binding of spliceosomal proteins. snRNA modifications appear to play important roles in snRNP biogenesis and spliceosome assembly, and have also been proposed to influence the efficiency and fidelity of pre-mRNAs splicing. Interestingly, alterations in the modification status of snRNAs have recently been observed in different cellular conditions, implying that some snRNA modifications are dynamic and raising the possibility that these modifications may fine-tune the spliceosome for particular functions. Here, we review the current knowledge on the snRNA modification machinery and discuss the timing, functions and dynamics of modifications in snRNAs.

Base modification strategies to modulate immune stimulation by an siRNA.

PubMed

Valenzuela, Rachel Anne P; Suter, Scott R; Ball-Jones, Alexi A; Ibarra-Soza, José M; Zheng, Yuxuan; Beal, Peter A

2015-01-19

Immune stimulation triggered by siRNAs is one of the major challenges in the development of safe RNAi-based therapeutics. Within an immunostimulatory siRNA sequence, this hurdle is commonly addressed by using ribose modifications (e.g., 2'-OMe or 2'-F), which results in decreased cytokine production. However, as immune stimulation by siRNAs is a sequence-dependent phenomenon, recognition of the nucleobases by the trigger receptor(s) is also likely. Here, we use the recently published crystal structures of Toll-like receptor 8 (TLR8) bound to small-molecule agonists to generate computational models for ribonucleotide binding by this immune receptor. Our modeling suggested that modification of either the Watson-Crick or Hoogsteen face of adenosine would disrupt nucleotide/TLR8 interactions. We employed chemical synthesis to alter either the Watson-Crick or Hoogsteen face of adenosine and evaluated the effect of these modifications in an siRNA guide strand by measuring the immunostimulatory and RNA interference properties. For the siRNA guide strand tested, we found that modifying the Watson-Crick face is generally more effective at blocking TNFα production in human peripheral blood mononuclear cells (PBMCs) than modification at the Hoogsteen edge. We also observed that modifications near the 5'-end were more effective at blocking cytokine production than those placed at the 3'-end. This work advances our understanding of how chemical modifications can be used to optimize siRNA performance. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Whole-Cell-Based Assay To Evaluate Structure Permeation Relationships for Carbapenem Passage through the Pseudomonas aeruginosa Porin OprD.

PubMed

Iyer, Ramkumar; Sylvester, Mark A; Velez-Vega, Camilo; Tommasi, Ruben; Durand-Reville, Thomas F; Miller, Alita A

2017-04-14

The global emergence of antibiotic resistance, especially in Gram-negative bacteria, is an urgent threat to public health. Discovery of novel classes of antibiotics with activity against these pathogens has been impeded by a fundamental lack of understanding of the molecular drivers underlying small molecule uptake. Although it is well-known that outer membrane porins represent the main route of entry for small, hydrophilic molecules across the Gram-negative cell envelope, the structure-permeation relationship for porin passage has yet to be defined. To address this knowledge gap, we developed a sensitive and specific whole-cell approach in Escherichia coli called titrable outer membrane permeability assay system (TOMAS). We used TOMAS to characterize the structure porin-permeation relationships of a set of novel carbapenem analogues through the Pseudomonas aeruginosa porin OprD. Our results show that small structural modifications, especially the number and nature of charges and their position, have dramatic effects on the ability of these molecules to permeate cells through OprD. This is the first demonstration of a defined relationship between specific molecular changes in a substrate and permeation through an isolated porin. Understanding the molecular mechanisms that impact antibiotic transit through porins should provide valuable insights to antibacterial medicinal chemistry and may ultimately allow for the rational design of porin-mediated uptake of small molecules into Gram-negative bacteria.

Electric-field-induced modification in Dzyaloshinskii-Moriya interaction of Co monolayer on Pt(111)

NASA Astrophysics Data System (ADS)

Nakamura, Kohji; Akiyama, Toru; Ito, Tomonori; Ono, Teruo; Weinert, Michael

Magnetism induced by an external electric field (E-field) has received much attention as a potential approach for controlling magnetism at the nano-scale with the promise of ultra-low energy power consumption. Here, the E-field-induced modification of the Dzyaloshinskii-Moriya interaction (DMI) for a prototypical transition-metal thin layer of a Co monolayer on Pt(111) is investigated by first-principles calculations by using the full-potential linearized augmented plane wave method that treats spin-spiral structures in an E-field. With inclusion of the spin-orbit coupling (SOC) by the second variational method for commensurate spin-spiral structures, the DMI constants were estimated from an asymmetric contribution in the total energy with respect to the spin-spiral wavevector. The results predicted that the DMI is modified by the E-field, but the change is found to be small compared to that in the exchange interaction (a symmetric contribution in the total energy) by a factor of ten.

Ball with hair: modular functionalization of highly stable G-quadruplex DNA nano-scaffolds through N2-guanine modification.

PubMed

Lech, Christopher Jacques; Phan, Anh Tuân

2017-06-20

Functionalized nanoparticles have seen valuable applications, particularly in the delivery of therapeutic and diagnostic agents in biological systems. However, the manufacturing of such nano-scale systems with the consistency required for biological application can be challenging, as variation in size and shape have large influences in nanoparticle behavior in vivo. We report on the development of a versatile nano-scaffold based on the modular functionalization of a DNA G-quadruplex. DNA sequences are functionalized in a modular fashion using well-established phosphoramidite chemical synthesis with nucleotides containing modification of the amino (N2) position of the guanine base. In physiological conditions, these sequences fold into well-defined G-quadruplex structures. The resulting DNA nano-scaffolds are thermally stable, consistent in size, and functionalized in a manner that allows for control over the density and relative orientation of functional chemistries on the nano-scaffold surface. Various chemistries including small modifications (N2-methyl-guanine), bulky aromatic modifications (N2-benzyl-guanine), and long chain-like modifications (N2-6-amino-hexyl-guanine) are tested and are found to be generally compatible with G-quadruplex formation. Furthermore, these modifications stabilize the G-quadruplex scaffold by 2.0-13.3 °C per modification in the melting temperature, with concurrent modifications producing extremely stable nano-scaffolds. We demonstrate the potential of this approach by functionalizing nano-scaffolds for use within the biotin-avidin conjugation approach. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Chemoenzymatic Labeling of Proteins: Techniques and Approaches

PubMed Central

Rashidian, Mohammad; Dozier, Jonathan K.; Distefano, Mark D.

2013-01-01

Site-specific modification of proteins is a major challenge in modern chemical biology due to the large number of reactive functional groups typically present in polypeptides. Because of its importance in biology and medicine, the development of methods for site-specific modification of proteins is an area of intense research. Selective protein modification procedures have been useful for oriented protein immobilization, for studies of naturally-occurring post-translational modifications, for creating antibody-drug conjugates, for the introduction of fluorophores and other small molecules on to proteins, for examining protein structure, folding, dynamics and protein-protein interactions and for the preparation of protein-polymer conjugates. One of the most important approaches for protein labeling is to incorporate bioorthogonal functionalities into proteins at specific sites via enzymatic reactions. The incorporated tags then enable reactions that are chemoselective, whose functional groups are not only inert in biological media, but also do not occur natively in proteins or other macromolecules. This review article summarizes the enzymatic strategies, which enable site-specific functionalization of proteins with a variety of different functional groups. The enzymes covered in this review include formylglycine generating enzyme, sialyltransferases, phosphopantetheinyltransferases, O-GlcNAc post-translational modification, sortagging, transglutaminase, farnesyltransferase, biotin ligase, lipoic acid ligase and N-myristoyl transferase. PMID:23837885

Laser Micro and Nano Processing of Metals , Ceramics , and Polymers

NASA Astrophysics Data System (ADS)

Pfleging, Wilhelm; Kohler, Robert; Südmeyer, Isabelle; Rohde, Magnus

Laser -based material processing is well investigated for structuring , modification , and bonding of metals , ceramics , glasses, and polymers . Especially for material processing on micrometer, and nanometer scale laser-assisted processes will very likely become more prevalent as lasers offer more cost-effective solutions for advanced material research, and application. Laser ablation , and surface modification are suitable for direct patterning of materials and their surface properties. Lasers allow rapid prototyping and small-batch manufacturing . They can also be used to pattern moving substrates, permitting fly-processing of large areas at reasonable speed. Different types of laser processes such as ablation, modification, and welding can be successfully combined in order to enable a high grade of bulk and surface functionality. Ultraviolet lasers favored for precise and debris-free patterns can be generated without the need for masks, resist materials, or chemicals. Machining of materials, for faster operation, thermally driven laser processes using NIR and IR laser radiation, could be increasingly attractive for a real rapid manufacturing.

Structure of Hydrophobically Modified Phytoglycogen Nanoparticles

NASA Astrophysics Data System (ADS)

Atkinson, John; Nickels, Jonathan; Dutcher, John; Katsaras, John

Phytoglycogen is a highly branched, polysaccharide nanoparticle produced by some varieties of plants including sweet corn. These particles are attractive candidates for cosmetic, industrial and biomedical applications. Many of these applications result from phytoglycogen's unique interaction with water: (1) high solubility; (2) low viscosity and high stability in aqueous dispersions; and (3) a remarkable capacity to sequester and retain water. Neutron scattering measurements of native phytoglycogen revealed that the particles have uniform size, uniform radial particle density, and a high level of hydration. Hydrophobically modifying the outer surface of the hydrophilic nanoparticles opens up new applications in food and biomedicine, such as solubilizing and stabilizing bioactive compounds. One such modification is octenyl succinate anhydride (OSA), where the hydrophobicity can be tuned by adjusting the degree of substitution. I will present the results of small angle neutron scattering (SANS) measurements of aqueous dispersions of OSA-modified phytoglycogen with two different degrees of modification. Contrast series SANS measurements have yielded information about the radial density profile, providing insight into the nature of the chemical modification of the particles.

Signaling gateway molecule pages—a data model perspective

PubMed Central

Dinasarapu, Ashok Reddy; Saunders, Brian; Ozerlat, Iley; Azam, Kenan; Subramaniam, Shankar

2011-01-01

Summary: The Signaling Gateway Molecule Pages (SGMP) database provides highly structured data on proteins which exist in different functional states participating in signal transduction pathways. A molecule page starts with a state of a native protein, without any modification and/or interactions. New states are formed with every post-translational modification or interaction with one or more proteins, small molecules or class molecules and with each change in cellular location. State transitions are caused by a combination of one or more modifications, interactions and translocations which then might be associated with one or more biological processes. In a characterized biological state, a molecule can function as one of several entities or their combinations, including channel, receptor, enzyme, transcription factor and transporter. We have also exported SGMP data to the Biological Pathway Exchange (BioPAX) and Systems Biology Markup Language (SBML) as well as in our custom XML. Availability: SGMP is available at www.signaling-gateway.org/molecule. Contact: shankar@ucsd.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21505029

Effect of deformation on the structural state of piracetam

NASA Astrophysics Data System (ADS)

Kanunnikova, O. M.; Mikhailova, S. S.; Karban', O. V.; Mukhgalin, V. V.; Aksenova, V. V.; Sen'kovskii, B. V.; Pechina, E. A.; Lad'yanov, V. I.

2016-04-01

The effect of various deformation actions on the structure-phase transformations in piracetam of modifications I and II with a sodium acetate addition is studied. Mechanical activation and pressing are shown to cause the polymorphic transformation of modification I into modification II, and modification III forms predominantly during severe plastic deformation by torsion. The structural difference between the piracetam molecules of modifications I and II is found to be retained in aqueous solutions.

Response modification for enhanced operation and safety of bridges.

DOT National Transportation Integrated Search

2011-08-01

This report shows that safe extension of the service life of existing bridge structures is possible through bridge : health monitoring and structural response modification. To understand bridge health monitoring and structural : response modification...

The Italian corporate system in a network perspective (1952-1983)

NASA Astrophysics Data System (ADS)

Bargigli, L.; Giannetti, R.

2018-03-01

We study the Italian network of boards in four benchmark years covering different decades, when important economic structural shifts occurred. We find that the latter did not significantly disturb its structure as a small world. At the same time, we do not find a strong peculiarity of the Italian variety of capitalism and its corporate governance system. Typical properties of small world networks are at levels which are not dissimilar from those of other developed economies. Even the steady decrease of density that we observe is recurrent in many other national systems. The composition of the core of the most connected boards remains also quite stable over time. Among the most central boards we always find those of banks and insurances, as well as those of State Owned Enterprises (SOEs). At the same time, the system underwent two significant dynamic adjustments in the Sixties (nationalization of electrical industry) and Seventies (financial restructuring after the "big inflation") which are revealed by modifications in the core and in the community structure.

On the adsorption properties of magnetic fluids: Impact of bulk structure

NASA Astrophysics Data System (ADS)

Kubovcikova, Martina; Gapon, Igor V.; Zavisova, Vlasta; Koneracka, Martina; Petrenko, Viktor I.; Soltwedel, Olaf; Almasy, László; Avdeev, Mikhail V.; Kopcansky, Peter

2017-04-01

Adsorption of nanoparticles from magnetic fluids (MFs) on solid surface (crystalline silicon) was studied by neutron reflectometry (NR) and related to the bulk structural organization of MFs concluded from small-angle neutron scattering (SANS). The initial aqueous MF with nanomagnetite (co-precipitation reaction) stabilized by sodium oleate and MF modified by a biocompatible polymer, poly(ethylene glycol) (PEG), were considered. Regarding the bulk structure it was confirmed in the SANS experiment that comparatively small and compact (size 30 nm) aggregates of nanoparticle in the initial sample transfer to large and developed (size>130 nm, fractal dimension 2.7) associates in the PEG modified MF. This reorganization in the aggregates correlates with the changes in the neutron reflectivity that showed that a single adsorption layer of individual nanoparticles on the oxidized silicon surface for the initial MF disappears after the PEG modification. It is concluded that all particles in the modified fluid are in the aggregates that are not adsorbed by silicon.

Surface Roughness Measurement on a Wing Aircraft by Speckle Correlation

PubMed Central

Salazar, Félix; Barrientos, Alberto

2013-01-01

The study of the damage of aeronautical materials is important because it may change the microscopic surface structure profiles. The modification of geometrical surface properties can cause small instabilities and then a displacement of the boundary layer. One of the irregularities we can often find is surface roughness. Due to an increase of roughness and other effects, there may be extra momentum losses in the boundary layer and a modification in the parasite drag. In this paper we present a speckle method for measuring the surface roughness on an actual unmanned aircraft wing. The results show an inhomogeneous roughness distribution on the wing, as expected according to the anisotropic influence of the winds over the entire wing geometry. A calculation of the uncertainty of the technique is given. PMID:24013488

Surface roughness measurement on a wing aircraft by speckle correlation.

PubMed

Salazar, Félix; Barrientos, Alberto

2013-09-05

The study of the damage of aeronautical materials is important because it may change the microscopic surface structure profiles. The modification of geometrical surface properties can cause small instabilities and then a displacement of the boundary layer. One of the irregularities we can often find is surface roughness. Due to an increase of roughness and other effects, there may be extra momentum losses in the boundary layer and a modification in the parasite drag. In this paper we present a speckle method for measuring the surface roughness on an actual unmanned aircraft wing. The results show an inhomogeneous roughness distribution on the wing, as expected according to the anisotropic influence of the winds over the entire wing geometry. A calculation of the uncertainty of the technique is given.

Determination of the structures of small gold clusters on stepped magnesia by density functional calculations.

PubMed

Damianos, Konstantina; Ferrando, Riccardo

2012-02-21

The structural modifications of small supported gold clusters caused by realistic surface defects (steps) in the MgO(001) support are investigated by computational methods. The most stable gold cluster structures on a stepped MgO(001) surface are searched for in the size range up to 24 Au atoms, and locally optimized by density-functional calculations. Several structural motifs are found within energy differences of 1 eV: inclined leaflets, arched leaflets, pyramidal hollow cages and compact structures. We show that the interaction with the step clearly modifies the structures with respect to adsorption on the flat defect-free surface. We find that leaflet structures clearly dominate for smaller sizes. These leaflets are either inclined and quasi-horizontal, or arched, at variance with the case of the flat surface in which vertical leaflets prevail. With increasing cluster size pyramidal hollow cages begin to compete against leaflet structures. Cage structures become more and more favourable as size increases. The only exception is size 20, at which the tetrahedron is found as the most stable isomer. This tetrahedron is however quite distorted. The comparison of two different exchange-correlation functionals (Perdew-Burke-Ernzerhof and local density approximation) show the same qualitative trends. This journal is © The Royal Society of Chemistry 2012

Reducing Aerodynamic Drag on Empty Open Cargo Vehicles

NASA Technical Reports Server (NTRS)

Ross, James C.; Storms, Bruce L.; Dzoan, Dan

2009-01-01

Some simple structural modifications have been demonstrated to be effective in reducing aerodynamic drag on vehicles that have empty open cargo bays. The basic idea is to break up the airflow in a large open cargo bay by inserting panels to divide the bay into a series of smaller bays. In the case of a coal car, this involves inserting a small number (typically between two and four) of vertical full-depth or partial-depth panels.

Epigenomics in cancer management

PubMed Central

Costa, Fabricio F

2010-01-01

The identification of all epigenetic modifications implicated in gene expression is the next step for a better understanding of human biology in both normal and pathological states. This field is referred to as epigenomics, and it is defined as epigenetic changes (ie, DNA methylation, histone modifications and regulation by noncoding RNAs such as microRNAs) on a genomic scale rather than a single gene. Epigenetics modulate the structure of the chromatin, thereby affecting the transcription of genes in the genome. Different studies have already identified changes in epigenetic modifications in a few genes in specific pathways in cancers. Based on these epigenetic changes, drugs against different types of tumors were developed, which mainly target epimutations in the genome. Examples include DNA methylation inhibitors, histone modification inhibitors, and small molecules that target chromatin-remodeling proteins. However, these drugs are not specific, and side effects are a major problem; therefore, new DNA sequencing technologies combined with epigenomic tools have the potential to identify novel biomarkers and better molecular targets to treat cancers. The purpose of this review is to discuss current and emerging epigenomic tools and to address how these new technologies may impact the future of cancer management. PMID:21188117

Small molecule alteration of RNA sequence in cells and animals.

PubMed

Guan, Lirui; Luo, Yiling; Ja, William W; Disney, Matthew D

2017-10-18

RNA regulation and maintenance are critical for proper cell function. Small molecules that specifically alter RNA sequence would be exceptionally useful as probes of RNA structure and function or as potential therapeutics. Here, we demonstrate a photochemical approach for altering the trinucleotide expanded repeat causative of myotonic muscular dystrophy type 1 (DM1), r(CUG) exp . The small molecule, 2H-4-Ru, binds to r(CUG) exp and converts guanosine residues to 8-oxo-7,8-dihydroguanosine upon photochemical irradiation. We demonstrate targeted modification upon irradiation in cell culture and in Drosophila larvae provided a diet containing 2H-4-Ru. Our results highlight a general chemical biology approach for altering RNA sequence in vivo by using small molecules and photochemistry. Furthermore, these studies show that addition of 8-oxo-G lesions into RNA 3' untranslated regions does not affect its steady state levels. Copyright © 2017 Elsevier Ltd. All rights reserved.

Study of the gel films of Acetobacter Xylinum cellulose and its modified samples by {sup 1}H NMR cryoporometry and small-angle X-ray scattering

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

Babushkina, T. A.; Klimova, T. P.; Shtykova, E. V.

2010-03-15

Gel films of Acetobacter Xylinum cellulose and its modified samples have been investigated by 1H nuclear magnetic resonance (NMR) cryoporometry and small-angle X-ray scattering. The joint use of these two methods made it possible to characterize the sizes of aqueous pores in gel films and estimate the sizes of structural inhomogeneities before and after the sorption of polyvinylpyrrolidone and Se{sub 0} nanoparticles (stabilized by polyvinylpyrrolidone) into the films. According to small-angle X-ray scattering data, the sizes of inhomogeneities in a gel film change only slightly upon the sorption of polyvinylpyrrolidone and nanoparticles. The impregnated material is sorbed into water-filled cavitiesmore » that are present in the gel film. {sup 1}H NMR cryoporometry allowed us to reveal the details of changes in the sizes of small aqueous pores during modifications.« less

Marine exposure of preservative-treated small wood panels

Treesearch

B. R. Johnson; D. I. Gutzmer

1984-01-01

Small wood panels treated with many different chemicals have been exposed to limnorian and teredine marine borers in the sea at Key West, Florida. These preservatives and treatments include creosotes with and without modification, waterborne salts, salt-creosote dual treatments, chemical modifications of wood, and modified polymers. In spite of the accelerated nature...

Noncentrosymmetric superconductor BeAu

NASA Astrophysics Data System (ADS)

Amon, A.; Svanidze, E.; Cardoso-Gil, R.; Wilson, M. N.; Rosner, H.; Bobnar, M.; Schnelle, W.; Lynn, J. W.; Gumeniuk, R.; Hennig, C.; Luke, G. M.; Borrmann, H.; Leithe-Jasper, A.; Grin, Yu.

2018-01-01

Mixed spin-singlet and spin-triplet pairing can occur in noncentrosymmetric superconductors. In this respect, a comprehensive characterization of the noncentrosymmetric superconductor BeAu was carried out. It was established that BeAu undergoes a structural phase transition from a low-temperature noncentrosymmetric FeSi structure type to a high-temperature centrosymmetric structure in the CsCl type at Ts=860 K. The low-temperature modification exhibits a superconducting transition below Tc=3.3 K. The values of lower (Hc1=32 Oe) and upper (Hc2=335 Oe) critical fields are rather small, confirming that this type-II (κG-L=2.3 ) weakly coupled (λe-p=0.5 ,Δ Ce/γnTc≈1.26 ) superconductor can be well understood within the Bardeen-Cooper-Schrieffer theory. The muon spin relaxation analysis indicates that the time-reversal symmetry is preserved when the superconducting state is entered, supporting conventional superconductivity in BeAu. From the density functional band structure calculations, a considerable contribution of the Be electrons to the superconducting state was established. On average, a rather small mass renormalization was found, consistent with the experimental data.

Tracking of Short Distance Transport Pathways in Biological Tissues by Ultra-Small Nanoparticles

NASA Astrophysics Data System (ADS)

Segmehl, Jana S.; Lauria, Alessandro; Keplinger, Tobias; Berg, John K.; Burgert, Ingo

2018-03-01

In this work, ultra-small europium-doped HfO2 nanoparticles were infiltrated into native wood and used as trackers for studying penetrability and diffusion pathways in the hierarchical wood structure. The high electron density, laser induced luminescence, and crystallinity of these particles allowed for a complementary detection of the particles in the cellular tissue. Confocal Raman microscopy and high-resolution synchrotron scanning wide-angle X-ray scattering (WAXS) measurements were used to detect the infiltrated particles in the native wood cell walls. This approach allows for simultaneously obtaining chemical information of the probed biological tissue and the spatial distribution of the integrated particles. The in-depth information about particle distribution in the complex wood structure can be used for revealing transport pathways in plant tissues, but also for gaining better understanding of modification treatments of plant scaffolds aiming at novel functionalized materials.

High-Mobility, Ultrathin Organic Semiconducting Films Realized by Surface-Mediated Crystallization.

PubMed

Vladimirov, I; Kellermeier, M; Geßner, T; Molla, Zarah; Grigorian, S; Pietsch, U; Schaffroth, L S; Kühn, M; May, F; Weitz, R T

2018-01-10

The functionality of common organic semiconductor materials is determined by their chemical structure and crystal modification. While the former can be fine-tuned via synthesis, a priori control over the crystal structure has remained elusive. We show that the surface tension is the main driver for the plate-like crystallization of a novel small organic molecule n-type semiconductor at the liquid-air interface. This interface provides an ideal environment for the growth of millimeter-sized semiconductor platelets that are only few nanometers thick and thus highly attractive for application in transistors. On the basis of the novel high-performance perylene diimide, we show in as-grown, only 3 nm thin crystals electron mobilities of above 4 cm 2 /(V s) and excellent bias stress stability. We suggest that the established systematics on solvent parameters can provide the basis of a general framework for a more deterministic crystallization of other small molecules.

Water transport mechanism through open capillaries analyzed by direct surface modifications on biological surfaces

NASA Astrophysics Data System (ADS)

Ishii, Daisuke; Horiguchi, Hiroko; Hirai, Yuji; Yabu, Hiroshi; Matsuo, Yasutaka; Ijiro, Kuniharu; Tsujii, Kaoru; Shimozawa, Tateo; Hariyama, Takahiko; Shimomura, Masatsugu

2013-10-01

Some small animals only use water transport mechanisms passively driven by surface energies. However, little is known about passive water transport mechanisms because it is difficult to measure the wettability of microstructures in small areas and determine the chemistry of biological surfaces. Herein, we developed to directly analyse the structural effects of wettability of chemically modified biological surfaces by using a nanoliter volume water droplet and a hi-speed video system. The wharf roach Ligia exotica transports water only by using open capillaries in its legs containing hair- and paddle-like microstructures. The structural effects of legs chemically modified with a self-assembled monolayer were analysed, so that the wharf roach has a smart water transport system passively driven by differences of wettability between the microstructures. We anticipate that this passive water transport mechanism may inspire novel biomimetic fluid manipulations with or without a gravitational field.

Recent Methods for Purification and Structure Determination of Oligonucleotides.

PubMed

Zhang, Qiulong; Lv, Huanhuan; Wang, Lili; Chen, Man; Li, Fangfei; Liang, Chao; Yu, Yuanyuan; Jiang, Feng; Lu, Aiping; Zhang, Ge

2016-12-18

Aptamers are single-stranded DNA or RNA oligonucleotides that can interact with target molecules through specific three-dimensional structures. The excellent features, such as high specificity and affinity for target proteins, small size, chemical stability, low immunogenicity, facile chemical synthesis, versatility in structural design and engineering, and accessible for site-specific modifications with functional moieties, make aptamers attractive molecules in the fields of clinical diagnostics and biopharmaceutical therapeutics. However, difficulties in purification and structural identification of aptamers remain a major impediment to their broad clinical application. In this mini-review, we present the recently attractive developments regarding the purification and identification of aptamers. We also discuss the advantages, limitations, and prospects for the major methods applied in purifying and identifying aptamers, which could facilitate the application of aptamers.

Small is beautiful: features of the smallest insects and limits to miniaturization.

PubMed

Polilov, Alexey A

2015-01-07

Miniaturization leads to considerable reorganization of structures in insects, affecting almost all organs and tissues. In the smallest insects, comparable in size to unicellular organisms, modifications arise not only at the level of organs, but also at the cellular level. Miniaturization is accompanied by allometric changes in many organ systems. The consequences of miniaturization displayed by different insect taxa include both common and unique changes. Because the smallest insects are among the smallest metazoans and have the most complex organization among organisms of the same size, their peculiar structural features and the factors that limit their miniaturization are of considerable theoretical interest to general biology.

Analyses of Fatigue and Fatigue-Crack Growth under Constant- and Variable-Amplitude Loading

NASA Technical Reports Server (NTRS)

Newman, J. C., Jr.

1999-01-01

Studies on the growth of small cracks have led to the observation that fatigue life of many engineering materials is primarily crack growth from micro-structural features, such as inclusion particles, voids, slip-bands or from manufacturing defects. This paper reviews the capabilities of a plasticity-induced crack-closure model to predict fatigue lives of metallic materials using small-crack theory under various loading conditions. Constraint factors, to account for three-dimensional effects, were selected to correlate large-crack growth rate data as a function of the effective stress-intensity factor range (delta K(sub eff)) under constant-amplitude loading. Modifications to the delta K(sub eff)-rate relations in the near-threshold regime were needed to fit measured small-crack growth rate behavior. The model was then used to calculate small- and large-crack growth rates, and to predict total fatigue lives, for notched and un-notched specimens under constant-amplitude and spectrum loading. Fatigue lives were predicted using crack-growth relations and micro-structural features like those that initiated cracks in the fatigue specimens for most of the materials analyzed. Results from the tests and analyses agreed well.

Effect of gamma radiation on low density polyethylene (LDPE) films: optical, dielectric and FTIR studies.

PubMed

Moez, A Abdel; Aly, S S; Elshaer, Y H

2012-07-01

The low density polyethylene (LDPE) films were irradiated with gamma radiation in the dose range varied from 20 to 400 kGy. The induced changes in the chemical structure and dielectric properties for the irradiated films were investigated. The structure modifications: crystallinity as well as possible molecular changes of the polymer were recognized using Fourier Transform Infrared Spectroscopy (FTIR). The optical results were determined from transmission, reflection and absorption spectra for these films. The dielectric properties of these films were calculated using optical methods. Result indicates small variation in crystallinity which could be increased or decreased depending on the relative importance of the structural and chemical changes. Copyright © 2012 Elsevier B.V. All rights reserved.

Composite casting/bonding construction of an air-cooled, high temperature radial turbine wheel

NASA Technical Reports Server (NTRS)

Hammer, A. N.; Aigret, G.; Rodgers, C.; Metcalfe, A. G.

1983-01-01

A composite casting/bonding technique has been developed for the fabrication of a unique air-cooled, high temperature radial inflow turbine wheel design applicable to auxilliary power units with small rotor diameters and blade entry heights. The 'split blade' manufacturing procedure employed is an alternative to complex internal ceramic coring. Attention is given to both aerothermodynamic and structural design, of which the latter made advantageous use of the exploration of alternative cooling passage configurations through CAD/CAM system software modification.

Post-transcriptional modifications in the small subunit ribosomal RNA from Thermotoga maritima, including presence of a novel modified cytidine

PubMed Central

Guymon, Rebecca; Pomerantz, Steven C.; Ison, J. Nicholas; Crain, Pamela F.; McCloskey, James A.

2007-01-01

Post-transcriptional modifications of RNA are nearly ubiquitous in the principal RNAs involved in translation. However, in the case of rRNA the functional roles of modification are far less established than for tRNA, and are subject to less knowledge in terms of specific nucleoside identities and their sequence locations. Post-transcriptional modifications have been studied in the SSU rRNA from Thermotoga maritima (optimal growth 80°C), one of the most deeply branched organisms in the Eubacterial phylogenetic tree. A total of 10 different modified nucleosides were found, the greatest number reported for bacterial SSU rRNA, occupying a net of ∼14 sequence sites, compared with a similar number of sites recently reported for Thermus thermophilus and 11 for Escherichia coli. The relatively large number of modifications in Thermotoga offers modest support for the notion that thermophile rRNAs are more extensively modified than those from mesophiles. Seven of the Thermotoga modified sites are identical (location and identity) to those in E. coli. An unusual derivative of cytidine was found, designated N-330 (M r 330.117), and was sequenced to position 1404 in the decoding region of the rRNA. It was unexpectedly found to be identical to an earlier reported nucleoside of unknown structure at the same location in the SSU RNA of the archaeal mesophile Haloferax volcanii. PMID:17255199

Evaluation of Heterogeneous Metal-Organic Framework Organocatalysts Prepared by Postsynthetic Modification

PubMed Central

Garibay, Sergio J.; Wang, Zhenqiang; Cohen, Seth M.

2010-01-01

A metal-organic framework (MOF) containing 2-amino-1,4-benzenedicarboxylate (NH2-BDC) as a building block is shown to undergo chemical modification with a set of cyclic anhydrides. The modification of the aluminum-based MOF known as MIL-53(Al)-NH2 (MIL = Matérial Institut Lavoisier) by these reagents is demonstrated by using a variety of methods, including NMR and ESI-MS, and the structural integrity of the modified MOFs has been confirmed by TGA, PXRD, and gas sorption analysis. Reaction with these cyclic anhydrides produces MOFs that display carboxylic acid functional groups within their pores. Furthermore, it is shown that maleic acid functionalized MIL-53(Al)-AMMal can act as a Brønsted acid catalyst and facilitate the methanolysis of several small epoxides. Experiments show that MIL-53(Al)-AMMal acts in a heterogeneous manner and is recyclable with consistent activity over at least three catalytic cycles. The findings presented here demonstrate several important features of covalent postsynthetic modification (PSM) on MOFs, including: 1) facile introduction of catalytic functionality using simple organic reagents (e.g. anhydrides); 2) the ability to utilize and recycle organocatalytic MOFs; 3) control of catalytic activity through choice of functional group. The findings clearly illustrate that covalent postsynthetic modification represents a powerful means to access new MOF compounds that serve as organocatalytic materials. PMID:20698561

Oligo/Polynucleotide-Based Gene Modification: Strategies and Therapeutic Potential

PubMed Central

Sargent, R. Geoffrey; Kim, Soya

2011-01-01

Oligonucleotide- and polynucleotide-based gene modification strategies were developed as an alternative to transgene-based and classical gene targeting-based gene therapy approaches for treatment of genetic disorders. Unlike the transgene-based strategies, oligo/polynucleotide gene targeting approaches maintain gene integrity and the relationship between the protein coding and gene-specific regulatory sequences. Oligo/polynucleotide-based gene modification also has several advantages over classical vector-based homologous recombination approaches. These include essentially complete homology to the target sequence and the potential to rapidly engineer patient-specific oligo/polynucleotide gene modification reagents. Several oligo/polynucleotide-based approaches have been shown to successfully mediate sequence-specific modification of genomic DNA in mammalian cells. The strategies involve the use of polynucleotide small DNA fragments, triplex-forming oligonucleotides, and single-stranded oligodeoxynucleotides to mediate homologous exchange. The primary focus of this review will be on the mechanistic aspects of the small fragment homologous replacement, triplex-forming oligonucleotide-mediated, and single-stranded oligodeoxynucleotide-mediated gene modification strategies as it relates to their therapeutic potential. PMID:21417933

Structural modification in the formation of starch – silver nanocomposites

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

Begum, S. N. Suraiya; Ramasamy, Radha Perumal, E-mail: perumal.ramasamy@gmail.com; Aswal, V. K.

Polymer based nanocomposites have gained wide applications in field of battery technology. Starch is a naturally occurring polysaccharide with sustainable properties such as biodegradable, non toxic, excellent film forming capacity and it also act as reducing agent for the metal nanoparticles. In our research various concentration of silver nitrate (AgNO{sub 3}) was added to the starch solution and films were obtained using solution casting method. Surface electron microscope (SEM) of the films shows modifications depending upon the concentration of AgNO{sub 3}. Small angle neutron scattering (SANS) analysis showed that addition of silver nitrate modifies the starch to disc like structuresmore » and with increasing the AgNO{sub 3} concentration leads to the formation of fractals. This research could benefit battery technology where solid polymer membranes using starch is used.« less

Effects of habitat fragmentation on a stream-dwelling species, the flattened musk turtle Sternotherus depressus

USGS Publications Warehouse

Dodd, C.K.

1990-01-01

The flattened musk turtle Sternotherus depressus has disappeared from more than half of its former range because of habitat modifications to stream and river channels in the Warrior River Basin, Alabama. Only 6·9% of its probable historic range contains relatively healthy populations, and most populations are fragmented by extensive areas of unsuitable habitat. Turtles in the best remaining habitats continue to be vulnerable to disease and human-related disturbance, collecting and habitat modification. These factors lead to population declines and abnormal population structure. Habitat fragmentation, especially in small populations, increases vulnerability to human-caused catastrophes and demographic accidents, and could lead to eventual extinction. The threats facing fragmented populations of this turtle probably parallel those affecting many other stream-dwelling species throughout the southeastern United States.

Synaptic structure and function are altered by the neddylation inhibitor MLN4924

PubMed Central

Scudder, Samantha L.; Patrick, Gentry N.

2015-01-01

The posttranslational modification of proteins by the ubiquitin-like small molecule NEDD8 has previously been shown to be vital in a number of cell signaling pathways. In particular, conjugation of NEDD8 (neddylation) serves to regulate protein ubiquitination through modifications to E3 ubiquitin ligases. Despite the prevalence of NEDD8 in neurons, very little work has been done to characterize the role of this modifier in these cells. Here, we use the recently developed NEDD8 Activating Enzyme (NAE) inhibitor MLN4924 and report evidence of a role for NEDD8 in regulating mammalian excitatory synapses. Application of this drug to dissociated rat hippocampal neurons caused reductions in synaptic strength, surface glutamate receptor levels, dendritic spine width, and spine density, suggesting that neddylation is involved in the maintenance of synapses. PMID:25701678

Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs

PubMed Central

Yip, W. S. Vincent; Shigematsu, Hideki; Taylor, David W.; Baserga, Susan J.

2016-01-01

Ribosomal RNA (rRNA) modifications are essential for ribosome function in all cellular organisms. Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze 2′-O-methylation, one rRNA modification type in Eukarya and Archaea. Negatively stained electron microscopy (EM) models of archaeal box C/D sRNPs have demonstrated the dimeric sRNP (di-sRNP) architecture, which has been corroborated by nuclear magnetic resonance (NMR) studies. Due to limitations of the structural techniques, the orientation of the box C/D sRNAs has remained unclear. Here, we have used cryo-EM to elucidate the sRNA orientation in a M. jannaschii box C/D di-sRNP. The cryo-EM reconstruction suggests a parallel orientation of the two sRNAs. Biochemical and structural analyses of sRNPs assembled with mutant sRNAs indicate a potential interaction between the sRNA stem ends. Our results suggest that the parallel arrangement of the sRNAs juxtaposes their stem ends into close proximity to allow for a stabilizing interaction that helps maintain the di-sRNP architecture. PMID:27342279

Recent advances on biological production of difructose dianhydride III.

PubMed

Zhu, Yingying; Yu, Shuhuai; Zhang, Wenli; Zhang, Tao; Guang, Cuie; Mu, Wanmeng

2018-04-01

Difructose dianhydride III (DFA III) is a cyclic difructose containing two reciprocal glycosidic linkages. It is easily generated with a small amount by sucrose caramelization and thus occurs in a wide range of food-stuffs during food processing. DFA III has half sweetness but only 1/15 energy of sucrose, showing potential industrial application as low-calorie sucrose substitute. In addition, it displays many benefits including prebiotic effect, low cariogenicity property, and hypocholesterolemic effect, and improves absorption of minerals, flavonoids, and immunoglobulin G. DFA III is biologically produced from inulin by inulin fructotransferase (IFTase, EC 4.2.2.18). Plenty of DFA III-producing enzymes have been identified. The crystal structure of inulin fructotransferase has been determined, and its molecular modification has been performed to improve the catalytic activity and structural stability. Large-scale production of DFA III has been studied by various IFTases, especially using an ultrafiltration membrane bioreactor. In this article, the recent findings on physiological effects of DFA III are briefly summarized; the research progresses on identification, expression, and molecular modification of IFTase and large-scale biological production of DFA III by IFTase are reviewed in detail.

Epigenetics and Epigenomics of Plants.

PubMed

Yadav, Chandra Bhan; Pandey, Garima; Muthamilarasan, Mehanathan; Prasad, Manoj

2018-01-23

The genetic material DNA in association with histone proteins forms the complex structure called chromatin, which is prone to undergo modification through certain epigenetic mechanisms including cytosine DNA methylation, histone modifications, and small RNA-mediated methylation. Alterations in chromatin structure lead to inaccessibility of genomic DNA to various regulatory proteins such as transcription factors, which eventually modulates gene expression. Advancements in high-throughput sequencing technologies have provided the opportunity to study the epigenetic mechanisms at genome-wide levels. Epigenomic studies using high-throughput technologies will widen the understanding of mechanisms as well as functions of regulatory pathways in plant genomes, which will further help in manipulating these pathways using genetic and biochemical approaches. This technology could be a potential research tool for displaying the systematic associations of genetic and epigenetic variations, especially in terms of cytosine methylation onto the genomic region in a specific cell or tissue. A comprehensive study of plant populations to correlate genotype to epigenotype and to phenotype, and also the study of methyl quantitative trait loci (QTL) or epiGWAS, is possible by using high-throughput sequencing methods, which will further accelerate molecular breeding programs for crop improvement. Graphical Abstract.

Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs

PubMed Central

Mutisya, Daniel; Hardcastle, Travis; Cheruiyot, Samwel K.; Pallan, Pradeep S.; Kennedy, Scott D.; Egli, Martin; Kelley, Melissa L.; Smith, Anja van Brabant

2017-01-01

Abstract While the use of RNA interference (RNAi) in molecular biology and functional genomics is a well-established technology, in vivo applications of synthetic short interfering RNAs (siRNAs) require chemical modifications. We recently found that amides as non-ionic replacements for phosphodiesters may be useful modifications for optimization of siRNAs. Herein, we report a comprehensive study of systematic replacement of a single phosphate with an amide linkage throughout the guide strand of siRNAs. The results show that amides are surprisingly well tolerated in the seed and central regions of the guide strand and increase the silencing activity when placed between nucleosides 10 and 12, at the catalytic site of Argonaute. A potential explanation is provided by the first crystal structure of an amide-modified RNA–DNA with Bacillus halodurans RNase H1. The structure reveals how small changes in both RNA and protein conformation allow the amide to establish hydrogen bonding interactions with the protein. Molecular dynamics simulations suggest that these alternative binding modes may compensate for interactions lost due to the absence of a phosphodiester moiety. Our results suggest that an amide can mimic important hydrogen bonding interactions with proteins required for RNAi activity and may be a promising modification for optimization of biological properties of siRNAs. PMID:28854734

Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs

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

Mutisya, Daniel; Hardcastle, Travis; Cheruiyot, Samwel K.

While the use of RNA interference (RNAi) in molecular biology and functional genomics is a well-established technology, in vivo applications of synthetic short interfering RNAs (siRNAs) require chemical modifications. We recently found that amides as non-ionic replacements for phosphodiesters may be useful modifications for optimization of siRNAs. Herein, we report a comprehensive study of systematic replacement of a single phosphate with an amide linkage throughout the guide strand of siRNAs. The results show that amides are surprisingly well tolerated in the seed and central regions of the guide strand and increase the silencing activity when placed between nucleosides 10 andmore » 12, at the catalytic site of Argonaute. A potential explanation is provided by the first crystal structure of an amide-modified RNA–DNA with Bacillus halodurans RNase H1. The structure reveals how small changes in both RNA and protein conformation allow the amide to establish hydrogen bonding interactions with the protein. Molecular dynamics simulations suggest that these alternative binding modes may compensate for interactions lost due to the absence of a phosphodiester moiety. Our results suggest that an amide can mimic important hydrogen bonding interactions with proteins required for RNAi activity and may be a promising modification for optimization of biological properties of siRNAs.« less

Exploiting tRNAs to Boost Virulence

PubMed Central

Albers, Suki; Czech, Andreas

2016-01-01

Transfer RNAs (tRNAs) are powerful small RNA entities that are used to translate nucleotide language of genes into the amino acid language of proteins. Their near-uniform length and tertiary structure as well as their high nucleotide similarity and post-transcriptional modifications have made it difficult to characterize individual species quantitatively. However, due to the central role of the tRNA pool in protein biosynthesis as well as newly emerging roles played by tRNAs, their quantitative assessment yields important information, particularly relevant for virus research. Viruses which depend on the host protein expression machinery have evolved various strategies to optimize tRNA usage—either by adapting to the host codon usage or encoding their own tRNAs. Additionally, several viruses bear tRNA-like elements (TLE) in the 5′- and 3′-UTR of their mRNAs. There are different hypotheses concerning the manner in which such structures boost viral protein expression. Furthermore, retroviruses use special tRNAs for packaging and initiating reverse transcription of their genetic material. Since there is a strong specificity of different viruses towards certain tRNAs, different strategies for recruitment are employed. Interestingly, modifications on tRNAs strongly impact their functionality in viruses. Here, we review those intersection points between virus and tRNA research and describe methods for assessing the tRNA pool in terms of concentration, aminoacylation and modification. PMID:26797637

Alternative approaches used to assess structural changes of natural zircon caused by heat treatment

NASA Astrophysics Data System (ADS)

Huong, L. T. T.; Thuyet, N. T. M.; Phan, T. L.; Tran, N.; Toan, D. N.; Thang, P. D.; Huy, B. T.

2018-03-01

It is known that large changes in the crystal structure of zircon (ZrSiO4) can be assessed through the linewidth of the characteristic Raman mode (Δν3) at 1008 cm-1. However, the use of Δν3 to assess small changes caused by heat treatment at temperatures below its decomposition temperature of 1670 °C is difficult. The present work points out that the combination of X-ray diffraction (XRD) analyses, and photoluminescence (PL) and Raman (RS) measurements with different excitation wavelengths is an effective approach to solve the above problem. In this context, we have selected natural zircon containing some rare-earth (RE) impurities, and then studied the changes in its crystal structure caused by heat treatment at temperatures Tan=400-1600 °C. XRD analyses reveal that small modifications of the unit-cell parameters occur as Tan>600 °C. Taking the intensity ratios of the ν3 mode to RE-related emissions (Iν3/IRE) or the PL intensity ratios between RE-related emissions into consideration, the similar results in good agreement with the XRD analyses are also found. We believe that the small structural changes are related to the migration and redistribution of defects and impurities, and re-crystallization of zircon. This could be further confirmed though the relation between paramagnetic and ferromagnetic signals when Tan changes.

Magnetically-induced forces on a ferromagnetic HT-9 first wall/blanket module

NASA Astrophysics Data System (ADS)

Lechtenberg, T. A.; Dahms, C. F.; Attaya, H.

1984-05-01

A model of the Starfire commercial tokamak reactor was used as the basis for calculating magnetic loads induced on typical fusion reactor first wall components fabricated of ferromagnetic material. The component analyzed was the first wall/blanket module because this structure experiences the greatest neutron fluence level and is the component for which the low swelling ferromagnetic Sandvik alloy, HT-9, may have the greatest benefit. The magnitudes of the magnetic body forces calculated were consistent with analyses performed on structures within other types of reactors. The loads generated within the module structure by the magnetic forces were found to be of the same order of magnitude as those arising from other sources such as pressure differential, dead weight, temperature distribution. Only small structural design modifications would be required if the magnetic alloy, Sandvik HT-9 were utilized.

Static shape control for adaptive wings

NASA Astrophysics Data System (ADS)

Austin, Fred; Rossi, Michael J.; van Nostrand, William; Knowles, Gareth; Jameson, Antony

1994-09-01

A theoretical method was developed and experimentally validated, to control the static shape of flexible structures by employing internal translational actuators. A finite element model of the structure, without the actuators present, is employed to obtain the multiple-input, multiple-output control-system gain matrices for actuator-load control as well as actuator-displacement control. The method is applied to the quasistatic problem of maintaining an optimum-wing cross section during various transonic-cruise flight conditions to obtain significant reductions in the shock-induced drag. Only small, potentially achievable, adaptive modifications to the profile are required. The adaptive-wing concept employs actuators as truss elements of active ribs to reshape the wing cross section by deforming the structure. Finite element analyses of an adaptive-rib model verify the controlled-structure theory. Experiments on the model were conducted, and arbitrarily selected deformed shapes were accurately achieved.

On Time Delay Margin Estimation for Adaptive Control and Optimal Control Modification

NASA Technical Reports Server (NTRS)

Nguyen, Nhan T.

2011-01-01

This paper presents methods for estimating time delay margin for adaptive control of input delay systems with almost linear structured uncertainty. The bounded linear stability analysis method seeks to represent an adaptive law by a locally bounded linear approximation within a small time window. The time delay margin of this input delay system represents a local stability measure and is computed analytically by three methods: Pade approximation, Lyapunov-Krasovskii method, and the matrix measure method. These methods are applied to the standard model-reference adaptive control, s-modification adaptive law, and optimal control modification adaptive law. The windowing analysis results in non-unique estimates of the time delay margin since it is dependent on the length of a time window and parameters which vary from one time window to the next. The optimal control modification adaptive law overcomes this limitation in that, as the adaptive gain tends to infinity and if the matched uncertainty is linear, then the closed-loop input delay system tends to a LTI system. A lower bound of the time delay margin of this system can then be estimated uniquely without the need for the windowing analysis. Simulation results demonstrates the feasibility of the bounded linear stability method for time delay margin estimation.

siRNAmod: A database of experimentally validated chemically modified siRNAs.

PubMed

Dar, Showkat Ahmad; Thakur, Anamika; Qureshi, Abid; Kumar, Manoj

2016-01-28

Small interfering RNA (siRNA) technology has vast potential for functional genomics and development of therapeutics. However, it faces many obstacles predominantly instability of siRNAs due to nuclease digestion and subsequently biologically short half-life. Chemical modifications in siRNAs provide means to overcome these shortcomings and improve their stability and potency. Despite enormous utility bioinformatics resource of these chemically modified siRNAs (cm-siRNAs) is lacking. Therefore, we have developed siRNAmod, a specialized databank for chemically modified siRNAs. Currently, our repository contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. It is developed and hosted using Linux Apache MySQL PHP (LAMP) software bundle. Standard user-friendly browse, search facility and analysis tools are also integrated. It would assist in understanding the effect of chemical modifications and further development of stable and efficacious siRNAs for research as well as therapeutics. siRNAmod is freely available at: http://crdd.osdd.net/servers/sirnamod.

Modification of the morphology of P(S-b-EO) templated thin TiO2 films by swelling with PS homopolymer.

PubMed

Perlich, J; Schulz, L; Abul Kashem, M M; Cheng, Y-J; Memesa, M; Gutmann, J S; Roth, S V; Müller-Buschbaum, P

2007-09-25

For the controlled modification of sol-gel-templated polymer nanocomposites, which are transferred to a nanostructured, crystalline TiO2 phase by a calcination process, the addition of a single homopolymer was investigated. For the preparation, the homopolymer polystyrene (PS) is added in different amounts to the diblock copolymer P(S-b-EO) acting as a templating agent. The homopolymer/diblock copolymer blend system is combined with sol-gel chemistry to provide and attach the TiO2 nanoparticles to the diblock copolymer. So-called good-poor solvent-pair-induced phase separation leads to the formation of nanostructures by film preparation via spin coating. The fabricated morphologies are studied as a function of added homopolymer before and after calcination with atomic force microscopy, field emission scanning electron microscopy, and grazing incidence small-angle X-ray scattering. The observed behavior is discussed in the framework of controlling the block copolymer morphologies by the addition of homopolymers. At small homopolymer concentrations, the increase in homopolymer concentration changes the structure size, whereas at high homopolymer concentrations, a change in morphology is triggered. Thus, the behavior of a pure polymer system is transferred to a more complex hybrid system.

Thermally Tunable Hydrogels Displaying Angle-Independent Structural Colors.

PubMed

Ohtsuka, Yumiko; Seki, Takahiro; Takeoka, Yukikazu

2015-12-14

We report the preparation of thermally tunable hydrogels displaying angle-independent structural colors. The porous structures were formed with short-range order using colloidal amorphous array templates and a small amount of carbon black (CB). The resultant porous hydrogels prepared using colloidal amorphous arrays without CB appeared white, whereas the hydrogels with CB revealed bright structural colors. The brightly colored hydrogels rapidly changed hues in a reversible manner, and the hues varied widely depending on the water temperature. Moreover, the structural colors were angle-independent under diffusive lighting because of the isotropic nanostructure generated from the colloidal amorphous arrays. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution Non-Commercial NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Structural modifications of graphyne layers consisting of carbon atoms in the sp- and sp{sup 2}-hybridized states

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

Belenkov, E. A., E-mail: belenkov@csu.ru; Mavrinskii, V. V.; Belenkova, T. E.

2015-05-15

A model scheme is proposed for obtaining layered compounds consisting of carbon atoms in the sp- and (vnsp){sup 2}-hybridized states. This model is used to find the possibility of existing the following seven basic structural modifications of graphyne: α-, β1-, β2-, β3-, γ1-, γ2-, and γ3-graphyne. Polymorphic modifications β3 graphyne and γ3 graphyne are described. The basic structural modifications of graphyne contain diatomic polyyne chains and consist only of carbon atoms in two different crystallographically equivalent states. Other nonbasic structural modifications of graphyne can be formed via the elongation of the carbyne chains that connect three-coordinated carbon atoms and viamore » the formation of graphyne layers with a mixed structure consisting of basic layer fragments, such as α-β-graphyne, α-γ-graphyne, and β-γ-graphyne. The semiempirical quantum-mechanical MNDO, AM1, and PM3 methods and ab initio STO6-31G basis calculations are used to find geometrically optimized structures of the basic graphyne layers, their structural parameters, and energies of their sublimation. The energy of sublimation is found to be maximal for γ2-graphyne, which should be the most stable structural modification of graphyne.« less

Optics-Only Calibration of a Neural-Net Based Optical NDE Method for Structural Health Monitoring

NASA Technical Reports Server (NTRS)

Decker, Arthur J.

2004-01-01

A calibration process is presented that uses optical measurements alone to calibrate a neural-net based NDE method. The method itself detects small changes in the vibration mode shapes of structures. The optics-only calibration process confirms previous work that the sensitivity to vibration-amplitude changes can be as small as 10 nanometers. A more practical value in an NDE service laboratory is shown to be 50 nanometers. Both model-generated and experimental calibrations are demonstrated using two implementations of the calibration technique. The implementations are based on previously published demonstrations of the NDE method and an alternative calibration procedure that depends on comparing neural-net and point sensor measurements. The optics-only calibration method, unlike the alternative method, does not require modifications of the structure being tested or the creation of calibration objects. The calibration process can be used to test improvements in the NDE process and to develop a vibration-mode-independence of damagedetection sensitivity. The calibration effort was intended to support NASA s objective to promote safety in the operations of ground test facilities or aviation safety, in general, by allowing the detection of the gradual onset of structural changes and damage.

Genome-wide analyses of four major histone modifications in Arabidopsis hybrids at the germinating seed stage.

PubMed

Zhu, Anyu; Greaves, Ian K; Dennis, Elizabeth S; Peacock, W James

2017-02-07

Hybrid vigour (heterosis) has been used for decades in cropping agriculture, especially in the production of maize and rice, because hybrid varieties exceed their parents in plant biomass and seed yield. The molecular basis of hybrid vigour is not fully understood. Previous studies have suggested that epigenetic systems could play a role in heterosis. In this project, we investigated genome-wide patterns of four histone modifications in Arabidopsis hybrids in germinating seeds. We found that although hybrids have similar histone modification patterns to the parents in most regions of the genome, they have altered patterns at specific loci. A small subset of genes show changes in histone modifications in the hybrids that correlate with changes in gene expression. Our results also show that genome-wide patterns of histone modifications in geminating seeds parallel those at later developmental stages of seedlings. Ler/C24 hybrids showed similar genome-wide patterns of histone modifications as the parents at an early germination stage. However, a small subset of genes, such as FLC, showed correlated changes in histone modification and in gene expression in the hybrids. The altered patterns of histone modifications for those genes in hybrids could be related to some heterotic traits in Arabidopsis, such as flowering time, and could play a role in hybrid vigour establishment.

Disconnect between alcohol-induced alterations in chromatin structure and gene transcription in a mouse embryonic stem cell model of exposure

PubMed Central

Veazey, Kylee J.; Wang, Haiqing; Behdi, Yudhishtar S.; Skiles, William M.; Chang, Richard Cheng-An; Golding, Michael C.

2017-01-01

Alterations to chromatin structure induced by environmental insults have become an attractive explanation for the persistence of exposure effects into subsequent life stages. However, a growing body of work examining the epigenetic impact alcohol and other drugs of abuse exert consistently note a disconnect between induced changes in chromatin structure and patterns of gene transcription. Thus, an important question is whether perturbations in the ‘histone code’ induced by prenatal exposures to alcohol implicitly subvert gene expression, or if the hierarchy of cellular signaling networks driving development is such that they retain control over the transcriptional program. To address this question, we examined the impact of ethanol exposure in mouse embryonic stem cells cultured under 2i conditions, where the transcriptional program is rigidly enforced through the use of small molecule inhibitors. We find that ethanol-induced changes in post-translational histone modifications are dose-dependent, unique to the chromatin modification under investigation, and that the extent and direction of the change differ between the period of exposure and the recovery phase. Similar to in vivo models, we find post-translational modifications affecting histone 3 lysine 9 are the most profoundly impacted, with the signature of exposure persisting long after alcohol has been removed. These changes in chromatin structure associate with dose-dependent alterations in the levels of transcripts encoding Dnmt1, Uhrf1, Tet1, Tet2, Tet3, and Polycomb complex members Eed and Ezh2. However, in this model, ethanol-induced changes to the chromatin template do not consistently associate with changes in gene transcription, impede the process of differentiation or impact the acquisition of monoallelic patterns of expression for the imprinted gene Igf2R. These findings question the inferred universal relevance of epigenetic changes induced by drugs of abuse and suggest changes in chromatin structure cannot unequivocally explain dysgenesis in isolation. PMID:28433419

Disconnect between alcohol-induced alterations in chromatin structure and gene transcription in a mouse embryonic stem cell model of exposure.

PubMed

Veazey, Kylee J; Wang, Haiqing; Bedi, Yudhishtar S; Skiles, William M; Chang, Richard Cheng-An; Golding, Michael C

2017-05-01

Alterations to chromatin structure induced by environmental insults have become an attractive explanation for the persistence of exposure effects into subsequent life stages. However, a growing body of work examining the epigenetic impact that alcohol and other drugs of abuse exert consistently notes a disconnection between induced changes in chromatin structure and patterns of gene transcription. Thus, an important question is whether perturbations in the 'histone code' induced by prenatal exposures to alcohol implicitly subvert gene expression, or whether the hierarchy of cellular signaling networks driving development is such that they retain control over the transcriptional program. To address this question, we examined the impact of ethanol exposure in mouse embryonic stem cells cultured under 2i conditions, where the transcriptional program is rigidly enforced through the use of small molecule inhibitors. We find that ethanol-induced changes in post-translational histone modifications are dose-dependent, unique to the chromatin modification under investigation, and that the extent and direction of the change differ between the period of exposure and the recovery phase. Similar to in vivo models, we find post-translational modifications affecting histone 3 lysine 9 are the most profoundly impacted, with the signature of exposure persisting long after alcohol has been removed. These changes in chromatin structure associate with dose-dependent alterations in the levels of transcripts encoding Dnmt1, Uhrf1, Tet1, Tet2, Tet3, and Polycomb complex members Eed and Ezh2. However, in this model, ethanol-induced changes to the chromatin template do not consistently associate with changes in gene transcription, impede the process of differentiation, or affect the acquisition of monoallelic patterns of expression for the imprinted gene Igf2R. These findings question the inferred universal relevance of epigenetic changes induced by drugs of abuse and suggest that changes in chromatin structure cannot unequivocally explain dysgenesis in isolation. Copyright © 2017 Elsevier Inc. All rights reserved.

Robust functional statistics applied to Probability Density Function shape screening of sEMG data.

PubMed

Boudaoud, S; Rix, H; Al Harrach, M; Marin, F

2014-01-01

Recent studies pointed out possible shape modifications of the Probability Density Function (PDF) of surface electromyographical (sEMG) data according to several contexts like fatigue and muscle force increase. Following this idea, criteria have been proposed to monitor these shape modifications mainly using High Order Statistics (HOS) parameters like skewness and kurtosis. In experimental conditions, these parameters are confronted with small sample size in the estimation process. This small sample size induces errors in the estimated HOS parameters restraining real-time and precise sEMG PDF shape monitoring. Recently, a functional formalism, the Core Shape Model (CSM), has been used to analyse shape modifications of PDF curves. In this work, taking inspiration from CSM method, robust functional statistics are proposed to emulate both skewness and kurtosis behaviors. These functional statistics combine both kernel density estimation and PDF shape distances to evaluate shape modifications even in presence of small sample size. Then, the proposed statistics are tested, using Monte Carlo simulations, on both normal and Log-normal PDFs that mimic observed sEMG PDF shape behavior during muscle contraction. According to the obtained results, the functional statistics seem to be more robust than HOS parameters to small sample size effect and more accurate in sEMG PDF shape screening applications.

A revisit to model the Cr i triplet at 5204-5208 Å and the Ba ii D2 line at 4554 Å in the Second Solar Spectrum

NASA Astrophysics Data System (ADS)

Smitha, H. N.; Nagendra, K. N.; Stenflo, J. O.; Bianda, M.; Sampoorna, M.; Ramelli, R.

2015-10-01

In our previous attempt to model the Stokes profiles of the Cr i triplet at 5204-5208 Å and the Ba ii D2 at 4554 Å, we found it necessary to slightly modify the standard FAL model atmospheres to fit the observed polarization profiles. In the case of Cr i triplet, this modification was done to reduce the theoretical continuum polarization, and in the case of Ba ii D2, it was needed to reproduce the central peak in Q/I. In this work, we revisit both these cases using different standard model atmospheres whose temperature structures closely resemble those of the modified FAL models, and explore the possibility of synthesizing the line profiles without the need for small modifications of the model atmosphere.

Regulation of parkin and PINK1 by neddylation

PubMed Central

Choo, Yeun Su; Vogler, Georg; Wang, Danling; Kalvakuri, Sreehari; Iliuk, Anton; Tao, W. Andy; Bodmer, Rolf; Zhang, Zhuohua

2012-01-01

Neddylation is a posttranslational modification that plays important roles in regulating protein structure and function by covalently conjugating NEDD8, an ubiquitin-like small molecule, to the substrate. Here, we report that Parkinson's disease (PD)-related parkin and PINK1 are NEDD8 conjugated. Neddylation of parkin and PINK1 results in increased E3 ligase activity of parkin and selective stabilization of the 55 kDa PINK1 fragment. Expression of dAPP-BP1, a NEDD8 activation enzyme subunit, in Drosophila suppresses abnormalities induced by dPINK1 RNAi. PD neurotoxin MPP+ inhibits neddylation of both parkin and PINK1. NEDD8 immunoreactivity is associated with Lewy bodies in midbrain dopaminergic neurons of PD patients. Together, these results suggest that parkin and PINK1 are regulated by neddylation and that impaired NEDD8 modification of these proteins likely contributes to PD pathogenesis. PMID:22388932

Expansion of Protein Farnesyltransferase Specificity Using “Tunable” Active Site Interactions

PubMed Central

Hougland, James L.; Gangopadhyay, Soumyashree A.; Fierke, Carol A.

2012-01-01

Post-translational modifications play essential roles in regulating protein structure and function. Protein farnesyltransferase (FTase) catalyzes the biologically relevant lipidation of up to several hundred cellular proteins. Site-directed mutagenesis of FTase coupled with peptide selectivity measurements demonstrates that molecular recognition is determined by a combination of multiple interactions. Targeted randomization of these interactions yields FTase variants with altered and, in some cases, bio-orthogonal selectivity. We demonstrate that FTase specificity can be “tuned” using a small number of active site contacts that play essential roles in discriminating against non-substrates in the wild-type enzyme. This tunable selectivity extends in vivo, with FTase variants enabling the creation of bioengineered parallel prenylation pathways with altered substrate selectivity within a cell. Engineered FTase variants provide a novel avenue for probing both the selectivity of prenylation pathway enzymes and the effects of prenylation pathway modifications on the cellular function of a protein. PMID:22992747

Synaptic structure and function are altered by the neddylation inhibitor MLN4924.

PubMed

Scudder, Samantha L; Patrick, Gentry N

2015-03-01

The posttranslational modification of proteins by the ubiquitin-like small molecule NEDD8 has previously been shown to be vital in a number of cell signaling pathways. In particular, conjugation of NEDD8 (neddylation) serves to regulate protein ubiquitination through modifications to E3 ubiquitin ligases. Despite the prevalence of NEDD8 in neurons, very little work has been done to characterize the role of this modifier in these cells. Here, we use the recently developed NEDD8 Activating Enzyme (NAE) inhibitor MLN4924 and report evidence of a role for NEDD8 in regulating mammalian excitatory synapses. Application of this drug to dissociated rat hippocampal neurons caused reductions in synaptic strength, surface glutamate receptor levels, dendritic spine width, and spine density, suggesting that neddylation is involved in the maintenance of synapses. Copyright © 2015 Elsevier Inc. All rights reserved.

Application of ion mobility-mass spectrometry to microRNA analysis.

PubMed

Takebayashi, Kosuke; Hirose, Kenji; Izumi, Yoshihiro; Bamba, Takeshi; Fukusaki, Eiichiro

2013-03-01

Liquid chromatography/mass spectrometry is widely used for studying sequence determination and modification analysis of small RNAs. However, the efficiency of liquid chromatography-based separation of intact small RNA species is insufficient, since the physiochemical properties among small RNAs are very similar. In this study, we focused on ion mobility-mass spectrometry (IM-MS), which is a gas-phase separation technique coupled with mass spectrometry; we have evaluated the utility of IM-MS for microRNA (miRNA) analysis. A multiply charged deprotonated ion derived from an 18-24-nt-long miRNA was formed by electrospray ionization, and then the time, called the "drift time", taken by each ion to migrate through a buffer gas was measured. Each multivalent ion was temporally separated on the basis of the charge state and structural formation; 3 types of unique mass-mobility correlation patterns (i.e., chainlike-form, hairpin-form, and dimer-form) were present on the two-dimensional mobility-mass spectrum. Moreover, we found that the ion size (sequence length) and the secondary structures of the small RNAs strongly contributed to the IM-MS-based separation, although solvent conditions such as pH had no effect. Therefore, sequence isomers could also be discerned by the selection of each specific charged ion, i.e., the 6(-) charged ion reflected a majority among chainlike-, hairpin-, and other structures. We concluded that the IM-MS provides additional capability for separation; thus, this analytical method will be a powerful tool for comprehensive small RNA analysis. Copyright © 2012. Published by Elsevier B.V.

Sonic hedgehog multimerization: a self-organizing event driven by post-translational modifications?

PubMed

Koleva, Mirella V; Rothery, Stephen; Spitaler, Martin; Neil, Mark A A; Magee, Anthony I

2015-01-01

Sonic hedgehog (Shh) is a morphogen active during vertebrate development and tissue homeostasis in adulthood. Dysregulation of the Shh signalling pathway is known to incite carcinogenesis. Due to the highly lipophilic nature of this protein imparted by two post-translational modifications, Shh's method of transit through the aqueous extracellular milieu has been a long-standing conundrum, prompting the proposition of numerous hypotheses to explain the manner of its displacement from the surface of the producing cell. Detection of high molecular-weight complexes of Shh in the intercellular environment has indicated that the protein achieves this by accumulating into multimeric structures prior to release from producing cells. The mechanism of assembly of the multimers, however, has hitherto remained mysterious and contentious. Here, with the aid of high-resolution optical imaging and post-translational modification mutants of Shh, we show that the C-terminal cholesterol and the N-terminal palmitate adducts contribute to the assembly of large multimers and regulate their shape. Moreover, we show that small Shh multimers are produced in the absence of any lipid modifications. Based on an assessment of the distribution of various dimensional characteristics of individual Shh clusters, in parallel with deductions about the kinetics of release of the protein from the producing cells, we conclude that multimerization is driven by self-assembly underpinned by the law of mass action. We speculate that the lipid modifications augment the size of the multimolecular complexes through prolonging their association with the exoplasmic membrane.

Targeting RNA in mammalian systems with small molecules.

PubMed

Donlic, Anita; Hargrove, Amanda E

2018-05-03

The recognition of RNA functions beyond canonical protein synthesis has challenged the central dogma of molecular biology. Indeed, RNA is now known to directly regulate many important cellular processes, including transcription, splicing, translation, and epigenetic modifications. The misregulation of these processes in disease has led to an appreciation of RNA as a therapeutic target. This potential was first recognized in bacteria and viruses, but discoveries of new RNA classes following the sequencing of the human genome have invigorated exploration of its disease-related functions in mammals. As stable structure formation is evolving as a hallmark of mammalian RNAs, the prospect of utilizing small molecules to specifically probe the function of RNA structural domains and their interactions is gaining increased recognition. To date, researchers have discovered bioactive small molecules that modulate phenotypes by binding to expanded repeats, microRNAs, G-quadruplex structures, and RNA splice sites in neurological disorders, cancers, and other diseases. The lessons learned from achieving these successes both call for additional studies and encourage exploration of the plethora of mammalian RNAs whose precise mechanisms of action remain to be elucidated. Efforts toward understanding fundamental principles of small molecule-RNA recognition combined with advances in methodology development should pave the way toward targeting emerging RNA classes such as long noncoding RNAs. Together, these endeavors can unlock the full potential of small molecule-based probing of RNA-regulated processes and enable us to discover new biology and underexplored avenues for therapeutic intervention in human disease. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA in Disease and Development > RNA in Disease. © 2018 Wiley Periodicals, Inc.

The effects of particle loading on turbulence structure and modelling

NASA Technical Reports Server (NTRS)

Squires, Kyle D.; Eaton, J. K.

1989-01-01

The objective of the present research was to extend the Direct Numerical Simulation (DNS) approach to particle-laden turbulent flows using a simple model of particle/flow interaction. The program addressed the simplest type of flow, homogeneous, isotropic turbulence, and examined interactions between the particles and gas phase turbulence. The specific range of problems examined include those in which the particle is much smaller than the smallest length scales of the turbulence yet heavy enough to slip relative to the flow. The particle mass loading is large enough to have a significant impact on the turbulence, while the volume loading was small enough such that particle-particle interactions could be neglected. Therefore, these simulations are relevant to practical problems involving small, dense particles conveyed by turbulent gas flows at moderate loadings. A sample of the results illustrating modifications of the particle concentration field caused by the turbulence structure is presented and attenuation of turbulence by the particle cloud is also illustrated.

Structural transitions and multiferroic properties of high Ni-doped BiFeO3

NASA Astrophysics Data System (ADS)

Betancourt-Cantera, L. G.; Bolarín-Miró, A. M.; Cortés-Escobedo, C. A.; Hernández-Cruz, L. E.; Sánchez-De Jesús, F.

2018-06-01

Nickel doped bismuth ferrite powders, BiFe1-x NixO3 (0 ≤ x ≤ 0.5), were synthesized by high-energy ball milling followed by an annealing at 700 °C. A detailed study about the substitution of Fe3+ by Ni2+ on the crystal structure and multiferroic properties is presented. The X-ray diffraction patterns reveal the formation of rhombohedral structure with small amounts of Bi2Fe4O9 as a secondary phase for x < 0.1. Also it is inferred the stabilization of a Bi25FeO40, sillenite phase, as the amount of Ni2+ substitution increases, reaching up 95.23% of sillenite for x = 0.5. The magnetic behavior indicates the frustration of the G-antiferromagnetic order typical of the un-doped BiFeO3, caused by the presence of small amounts of Ni2+ (x < 0.1) on the structure. The DC conductivity exhibited a little increment with increasing Ni content (up to x = 0.1). Although the conductivity increases, for nickel concentrations of 0.2-0.5, the bismuth ferrites doped with nickel retain their property of being an electrical insulating material. Behavior modifications of electrical conductivity, permittivity and dielectric loss versus frequency are related with crystal structure transformations, when nickel concentration is increased.

Low genetic diversity and strong population structure shaped by anthropogenic habitat fragmentation in a critically endangered primate, Trachypithecus leucocephalus.

PubMed

Wang, W; Qiao, Y; Li, S; Pan, W; Yao, M

2017-06-01

Habitat fragmentation may strongly impact population genetic structure and reduce the genetic diversity and viability of small and isolated populations. The white-headed langur (Trachypithecus leucocephalus) is a critically endangered primate species living in a highly fragmented and human-modified habitat in southern China. We examined the population genetic structure and genetic diversity of the species and investigated the environmental and anthropogenic factors that may have shaped its population structure. We used 214 unique multi-locus genotypes from 41 social groups across the main distribution area of T. leucocephalus, and found strong genetic structure and significant genetic differentiation among local populations. Our landscape genetic analyses using a causal modelling framework suggest that a large habitat gap and geographical distance represent the primary landscape elements shaping genetic structure, yet high levels of genetic differentiation also exist between patches separated by a small habitat gap or road. This is the first comprehensive study that has evaluated the population genetic structure and diversity of T. leucocephalus using nuclear markers. Our results indicate strong negative impacts of anthropogenic land modifications and habitat fragmentation on primate genetic connectivity between forest patches. Our analyses suggest that two management units of the species could be defined, and indicate that habitat continuity should be enforced and restored to reduce genetic isolation and enhance population viability.

A series of simple oligomer-like small molecules based on oligothiophenes for solution-processed solar cells with high efficiency.

PubMed

Kan, Bin; Li, Miaomiao; Zhang, Qian; Liu, Feng; Wan, Xiangjian; Wang, Yunchuang; Ni, Wang; Long, Guankui; Yang, Xuan; Feng, Huanran; Zuo, Yi; Zhang, Mingtao; Huang, Fei; Cao, Yong; Russell, Thomas P; Chen, Yongsheng

2015-03-25

A series of acceptor-donor-acceptor simple oligomer-like small molecules based on oligothiophenes, namely, DRCN4T-DRCN9T, were designed and synthesized. Their optical, electrical, and thermal properties and photovoltaic performances were systematically investigated. Except for DRCN4T, excellent performances were obtained for DRCN5T-DRCN9T. The devices based on DRCN5T, DRCN7T, and DRCN9T with axisymmetric chemical structures exhibit much higher short-circuit current densities than those based on DRCN6T and DRCN8T with centrosymmetric chemical structures, which is attributed to their well-developed fibrillar network with a feature size less than 20 nm. The devices based on DRCN5T/PC71BM showed a notable certified power conversion efficiency (PCE) of 10.10% under AM 1.5G irradiation (100 mW cm(-2)) using a simple solution spin-coating fabrication process. This is the highest PCE for single-junction small-molecule-based organic photovoltaics (OPVs) reported to date. DRCN5T is a rather simpler molecule compared with all of the other high-performance molecules in OPVs to date, and this might highlight its advantage in the future possible commercialization of OPVs. These results demonstrate that a fine and balanced modification/design of chemical structure can make significant performance differences and that the performance of solution-processed small-molecule-based solar cells can be comparable to or even surpass that of their polymer counterparts.

Crystal structure of laser-induced subsurface modifications in Si

NASA Astrophysics Data System (ADS)

Verburg, P. C.; Smillie, L. A.; Römer, G. R. B. E.; Haberl, B.; Bradby, J. E.; Williams, J. S.; Huis in't Veld, A. J.

2015-08-01

Laser-induced subsurface modification of dielectric materials is a well-known technology. Applications include the production of optical components and selective etching. In addition to dielectric materials, the subsurface modification technology can be applied to silicon, by employing near to mid-infrared radiation. An application of subsurface modifications in silicon is laser-induced subsurface separation, which is a method to separate wafers into individual dies. Other applications for which proofs of concept exist are the formation of waveguides and resistivity tuning. However, limited knowledge is available about the crystal structure of subsurface modifications in silicon. In this work, we investigate the geometry and crystal structure of laser-induced subsurface modifications in monocrystalline silicon wafers. In addition to the generation of lattice defects, we found that transformations to amorphous silicon and Si -iii/Si -xii occur as a result of the laser irradiation.

Damage severity assessment in wind turbine blade laboratory model through fuzzy finite element model updating

NASA Astrophysics Data System (ADS)

Turnbull, Heather; Omenzetter, Piotr

2017-04-01

The recent shift towards development of clean, sustainable energy sources has provided a new challenge in terms of structural safety and reliability: with aging, manufacturing defects, harsh environmental and operational conditions, and extreme events such as lightning strikes wind turbines can become damaged resulting in production losses and environmental degradation. To monitor the current structural state of the turbine, structural health monitoring (SHM) techniques would be beneficial. Physics based SHM in the form of calibration of a finite element model (FEMs) by inverse techniques is adopted in this research. Fuzzy finite element model updating (FFEMU) techniques for damage severity assessment of a small-scale wind turbine blade are discussed and implemented. The main advantage is the ability of FFEMU to account in a simple way for uncertainty within the problem of model updating. Uncertainty quantification techniques, such as fuzzy sets, enable a convenient mathematical representation of the various uncertainties. Experimental frequencies obtained from modal analysis on a small-scale wind turbine blade were described by fuzzy numbers to model measurement uncertainty. During this investigation, damage severity estimation was investigated through addition of small masses of varying magnitude to the trailing edge of the structure. This structural modification, intended to be in lieu of damage, enabled non-destructive experimental simulation of structural change. A numerical model was constructed with multiple variable additional masses simulated upon the blades trailing edge and used as updating parameters. Objective functions for updating were constructed and minimized using both particle swarm optimization algorithm and firefly algorithm. FFEMU was able to obtain a prediction of baseline material properties of the blade whilst also successfully predicting, with sufficient accuracy, a larger magnitude of structural alteration and its location.

Small-molecule inhibitors of multidrug resistance-associated protein 1 and related processes: A historic approach and recent advances.

PubMed

Stefan, Sven Marcel; Wiese, Michael

2018-05-29

Multidrug resistance-associated protein 1 (MRP1, ABCC1) is an ATP-binding cassette (ABC) transport protein. This efflux pump uses the energy of ATP hydrolysis to export structurally diverse antineoplastic agents in human cancers. The upregulation of MRP1 (either inherent or acquired) is one major reason for the occurrence of the phenomenon called multidrug resistance (MDR). MDR is characterized by a reduced outcome of chemotherapy due to the active intracellular clearance of cytostatic drugs below the necessary effect concentration. Much effort has been made to overcome MDR, which implied high-throughput screenings of already known pharmacological and natural compounds, modification of intrinsic substrates, as well as design and synthesis of new inhibitors. This review is meant not only to summarize the most recent results over the past 10 years, but also to highlight major achievements regarding reversal of MRP1-mediated MDR, from the time of its discovery until today. The focus lies on small-molecule compounds that feature either direct MRP1 inhibition/transport blockage, toxicity against MRP1-overexpressing cells, inhibition/modification of intracellular processes necessary for MRP1 function, or modification of MRP1-related metabolic and genomic mechanisms. Considering all aspects, this review might be useful to (re)consider possible strategies to overcome MRP1-mediated MDR. Furthermore, it may be the basis for developing new, even better, highly potent, less toxic, and selective (as well as broad-spectrum) MRP1 inhibitors that will enter clinical evaluations in different malignancies and finally conduce to overcome MDR in general. © 2018 Wiley Periodicals, Inc.

Modulation of structural, electrical, and magnetic features with dilute Zr substitution in Bi0.8La0.2Fe1-xZrxO3 system

NASA Astrophysics Data System (ADS)

Usama, Hasan M.; Akter, Ayesha; Zubair, M. A.

2017-12-01

A significant structural modification and enhancement of the electrical and magnetic properties with dilute substitution of Zr (≤1 mol. %) in the Bi0.8La0.2Fe1-xZrxO3 system has been reported. A mixture of rhombohedral and orthorhombic phases was detected in these conventionally sintered ceramics. Transition from a leaky state to an insulating state was observed upon Zr substitution. This is the first time that a drop in the electrical conductivity as large as 6 orders of magnitude for doping as small as 0.25 mol. % in bismuth ferrite systems has been reported. An investigation on the nature of this abrupt transition revealed the dominant role of defects. A proper consideration of possible defect reactions taking place during and after sintering satisfactorily accounts for the observed modulation in the electrical properties. Both AC and DC measurements indicate that, before Zr substitution, p-type hopping conduction prevails with an activation energy as low as ˜0.57 eV, whereas the Zr substitution makes oxide ion migration the central mechanism for conduction with the activation energy of ˜0.96-1.08 eV. In contrast to that, the magnetic properties of the compounds experience a more subtle effect; a gradual modification of saturation magnetization and coercivity with Zr substitution is observed. Curve fitting of the magnetic hysteresis loops not only allowed extraction of three separate contributions from the magnetic response but also helped to explain the effects of Zr on the magnetic properties. Modifications of structural characteristics and magnetic anisotropy of the samples are believed to be the primary driving force behind the improvement in the magnetic properties.

Tuning reactivity of diphenylpropynone derivatives with metal-associated amyloid-β species via structural modifications.

PubMed

Liu, Yuzhong; Kochi, Akiko; Pithadia, Amit S; Lee, Sanghyun; Nam, Younwoo; Beck, Michael W; He, Xiaoming; Lee, Dongkuk; Lim, Mi Hee

2013-07-15

A diphenylpropynone derivative, DPP2, has been recently demonstrated to target metal-associated amyloid-β (metal-Aβ) species implicated in Alzheimer's disease (AD). DPP2 was shown to interact with metal-Aβ species and subsequently control Aβ aggregation (reactivity) in vitro; however, its cytotoxicity has limited further biological applications. In order to improve reactivity toward Aβ species and lower cytotoxicity, along with gaining an understanding of a structure-reactivity-cytotoxicity relationship, we designed, prepared, and characterized a series of small molecules (C1/C2, P1/P2, and PA1/PA2) as structurally modified DPP2 analogues. A similar metal binding site to that of DPP2 was contained in these compounds while their structures were varied to afford different interactions and reactivities with metal ions, Aβ species, and metal-Aβ species. Distinct reactivities of our chemical family toward in vitro Aβ aggregation in the absence and presence of metal ions were observed. Among our chemical series, the compound (C2) with a relatively rigid backbone and a dimethylamino group was observed to noticeably regulate both metal-free and metal-mediated Aβ aggregation to different extents. Using our compounds, cell viability was significantly improved, compared to that with DPP2. Lastly, modifications on the DPP framework maintained the structural properties for potential blood-brain barrier (BBB) permeability. Overall, our studies demonstrated that structural variations adjacent to the metal binding site of DPP2 could govern different metal binding properties, interactions with Aβ and metal-Aβ species, reactivity toward metal-free and metal-induced Aβ aggregation, and cytotoxicity of the compounds, establishing a structure-reactivity-cytotoxicity relationship. This information could help gain insight into structural optimization for developing nontoxic chemical reagents toward targeting metal-Aβ species and modulating their reactivity in biological systems.

Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs.

PubMed

Mutisya, Daniel; Hardcastle, Travis; Cheruiyot, Samwel K; Pallan, Pradeep S; Kennedy, Scott D; Egli, Martin; Kelley, Melissa L; Smith, Anja van Brabant; Rozners, Eriks

2017-08-21

While the use of RNA interference (RNAi) in molecular biology and functional genomics is a well-established technology, in vivo applications of synthetic short interfering RNAs (siRNAs) require chemical modifications. We recently found that amides as non-ionic replacements for phosphodiesters may be useful modifications for optimization of siRNAs. Herein, we report a comprehensive study of systematic replacement of a single phosphate with an amide linkage throughout the guide strand of siRNAs. The results show that amides are surprisingly well tolerated in the seed and central regions of the guide strand and increase the silencing activity when placed between nucleosides 10 and 12, at the catalytic site of Argonaute. A potential explanation is provided by the first crystal structure of an amide-modified RNA-DNA with Bacillus halodurans RNase H1. The structure reveals how small changes in both RNA and protein conformation allow the amide to establish hydrogen bonding interactions with the protein. Molecular dynamics simulations suggest that these alternative binding modes may compensate for interactions lost due to the absence of a phosphodiester moiety. Our results suggest that an amide can mimic important hydrogen bonding interactions with proteins required for RNAi activity and may be a promising modification for optimization of biological properties of siRNAs. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Synthetic Modifications In the Frequency Domain for Finite Element Model Update and Damage Detection

DTIC Science & Technology

2017-09-01

Sensitivity-based finite element model updating and structural damage detection has been limited by the number of modes available in a vibration test and...increase the number of modes and corresponding sensitivity data by artificially constraining the structure under test, producing a large number of... structural modifications to the measured data, including both springs-to-ground and mass modifications. This is accomplished with frequency domain

TU-H-CAMPUS-JeP2-05: Can Automatic Delineation of Cardiac Substructures On Noncontrast CT Be Used for Cardiac Toxicity Analysis?

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

Luo, Y; Liao, Z; Jiang, W

Purpose: To evaluate the feasibility of using an automatic segmentation tool to delineate cardiac substructures from computed tomography (CT) images for cardiac toxicity analysis for non-small cell lung cancer (NSCLC) patients after radiotherapy. Methods: A multi-atlas segmentation tool developed in-house was used to delineate eleven cardiac substructures including the whole heart, four heart chambers, and six greater vessels automatically from the averaged 4DCT planning images for 49 NSCLC patients. The automatic segmented contours were edited appropriately by two experienced radiation oncologists. The modified contours were compared with the auto-segmented contours using Dice similarity coefficient (DSC) and mean surface distance (MSD)more » to evaluate how much modification was needed. In addition, the dose volume histogram (DVH) of the modified contours were compared with that of the auto-segmented contours to evaluate the dosimetric difference between modified and auto-segmented contours. Results: Of the eleven structures, the averaged DSC values ranged from 0.73 ± 0.08 to 0.95 ± 0.04 and the averaged MSD values ranged from 1.3 ± 0.6 mm to 2.9 ± 5.1mm for the 49 patients. Overall, the modification is small. The pulmonary vein (PV) and the inferior vena cava required the most modifications. The V30 (volume receiving 30 Gy or above) for the whole heart and the mean dose to the whole heart and four heart chambers did not show statistically significant difference between modified and auto-segmented contours. The maximum dose to the greater vessels did not show statistically significant difference except for the PV. Conclusion: The automatic segmentation of the cardiac substructures did not require substantial modification. The dosimetric evaluation showed no statistically significant difference between auto-segmented and modified contours except for the PV, which suggests that auto-segmented contours for the cardiac dose response study are feasible in the clinical practice with a minor modification to the PV vessel.« less

Crystal structure of laser-induced subsurface modifications in Si

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

Verburg, P. C.; Smillie, L. A.; Römer, G. R. B. E.

2015-06-04

Laser-induced subsurface modification of dielectric materials is a well-known technology. Applications include the production of optical components and selective etching. In addition to dielectric materials, the subsurface modification technology can be applied to silicon, by employing near to mid-infrared radiation. An application of subsurface modifications in silicon is laser-induced subsurface separation, which is a method to separate wafers into individual dies. Other applications for which proofs of concept exist are the formation of waveguides and resistivity tuning. However, limited knowledge is available about the crystal structure of subsurface modifications in silicon. In this paper, we investigate the geometry and crystalmore » structure of laser-induced subsurface modifications in monocrystalline silicon wafers. Finally, in addition to the generation of lattice defects, we found that transformations to amorphous silicon and Si-iii/Si-xii occur as a result of the laser irradiation.« less

General Characteristics of the Changes in the Thermal Stability of Proteins and Enzymes After the Chemical Modification of Their Functional Groups

NASA Astrophysics Data System (ADS)

Kutuzova, G. D.; Ugarova, N. N.; Berezin, Ilya V.

1984-11-01

The principal structural and physicochemical factors determining the stability of protein macromolecules in solution and the characteristics of the structure of the proteins from thermophilic microorganisms are examined. The mechanism of the changes in the thermal stability of proteins and enzymes after the chemical modification of their functional side groups and the experimental data concerning the influence of chemical modification on the thermal stability of proteins are analysed. The dependence of the stabilisation effect and of the changes in the structure of protein macromolecules on the degree of modification and on the nature of the modified groups and the groups introduced into proteins in the course of modification (their charge and hydrophobic properties) is demonstrated. The great practical value of the method of chemical modification for the preparation of stabilised forms of biocatalysts is shown in relation to specific examples. The bibliography includes 178 references.

Advances on Semisynthesis, Total Synthesis, and Structure-Activity Relationships of Honokiol and Magnolol Derivatives.

PubMed

Yang, Chun; Zhi, Xiaoyan; Xu, Hui

2016-01-01

Honokiol and magnolol (an isomer of honokiol) are small-molecule polyphenols isolated from the barks of Magnolia officinalis, which have been widely used in traditional Chinese and Japanese medicines. In the last decade, a variety of biological properties of honokiol and magnolol (e.g., anti-oxidativity, antitumor activity, anti-depressant activity, anti-inflammatory activity, neuroprotective activity, anti-diabetic activity, antiviral activity, and antimicrobial activity) have been reported. Meanwhile, certain mechanisms of action of some biological activities were also investigated. Moreover, many analogs of honokiol and magnolol were prepared by structural modification or total synthesis, and some exhibited very potent pharmacological activities with improved water solubility. Therefore, the present review will provide a systematic coverage on recent developments of honokiol and magnolol derivatives in regard to semisynthesis, total synthesis, and structure-activity relationships from 2000 up to now.

Split of Chiral Degeneracy in Mechanical and Structural Properties of Oligopeptide-Polysaccharide Biomaterials

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

Taraban, Marc B.; Hyland, Laura L.; Yu, Y. Bruce

Enantiomeric biomaterials which are mirror images of each other are characterized by chiral degeneracy—identical structural characteristics and bulk material properties. The addition of another chiral component, d-polysaccharide, has been shown to split such degeneracy and result in two distinct biomaterials. Dynamic oscillatory rheometry and small-angle X-ray scattering demonstrate that the natural biochirality combination of l-peptides and d-polysaccharides assembles faster, has higher elastic moduli (G'), and is structurally more beneficial as opposed to the alternative d-peptide and d-polysaccharide combination. Chemical modifications of the OH-groups in α-d-glucose units in d-polysaccharides weaken such splitting of chiral degeneracy. These findings form a basis tomore » design novel biomaterials and provide additional insight on why proteins and polysaccharides have oppoiste chirality in the biological world.« less

Exploring the wake of a dust particle by a continuously approaching test grain

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

Jung, Hendrik, E-mail: hjung@physik.uni-kiel.de; Greiner, Franko; Asnaz, Oguz Han

2015-05-15

The structure of the ion wake behind a dust particle in the plasma sheath of an rf discharge is studied in a two-particle system. The wake formation leads to attractive forces between the negatively charged dust and can cause a reduction of the charge of a particle. By evaluating the dynamic response of the particle system to small external perturbations, these quantities can be measured. Plasma inherent etching processes are used to achieve a continuous mass loss and hence an increasing levitation height of the lower particle, so that the structure of the wake of the upper particle, which ismore » nearly unaffected by etching, can be probed. The results show a significant modification of the wake structure in the plasma sheath to one long potential tail.« less

Plasma modification of spoof plasmon propagation along metamaterial-air interfaces

NASA Astrophysics Data System (ADS)

Lee, R.; Wang, B.; Cappelli, M. A.

2017-12-01

We report on measurements of the shift in resonance frequency of "spoof" surface plasmon polariton propagation along a 2-D metamaterial slow-wave structure induced by a gaseous plasma near the metamaterial/air interface. A transmission line circuit model for the metamaterial structure interprets the introduction of a plasma as a decrease in unit cell capacitance, causing a shift in the plasmon dispersion to higher frequency. We show through simulations and experiments that the effects of this shift at the resonance frequency and attenuation below and above resonance depend on the plasma density. The shifts recorded experimentally are small owing to the low plasma densities generated near the structure, ˜ 10 11 cm - 3 , but simulations show that a shift of ˜ 3 % of the resonance frequency can be generated at plasma densities of ˜ 10 12 cm - 3 .

Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology

PubMed Central

Galdeano, Carles; Ciulli, Alessio

2017-01-01

Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity. PMID:27193077

Molecular-Scale Features that Govern the Effects of O-Glycosylation on a Carbohydrate-Binding Module

DOE PAGES

Guan, Xiaoyang; Chaffey, Patrick K.; Zeng, Chen; ...

2015-09-21

The protein glycosylation is a ubiquitous post-translational modification in all kingdoms of life. Despite its importance in molecular and cellular biology, the molecular-level ramifications of O-glycosylation on biomolecular structure and function remain elusive. Here, we took a small model glycoprotein and changed the glycan structure and size, amino acid residues near the glycosylation site, and glycosidic linkage while monitoring any corresponding changes to physical stability and cellulose binding affinity. The results of this study reveal the collective importance of all the studied features in controlling the most pronounced effects of O-glycosylation in this system. This study suggests the possibility ofmore » designing proteins with multiple improved properties by simultaneously varying the structures of O-glycans and amino acids local to the glycosylation site.« less

Argonne Physics Division - E-906/SeaQuest

Science.gov Websites

measure the quark and antiquark structure of the nucleon and the modifications to that structure which experiment will also examine the modifications to the antiquark structure of the proton from nuclear binding

The small-x gluon distribution in centrality biased pA and pp collisions

NASA Astrophysics Data System (ADS)

Dumitru, Adrian; Kapilevich, Gary; Skokov, Vladimir

2018-06-01

The nuclear modification factor RpA (pT) provides information on the small-x gluon distribution of a nucleus at hadron colliders. Several experiments have recently measured the nuclear modification factor not only in minimum bias but also for central pA collisions. In this paper we analyze the bias on the configurations of soft gluon fields introduced by a centrality selection via the number of hard particles. Such bias can be viewed as reweighting of configurations of small-x gluons. We find that the biased nuclear modification factor QpA (pT) for central collisions is above RpA (pT) for minimum bias events, and that it may redevelop a "Cronin peak" even at small x. The magnitude of the peak is predicted to increase approximately like 1 /A⊥ ν, ν ∼ 0.6 ± 0.1, if one is able to select more compact configurations of the projectile proton where its gluons occupy a smaller transverse area A⊥. We predict an enhanced Qpp (pT) - 1 ∼ 1 /(pT2) ν and a Cronin peak even for central pp collisions.

A bio-enabled maximally mild layer-by-layer Kapton surface modification approach for the fabrication of all-inkjet-printed flexible electronic devices

PubMed Central

Fang, Yunnan; Hester, Jimmy G. D.; Su, Wenjing; Chow, Justin H.; Sitaraman, Suresh K.; Tentzeris, Manos M.

2016-01-01

A bio-enabled, environmentally-friendly, and maximally mild layer-by-layer approach has been developed to surface modify inherently hydrophobic Kapton HN substrates to allow for great printability of both water- and organic solvent-based inks thus facilitating the full-inkjet-printing of flexible electronic devices. Different from the traditional Kapton surface modification approaches which are structure-compromising and use harsh conditions to target, and oxidize and/or remove part of, the surface polyimide of Kapton, the present Kapton surface modification approach targeted the surface electric charges borne by its additive particles, and was not only the first to utilize environmentally-friendly clinical biomolecules to build up a thin film of protamine-heparin complex on Kapton, but also the first to be conducted under minimally destructive and maximally mild conditions. Besides, for electrically charged ink particles, the present surface modification method can enhance the uniformity of the inkjet-printed films by reducing the “coffee ring effect”. As a proof-of-concept demonstration, reduced graphene oxide-based gas sensors, which were flexible, ultra-lightweight, and miniature-sized, were fully-inkjet-printed on surface modified Kapton HN films and tested for their sensitivity to dimethyl methylphosphonate (a nerve agent simulant). Such fabricated sensors survived a Scotch-tape peel test and were found insensitive to repeated bending to a small 0.5 cm radius. PMID:28008987

A bio-enabled maximally mild layer-by-layer Kapton surface modification approach for the fabrication of all-inkjet-printed flexible electronic devices

NASA Astrophysics Data System (ADS)

Fang, Yunnan; Hester, Jimmy G. D.; Su, Wenjing; Chow, Justin H.; Sitaraman, Suresh K.; Tentzeris, Manos M.

2016-12-01

A bio-enabled, environmentally-friendly, and maximally mild layer-by-layer approach has been developed to surface modify inherently hydrophobic Kapton HN substrates to allow for great printability of both water- and organic solvent-based inks thus facilitating the full-inkjet-printing of flexible electronic devices. Different from the traditional Kapton surface modification approaches which are structure-compromising and use harsh conditions to target, and oxidize and/or remove part of, the surface polyimide of Kapton, the present Kapton surface modification approach targeted the surface electric charges borne by its additive particles, and was not only the first to utilize environmentally-friendly clinical biomolecules to build up a thin film of protamine-heparin complex on Kapton, but also the first to be conducted under minimally destructive and maximally mild conditions. Besides, for electrically charged ink particles, the present surface modification method can enhance the uniformity of the inkjet-printed films by reducing the “coffee ring effect”. As a proof-of-concept demonstration, reduced graphene oxide-based gas sensors, which were flexible, ultra-lightweight, and miniature-sized, were fully-inkjet-printed on surface modified Kapton HN films and tested for their sensitivity to dimethyl methylphosphonate (a nerve agent simulant). Such fabricated sensors survived a Scotch-tape peel test and were found insensitive to repeated bending to a small 0.5 cm radius.

Box C/D sRNA stem ends act as stabilizing anchors for box C/D di-sRNPs.

PubMed

Yip, W S Vincent; Shigematsu, Hideki; Taylor, David W; Baserga, Susan J

2016-10-14

Ribosomal RNA (rRNA) modifications are essential for ribosome function in all cellular organisms. Box C/D small (nucleolar) ribonucleoproteins [s(no)RNPs] catalyze 2'-O-methylation, one rRNA modification type in Eukarya and Archaea. Negatively stained electron microscopy (EM) models of archaeal box C/D sRNPs have demonstrated the dimeric sRNP (di-sRNP) architecture, which has been corroborated by nuclear magnetic resonance (NMR) studies. Due to limitations of the structural techniques, the orientation of the box C/D sRNAs has remained unclear. Here, we have used cryo-EM to elucidate the sRNA orientation in a M. jannaschii box C/D di-sRNP. The cryo-EM reconstruction suggests a parallel orientation of the two sRNAs. Biochemical and structural analyses of sRNPs assembled with mutant sRNAs indicate a potential interaction between the sRNA stem ends. Our results suggest that the parallel arrangement of the sRNAs juxtaposes their stem ends into close proximity to allow for a stabilizing interaction that helps maintain the di-sRNP architecture. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nanoscale measurements of phosphorous-induced lattice expansion in nanosecond laser annealed germanium

NASA Astrophysics Data System (ADS)

Boninelli, S.; Milazzo, R.; Carles, R.; Houdellier, F.; Duffy, R.; Huet, K.; La Magna, A.; Napolitani, E.; Cristiano, F.

2018-05-01

Laser Thermal Annealing (LTA) at various energy densities was used to recrystallize and activate amorphized germanium doped with phosphorous by ion implantation. The structural modifications induced during the recrystallization and the related dopant diffusion were first investigated. After LTA at low energy densities, the P electrical activation was poor while the dopant distribution was mainly localized in the polycrystalline Ge resulting from the anneal. Conversely, full dopant activation (up to 1 × 1020 cm-3) in a perfectly recrystallized material was observed after annealing at higher energy densities. Measurements of lattice parameters performed on the fully activated structures show that P doping results in a lattice expansion, with a perpendicular lattice strain per atom βPs = +0.7 ± 0.1 Å3. This clearly indicates that, despite the small atomic radius of P compared to Ge, the "electronic contribution" to the lattice parameter modification (due to the increased hydrostatic deformation potential in the conduction band of P doped Ge) is larger than the "size mismatch contribution" associated with the atomic radii. Such behavior, predicted by theory, is observed experimentally for the first time, thanks to the high sensitivity of the measurement techniques used in this work.

Influences of surface modification of nano-silica by silane coupling agents on the thermal and frictional properties of cyanate ester resin

NASA Astrophysics Data System (ADS)

Chuang, Wang; Geng-sheng, Jiao; Lei, Peng; Bao-lin, Zhu; Ke-zhi, Li; Jun-long, Wang

2018-06-01

The surface of nano-silicon dioxide (nano-SiO2) particles was modified by small molecular coupling agent KH-560 and macromolecular coupling agent SEA-171, respectively, to change the surface activity and structure. The modified nano-SiO2 was then used for reinforcing cyanate ester resin (CE). Influences of the content of nano-SiO2 and the interfacial structure over the thermal and frictional properties of nano-SiO2/CE composites were investigated. The mechanism of the surface modification of silicon dioxide by KH-560 and SEA-171 was discussed. The experimental results show that the addition of coupling agents increased the interfacial bonding between nano-SiO2 particles and the CE resin so that the heat resistance and friction properties of the composites were improved. After surface treatment of nano-SiO2 by SEA-171, the thermal decomposition temperature of the 3.0 wt% nano-SiO2/CE composites increased nearly by 75 °C and the frictional coefficient was reduced by 25% compared with that of the pure CE, and the wear resistance increased by 77%.

TiO2 induced structural modifications in Cs containing borosilicate glasses: Raman and infrared studies

NASA Astrophysics Data System (ADS)

Pandey, M.; Banerjee, D.; Sudarsan, V.; Kshirsagar, R. J.

2018-04-01

Effect of TiO2 addition in Cs containing Sodium-borosilicate glasses is studied using Raman and infrared spectroscopic techniques. As revealed from infrared and Raman studies, TiO2 does not form segregated phase, but instead enters into the borosilicate network. It is further observed that TiO2 addition results in modifications of the borate and silicate structural units by transforming into tetraborates and metasilicate structural units. These structural modifications are responsible for Cs immobilization, leach rate and chemical durability of these glasses.

Functional group and stereochemical requirements for substrate binding by ghrelin O-acyltransferase revealed by unnatural amino acid incorporation.

PubMed

Cleverdon, Elizabeth R; Davis, Tasha R; Hougland, James L

2018-04-21

Ghrelin is a small peptide hormone that undergoes a unique posttranslational modification, serine octanoylation, to play its physiological roles in processes including hunger signaling and glucose metabolism. Ghrelin O-acyltransferase (GOAT) catalyzes this posttranslational modification, which is essential for ghrelin to bind and activate its cognate GHS-R1a receptor. Inhibition of GOAT offers a potential avenue for modulating ghrelin signaling for therapeutic effect. Defining the molecular characteristics of ghrelin that lead to binding and recognition by GOAT will facilitate the development and optimization of GOAT inhibitors. We show that small peptide mimics of ghrelin substituted with 2,3-diaminopropanoic acid in place of the serine at the site of octanoylation act as submicromolar inhibitors of GOAT. Using these chemically modified analogs of desacyl ghrelin, we define key functional groups within the N-terminal sequence of ghrelin essential for binding to GOAT and determine GOAT's tolerance to backbone methylations and altered amino acid stereochemistry within ghrelin. Our study provides a structure-activity analysis of ghrelin binding to GOAT that expands upon activity-based investigations of ghrelin recognition and establishes a new class of potent substrate-mimetic GOAT inhibitors for further investigation and therapeutic interventions targeting ghrelin signaling. Copyright © 2018 Elsevier Inc. All rights reserved.

Structural Analysis of PTM Hotspots (SAPH-ire) – A Quantitative Informatics Method Enabling the Discovery of Novel Regulatory Elements in Protein Families*

PubMed Central

Dewhurst, Henry M.; Choudhury, Shilpa; Torres, Matthew P.

2015-01-01

Predicting the biological function potential of post-translational modifications (PTMs) is becoming increasingly important in light of the exponential increase in available PTM data from high-throughput proteomics. We developed structural analysis of PTM hotspots (SAPH-ire)—a quantitative PTM ranking method that integrates experimental PTM observations, sequence conservation, protein structure, and interaction data to allow rank order comparisons within or between protein families. Here, we applied SAPH-ire to the study of PTMs in diverse G protein families, a conserved and ubiquitous class of proteins essential for maintenance of intracellular structure (tubulins) and signal transduction (large and small Ras-like G proteins). A total of 1728 experimentally verified PTMs from eight unique G protein families were clustered into 451 unique hotspots, 51 of which have a known and cited biological function or response. Using customized software, the hotspots were analyzed in the context of 598 unique protein structures. By comparing distributions of hotspots with known versus unknown function, we show that SAPH-ire analysis is predictive for PTM biological function. Notably, SAPH-ire revealed high-ranking hotspots for which a functional impact has not yet been determined, including phosphorylation hotspots in the N-terminal tails of G protein gamma subunits—conserved protein structures never before reported as regulators of G protein coupled receptor signaling. To validate this prediction we used the yeast model system for G protein coupled receptor signaling, revealing that gamma subunit–N-terminal tail phosphorylation is activated in response to G protein coupled receptor stimulation and regulates protein stability in vivo. These results demonstrate the utility of integrating protein structural and sequence features into PTM prioritization schemes that can improve the analysis and functional power of modification-specific proteomics data. PMID:26070665

Surface charge dependent separation of modified and hybrid ferritin in native PAGE: Impact of lysine 104.

PubMed

Subhadarshanee, Biswamaitree; Mohanty, Abhinav; Jagdev, Manas Kumar; Vasudevan, Dileep; Behera, Rabindra K

2017-10-01

Preparation of modified and hybrid ferritin provides a great opportunity to understand the mechanisms of iron loading/unloading, protein self-assembly, size constrained nanomaterial synthesis and targeted drug delivery. However, the large size (M.W.=490kDa) has been limiting the separation of different modified and/or hybrid ferritin nanocages from each other in their intact assembled form and further characterization. Native polyacrylamide gel electrophoresis (PAGE) separates proteins on the basis of both charge and mass, while maintaining their overall native structure and activity. Altering surface charge distribution by substitution of amino acid residues located at the external surface of ferritin (K104E & D40A) affected the migration rate in native PAGE while internal modification had little effect. Crystal structures confirmed that ferritin nanocages made up of subunits with single amino acid substitutions retain the overall structure of ferritin nanocage. Taking advantage of K104E migration behavior, formation of hybrid ferritins with subunits of wild type (WT) and K104E were confirmed and separated in native PAGE. Cage integrity and iron loading ability (ferritin activity) were also tested. The migration pattern of hybrid ferritins in native PAGE depends on the subunit ratio (WT: K104E) in the ferritin cage. Our work shows that native PAGE can be exploited in nanobiotechnology, by analyzing modifications of large proteins like ferritin. Native PAGE, a simple, straight-forward technique, can be used to analyze small modification (by altering external surface charge) in large proteins like ferritin, without disintegrating its self-assembled nanocage structure. In doing so, native PAGE can complement the information obtained from mass spectrometry. The confirmation and separation of modified and hybrid ferritin protein nanocages in native PAGE, opens up various prospects of bio-conjugation, which can be useful in targeted drug delivery, nanobiotechnology and in understanding nature's idea of synthesizing hybrid ferritins in different human tissues. Copyright © 2017 Elsevier B.V. All rights reserved.

Optimal charges in lead progression: a structure-based neuraminidase case study.

PubMed

Armstrong, Kathryn A; Tidor, Bruce; Cheng, Alan C

2006-04-20

Collective experience in structure-based lead progression has found electrostatic interactions to be more difficult to optimize than shape-based ones. A major reason for this is that the net electrostatic contribution observed includes a significant nonintuitive desolvation component in addition to the more intuitive intermolecular interaction component. To investigate whether knowledge of the ligand optimal charge distribution can facilitate more intuitive design of electrostatic interactions, we took a series of small-molecule influenza neuraminidase inhibitors with known protein cocrystal structures and calculated the difference between the optimal and actual charge distributions. This difference from the electrostatic optimum correlates with the calculated electrostatic contribution to binding (r(2) = 0.94) despite small changes in binding modes caused by chemical substitutions, suggesting that the optimal charge distribution is a useful design goal. Furthermore, detailed suggestions for chemical modification generated by this approach are in many cases consistent with observed improvements in binding affinity, and the method appears to be useful despite discrete chemical constraints. Taken together, these results suggest that charge optimization is useful in facilitating generation of compound ideas in lead optimization. Our results also provide insight into design of neuraminidase inhibitors.

Small Molecule Anticonvulsant Agents with Potent In Vitro Neuroprotection

PubMed Central

Smith, Garry R.; Zhang, Yan; Du, Yanming; Kondaveeti, Sandeep K.; Zdilla, Michael J.; Reitz, Allen B.

2012-01-01

Severe seizure activity is associated with recurring cycles of excitotoxicity and oxidative stress that result in progressive neuronal damage and death. Intervention to halt these pathological processes is a compelling disease-modifying strategy for the treatment of seizure disorders. In the present study, a core small molecule with anticonvulsant activity has been structurally optimized for neuroprotection. Phenotypic screening of rat hippocampal cultures with nutrient medium depleted of antioxidants was utilized as a disease model. Increased cell death and decreased neuronal viability produced by acute treatment with glutamate or hydrogen peroxide were prevented by our novel molecules. The neuroprotection associated with this chemical series has marked structure activity relationships that focus on modification of the benzylic position of a 2-phenyl-2-hydroxyethyl sulfamide core structure. Complete separation between anticonvulsant activity and neuroprotective action was dependent on substitution at the benzylic carbon. Chiral selectivity was evident in that the S-enantiomer of the benzylic hydroxy group had neither neuroprotective nor anticonvulsant activity, while the R-enantiomer of the lead compound had full neuroprotective action at ≤40 nM and antiseizure activity in three animal models. These studies indicate that potent, multifunctional neuroprotective anticonvulsants are feasible within a single molecular entity. PMID:22535312

Mechanisms and chemistry of dye adsorption on manganese oxides-modified diatomite.

PubMed

Al-Ghouti, Mohammad A; Al-Degs, Yehya S; Khraisheh, Majeda A M; Ahmad, Mohammad N; Allen, Stephen J

2009-08-01

The investigations into structural changes which occur during adsorbent modification and the adsorption mechanisms are essential for an effective design of adsorption systems. Manganese oxides were impregnated onto diatomite to form the type known as delta-birnessite. Initial investigations established the effectiveness of manganese oxides-modified diatomite (MOMD) to remove basic and reactive dyes from aqueous solution. The adsorption capacity of MOMD for methylene blue (MB), hydrolysed reactive black (RB) and hydrolysed reactive yellow (RY) was 320, 419, and 204mg/g, respectively. Various analytical techniques were used to characterise the structure and the mechanisms of the dye adsorption process onto MOMD such as Fourier transform infrared (FTIR), X-ray diffraction (XRD) and atomic absorption spectrometry (A.A.). A small shift to higher values of the d-spacing of dye/MOMD was observed indicating that a small amount of the dye molecules were intercalated in the MOMD structure and other molecules were adsorbed on the external surface of MOMD. Two mechanisms of dye adsorption onto MOMD were proposed; intercalation of the dye in the octahedral layers and adsorption of the dye on the MOMD external surface. Moreover, the results demonstrated that the MOMD structure was changed upon insertion of MB and RY with an obvious decrease in the intensity of the second main peak of the MOMD X-ray pattern.

Sterile neutrinos with secret interactions—lasting friendship with cosmology

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

Chu, Xiaoyong; Dasgupta, Basudeb; Kopp, Joachim, E-mail: xchu@ictp.it, E-mail: bdasgupta@theory.tifr.res.in, E-mail: jkopp@uni-mainz.de

Sterile neutrinos with mass ≅ 1 eV and order 10% mixing with active neutrinos have been proposed as a solution to anomalies in neutrino oscillation data, but are tightly constrained by cosmological limits. It was recently shown that these constraints are avoided if sterile neutrinos couple to a new MeV-scale gauge boson A'. However, even this scenario is restricted by structure formation constraints when A'-mediated collisional processes lead to efficient active-to-sterile neutrino conversion after neutrinos have decoupled. In view of this, we reevaluate in this paper the viability of sterile neutrinos with such ''secret'' interactions. We carefully dissect their evolution inmore » the early Universe, including the various production channels and the expected modifications to large scale structure formation. We argue that there are two regions in parameter space—one at very small A' coupling, one at relatively large A' coupling—where all constraints from big bang nucleosynthesis (BBN), cosmic microwave background (CMB), and large scale structure (LSS) data are satisfied. Interestingly, the large A' coupling region is precisely the region that was previously shown to have potentially important consequences for the small scale structure of dark matter halos if the A' boson couples also to the dark matter in the Universe.« less

14 CFR 121.1109 - Supplemental inspections.

Code of Federal Regulations, 2010 CFR

2010-01-01

... damage-tolerance-based inspections and procedures for airplane structure susceptible to fatigue cracking... termed “fatigue critical structure.” (2) Adverse effects of repairs, alterations, and modifications. The..., and modifications may have on fatigue critical structure and on inspections required by paragraph (c...

Chronic uremia induces permeability changes, increased nitric oxide synthase expression, and structural modifications in the peritoneum.

PubMed

Combet, S; Ferrier, M L; Van Landschoot, M; Stoenoiu, M; Moulin, P; Miyata, T; Lameire, N; Devuyst, O

2001-10-01

Advanced glycation end products (AGE), growth factors, and nitric oxide contribute to alterations of the peritoneum during peritoneal dialysis (PD). These mediators are also involved in chronic uremia, a condition associated with increased permeability of serosal membranes. It is unknown whether chronic uremia per se modifies the peritoneum before PD initiation. A rat model of subtotal nephrectomy was used to measure peritoneal permeability after 3, 6, and 9 wk, in parallel with peritoneal nitric oxide synthase (NOS) isoform expression and activity and structural changes. Uremic rats were characterized by a higher peritoneal permeability for small solutes and an increased NOS activity due to the up-regulation of endothelial and neuronal NOS. The permeability changes and increased NOS activities correlated with the degree of renal failure. Focal areas of vascular proliferation and fibrosis were detected in uremic rats, in relation with a transient up-regulation of vascular endothelial growth factor and basic fibroblast growth factor, as well as vascular deposits of the AGE carboxymethyllysine and pentosidine. Correction of anemia with erythropoietin did not prevent the permeability or structural changes in uremic rats. Thus, in this rat model, uremia induces permeability and structural changes in the peritoneum, in parallel with AGE deposits and up-regulation of specific NOS isoforms and growth factors. These data suggest an independent contribution of uremia in the peritoneal changes during PD and offer a paradigm to better understand the modifications of serosal membranes in uremia.

Heparin sodium compliance to the new proposed USP monograph: elucidation of a minor structural modification responsible for a process dependent 2.10 ppm NMR signal.

PubMed

Mourier, Pierre A J; Guichard, Olivier Y; Herman, Fréderic; Viskov, Christian

2011-01-25

Heparin is a highly sulfated hetero polysaccharide mixture found and extracted from mammalian tissues. It has been widely used as an anticoagulant drug during the past decades. In the new proposed USP heparin monograph, the ¹H NMR acceptance criteria to prevent contamination by over sulfated chondroitin sulfate (OSCS), or other persulfated glycosaminoglycans, specifies that no unidentified signals greater than 4% of the mean of signal height of 1 and 2 should be present in the following ranges: 0.10-2.00, 2.10-3.20, and 5.70-8.00 ppm. However, those criteria do not take into account the impact of potential structural modifications generated by the heparin manufacturing processes. In fact, starting from pig mucosa, heparin purification involves oxidizing reagents such as sodium peroxide, potassium permanganate and peracetic acid. In the present work, we demonstrate that potassium permanganate treated heparins show a small but characteristic extra signal at 2.10 ppm. Controlled heparinase I depolymerisation is used to target and excise the oligosaccharide responsible for this extra signal from the polysaccharide backbone. By using orthogonal chromatographic techniques, the fingerprint oligosaccharide was isolated and its structure elucidated. Without the identification of this structural moiety, such purified heparins may have been considered as non-compliant drug substance and not suitable for pharmaceutical use. Copyright © 2010 Elsevier B.V. All rights reserved.

Quantitative comparison of structure and dynamics of elastin following three isolation schemes by 13C solid state NMR and MALDI mass spectrometry.

PubMed

Papaioannou, A; Louis, M; Dhital, B; Ho, H P; Chang, E J; Boutis, G S

2015-05-01

Methods for isolating elastin from fat, collagen, and muscle, commonly used in the design of artificial elastin based biomaterials, rely on exposing tissue to harsh pH levels and temperatures that usually denature many proteins. At present, a quantitative measurement of the modifications to elastin following isolation from other extracellular matrix constituents has not been reported. Using magic angle spinning (13)C NMR spectroscopy and relaxation methodologies, we have measured the modification in structure and dynamics following three known purification protocols. Our experimental data reveal that the (13)C spectra of the hydrated samples appear remarkably similar across the various purification methods. Subtle differences in the half maximum widths were observed in the backbone carbonyl suggesting possible structural heterogeneity across the different methods of purification. Additionally, small differences in the relative signal intensities were observed between purified samples. Lyophilizing the samples results in a reduction of backbone motion and reveals additional differences across the purification methods studied. These differences were most notable in the alanine motifs indicating possible changes in cross-linking or structural rigidity. The measured correlation times of glycine and proline moieties are observed to also vary considerably across the different purification methods, which may be related to peptide bond cleavage. Lastly, the relative concentration of desmosine cross-links in the samples quantified by MALDI mass spectrometry is reported. Copyright © 2015 Elsevier B.V. All rights reserved.

Dynamic protein interaction networks and new structural paradigms in signaling

PubMed Central

Csizmok, Veronika; Follis, Ariele Viacava; Kriwacki, Richard W.; Forman-Kay, Julie D.

2017-01-01

Understanding signaling and other complex biological processes requires elucidating the critical roles of intrinsically disordered proteins and regions (IDPs/IDRs), which represent ~30% of the proteome and enable unique regulatory mechanisms. In this review we describe the structural heterogeneity of disordered proteins that underpins these mechanisms and the latest progress in obtaining structural descriptions of ensembles of disordered proteins that are needed for linking structure and dynamics to function. We describe the diverse interactions of IDPs that can have unusual characteristics such as “ultrasensitivity” and “regulated folding and unfolding”. We also summarize the mounting data showing that large-scale assembly and protein phase separation occurs within a variety of signaling complexes and cellular structures. In addition, we discuss efforts to therapeutically target disordered proteins with small molecules. Overall, we interpret the remodeling of disordered state ensembles due to binding and post-translational modifications within an expanded framework for allostery that provides significant insights into how disordered proteins transmit biological information. PMID:26922996

MET-2-Dependent H3K9 Methylation Suppresses Transgenerational Small RNA Inheritance.

PubMed

Lev, Itamar; Seroussi, Uri; Gingold, Hila; Bril, Roberta; Anava, Sarit; Rechavi, Oded

2017-04-24

In C. elegans, alterations to chromatin produce transgenerational effects, such as inherited increase in lifespan and gradual loss of fertility. Inheritance of histone modifications can be induced by double-stranded RNA-derived heritable small RNAs. Here, we show that the mortal germline phenotype, which is typical of met-2 mutants, defective in H3K9 methylation, depends on HRDE-1, an argonaute that carries small RNAs across generations, and is accompanied by accumulated transgenerational misexpression of heritable small RNAs. We discovered that MET-2 inhibits small RNA inheritance, and, as a consequence, induction of RNAi in met-2 mutants leads to permanent RNAi responses that do not terminate even after more than 30 generations. We found that potentiation of heritable RNAi in met-2 animals results from global hyperactivation of the small RNA inheritance machinery. Thus, changes in histone modifications can give rise to drastic transgenerational epigenetic effects, by controlling the overall potency of small RNA inheritance. Copyright © 2017 Elsevier Ltd. All rights reserved.

Modification in structure, phase transition, and magnetic property of metallic gallium driven by atom-molecule interactions.

PubMed

Song, Le Xin; Chen, Jie; Zhu, Lin Hong; Xia, Juan; Yang, Jun

2011-09-05

The present work supports a novel paradigm in which the surface structure and stacking behavior of metallic gallium (Ga) were significantly influenced by the preparation process in the presence of organic small molecules (ethanol, acetone, dichloromethane, and diethyl ether). The extent of the effect strongly depends on the polarity of the molecules. Especially, a series of new atom-molecule aggregates consisting of metallic Ga and macrocyclic hosts (cyclodextrins, CDs) were prepared and characterized by various techniques. A comprehensive comparative analysis between free metallic Ga and the Ga samples obtained provides important and at present rare information on the modification in structure, phase transition, and magnetic property of Ga driven by atom-molecule interactions. First, there is a notable difference in microstructure and electronic structure between the different types of Ga samples. Second, differential scanning calorimetry analysis gives us a complete picture (such as the occurrence of a series of metastable phases of Ga in the presence of CDs) that has allowed us to consider that Ga atoms were protected by the shielding effect provided by the cavities of CDs. Third, the metallic Ga distributed in the aggregates exhibits very interesting magnetic property compared to free metallic Ga, such as the uniform zero-field-cooled and field-cooled magnetization processes, the enhanced responses in magnetization to temperature and applied field, and the fundamental change in shape of magnetic hysteresis loops. These significant changes in structural transformation and physical property of Ga provide a novel insight into the understanding of atom-molecule interactions between metallic atoms and organic molecules.

The effect of ultrasonic nanocrystalline surface modification on the high-frequency fretting wear behavior of AISI304 steel.

PubMed

Cho, In-Shik; Lee, Chang-Soon; Amanov, Auezhan; Pyoun, Young-Shik; Park, In-Gyu

2011-01-01

The fact that one of fundamental characteristics of fretting is the very small sliding amplitude dictates the unique feature of wear mechanism. Ultrasonic Nanocrystalline Surface Modification (UNSM) technology was applied in order to investigate its effect on the high-frequency fretting wear behavior of AISI304 steel. Its influence on the fretting wear is also reported in this paper with these treated and untreated samples. UNSM delivers force onto the workpiece surface 20,000 times per second with 1,000 to 4,000 contact counts per square millimeter. UNSM creates homogenous nanocrystalline structures as well on the surface. UNSM process is expected to eliminate or significantly retard the formation of fretting wear. Nanocrystalline structure generation after UNSM has been reported to produce its unique structure and to offer a variety of beneficial properties compared to conventionally treated materials. A deformed layer of 220 microm exhibits high dislocation density, where top layer transformed to a nanostructure of the grain size in 23 nm and mechanical twins were observed. Deformation-induced martensite was observed to form at the intersections of mechanical twins, whose volume fraction has increased up to 38.4% and wear loss rate at 800,000 cycles has decreased by 40%. In this paper, experimental results are discussed to elucidate potential mechanism of high-frequency fretting wear.

Modern chromatographic and mass spectrometric techniques for protein biopharmaceutical characterization.

PubMed

Sandra, Koen; Vandenheede, Isabel; Sandra, Pat

2014-03-28

Protein biopharmaceuticals such as monoclonal antibodies and therapeutic proteins are currently in widespread use for the treatment of various life-threatening diseases including cancer, autoimmune disorders, diabetes and anemia. The complexity of protein therapeutics is far exceeding that of small molecule drugs; hence, unraveling this complexity represents an analytical challenge. The current review provides the reader with state-of-the-art chromatographic and mass spectrometric tools available to dissect primary and higher order structures, post-translational modifications, purity and impurity profiles and pharmacokinetic properties of protein therapeutics. Copyright © 2013 Elsevier B.V. All rights reserved.

Covalent modification of soy protein isolate by (-)-epigallocatechin-3-gallate: effects on structural and emulsifying properties.

PubMed

Tao, Fei; Jiang, He; Chen, Wenwei; Zhang, Yongyong; Pan, Jiarong; Jiang, Jiaxin; Jia, Zhenbao

2018-05-07

Soy protein isolate (SPI) has promising applications in various food products because of its excellent functional properties and nutritional quality. The structural and emulsifying properties of covalently modified SPI by (-)-epigallocatechin-3-gallate (EGCG) were investigated. SPI was covalently modified by EGCG under alkaline conditions. SDS-PAGE analysis revealed that EGCG modification caused cross-linking of SPI proteins. Circular dichroism spectra demonstrated that the secondary structure of SPI proteins was changed by EGCG modification. In addition, the modifications resulted in the perturbation of the tertiary structure of SPI as evidenced by intrinsic fluorescence spectra and surface hydrophobicity measurements. Oil-in-water emulsions of modified SPI had smaller droplet sizes and better creaming stability compared to those from unmodified SPI. The covalent modification by EGCG improved the emulsifying property of SPI. This study provided an innovative approach for improving the emulsifying properties of proteins. This article is protected by copyright. All rights reserved.

Warm dark matter

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

Horiuchi, Shunsaku, E-mail: horiuchi@vt.edu

2016-06-21

The cold dark matter paradigm has been extremely successful in explaining the large-scale structure of the Universe. However, it continues to face issues when confronted by observations on sub-Galactic scales. A major caveat, now being addressed, has been the incomplete treatment of baryon physics. We first summarize the small-scale issues surrounding cold dark matter and discuss the solutions explored by modern state-of-the-art numerical simulations including treatment of baryonic physics. We identify the too big to fail in field galaxies as among the best targets to study modifications to dark matter, and discuss the particular connection with sterile neutrino warm darkmore » matter. We also discuss how the recently detected anomalous 3.55 keV X-ray lines, when interpreted as sterile neutrino dark matter decay, provide a very good description of small-scale observations of the Local Group.« less

Construction of nanostructures for selective lithium ion conduction using self-assembled molecular arrays in supramolecular solids

NASA Astrophysics Data System (ADS)

Moriya, Makoto

2017-12-01

In the development of innovative molecule-based materials, the identification of the structural features in supramolecular solids and the understanding of the correlation between structure and function are important factors. The author investigated the development of supramolecular solid electrolytes by constructing ion conduction paths using a supramolecular hierarchical structure in molecular crystals because the ion conduction path is an attractive key structure due to its ability to generate solid-state ion diffusivity. The obtained molecular crystals exhibited selective lithium ion diffusion via conduction paths consisting of lithium bis(trifluoromethanesulfonyl)amide (LiTFSA) and small molecules such as ether or amine compounds. In the present review, the correlation between the crystal structure and ion conductivity of the obtained molecular crystals is addressed based on the systematic structural control of the ionic conduction paths through the modification of the component molecules. The relationship between the crystal structure and ion conductivity of the molecular crystals provides a guideline for the development of solid electrolytes based on supramolecular solids exhibiting rapid and selective lithium ion conduction.

Chemical biology on the genome.

PubMed

Balasubramanian, Shankar

2014-08-15

In this article I discuss studies towards understanding the structure and function of DNA in the context of genomes from the perspective of a chemist. The first area I describe concerns the studies that led to the invention and subsequent development of a method for sequencing DNA on a genome scale at high speed and low cost, now known as Solexa/Illumina sequencing. The second theme will feature the four-stranded DNA structure known as a G-quadruplex with a focus on its fundamental properties, its presence in cellular genomic DNA and the prospects for targeting such a structure in cels with small molecules. The final topic for discussion is naturally occurring chemically modified DNA bases with an emphasis on chemistry for decoding (or sequencing) such modifications in genomic DNA. The genome is a fruitful topic to be further elucidated by the creation and application of chemical approaches. Copyright © 2014 Elsevier Ltd. All rights reserved.

Recrystallization inhibition in ice due to ice binding protein activity detected by nuclear magnetic resonance.

PubMed

Brown, Jennifer R; Seymour, Joseph D; Brox, Timothy I; Skidmore, Mark L; Wang, Chen; Christner, Brent C; Luo, Bing-Hao; Codd, Sarah L

2014-09-01

Liquid water present in polycrystalline ice at the interstices between ice crystals results in a network of liquid-filled veins and nodes within a solid ice matrix, making ice a low porosity porous media. Here we used nuclear magnetic resonance (NMR) relaxation and time dependent self-diffusion measurements developed for porous media applications to monitor three dimensional changes to the vein network in ices with and without a bacterial ice binding protein (IBP). Shorter effective diffusion distances were detected as a function of increased irreversible ice binding activity, indicating inhibition of ice recrystallization and persistent small crystal structure. The modification of ice structure by the IBP demonstrates a potential mechanism for the microorganism to enhance survivability in ice. These results highlight the potential of NMR techniques in evaluation of the impact of IBPs on vein network structure and recrystallization processes; information useful for continued development of ice-interacting proteins for biotechnology applications.

Structural Determinants of the Closed KCa3.1 Channel Pore in Relation to Channel Gating: Results from a Substituted Cysteine Accessibility Analysis

PubMed Central

Klein, Hélène; Garneau, Line; Banderali, Umberto; Simoes, Manuel; Parent, Lucie; Sauvé, Rémy

2007-01-01

In this work we address the question of the KCa3.1 channel pore structure in the closed configuration in relation to the contribution of the C-terminal end of the S6 segments to the Ca2+-dependent gating process. Our results based on SCAM (substituted cysteine accessibility method) experiments first demonstrate that the S6 transmembrane segment of the open KCa3.1 channel contains two distinct functional domains delimited by V282 with MTSEA and MTSET binding leading to a total channel inhibition at positions V275, T278, and V282 and to a steep channel activation at positions A283 and A286. The rates of modification by MTSEA (diameter 4.6 Å) of the 275C (central cavity) and 286C residues (S6 C-terminal end) for the closed channel configuration were found to differ by less than sevenfold, whereas experiments performed with the larger MTSET reagent (diameter 5.8 Å) resulted in modification rates 103–104 faster for cysteines at 286 compared with 275. Consistent with these results, the modification rates of the cavity lining 275C residue by MTSEA, Et-Hg+, and Ag+ appeared poorly state dependent, whereas modification rates by MTSET were 103 faster for the open than the closed configuration. A SCAM analysis of the channel inner vestibule in the closed state revealed in addition that cysteine residues at 286 were accessible to MTS reagents as large as MTS-PtrEA, a result supported by the observation that binding of MTSET to cysteines at positions 283 or 286 could neither sterically nor electrostatically block the access of MTSEA to the closed channel cavity (275C). It follows that the closed KCa3.1 structure can hardly be accountable by an inverted teepee-like structure as described for KcsA, but is better represented by a narrow passage centered at V282 (equivalent to V474 in Shaker) connecting the channel central cavity to the cytosolic medium. This passage would not be however restrictive to the diffusion of small reagents such as MTSEA, Et-Hg+, and Ag+, arguing against the C-terminal end of S6 forming an obstructive barrier to the diffusion of K+ ions for the closed channel configuration. PMID:17353352

The small-x gluon distribution in centrality biased pA and pp collisions

DOE PAGES

Dumitru, Adrian; Kapilevich, Gary; Skokov, Vladimir

2018-04-04

Here, the nuclear modification factor R pA(p T) provides information on the small- x gluon distribution of a nucleus at hadron colliders. Several experiments have recently measured the nuclear modification factor not only in minimum bias but also for central pA collisions. In this paper we analyze the bias on the configurations of soft gluon fields introduced by a centrality selection via the number of hard particles. Such bias can be viewed as reweighting of configurations of small- x gluons. We find that the biased nuclear modification factor Q pA(p T) for central collisions is above R pA(p T) formore » minimum bias events, and that it may redevelop a “Cronin peak” even at small x . The magnitude of the peak is predicted to increase approximately like 1/A ⊥ ν, ν~0.6±0.1 , if one is able to select more compact configurations of the projectile proton where its gluons occupy a smaller transverse area A ⊥. We predict an enhanced Q pp(p T)–1~1/(p T 2) ν and a Cronin peak even for central pp collisions.« less

The small-x gluon distribution in centrality biased pA and pp collisions

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

Dumitru, Adrian; Kapilevich, Gary; Skokov, Vladimir

Here, the nuclear modification factor R pA(p T) provides information on the small- x gluon distribution of a nucleus at hadron colliders. Several experiments have recently measured the nuclear modification factor not only in minimum bias but also for central pA collisions. In this paper we analyze the bias on the configurations of soft gluon fields introduced by a centrality selection via the number of hard particles. Such bias can be viewed as reweighting of configurations of small- x gluons. We find that the biased nuclear modification factor Q pA(p T) for central collisions is above R pA(p T) formore » minimum bias events, and that it may redevelop a “Cronin peak” even at small x . The magnitude of the peak is predicted to increase approximately like 1/A ⊥ ν, ν~0.6±0.1 , if one is able to select more compact configurations of the projectile proton where its gluons occupy a smaller transverse area A ⊥. We predict an enhanced Q pp(p T)–1~1/(p T 2) ν and a Cronin peak even for central pp collisions.« less

Modulation of Epigenetic Targets for Anticancer Therapy: Clinicopathological Relevance, Structural Data and Drug Discovery Perspectives

PubMed Central

Andreol, Federico; Barbosa, Arménio Jorge Moura; Daniele Parenti, Marco; Rio, Alberto Del

2013-01-01

Research on cancer epigenetics has flourished in the last decade. Nevertheless growing evidence point on the importance to understand the mechanisms by which epigenetic changes regulate the genesis and progression of cancer growth. Several epigenetic targets have been discovered and are currently under validation for new anticancer therapies. Drug discovery approaches aiming to target these epigenetic enzymes with small-molecules inhibitors have produced the first pre-clinical and clinical outcomes and many other compounds are now entering the pipeline as new candidate epidrugs. The most studied targets can be ascribed to histone deacetylases and DNA methyltransferases, although several other classes of enzymes are able to operate post-translational modifications to histone tails are also likely to represent new frontiers for therapeutic interventions. By acknowledging that the field of cancer epigenetics is evolving with an impressive rate of new findings, with this review we aim to provide a current overview of pre-clinical applications of small-molecules for cancer pathologies, combining them with the current knowledge of epigenetic targets in terms of available structural data and drug design perspectives. PMID:23016851

Combined aerodynamic and structural dynamic problem emulating routines (CASPER): Theory and implementation

NASA Technical Reports Server (NTRS)

Jones, William H.

1985-01-01

The Combined Aerodynamic and Structural Dynamic Problem Emulating Routines (CASPER) is a collection of data-base modification computer routines that can be used to simulate Navier-Stokes flow through realistic, time-varying internal flow fields. The Navier-Stokes equation used involves calculations in all three dimensions and retains all viscous terms. The only term neglected in the current implementation is gravitation. The solution approach is of an interative, time-marching nature. Calculations are based on Lagrangian aerodynamic elements (aeroelements). It is assumed that the relationships between a particular aeroelement and its five nearest neighbor aeroelements are sufficient to make a valid simulation of Navier-Stokes flow on a small scale and that the collection of all small-scale simulations makes a valid simulation of a large-scale flow. In keeping with these assumptions, it must be noted that CASPER produces an imitation or simulation of Navier-Stokes flow rather than a strict numerical solution of the Navier-Stokes equation. CASPER is written to operate under the Parallel, Asynchronous Executive (PAX), which is described in a separate report.

Association of herpes simplex virus regulatory protein ICP22 with transcriptional complexes containing EAP, ICP4, RNA polymerase II, and viral DNA requires posttranslational modification by the U(L)13 proteinkinase.

PubMed Central

Leopardi, R; Ward, P L; Ogle, W O; Roizman, B

1997-01-01

The expression of herpes simplex virus 1 gamma (late) genes requires functional alpha proteins (gamma1 genes) and the onset of viral DNA synthesis (gamma2 genes). We report that late in infection after the onset of viral DNA synthesis, cell nuclei exhibit defined structures which contain two viral regulatory proteins (infected cell proteins 4 and 22) required for gamma gene expression, RNA polymerase II, a host nucleolar protein (EAP or L22) known to be associated with ribosomes and to bind small RNAs, including the Epstein-Barr virus small nuclear RNAs, and newly synthesized progeny DNA. The formation of these complexes required the onset of viral DNA synthesis. The association of infected cell protein 22, a highly posttranslationally processed protein, with these structures did not occur in cells infected with a viral mutant deleted in the genes U(L)13 and U(S)3, each of which specifies a protein kinase known to phosphorylate the protein. PMID:8995634

Reconfigurable modified surface layers using plasma capillaries around the neutral inclusion regime

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

Varault, S.; Universite Paul Sabatier—CNRS-Laplace 118, Route de Narbonne, F-31062 Toulouse Cedex 9; Gabard, B.

We show both theoretically and experimentally reconfigurable properties achieved by plasma inclusions placed in modified surface layers generally used to tailor the transmission and beaming properties of electromagnetic bandgap based waveguiding structures. A proper parametrization of the plasma capillaries allows to reach the neutral inclusion regime, where the inclusions appear to be electromagnetically transparent, letting the surface mode characteristics unaltered. Varying the electron density of the plasma inclusions provoques small perturbations around this peculiar regime, and we observe significant modifications of the transmission/beaming properties. This offers a way to dynamically select the enhanced transmission frequency or to modify the radiationmore » pattern of the structure, depending on whether the modified surface layer is placed at the entrance/exit of the waveguide.« less

Experimental study of the fracture toughness of a ceramic/ceramic-matrix composite sandwich structure

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

Li, Z.; Taya, M.; Dunn, M.L.

A hybrid experimental-numerical approach has been used to measure the fracture resistance of a sandwich structure consisting of a 304 stainless steel/partially stabilized zirconia ceramic-matrix composite crack-arresting layer embedded in a partially stabilized zirconia ceramic specimen. The mode 1 fracture toughness increases significantly when the crack propagates from the ceramic into the ceramic-matrix composite region. The increased toughening due to the stainless steel particles is explained reasonably well by a toughening model based on processing-induced thermal residual stresses. In addition, several experimental modifications were made to the chevron-notch wedge-loaded double cantilever beam specimen to overcome numerous problems encountered in generatingmore » a precrack in the small, brittle specimens used in this study.« less

An efficient approach for the assembly of mass and stiffness matrices of structures with modifications

NASA Astrophysics Data System (ADS)

Wagner, Andreas; Spelsberg-Korspeter, Gottfried

2013-09-01

The finite element method is one of the most common tools for the comprehensive analysis of structures with applications reaching from static, often nonlinear stress-strain, to transient dynamic analyses. For single calculations the expense to generate an appropriate mesh is often insignificant compared to the analysis time even for complex geometries and therefore negligible. However, this is not the case for certain other applications, most notably structural optimization procedures, where the (re-)meshing effort is very important with respect to the total runtime of the procedure. Thus it is desirable to find methods to efficiently generate mass and stiffness matrices allowing to reduce this effort, especially for structures with modifications of minor complexity, e.g. panels with cutouts. Therefore, a modeling approach referred to as Energy Modification Method is proposed in this paper. The underlying idea is to model and discretize the basis structure, e.g. a plate, and the modifications, e.g. holes, separately. The discretized energy expressions of the modifications are then subtracted from (or added to) the energy expressions of the basis structure and the coordinates are related to each other by kinematical constraints leading to the mass and stiffness matrices of the complete structure. This approach will be demonstrated by two simple examples, a rod with varying material properties and a rectangular plate with a rectangular or circular hole, using a finite element discretization as basis. Convergence studies of the method based on the latter example follow demonstrating the rapid convergence and efficiency of the method. Finally, the Energy Modification Method is successfully used in the structural optimization of a circular plate with holes, with the objective to split all its double eigenfrequencies.

Investigation of Solar Wind Correlations and Solar Wind Modifications Near Earth by Multi-Spacecraft Observations: IMP 8, WIND and INTERBALL-1

NASA Technical Reports Server (NTRS)

Paularena, Karolen I.; Richardson, John D.; Zastenker, Georgy N.

2002-01-01

The foundation of this Project is use of the opportunity available during the ISTP (International Solar-Terrestrial Physics) era to compare solar wind measurements obtained simultaneously by three spacecraft - IMP 8, WIND and INTERBALL-1 at wide-separated points. Using these data allows us to study three important topics: (1) the size and dynamics of near-Earth mid-scale (with dimension about 1-10 million km) and small-scale (with dimension about 10-100 thousand km) solar wind structures; (2) the reliability of the common assumption that solar wind conditions at the upstream Lagrangian (L1) point accurately predict the conditions affecting Earth's magnetosphere; (3) modification of the solar wind plasma and magnetic field in the regions near the Earth magnetosphere, the foreshock and the magnetosheath. Our Project was dedicated to these problems. Our research has made substantial contributions to the field and has lead others to undertake similar work.

Phosphomimics destabilize Hsp27 oligomeric assemblies and enhance chaperone activity.

PubMed

Jovcevski, Blagojce; Kelly, Megan A; Rote, Anthea P; Berg, Tracey; Gastall, Heidi Y; Benesch, Justin L P; Aquilina, J Andrew; Ecroyd, Heath

2015-02-19

Serine phosphorylation of the mammalian small heat-shock protein Hsp27 at residues 15, 78, and 82 is thought to regulate its structure and chaperone function; however, the site-specific impact has not been established. We used mass spectrometry to assess the combinatorial effect of mutations that mimic phosphorylation upon the oligomeric state of Hsp27. Comprehensive dimerization yielded a relatively uncrowded spectrum, composed solely of even-sized oligomers. Modification at one or two serines decreased the average oligomeric size, while the triple mutant was predominantly a dimer. These changes were reflected in a greater propensity for oligomers to dissociate upon increased modification. The ability of Hsp27 to prevent amorphous or fibrillar aggregation of target proteins was enhanced and correlated with the amount of dissociated species present. We propose that, in vivo, phosphorylation promotes oligomer dissociation, thereby enhancing chaperone activity. Our data support a model in which dimers are the chaperone-active component of Hsp27. Copyright © 2015 Elsevier Ltd. All rights reserved.

White dwarfs and revelations

NASA Astrophysics Data System (ADS)

Saltas, Ippocratis D.; Sawicki, Ignacy; Lopes, Ilidio

2018-05-01

We use the most recent, complete and independent measurements of masses and radii of white dwarfs in binaries to bound the class of non-trivial modified gravity theories, viable after GW170817/GRB170817, using its effect on the mass-radius relation of the stars. We show that the uncertainty in the latest data is sufficiently small that residual evolutionary effects, most notably the effect of core composition, finite temperature and envelope structure, must now accounted for if correct conclusions about the nature of gravity are to be made. We model corrections resulting from finite temperature and envelopes to a base Hamada-Salpeter cold equation of state and derive consistent bounds on the possible modifications of gravity in the stars' interiors, finding that the parameter quantifying the strength of the modification Y< 0.14 at 95% confidence, an improvement of a factor of three with respect to previous bounds. Finally, our analysis reveals some fundamental degeneracies between the theory of gravity and the precise chemical makeup of white dwarfs.

Tunable and reversible drug control of protein production via a self-excising degron.

PubMed

Chung, Hokyung K; Jacobs, Conor L; Huo, Yunwen; Yang, Jin; Krumm, Stefanie A; Plemper, Richard K; Tsien, Roger Y; Lin, Michael Z

2015-09-01

An effective method for direct chemical control over the production of specific proteins would be widely useful. We describe small molecule-assisted shutoff (SMASh), a technique in which proteins are fused to a degron that removes itself in the absence of drug, resulting in the production of an untagged protein. Clinically tested HCV protease inhibitors can then block degron removal, inducing rapid degradation of subsequently synthesized copies of the protein. SMASh allows reversible and dose-dependent shutoff of various proteins in multiple mammalian cell types and in yeast. We also used SMASh to confer drug responsiveness onto an RNA virus for which no licensed inhibitors exist. As SMASh does not require the permanent fusion of a large domain, it should be useful when control over protein production with minimal structural modification is desired. Furthermore, as SMASh involves only a single genetic modification and does not rely on modulating protein-protein interactions, it should be easy to generalize to multiple biological contexts.

Cross-linking of the electron-transfer flavoprotein to electron-transfer flavoprotein-ubiquinone oxidoreductase with heterobifunctional reagents.

PubMed Central

Steenkamp, D J

1988-01-01

The mitochondrial electron-transfer flavoprotein (ETF) is a heterodimer containing only one FAD. In previous work on the structure-function relationships of ETF, its interaction with the general acyl-CoA dehydrogenase (GAD) was studied by chemical cross-linking with heterobifunctional reagents [D. J. Steenkamp (1987) Biochem. J. 243, 519-524]. GAD whose lysine residues were substituted with 3-(2-pyridyldithio)propionyl groups was preferentially cross-linked to the small subunit of ETF, the lysine residues of which had been substituted with 4-mercaptobutyramidine (MBA) groups. This work was extended to the interaction of ETF with ETF-ubiquinone oxidoreductase (ETF-Q ox). ETF-Q ox was partially inactivated by modification with N-succinimidyl 3-(2-pyridyldithio)propionate to introduce pyridyl disulphide structures. A similar modification of ETF caused a large increase in the apparent Michaelis constant of ETF-Q ox for modified ETF owing to the loss of positive charge on some critical lysines of ETF. When ETF-Q ox was modified with 2-iminothiolane to introduce 4-mercaptobutyramidine groups, only a minor effect on the activity of the enzyme was observed. To retain the positive charges on the lysine residues of ETF, pyridyl disulphide structures were introduced by treating ETF with 2-iminothiolane in the presence of 2,2'-dithiodipyridyl. The electron-transfer activity of the resultant ETF preparation containing 4-(2-pyridyldithio)butyramidine (PDBA) groups was only slightly affected. When ETF-Q ox substituted with MBA groups was mixed with ETF bearing PDBA groups, at least 70% of the cross-links formed between the two proteins were between the small subunit of ETF and ETF-Q ox. ETF-Q ox, therefore, interacts predominantly with the same subunit of ETF as GAD. Variables which affect the selectivity of ETF-Q ox cross-linking to the subunits of ETF are considered. Images Fig. 4. Fig. 5. Fig. 6. PMID:3145738

Age-related carbonylation of fibrocartilage structural proteins drives tissue degenerative modification.

PubMed

Scharf, Brian; Clement, Cristina C; Yodmuang, Supansa; Urbanska, Aleksandra M; Suadicani, Sylvia O; Aphkhazava, David; Thi, Mia M; Perino, Giorgio; Hardin, John A; Cobelli, Neil; Vunjak-Novakovic, Gordana; Santambrogio, Laura

2013-07-25

Aging-related oxidative stress has been linked to degenerative modifications in different organs and tissues. Using redox proteomic analysis and illustrative tandem mass spectrometry mapping, we demonstrate oxidative posttranslational modifications in structural proteins of intervertebral discs (IVDs) isolated from aging mice. Increased protein carbonylation was associated with protein fragmentation and aggregation. Complementing these findings, a significant loss of elasticity and increased stiffness was measured in fibrocartilage from aging mice. Studies using circular dichroism and intrinsic tryptophan fluorescence revealed a significant loss of secondary and tertiary structures of purified collagens following oxidation. Collagen unfolding and oxidation promoted both nonenzymatic and enzymatic degradation. Importantly, induction of oxidative modification in healthy fibrocartilage recapitulated the biochemical and biophysical modifications observed in the aging IVD. Together, these results suggest that protein carbonylation, glycation, and lipoxidation could be early events in promoting IVD degenerative changes. Copyright © 2013 Elsevier Ltd. All rights reserved.

An Overview of Structurally Modified Glycyrrhetinic Acid Derivatives as Antitumor Agents.

PubMed

Xu, Bing; Wu, Gao-Rong; Zhang, Xin-Yu; Yan, Meng-Meng; Zhao, Rui; Xue, Nan-Nan; Fang, Kang; Wang, Hui; Chen, Meng; Guo, Wen-Bo; Wang, Peng-Long; Lei, Hai-Min

2017-06-02

Glycyrrhetinic Acid ( GA ), a triterpenoid aglycone component of the natural product glycyrrhizinic acid, was found to possess remarkable anti-proliferative and apoptosis-inducing activity in various cancer cell lines. Though GA was not as active as other triterpenes, such as betulinic acid and oleanolic acid, it could trigger apoptosis in tumor cells and it can be obtained easily and cheaply, which has stimulated scientific interest in using GA as a scaffold to synthesize new antitumor agents. The structural modifications of GA reported in recent decades can be divided into four groups, which include structural modifications on ring-A, ring-C, ring-E and multiple ring modifications. The lack of a comprehensive and recent review on this topic prompted us to gather more new information. This overview is dedicated to summarizing and updating the structural modification of GA to improve its antitumor activity published between 2005 and 2016. We reviewed a total of 210 GA derivatives that we encountered and compiled the most active GA derivatives along with their activity profile in different series. Furthermore, the structure activity relationships of these derivatives are briefly discussed. The included information is expected to be of benefit to further studies of structural modifications of GA to enhance its antitumor activity.

Mod5 protein binds to tRNA gene complexes and affects local transcriptional silencing

PubMed Central

Pratt-Hyatt, Matthew; Pai, Dave A.; Haeusler, Rebecca A.; Wozniak, Glenn G.; Good, Paul D.; Miller, Erin L.; McLeod, Ian X.; Yates, John R.; Hopper, Anita K.; Engelke, David R.

2013-01-01

The tRNA gene-mediated (tgm) silencing of RNA polymerase II promoters is dependent on subnuclear clustering of the tRNA genes, but genetic analysis shows that the silencing requires additional mechanisms. We have identified proteins that bind tRNA gene transcription complexes and are required for tgm silencing but not required for gene clustering. One of the proteins, Mod5, is a tRNA modifying enzyme that adds an N6-isopentenyl adenosine modification at position 37 on a small number of tRNAs in the cytoplasm, although a subpopulation of Mod5 is also found in the nucleus. Recent publications have also shown that Mod5 has tumor suppressor characteristics in humans as well as confers drug resistance through prion-like misfolding in yeast. Here, we show that a subpopulation of Mod5 associates with tRNA gene complexes in the nucleolus. This association occurs and is required for tgm silencing regardless of whether the pre-tRNA transcripts are substrates for Mod5 modification. In addition, Mod5 is bound to nuclear pre-tRNA transcripts, although they are not substrates for the A37 modification. Lastly, we show that truncation of the tRNA transcript to remove the normal tRNA structure also alleviates silencing, suggesting that synthesis of intact pre-tRNAs is required for the silencing mechanism. These results are discussed in light of recent results showing that silencing near tRNA genes also requires chromatin modification. PMID:23898186

Using the Modification Index and Standardized Expected Parameter Change for Model Modification

ERIC Educational Resources Information Center

Whittaker, Tiffany A.

2012-01-01

Model modification is oftentimes conducted after discovering a badly fitting structural equation model. During the modification process, the modification index (MI) and the standardized expected parameter change (SEPC) are 2 statistics that may be used to aid in the selection of parameters to add to a model to improve the fit. The purpose of this…

Modification of the supramolecular structure of collagen with nanodisperse hydroxyapatite

NASA Astrophysics Data System (ADS)

Voloskova, E. V.; Berdnikova, L. K.; Poluboyarov, V. A.; Gur'yanova, T. I.

2015-02-01

The influence of nanodisperse particles of hydroxyapatite on the structure of films based on collagen with a molecular mass of 360 kDa was studied. When coatings formed, the collagen macromolecules aggregated into spherulites; modification led to structural changes related to the decomposition of the spherulite structure and the formation of a grain structure. The variation of the physicomechanical properties of film materials directly depends on the size of the structural units.

Retrofit designs for small bench-type blood cell counters.

PubMed

Ferris, C D

1991-01-01

This paper describes several retrofit designs to correct operational problems associated with small bench-type blood cell counters. Replacement electronic circuits as well as modifications to the vacuum systems are discussed.

Evaluation of the effect of post-translational modification toward protein structure: Chemical synthesis of glycosyl crambins having either a high mannose-type or a complex-type oligosaccharide.

PubMed

Dedola, Simone; Izumi, Masayuki; Makimura, Yutaka; Ito, Yukishige; Kajihara, Yasuhiro

2016-11-04

Glycoproteins are assembled and folded in the endoplasmic reticulum (ER) and transported to the Golgi for further processing of their oligosaccharides. During these processes, two types of oligosaccharides are used: that is, high mannose-type oligosaccharide in the ER and complex-type oligosaccharide in the Golgi. We were interested to know how two different types of oligosaccharides could influence the folding pathway or the final three-dimensional structure of the glycoproteins. For this purpose, we synthesized a new glycosyl crambin having complex-type oligosaccharide and evaluated the folding process, the final protein structure analyzed by NMR, and compared the CD spectra with previously synthesized glycosyl crambin bearing high mannose-type oligosaccharides. From our analysis, we found that the two different oligosaccharides do not influence the folding pathway in vitro and the final structure of the small glycoproteins. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 446-452, 2016. © 2015 Wiley Periodicals, Inc.

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

Winter, Frank; Detmold, William; Gambhir, Arjun S.

The role of gluons in the structure of the nucleon and light nuclei is investigated using lattice quantum chromodynamics (QCD) calculations. The first moment of the unpolarised gluon distribution is studied in nuclei up to atomic numbermore » $A=3$ at quark masses corresponding to pion masses of $$m_\\pi\\sim 450$$ and $806$ MeV. Nuclear modification of this quantity defines a gluonic analogue of the EMC effect and is constrained to be less than $$\\sim 10$$% in these nuclei. This is consistent with expectations from phenomenological quark distributions and the momentum sum rule. In the deuteron, the combination of gluon distributions corresponding to the $$b_1$$ structure function is found to have a small first moment compared with the corresponding momentum fraction. The first moment of the gluon transversity structure function is also investigated in the spin-1 deuteron, where a non-zero signal is observed at $$m_\\pi \\sim 806$$ MeV. In conclusion, this is the first indication of gluon contributions to nuclear structure that can not be associated with an individual nucleon.« less

Mammalian HspB1 (Hsp27) is a molecular sensor linked to the physiology and environment of the cell.

PubMed

Arrigo, André-Patrick

2017-07-01

Constitutively expressed small heat shock protein HspB1 regulates many fundamental cellular processes and plays major roles in many human pathological diseases. In that regard, this chaperone has a huge number of apparently unrelated functions that appear linked to its ability to recognize many client polypeptides that are subsequently modified in their activity and/or half-life. A major parameter to understand how HspB1 is dedicated to interact with particular clients in defined cellular conditions relates to its complex oligomerization and phosphorylation properties. Indeed, HspB1 structural organization displays dynamic and complex rearrangements in response to changes in the cellular environment or when the cell physiology is modified. These structural modifications probably reflect the formation of structural platforms aimed at recognizing specific client polypeptides. Here, I have reviewed data from the literature and re-analyzed my own studies to describe and discuss these fascinating changes in HspB1 structural organization.

ARCIMBOLDO_LITE: single-workstation implementation and use.

PubMed

Sammito, Massimo; Millán, Claudia; Frieske, Dawid; Rodríguez-Freire, Eloy; Borges, Rafael J; Usón, Isabel

2015-09-01

ARCIMBOLDO solves the phase problem at resolutions of around 2 Å or better through massive combination of small fragments and density modification. For complex structures, this imposes a need for a powerful grid where calculations can be distributed, but for structures with up to 200 amino acids in the asymmetric unit a single workstation may suffice. The use and performance of the single-workstation implementation, ARCIMBOLDO_LITE, on a pool of test structures with 40-120 amino acids and resolutions between 0.54 and 2.2 Å is described. Inbuilt polyalanine helices and iron cofactors are used as search fragments. ARCIMBOLDO_BORGES can also run on a single workstation to solve structures in this test set using precomputed libraries of local folds. The results of this study have been incorporated into an automated, resolution- and hardware-dependent parameterization. ARCIMBOLDO has been thoroughly rewritten and three binaries are now available: ARCIMBOLDO_LITE, ARCIMBOLDO_SHREDDER and ARCIMBOLDO_BORGES. The programs and libraries can be downloaded from http://chango.ibmb.csic.es/ARCIMBOLDO_LITE.

The Load Distribution in Bolted or Riveted Joints in Light-Alloy Structures

NASA Technical Reports Server (NTRS)

Vogt, F.

1947-01-01

This report contains a theoretical discussion of the load distribution in bolted or riveted joints in light-alloy structures which is applicable not only for loads below the limit of proportionality but also for loads above this limit. The theory is developed for double and single shear joints. The methods given are illustrated by numerical examples and the values assumed for the bolt (or rivet) stiffnesses are based partly on theory and partly on known experimental values. It is shown that the load distribution does not vary greatly with the bolt (or rivet) stiffnesses and that for design purposes it is usually sufficient to know their order of magnitude. The theory may also be directly used for spot-welded structures and, with small modifications, for seam-welded structures, The computational work involved in the methods described is simple and may be completed in a reasonable time for most practical problems. A summary of earlier theoretical and experimental investigations on the subject is included in the report.

Micro- and nano-CT textural analysis of an experimental volcanic fulgurite.

NASA Astrophysics Data System (ADS)

Cimarelli, Corrado; Yilmaz, Tim; Colombier, Mathieu; Villanova, Julie; Höfer, Lucas; Hess, Kai-Uwe; Ruthensteiner, Bernhard; Dingwell, Donald

2017-04-01

Fulgurites are natural glasses formed by cloud to ground lightning discharges causing rapid heating into rocks or unconsolidated sediments. Volcanic lightning can determine the re-melting and even ablation of newly formed or just deposited volcanic tephra during explosive eruptions. In this case the pristine material is already constituted by glass that can be further modified by the discharge. Although volcanic lightning discharges are generally less energetic than those produced by thunderclouds, the high temperatures reached by the lightning channel are well in excess of the low melting temperature of glass material. Here we have experimentally reproduced a fulgurite by single impulse voltage discharges (134 kV, 331 A, 10.5 J) on a target glass material. We have chosen borosilicate glass fibers (180 microns nominal length) as starting material to better account for the structural and chemical modification of the single particles after discharge-melting. The structure of the small fulgurite is best resolved through X-ray micro- and nano-computed tomography. Micro-CT analysis was carried out on a phoenix nanotom m with a voxelsize of 1 µm3. Additionally a 3D reconstruction with a voxel size of 150 nm3 has been analyzed at the new nano-analysis beamline ID16B at the ESRF. 3D analysis was carried out using Avizo 9.2 software, which allows non-destructive analysis of the fragile structure of the sample. The sample shows the channel-like structure typical for natural fulgurites with an inner void channel and internal wall constituted by the melted fibers. About 33% of the total solid volume of the fulgurite is melted to form the inner wall. The inner wall is characterized by nano- to micro-metric vesicles determined by volatile exsolution (mainly H2O) during the instantaneous heating and trapped in the low viscosity melt by the subsequent rapid quenching. Progressively outward the fulgurite shows the intricate delicate structure of the pristine glass fibers. Our results demonstrate that structural and chemical alteration of low viscosity glass material is possible by small impulse discharges with relatively low currents, thus reproducing a plausible scenario for electrical discharges during volcanic eruptions. Our experiment opens the opportunity for systematic constrained experimental investigation of the modification induced by volcanic lightning on tephra.

Methoxydiphenylamine-substituted fluorene derivatives as hole transporting materials: role of molecular interaction on device photovoltaic performance.

PubMed

Tiazkis, Robertas; Paek, Sanghyun; Daskeviciene, Maryte; Malinauskas, Tadas; Saliba, Michael; Nekrasovas, Jonas; Jankauskas, Vygintas; Ahmad, Shahzada; Getautis, Vytautas; Khaja Nazeeruddin, Mohammad

2017-03-10

The molecular structure of the hole transporting material (HTM) play an important role in hole extraction in a perovskite solar cells. It has a significant influence on the molecular planarity, energy level, and charge transport properties. Understanding the relationship between the chemical structure of the HTM's and perovskite solar cells (PSCs) performance is crucial for the continued development of the efficient organic charge transporting materials. Using molecular engineering approach we have constructed a series of the hole transporting materials with strategically placed aliphatic substituents to investigate the relationship between the chemical structure of the HTMs and the photovoltaic performance. PSCs employing the investigated HTMs demonstrate power conversion efficiency values in the range of 9% to 16.8% highlighting the importance of the optimal molecular structure. An inappropriately placed side group could compromise the device performance. Due to the ease of synthesis and moieties employed in its construction, it offers a wide range of possible structural modifications. This class of molecules has a great potential for structural optimization in order to realize simple and efficient small molecule based HTMs for perovskite solar cells application.

Features of the structural states of KNbO{sub 3} single crystals before and after fast-neutron irradiation

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

Stash, A. I., E-mail: astas@yandex.ru; Ivanov, S. A.; Stefanovich, S. Yu.

Neutron irradiation is a unique tool for forming new structural states of ferroelectrics, which cannot be obtained by conventional methods. The inf luence of the irradiation by two doses of fast neutrons (F = 1 × 10{sup 17} and 3 × 10{sup 17} cm{sup –2}) on the structure and properties of KNbO{sub 3} single crystals has been considered for the first time. The developed method for taking into account the experimental correction to the diffuse scattering has been used to analyze the structural changes occurring in KNbO{sub 3} samples at T = 295 K and their correlations with the behaviormore » of dielectric and nonlinear optical characteristics. The irradiation to the aforementioned doses retains the KNbO{sub 3} polar structure, shifting Т{sub Ð}¡ to lower temperatures and significantly affecting only the thermal parameters and microstructure of single crystals. Neutron irradiation with small atomic displacements provides a structure similar to the high-temperature modification of an unirradiated KNbO{sub 3} crystal.« less

Grading sugar pine saw logs in trees.

Treesearch

John W. Henley

1972-01-01

Small limbs and small overgrown limbs cause problems when grading saw logs in sugar pine trees. Surface characteristics and lumber recovery information for 426 logs from 64 sugar pine trees were examined. Resulting modifications in the grading specification that allow a grader to ignore small limbs and small limb indicators do not appear to decrease the performance of...

Gas-Phase Enrichment of Multiply Charged Peptide Ions by Differential Ion Mobility Extend the Comprehensiveness of SUMO Proteome Analyses

NASA Astrophysics Data System (ADS)

Pfammatter, Sibylle; Bonneil, Eric; McManus, Francis P.; Thibault, Pierre

2018-04-01

The small ubiquitin-like modifier (SUMO) is a member of the family of ubiquitin-like modifiers (UBLs) and is involved in important cellular processes, including DNA damage response, meiosis and cellular trafficking. The large-scale identification of SUMO peptides in a site-specific manner is challenging not only because of the low abundance and dynamic nature of this modification, but also due to the branched structure of the corresponding peptides that further complicate their identification using conventional search engines. Here, we exploited the unusual structure of SUMO peptides to facilitate their separation by high-field asymmetric waveform ion mobility spectrometry (FAIMS) and increase the coverage of SUMO proteome analysis. Upon trypsin digestion, branched peptides contain a SUMO remnant side chain and predominantly form triply protonated ions that facilitate their gas-phase separation using FAIMS. We evaluated the mobility characteristics of synthetic SUMO peptides and further demonstrated the application of FAIMS to profile the changes in protein SUMOylation of HEK293 cells following heat shock, a condition known to affect this modification. FAIMS typically provided a 10-fold improvement of detection limit of SUMO peptides, and enabled a 36% increase in SUMO proteome coverage compared to the same LC-MS/MS analyses performed without FAIMS. [Figure not available: see fulltext.

Quantifying structural modifications of gills of two fish species Astyanax altiparanae (Lambari) and Prochilodus lineatus (Curimbatá) after exposure to biodegradable detergents in urban lake water.

PubMed

Fiorelini Pereira, Bruno; Alves, Anderson Luis; Senhorini, José Augusto; Hakime Scalize, Priscilla; Tocchini De Figueiredo, Fellipe Augusto; Pitol, Dimítrius Leonardo; Caetano, Flávio Henrique

2017-01-01

Anthropic actions in rivers and urban lakes are a cause for concern to our ecosystem. The effects on fauna and flora of substances discharged into waterways have become a focus for investigations globally. Biodegradable detergents are widely used in residences and small industries, but little is known regarding the consequences on fish fauna. The objective of the present study was to identify modifications in gill structure in two fish species, Astyanax altiparanae and Prochilodus lineatus, after treatment with water obtained from an urban lake and an exposure to 1 ppm diluted biodegradable detergents (linear alkylbenzene sulfonate). Data demonstrated exposure to urban lake produced various alterations in gill functions such as lamellar fusions, aneurysms, mucous, and chlorine cell proliferation, which may be attributed to the presence of detergents in the water but may also be a consequence of synergetic actions of detergents with other pollutants. Results showed that the levels of NO - 2 , Na, F - , Cl - , and Fe were significantly higher in urban lake water but in the presence of detergents Ni was also detected. Evidence indicates that biodegradable detergents produce damage to gill functions, which subsequently alters the fish physiology and reduces the ability to cope with stress and survival.

Biochemical and Structural Studies of RNA Modification and Repair

ERIC Educational Resources Information Center

Chan, Chio Mui

2009-01-01

RNA modification, RNA interference, and RNA repair are important events in the cell. This thesis presents three projects related to these three fields. By using both biochemical and structural methods, we characterized enzymatic activities of pseudouridine synthase TruD, solved the structure of "A. aeolicus" GidA, and reconstituted a novel…

Methodological guidelines for developing accident modification functions.

PubMed

Elvik, Rune

2015-07-01

This paper proposes methodological guidelines for developing accident modification functions. An accident modification function is a mathematical function describing systematic variation in the effects of road safety measures. The paper describes ten guidelines. An example is given of how to use the guidelines. The importance of exploratory analysis and an iterative approach in developing accident modification functions is stressed. The example shows that strict compliance with all the guidelines may be difficult, but represents a level of stringency that should be strived for. Currently the main limitations in developing accident modification functions are the small number of good evaluation studies and the often huge variation in estimates of effect. It is therefore still not possible to develop accident modification functions for very many road safety measures. Copyright © 2015 Elsevier Ltd. All rights reserved.

Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids.

PubMed

Iyer, Lakshminarayan M; Tahiliani, Mamta; Rao, Anjana; Aravind, L

2009-06-01

Modified bases in nucleic acids present a layer of information that directs biological function over and beyond the coding capacity of the conventional bases. While a large number of modified bases have been identified, many of the enzymes generating them still remain to be discovered. Recently, members of the 2-oxoglutarate- and iron(II)-dependent dioxygenase super-family, which modify diverse substrates from small molecules to biopolymers, were predicted and subsequently confirmed to catalyze oxidative modification of bases in nucleic acids. Of these, two distinct families, namely the AlkB and the kinetoplastid base J binding proteins (JBP) catalyze in situ hydroxylation of bases in nucleic acids. Using sensitive computational analysis of sequences, structures and contextual information from genomic structure and protein domain architectures, we report five distinct families of 2-oxoglutarate- and iron(II)-dependent dioxygenase that we predict to be involved in nucleic acid modifications. Among the DNA-modifying families, we show that the dioxygenase domains of the kinetoplastid base J-binding proteins belong to a larger family that includes the Tet proteins, prototyped by the human oncogene Tet1, and proteins from basidiomycete fungi, chlorophyte algae, heterolobosean amoeboflagellates and bacteriophages. We present evidence that some of these proteins are likely to be involved in oxidative modification of the 5-methyl group of cytosine leading to the formation of 5-hydroxymethylcytosine. The Tet/JBP homologs from basidiomycete fungi such as Laccaria and Coprinopsis show large lineage-specific expansions and a tight linkage with genes encoding a novel and distinct family of predicted transposases, and a member of the Maelstrom-like HMG family. We propose that these fungal members are part of a mobile transposon. To the best of our knowledge, this is the first report of a eukaryotic transposable element that encodes its own DNA-modification enzyme with a potential regulatory role. Through a wider analysis of other poorly characterized DNA-modifying enzymes we also show that the phage Mu Mom-like proteins, which catalyze the N6-carbamoylmethylation of adenines, are also linked to diverse families of bacterial transposases, suggesting that DNA modification by transposable elements might have a more general presence than previously appreciated. Among the other families of 2-oxoglutarate- and iron(II)-dependent dioxygenases identified in this study, one which is found in algae, is predicted to mainly comprise of RNA-modifying enzymes and shows a striking diversity in protein domain architectures suggesting the presence of RNA modifications with possibly unique adaptive roles. The results presented here are likely to provide the means for future investigation of unexpected epigenetic modifications, such as hydroxymethyl cytosine, that could profoundly impact our understanding of gene regulation and processes such as DNA demethylation.

Porphyrin mediated photo-modification of the structure and function of human serum albumin

NASA Astrophysics Data System (ADS)

Rozinek, Sarah C.

Photosensitization reactions involve irradiating (with visible light) molecules with a high efficiency for either electron transfer or entering an excited triplet state (photosensitizer). Such reactions are applied to photodynamic cancer therapy, many medical laser-treatments, and a potential array of disinfection and pest elimination techniques. To understand the biophysical mechanisms of how these applications are effective at the protein level, the group of Dr. Brancaleon (UTSA) has investigated the irradiation of several dye-protein combinations, and discovered effects on protein structure and function. To further that work, we have investigated irradiation of the protein, human serum albumin (HSA), photosensitized by either protoporphyrin IX (PPIX) or meso-tetrakis(4-sulfonatophenyl)porphyrin (TSPP). HSA is the most abundant plasma protein, making it a likely substrate in PDT, and it possesses a specific binding pocket for iron-PPIX (heme) and possibly other porphyrin derivatives. The results of our research are summarized as follows. First, a thorough characterization of the binding of each photosensitizer to albumin was completed, elucidating a probable binding location for TSPP. Next, fluorescence lifetime emission of the single tryptophan residue, alongside circular dichroism, found tertiary structural changes around tryptophan and an overall 20% decrease in protein secondary structure after irradiation with TSPP bound. Finally, to determine if protein function was lost after photosensitization, size exclusion chromatography found modified albumin still recognizable by its receptor-protein, and comparative ex vivo up-take studies revealed that modified albumin is not processed the same way as native albumin in live tapeworm larva (Mesocestoides corti). Thus we found that visible light can induce partial unfolding of a protein by using a photo-activated ligand. These small structural modifications were sufficient to affect the protein's biological function.

Sterile neutrinos with secret interactions — lasting friendship with cosmology

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

Chu, Xiaoyong; Dasgupta, Basudeb; Kopp, Joachim

Sterile neutrinos with mass ≃1 eV and order 10% mixing with active neutrinos have been proposed as a solution to anomalies in neutrino oscillation data, but are tightly constrained by cosmological limits. It was recently shown that these constraints are avoided if sterile neutrinos couple to a new MeV-scale gauge boson A{sup ′}. However, even this scenario is restricted by structure formation constraints when A{sup ′}-mediated collisional processes lead to efficient active-to-sterile neutrino conversion after neutrinos have decoupled. In view of this, we reevaluate in this paper the viability of sterile neutrinos with such “secret” interactions. We carefully dissect theirmore » evolution in the early Universe, including the various production channels and the expected modifications to large scale structure formation. We argue that there are two regions in parameter space — one at very small A{sup ′} coupling, one at relatively large A{sup ′} coupling — where all constraints from big bang nucleosynthesis (BBN), cosmic microwave background (CMB), and large scale structure (LSS) data are satisfied. Interestingly, the large A{sup ′} coupling region is precisely the region that was previously shown to have potentially important consequences for the small scale structure of dark matter halos if the A{sup ′} boson couples also to the dark matter in the Universe.« less

Manipulating explosive sensitivity through structural modifications in a nitrate ester system

NASA Astrophysics Data System (ADS)

Manner, Virginia

2017-06-01

Understanding how condensed phase effects influence sensitivity is essential for developing next generation insensitive high explosives. However, the ability to predictably manipulate explosive sensitivity remains an elusive goal. Explosive sensitivity has been suggested to be governed by multiple factors, from intramolecular effects such as bond dissociation energy, oxygen balance, and the electrostatic potential of reactive functional groups, to larger scale effects, such as crystal structure and hot spot formation. We have developed derivatives of the explosive pentaerythritol tetranitrate (PETN) and examined them experimentally and theoretically, in order to better understand which properties influence sensitivity. With this molecular framework, we can evaluate how small changes to the structure of the molecule influence qualities such as oxygen balance, heat of formation, heat capacity, compressibility, crystal packing, and hydrogen bonding, through techniques such as differential scanning calorimetry, x-ray crystallography, and atomistic simulation. We have also used small-scale sensitivity testing as an initial tool to screen for large and consistent differences in handling sensitivity. We will discuss the many factors that contribute to sensitivity in this series of systematically-modified molecules as well as in existing well-studied explosive systems, such as triaminotrinitrobenzene (TATB) and nitroglycerin (NG). In collaboration with: Thomas Myers, Marc Cawkwell, Edward Kober, Bryce Tappan, Geoffrey Brown, Mary Sandstrom, LOS ALAMOS NATL LAB.

A tandem regression-outlier analysis of a ligand cellular system for key structural modifications around ligand binding.

PubMed

Lin, Ying-Ting

2013-04-30

A tandem technique of hard equipment is often used for the chemical analysis of a single cell to first isolate and then detect the wanted identities. The first part is the separation of wanted chemicals from the bulk of a cell; the second part is the actual detection of the important identities. To identify the key structural modifications around ligand binding, the present study aims to develop a counterpart of tandem technique for cheminformatics. A statistical regression and its outliers act as a computational technique for separation. A PPARγ (peroxisome proliferator-activated receptor gamma) agonist cellular system was subjected to such an investigation. Results show that this tandem regression-outlier analysis, or the prioritization of the context equations tagged with features of the outliers, is an effective regression technique of cheminformatics to detect key structural modifications, as well as their tendency of impact to ligand binding. The key structural modifications around ligand binding are effectively extracted or characterized out of cellular reactions. This is because molecular binding is the paramount factor in such ligand cellular system and key structural modifications around ligand binding are expected to create outliers. Therefore, such outliers can be captured by this tandem regression-outlier analysis.

Lactose-modified DNA tile nanostructures as drug carriers.

PubMed

Akkus Sut, Pinar; Tunc, Cansu Umran; Culha, Mustafa

2016-09-01

DNA hybridization allows the preparation of nanoscale DNA structures with desired shape and size. DNA structures using simple base pairing can be used for the delivery of drug molecules into the cells. Since DNA carries multiple negative charges, their cellular uptake efficiency is low. Thus, the modification of the DNA structures with molecules that may enhance the cellular internalization may be an option. The objective of this study is to construct DNA-based nanocarrier system and to investigate the cellular uptake of DNA tile with/without lactose modification. Doxorubicin was intercalated to DNA tile and cellular uptake of drug-loaded DNA-based carrier with/without lactose modification was investigated in vitro. HeLa, BT-474, and MDA-MB-231 cancer cells were used for cellular uptake studies and cytotoxicity assays. Using fluorescence spectroscopy, flow cytometry, and confocal microscopy, cellular uptake behavior of DNA tile was investigated. The cytotoxicity of DNA tile structures was determined with WST-1 assay. The results show that modification with lactose effectively increases the intracellular uptake of doxorubicin loaded DNA tile structure by cancer cells compared with the unmodified DNA tile. The findings of this study suggest that DNA-based nanostructures modified with carbohydrates can be used as suitable multifunctional nanocarriers with simple chemical modifications.

Euglena Transcript Processing.

PubMed

McWatters, David C; Russell, Anthony G

2017-01-01

RNA transcript processing is an important stage in the gene expression pathway of all organisms and is subject to various mechanisms of control that influence the final levels of gene products. RNA processing involves events such as nuclease-mediated cleavage, removal of intervening sequences referred to as introns and modifications to RNA structure (nucleoside modification and editing). In Euglena, RNA transcript processing was initially examined in chloroplasts because of historical interest in the secondary endosymbiotic origin of this organelle in this organism. More recent efforts to examine mitochondrial genome structure and RNA maturation have been stimulated by the discovery of unusual processing pathways in other Euglenozoans such as kinetoplastids and diplonemids. Eukaryotes containing large genomes are now known to typically contain large collections of introns and regulatory RNAs involved in RNA processing events, and Euglena gracilis in particular has a relatively large genome for a protist. Studies examining the structure of nuclear genes and the mechanisms involved in nuclear RNA processing have revealed that indeed Euglena contains large numbers of introns in the limited set of genes so far examined and also possesses large numbers of specific classes of regulatory and processing RNAs, such as small nucleolar RNAs (snoRNAs). Most interestingly, these studies have also revealed that Euglena possesses novel processing pathways generating highly fragmented cytosolic ribosomal RNAs and subunits and non-conventional intron classes removed by unknown splicing mechanisms. This unexpected diversity in RNA processing pathways emphasizes the importance of identifying the components involved in these processing mechanisms and their evolutionary emergence in Euglena species.

Ring structure modifications of phenylalanine 19 increase fibrillation kinetics and reduce toxicity of amyloid β (1-40).

PubMed

Korn, Alexander; Surendran, Dayana; Krueger, Martin; Maiti, Sudipta; Huster, Daniel

2018-05-24

We investigated the influence of the chemical structure of the phenylalanine side chain in position 19 of the 40 residue amyloid β peptide. Side chain modifications in this position yielded fibrils of essentially unaltered morphology, structure, and dynamics, but significantly increased fibrillation kinetics and diminished the toxicity of the peptides.

The Endoplasmic Reticulum Membrane Is Permeable to Small Molecules

PubMed Central

Le Gall, Sylvie; Neuhof, Andrea; Rapoport, Tom

2004-01-01

The lumen of the endoplasmic reticulum (ER) differs from the cytosol in its content of ions and other small molecules, but it is unclear whether the ER membrane is as impermeable as other membranes in the cell. Here, we have tested the permeability of the ER membrane to small, nonphysiological molecules. We report that isolated ER vesicles allow different chemical modification reagents to pass from the outside into the lumen with little hindrance. In permeabilized cells, the ER membrane allows the passage of a small, charged modification reagent that is unable to cross the plasma membrane or the lysosomal and trans-Golgi membranes. A larger polar reagent of ∼5 kDa is unable to pass through the ER membrane. Permeation of the small molecules is passive because it occurs at low temperature in the absence of energy. These data indicate that the ER membrane is significantly more leaky than other cellular membranes, a property that may be required for protein folding and other functions of the ER. PMID:14617815

The influence of chemical structure on thermal properties and surface morphology of polyurethane materials.

PubMed

Brzeska, Joanna; Morawska, Magda; Heimowska, Aleksandra; Sikorska, Wanda; Wałach, Wojciech; Hercog, Anna; Kowalczuk, Marek; Rutkowska, Maria

2018-01-01

The surface morphology and thermal properties of polyurethanes can be correlated to their chemical composition. The hydrophilicity, surface morphology, and thermal properties of polyurethanes (differed in soft segments and in linear/cross-linked structure) were investigated. The influence of poly([ R , S ]-3-hydroxybutyrate) presence in soft segments and blending of polyurethane with polylactide on surface topography were also estimated. The linear polyurethanes (partially crystalline) had the granular surface, whereas the surface of cross-linked polyurethanes (almost amorphous) was smooth. Round aggregates of polylactide un-uniformly distributed in matrix of polyurethane were clearly visible. It was concluded that some modification of soft segment (by mixing of poly([ R , S ]-3-hydroxybutyrate) with different polydiols and polytriol) and blending of polyurethanes with small amount of polylactide influence on crystallinity and surface topography of obtained polyurethanes.

Theoretical study of the influence of the electric field on the electronic properties of armchair boron nitride nanoribbon

NASA Astrophysics Data System (ADS)

Chegel, Raad; Behzad, Somayeh

2014-11-01

We have investigated the electronic properties of A-BNNRs in the external electric field using third nearest neighbor tight binding approximation including edge effects. We found that the dependence of on-site energy to the external electric field for edge atoms and center part atoms is different. By comparing the band structure in the different fields, several differences are clearly seen such as modification of energy dispersions, creation of additional band edge states and band gap reduction. By increasing the electric field the band gap reduces linearly until reaches zero and BNNRs with larger width are more sensitive than small ones. All changes in the band structure are directly reflected in the DOS spectrum. The numbers and the energies of the DOS peaks are dependent on the electric field strength.

Variation of transition temperatures and residual resistivity ratio in vapor-grown FeSe

DOE PAGES

Böhmer, A. E.; Taufour, V.; Straszheim, W. E.; ...

2016-07-29

The study of the iron-based superconductor FeSe has blossomed with the availability of high-quality single crystals, obtained through flux/vapor-transport growth techniques below the structural transformation temperature of its tetragonal phase, T≈450°C. Here, we report on the variation of sample morphology and properties due to small modifications in the growth conditions. A considerable variation of the superconducting transition temperature T c, from 8.8 K to 3 K, which cannot be correlated with the sample composition, is observed. Instead, we point out a clear correlation between T c and disorder, as measured by the residual resistivity ratio. Notably, the tetragonal-to-orthorhombic structural transitionmore » is also found to be quite strongly disorder dependent (T s≈72–90K) and linearly correlated with T c.« less

Role of composition, bond covalency, and short-range order in the disordering of stannate pyrochlores by swift heavy ion irradiation

NASA Astrophysics Data System (ADS)

Tracy, Cameron L.; Shamblin, Jacob; Park, Sulgiye; Zhang, Fuxiang; Trautmann, Christina; Lang, Maik; Ewing, Rodney C.

2016-08-01

A2S n2O7 (A =Nd ,Sm,Gd,Er,Yb,and Y) materials with the pyrochlore structure were irradiated with 2.2 GeV Au ions to systematically investigate disordering of this system in response to dense electronic excitation. Structural modifications were characterized, over multiple length scales, by transmission electron microscopy, x-ray diffraction, and Raman spectroscopy. Transformations to amorphous and disordered phases were observed, with disordering dominating the structural response of materials with small A -site cation ionic radii. Both the disordered and amorphous phases were found to possess weberite-type local ordering, differing only in that the disordered phase exhibits a long-range, modulated arrangement of weberite-type structural units into an average defect-fluorite structure, while the amorphous phase remains fully aperiodic. Comparison with the behavior of titanate and zirconate pyrochlores showed minimal influence of the high covalency of the Sn-O bond on this phase behavior. An analytical model of damage accumulation was developed to account for simultaneous amorphization and recrystallization of the disordered phase during irradiation.

First lattice QCD study of the gluonic structure of light nuclei

NASA Astrophysics Data System (ADS)

Winter, Frank; Detmold, William; Gambhir, Arjun S.; Orginos, Kostas; Savage, Martin J.; Shanahan, Phiala E.; Wagman, Michael L.; Nplqcd Collaboration

2017-11-01

The role of gluons in the structure of the nucleon and light nuclei is investigated using lattice quantum chromodynamics (QCD) calculations. The first moment of the unpolarized gluon distribution is studied in nuclei up to atomic number A =3 at quark masses corresponding to pion masses of mπ˜450 and 806 MeV. Nuclear modification of this quantity defines a gluonic analogue of the EMC effect and is constrained to be less than ˜10 % in these nuclei. This is consistent with expectations from phenomenological quark distributions and the momentum sum rule. In the deuteron, the combination of gluon distributions corresponding to the b1 structure function is found to have a small first moment compared with the corresponding momentum fraction. The first moment of the gluon transversity structure function is also investigated in the spin-1 deuteron, where a nonzero signal is observed at mπ˜806 MeV . This is the first indication of gluon contributions to nuclear structure that can not be associated with an individual nucleon.

Chemical and structural biology of protein lysine deacetylases

PubMed Central

YOSHIDA, Minoru; KUDO, Norio; KOSONO, Saori; ITO, Akihiro

2017-01-01

Histone acetylation is a reversible posttranslational modification that plays a fundamental role in regulating eukaryotic gene expression and chromatin structure/function. Key enzymes for removing acetyl groups from histones are metal (zinc)-dependent and NAD+-dependent histone deacetylases (HDACs). The molecular function of HDACs have been extensively characterized by various approaches including chemical, molecular, and structural biology, which demonstrated that HDACs regulate cell proliferation, differentiation, and metabolic homeostasis, and that their alterations are deeply involved in various human disorders including cancer. Notably, drug discovery efforts have achieved success in developing HDAC-targeting therapeutics for treatment of several cancers. However, recent advancements in proteomics technology have revealed much broader aspects of HDACs beyond gene expression control. Not only histones but also a large number of cellular proteins are subject to acetylation by histone acetyltransferases (HATs) and deacetylation by HDACs. Furthermore, some of their structures can flexibly accept and hydrolyze other acyl groups on protein lysine residues. This review mainly focuses on structural aspects of HDAC enzymatic activity regulated by interaction with substrates, co-factors, small molecule inhibitors, and activators. PMID:28496053

First lattice QCD study of the gluonic structure of light nuclei

DOE PAGES

Winter, Frank; Detmold, William; Gambhir, Arjun S.; ...

2017-11-28

The role of gluons in the structure of the nucleon and light nuclei is investigated using lattice quantum chromodynamics (QCD) calculations. The first moment of the unpolarised gluon distribution is studied in nuclei up to atomic numbermore » $A=3$ at quark masses corresponding to pion masses of $$m_\\pi\\sim 450$$ and $806$ MeV. Nuclear modification of this quantity defines a gluonic analogue of the EMC effect and is constrained to be less than $$\\sim 10$$% in these nuclei. This is consistent with expectations from phenomenological quark distributions and the momentum sum rule. In the deuteron, the combination of gluon distributions corresponding to the $$b_1$$ structure function is found to have a small first moment compared with the corresponding momentum fraction. The first moment of the gluon transversity structure function is also investigated in the spin-1 deuteron, where a non-zero signal is observed at $$m_\\pi \\sim 806$$ MeV. In conclusion, this is the first indication of gluon contributions to nuclear structure that can not be associated with an individual nucleon.« less

Heavy Chronic Intermittent Ethanol Exposure Alters Small Noncoding RNAs in Mouse Sperm and Epididymosomes.

PubMed

Rompala, Gregory R; Mounier, Anais; Wolfe, Cody M; Lin, Qishan; Lefterov, Iliya; Homanics, Gregg E

2018-01-01

While the risks of maternal alcohol abuse during pregnancy are well-established, several preclinical studies suggest that chronic preconception alcohol consumption by either parent may also have significance consequences for offspring health and development. Notably, since isogenic male mice used in these studies are not involved in gestation or rearing of offspring, the cross-generational effects of paternal alcohol exposure suggest a germline-based epigenetic mechanism. Many recent studies have demonstrated that the effects of paternal environmental exposures such as stress or malnutrition can be transmitted to the next generation via alterations to small noncoding RNAs in sperm. Therefore, we used high throughput sequencing to examine the effect of preconception ethanol on small noncoding RNAs in sperm. We found that chronic intermittent ethanol exposure altered several small noncoding RNAs from three of the major small RNA classes in sperm, tRNA-derived small RNA (tDR), mitochondrial small RNA, and microRNA. Six of the ethanol-responsive small noncoding RNAs were evaluated with RT-qPCR on a separate cohort of mice and five of the six were confirmed to be altered by chronic ethanol exposure, supporting the validity of the sequencing results. In addition to altered sperm RNA abundance, chronic ethanol exposure affected post-transcriptional modifications to sperm small noncoding RNAs, increasing two nucleoside modifications previously identified in mitochondrial tRNA. Furthermore, we found that chronic ethanol reduced epididymal expression of a tRNA methyltransferase, Nsun2 , known to directly regulate tDR biogenesis. Finally, ethanol-responsive sperm tDR are similarly altered in extracellular vesicles of the epididymis (i.e., epididymosomes), supporting the hypothesis that alterations to sperm tDR emerge in the epididymis and that epididymosomes are the primary source of small noncoding RNAs in sperm. These results add chronic ethanol to the growing list of paternal exposures that can affect small noncoding RNA abundance and nucleoside modifications in sperm. As small noncoding RNAs in sperm have been shown to causally induce heritable phenotypes in offspring, additional research is warranted to understand the potential effects of ethanol-responsive sperm small noncoding RNAs on offspring health and development.

Heavy Chronic Intermittent Ethanol Exposure Alters Small Noncoding RNAs in Mouse Sperm and Epididymosomes

PubMed Central

Rompala, Gregory R.; Mounier, Anais; Wolfe, Cody M.; Lin, Qishan; Lefterov, Iliya; Homanics, Gregg E.

2018-01-01

While the risks of maternal alcohol abuse during pregnancy are well-established, several preclinical studies suggest that chronic preconception alcohol consumption by either parent may also have significance consequences for offspring health and development. Notably, since isogenic male mice used in these studies are not involved in gestation or rearing of offspring, the cross-generational effects of paternal alcohol exposure suggest a germline-based epigenetic mechanism. Many recent studies have demonstrated that the effects of paternal environmental exposures such as stress or malnutrition can be transmitted to the next generation via alterations to small noncoding RNAs in sperm. Therefore, we used high throughput sequencing to examine the effect of preconception ethanol on small noncoding RNAs in sperm. We found that chronic intermittent ethanol exposure altered several small noncoding RNAs from three of the major small RNA classes in sperm, tRNA-derived small RNA (tDR), mitochondrial small RNA, and microRNA. Six of the ethanol-responsive small noncoding RNAs were evaluated with RT-qPCR on a separate cohort of mice and five of the six were confirmed to be altered by chronic ethanol exposure, supporting the validity of the sequencing results. In addition to altered sperm RNA abundance, chronic ethanol exposure affected post-transcriptional modifications to sperm small noncoding RNAs, increasing two nucleoside modifications previously identified in mitochondrial tRNA. Furthermore, we found that chronic ethanol reduced epididymal expression of a tRNA methyltransferase, Nsun2, known to directly regulate tDR biogenesis. Finally, ethanol-responsive sperm tDR are similarly altered in extracellular vesicles of the epididymis (i.e., epididymosomes), supporting the hypothesis that alterations to sperm tDR emerge in the epididymis and that epididymosomes are the primary source of small noncoding RNAs in sperm. These results add chronic ethanol to the growing list of paternal exposures that can affect small noncoding RNA abundance and nucleoside modifications in sperm. As small noncoding RNAs in sperm have been shown to causally induce heritable phenotypes in offspring, additional research is warranted to understand the potential effects of ethanol-responsive sperm small noncoding RNAs on offspring health and development. PMID:29472946

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo.

PubMed

Zubradt, Meghan; Gupta, Paromita; Persad, Sitara; Lambowitz, Alan M; Weissman, Jonathan S; Rouskin, Silvi

2017-01-01

Coupling of structure-specific in vivo chemical modification to next-generation sequencing is transforming RNA secondary structure studies in living cells. The dominant strategy for detecting in vivo chemical modifications uses reverse transcriptase truncation products, which introduce biases and necessitate population-average assessments of RNA structure. Here we present dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase. DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features per molecule, and allows both genome-wide studies and focused in vivo investigations of even low-abundance RNAs. We apply DMS-MaPseq for the first analysis of RNA structure within an animal tissue and to identify a functional structure involved in noncanonical translation initiation. Additionally, we use DMS-MaPseq to compare the in vivo structure of pre-mRNAs with their mature isoforms. These applications illustrate DMS-MaPseq's capacity to dramatically expand in vivo analysis of RNA structure.

A Vastly Increased Chemical Variety of RNA Modifications Containing a Thioacetal Structure.

PubMed

Dal Magro, Christina; Keller, Patrick; Kotter, Annika; Werner, Stephan; Duarte, Victor; Marchand, Virginie; Ignarski, Michael; Freiwald, Anja; Müller, Roman-Ulrich; Dieterich, Christoph; Motorin, Yuri; Butter, Falk; Atta, Mohamed; Helm, Mark

2018-06-25

Recently discovered new chemical entities in RNA modifications have involved surprising functional groups that enlarge the chemical space of RNA. Using LC-MS, we found over 100 signals of RNA constituents that contained a ribose moiety in tRNAs from E. coli. Feeding experiments with variegated stable isotope labeled compounds identified 37 compounds that are new structures of RNA modifications. One structure was elucidated by deuterium exchange and high-resolution mass spectrometry. The structure of msms 2 i 6 A (2-methylthiomethylenethio-N6-isopentenyl-adenosine) was confirmed by methione-D3 feeding experiments and by synthesis of the nucleobase. The msms 2 i 6 A contains a thioacetal, shown in vitro to be biosynthetically derived from ms 2 i 6 A by the radical-SAM enzyme MiaB. This enzyme performs thiomethylation, forming ms 2 i 6 A from i 6 A in a first turnover. The new thioacetal is formed by a second turnover. Along with the pool of 36 new modifications, this work describes a new layer of RNA modification chemistry. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

[The psychometric properties of the new Turkish generic health-related quality of life questionnaire for children (Kid-KINDL)].

PubMed

Eser, Erhan; Yüksel, Hasan; Baydur, Hakan; Erhart, Michael; Saatli, Gül; Cengiz Ozyurt, Beyhan; Ozcan, Cemil; Ravens-Sieberer, Ulrike

2008-01-01

There are few health-related quality of life (HRQOL) instruments available that have been validated for use with Turkish children. The Kid-KINDL is a generic measure of children's (8-12 years) HRQOL, which contains 24 categorical items that assess 6 dimensions (physical well-being, emotional well-being, self-esteem, family, friends, and school). The Kid-KINDL is available in many languages. Following an elaborate translation procedure and cognitive focus group interviews, the Kid-KINDL was adopted into Turkish. This paper describes the psychometric properties of the new Turkish Kid-KINDL. In total, 1918 children aged 8-12 years at a school in Manisa completed the Kid-KINDL. A confirmatory approach was used for validity and reliability analysis. Using the Multi-trait/Multi-item analysis program (MAP) item-internal consistency and item-discriminant validity were calculated to confirm the instrument's structure. Likert scaling assumptions were tested and confirmatory factor analysis (CFA) was applied as well. After modification of 2 unsatisfactory items the Kid-KINDL was administered to a different group of 84 randomly selected children and the analyses were repeated. Cronbach's alpha was 0.35-0.78 before and 0.54-0.78 after the scales was modified. MAP-scaling success was 60%-100% before and 90%-100% after the modification. CFA confirmed the Kid-KINDL structure for the original version (RMSEA = 0.077) was less than the modified version (RMSEA = 0.059), although for the latter the sample was rather small. Floor effects were negligible, and ceiling effects reached 19%. The results indicate that the Turkish Kid-KINDL was a reliable and factorially valid assessment of the children's HRQOL. The modifications made to the 2 unsatisfactory items increased the psychometric quality of the scale.

Molecular recognition of a model globular protein apomyoglobin by synthetic receptor cyclodextrin: effect of fluorescence modification of the protein and cavity size of the receptor in the interaction.

PubMed

Saha, Ranajay; Rakshit, Surajit; Pal, Samir Kumar

2013-11-01

Labelling of proteins with some extrinsic probe is unavoidable in molecular biology research. Particularly, spectroscopic studies in the optical region require fluorescence modification of native proteins by attaching polycyclic aromatic fluoroprobe with the proteins under investigation. Our present study aims to address the consequence of the attachment of a fluoroprobe at the protein surface in the molecular recognition of the protein by selectively small model receptor. A spectroscopic study involving apomyoglobin (Apo-Mb) and cyclodextrin (CyD) of various cavity sizes as model globular protein and synthetic receptors, respectively, using steady-state and picosecond-resolved techniques, is detailed here. A study involving Förster resonance energy transfer, between intrinsic amino acid tryptophan (donor) and N, N-dimethyl naphthalene moiety of the extrinsic dansyl probes at the surface of Apo-Mb, precisely monitor changes in donor acceptor distance as a consequence of interaction of the protein with CyD having different cavity sizes (β and γ variety). Molecular modelling studies on the interaction of tryptophan and dansyl probe with β-CyD is reported here and found to be consistent with the experimental observations. In order to investigate structural aspects of the interacting protein, we have used circular dichroism spectroscopy. Temperature-dependent circular dichroism studies explore the change in the secondary structure of Apo-Mb in association with CyD, before and after fluorescence modification of the protein. Overall, the study well exemplifies approaches to protein recognition by CyD as a synthetic receptor and offers a cautionary note on the use of hydrophobic fluorescent labels for proteins in biochemical studies involving recognition of molecules. Copyright © 2013 John Wiley & Sons, Ltd.

Hydro-Geomorphic Connectivity in Arid Watershed: Anthropogenic Effects and Extreme Flash flood

NASA Astrophysics Data System (ADS)

Egozi, Roey

2017-04-01

Arid watersheds are excellent settings to study water and sediment connectivity because of spars vegetation and the possibility to make clearer links between climate parameters and topographical changes. However different flood event magnitudes may result in different degrees of connectivity. This even gets more complicated when man made modifications to the drainage system are done without considering the outcomes in terms of the potential of flood damage and risks, i.e. in the case of extreme flash floods. Herein we report on the results from two studies conducted in two different small catchments along the dead sea rift: Wadi A Dalia and Wadi Ras Moakif. The studies conducted as part of a larger project aimed at investigating the floods and damages triggered by a rare storm event occurred at the end of October 2015. This storm event covered all of Israel and characterized with rare rainfall depths and intensities as well as floods with rare pick discharges. Observations and field measurements of bed material, river cross sections and water elevation markers were done and statistical analysis has been performed to estimate the exceed probability of the different measured and estimated hydro-climatic values. In Wadi-A-Dalia the coupling of rare rainfall depths over the watershed area which itself was bare due to over grazing result in a major flood. The severe damage caused by this flood was intensified due to the increase of structural hydrologic connectivity, i.e. flood protection canal discharged higher volumes of water collected from small Wadi systems at the same time. In Wadi Ras Moakif the rainfall cells did not produced rare rainfall, but still a major flood occurred over a very short distance of the main channel transporting huge amount of bed material deposited and blocked the main road along the dead sea western coast. In this case the cause was similar - a modification to the drainage system result in increase structural hydrologic connectivity lead to runoff concentration and higher stream power value. The results suggest that in arid watersheds flood protection measures that involve modifications to the drainage system such that the structural hydrologic connectivity improves with the aim to conduit the volume of water away may fail to provide the protection planned and may cause higher damage to infrastructures. Therefore, hydrologic connectivity should become a parameter in flood control design. Moreover, studying hydrologic connectivity in natural landscapes may provide valid solutions for flood control design projects.

48 CFR 307.7101 - Policy.

Code of Federal Regulations, 2010 CFR

2010-10-01

... services available from only one source. (4) Proposals under the Small Business Innovative Research (SBIR) and Small Business Technology Transfer (STTR) programs. (5) Acquisition of commercial items/services... under HHS-wide strategic sourcing vehicles. (8) Contract/order modifications that— (i) Exercise options...

A Method for Selecting Structure-switching Aptamers Applied to a Colorimetric Gold Nanoparticle Assay

PubMed Central

Martin, Jennifer A.; Smith, Joshua E.; Warren, Mercedes; Chávez, Jorge L.; Hagen, Joshua A.; Kelley-Loughnane, Nancy

2015-01-01

Small molecules provide rich targets for biosensing applications due to their physiological implications as biomarkers of various aspects of human health and performance. Nucleic acid aptamers have been increasingly applied as recognition elements on biosensor platforms, but selecting aptamers toward small molecule targets requires special design considerations. This work describes modification and critical steps of a method designed to select structure-switching aptamers to small molecule targets. Binding sequences from a DNA library hybridized to complementary DNA capture probes on magnetic beads are separated from nonbinders via a target-induced change in conformation. This method is advantageous because sequences binding the support matrix (beads) will not be further amplified, and it does not require immobilization of the target molecule. However, the melting temperature of the capture probe and library is kept at or slightly above RT, such that sequences that dehybridize based on thermodynamics will also be present in the supernatant solution. This effectively limits the partitioning efficiency (ability to separate target binding sequences from nonbinders), and therefore many selection rounds will be required to remove background sequences. The reported method differs from previous structure-switching aptamer selections due to implementation of negative selection steps, simplified enrichment monitoring, and extension of the length of the capture probe following selection enrichment to provide enhanced stringency. The selected structure-switching aptamers are advantageous in a gold nanoparticle assay platform that reports the presence of a target molecule by the conformational change of the aptamer. The gold nanoparticle assay was applied because it provides a simple, rapid colorimetric readout that is beneficial in a clinical or deployed environment. Design and optimization considerations are presented for the assay as proof-of-principle work in buffer to provide a foundation for further extension of the work toward small molecule biosensing in physiological fluids. PMID:25870978

Wheat hybridization and polyploidization results in deregulation of small RNAs.

PubMed

Kenan-Eichler, Michal; Leshkowitz, Dena; Tal, Lior; Noor, Elad; Melamed-Bessudo, Cathy; Feldman, Moshe; Levy, Avraham A

2011-06-01

Speciation via interspecific or intergeneric hybridization and polyploidization triggers genomic responses involving genetic and epigenetic alterations. Such modifications may be induced by small RNAs, which affect key cellular processes, including gene expression, chromatin structure, cytosine methylation and transposable element (TE) activity. To date, the role of small RNAs in the context of wide hybridization and polyploidization has received little attention. In this work, we performed high-throughput sequencing of small RNAs of parental, intergeneric hybrid, and allopolyploid plants that mimic the genomic changes occurring during bread wheat speciation. We found that the percentage of small RNAs corresponding to miRNAs increased with ploidy level, while the percentage of siRNAs corresponding to TEs decreased. The abundance of most miRNA species was similar to midparent values in the hybrid, with some deviations, as seen in overrepresentation of miR168, in the allopolyploid. In contrast, the number of siRNAs corresponding to TEs strongly decreased upon allopolyploidization, but not upon hybridization. The reduction in corresponding siRNAs, together with decreased CpG methylation, as shown here for the Veju element, represent hallmarks of TE activation. TE-siRNA downregulation in the allopolyploid may contribute to genome destabilization at the initial stages of speciation. This phenomenon is reminiscent of hybrid dysgenesis in Drosophila.

From Deuterium to Free Neutrons - Recent Experimental Results

NASA Astrophysics Data System (ADS)

Kuhn, Sebastian

2009-05-01

Lepton scattering has long been used to gather data on the internal structure of both protons and neutrons. Assuming isospin symmetry, these data can be used to pin down the contributions of both u and d quarks to the spatial and momentum-spin structure of the nucleon and its excitations. In this context, information on the neutron is crucial and is typically obtained from experiments on few-body nuclear targets (predominantly ^3He and deuterium). However, the need to account for binding effects complicates the interpretation of these experiments. On the other hand, detailed studies of the reaction mechanism can yield important new information on the structure of few-body nuclei and the interplay of nuclear and quark degrees of freedom. Recent theoretical and experimental advances have allowed us to make significant progress on both fronts -- a cleaner extraction of neutron properties from nuclear data and a better understanding of nuclear modifications of the bound neutron structure. I will concentrate on recent results on the deuteron. I will present a new extraction of neutron spin structure functions in the resonance and large-x region (from the EG1 experiment with CLAS at Jefferson Lab). The same data can also be used for a detailed comparison with modern calculations of quasi-elastic spin-dependent scattering on the deuteron. A second experimental program with CLAS uses the technique of ``spectator tagging'' to extract the unpolarized structure functions of the neutron with minimal uncertainties from nuclear effects. By mapping out the dependence of the cross section on the ``spectator'' momentum, we can learn about final state interactions between the struck nucleon and the spectator, as well as modifications of the neutron structure due to nuclear binding. I will present preliminary results from the ``BoNuS'' experiment which pushed the detection limit of the spectator proton down to momenta of 70 MeV/c, where nuclear corrections should become small.

Structural Analysis of PTM Hotspots (SAPH-ire)--A Quantitative Informatics Method Enabling the Discovery of Novel Regulatory Elements in Protein Families.

PubMed

Dewhurst, Henry M; Choudhury, Shilpa; Torres, Matthew P

2015-08-01

Predicting the biological function potential of post-translational modifications (PTMs) is becoming increasingly important in light of the exponential increase in available PTM data from high-throughput proteomics. We developed structural analysis of PTM hotspots (SAPH-ire)--a quantitative PTM ranking method that integrates experimental PTM observations, sequence conservation, protein structure, and interaction data to allow rank order comparisons within or between protein families. Here, we applied SAPH-ire to the study of PTMs in diverse G protein families, a conserved and ubiquitous class of proteins essential for maintenance of intracellular structure (tubulins) and signal transduction (large and small Ras-like G proteins). A total of 1728 experimentally verified PTMs from eight unique G protein families were clustered into 451 unique hotspots, 51 of which have a known and cited biological function or response. Using customized software, the hotspots were analyzed in the context of 598 unique protein structures. By comparing distributions of hotspots with known versus unknown function, we show that SAPH-ire analysis is predictive for PTM biological function. Notably, SAPH-ire revealed high-ranking hotspots for which a functional impact has not yet been determined, including phosphorylation hotspots in the N-terminal tails of G protein gamma subunits--conserved protein structures never before reported as regulators of G protein coupled receptor signaling. To validate this prediction we used the yeast model system for G protein coupled receptor signaling, revealing that gamma subunit-N-terminal tail phosphorylation is activated in response to G protein coupled receptor stimulation and regulates protein stability in vivo. These results demonstrate the utility of integrating protein structural and sequence features into PTM prioritization schemes that can improve the analysis and functional power of modification-specific proteomics data. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Resilience of biochemical activity in protein domains in the face of structural divergence.

PubMed

Zhang, Dapeng; Iyer, Lakshminarayan M; Burroughs, A Maxwell; Aravind, L

2014-06-01

Recent studies point to the prevalence of the evolutionary phenomenon of drastic structural transformation of protein domains while continuing to preserve their basic biochemical function. These transformations span a wide spectrum, including simple domains incorporated into larger structural scaffolds, changes in the structural core, major active site shifts, topological rewiring and extensive structural transmogrifications. Proteins from biological conflict systems, such as toxin-antitoxin, restriction-modification, CRISPR/Cas, polymorphic toxin and secondary metabolism systems commonly display such transformations. These include endoDNases, metal-independent RNases, deaminases, ADP ribosyltransferases, immunity proteins, kinases and E1-like enzymes. In eukaryotes such transformations are seen in domains involved in chromatin-related peptide recognition and protein/DNA-modification. Intense selective pressures from 'arms-race'-like situations in conflict and macromolecular modification systems could favor drastic structural divergence while preserving function. Published by Elsevier Ltd.

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

PubMed Central

Schadt, Eric E.; Banerjee, Onureena; Fang, Gang; Feng, Zhixing; Wong, Wing H.; Zhang, Xuegong; Kislyuk, Andrey; Clark, Tyson A.; Luong, Khai; Keren-Paz, Alona; Chess, Andrew; Kumar, Vipin; Chen-Plotkin, Alice; Sondheimer, Neal; Korlach, Jonas; Kasarskis, Andrew

2013-01-01

Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of interest, progress has not been as dramatic regarding epigenetic changes and base-level damage to DNA, largely due to technological limitations in assaying all known and unknown types of modifications at genome scale. Recently, single-molecule real time (SMRT) sequencing has been reported to identify kinetic variation (KV) events that have been demonstrated to reflect epigenetic changes of every known type, providing a path forward for detecting base modifications as a routine part of sequencing. However, to date no statistical framework has been proposed to enhance the power to detect these events while also controlling for false-positive events. By modeling enzyme kinetics in the neighborhood of an arbitrary location in a genomic region of interest as a conditional random field, we provide a statistical framework for incorporating kinetic information at a test position of interest as well as at neighboring sites that help enhance the power to detect KV events. The performance of this and related models is explored, with the best-performing model applied to plasmid DNA isolated from Escherichia coli and mitochondrial DNA isolated from human brain tissue. We highlight widespread kinetic variation events, some of which strongly associate with known modification events, while others represent putative chemically modified sites of unknown types. PMID:23093720

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases.

PubMed

Schadt, Eric E; Banerjee, Onureena; Fang, Gang; Feng, Zhixing; Wong, Wing H; Zhang, Xuegong; Kislyuk, Andrey; Clark, Tyson A; Luong, Khai; Keren-Paz, Alona; Chess, Andrew; Kumar, Vipin; Chen-Plotkin, Alice; Sondheimer, Neal; Korlach, Jonas; Kasarskis, Andrew

2013-01-01

Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of interest, progress has not been as dramatic regarding epigenetic changes and base-level damage to DNA, largely due to technological limitations in assaying all known and unknown types of modifications at genome scale. Recently, single-molecule real time (SMRT) sequencing has been reported to identify kinetic variation (KV) events that have been demonstrated to reflect epigenetic changes of every known type, providing a path forward for detecting base modifications as a routine part of sequencing. However, to date no statistical framework has been proposed to enhance the power to detect these events while also controlling for false-positive events. By modeling enzyme kinetics in the neighborhood of an arbitrary location in a genomic region of interest as a conditional random field, we provide a statistical framework for incorporating kinetic information at a test position of interest as well as at neighboring sites that help enhance the power to detect KV events. The performance of this and related models is explored, with the best-performing model applied to plasmid DNA isolated from Escherichia coli and mitochondrial DNA isolated from human brain tissue. We highlight widespread kinetic variation events, some of which strongly associate with known modification events, while others represent putative chemically modified sites of unknown types.

Design of S-Allylcysteine in Situ Production and Incorporation Based on a Novel Pyrrolysyl-tRNA Synthetase Variant.

PubMed

Exner, Matthias P; Kuenzl, Tilmann; To, Tuyet Mai T; Ouyang, Zhaofei; Schwagerus, Sergej; Hoesl, Michael G; Hackenberger, Christian P R; Lensen, Marga C; Panke, Sven; Budisa, Nediljko

2017-01-03

The noncanonical amino acid S-allyl cysteine (Sac) is one of the major compounds of garlic extract and exhibits a range of biological activities. It is also a small bioorthogonal alkene tag capable of undergoing controlled chemical modifications, such as photoinduced thiol-ene coupling or Pd-mediated deprotection. Its small size guarantees minimal interference with protein structure and function. Here, we report a simple protocol efficiently to couple in-situ semisynthetic biosynthesis of Sac and its incorporation into proteins in response to amber (UAG) stop codons. We exploited the exceptional malleability of pyrrolysyl-tRNA synthetase (PylRS) and evolved an S-allylcysteinyl-tRNA synthetase (SacRS) capable of specifically accepting the small, polar amino acid instead of its long and bulky aliphatic natural substrate. We succeeded in generating a novel and inexpensive strategy for the incorporation of a functionally versatile amino acid. This will help in the conversion of orthogonal translation from a standard technique in academic research to industrial biotechnology. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure, chaperone-like activity and allergenicity profile of bovine caseins upon peroxynitrite modification: New evidences underlying mastitis pathomechanisms.

PubMed

Sadeghian, Tanaz; Tavaf, Zohreh; Oryan, Ahmad; Shokouhi, Raheleh; Pourpak, Zahra; Moosavi-Movahedi, Ali Akbar; Yousefi, Reza

2018-01-01

Mastitis, an inflammatory reaction frequently develops in response to intra-mammary bacterial infection‌‌, may induce the generation of peroxynitrite (PON)‌ which is a highly potent reactive oxygen and nitrogen species. Caseins as the intrinsically unfolded proteins seem feasible substrates to react with PON. Therefore, in the current study, structural and functional aspects of both β-casein (β-CN) and whole casein fraction (WCF) were evaluated after PON modification, using a variety of techniques. Modification of the bovine caseins with PON results in an important enhancement in the carbonyl, nitrotryptophan, nitrotyrosine and dityrosine content of these proteins‌. The results of fluorescence and far UV-CD assessments suggested significant structural alteration of caseins upon PON-modification. The chaperone-like activity of β-casein was significantly altered after PON modification. The results of scanning electron microscopy suggest that bovine caseins display unique morphological features after treatment with PON. Also, the PON-modified caseins preserved their allergenicity profile and displayed partial resistance against digestion by the pancreatic proteases. Ascorbic acid, an important antioxidant component of milk, was also capable to significantly prevent the PON-induced structural damages in bovine milk caseins. In conclusion, our results suggest that PON may have significant role in the structural and functional alteration of milk caseins. Also, the PON-induced structural damaging effects of caseins might be effectively prevented by a sufficient level of milk antioxidant components particularly by ascorbic acid. Copyright © 2017 Elsevier B.V. All rights reserved.

Favorable 2'-substitution in the loop region of a thrombin-binding DNA aptamer.

PubMed

Awachat, Ragini; Wagh, Atish A; Aher, Manisha; Fernandes, Moneesha; Kumar, Vaijayanti A

2018-06-01

Simple 2'-OMe-chemical modification in the loop region of the 15mer G-rich DNA sequence GGTTGGTGTGGTTGG is reported. The G-quadruplex structure of this thrombin-binding aptamer (TBA), is stabilized by single modifications (T → 2'-OMe-U), depending on the position of the modification. The structural stability also renders significantly increased inhibition of thrombin-induced fibrin polymerization, a process closely associated with blood-clotting. Copyright © 2018 Elsevier Ltd. All rights reserved.

In vitro isolation of small-molecule-binding aptamers with intrinsic dye-displacement functionality

PubMed Central

Yu, Haixiang; Yang, Weijuan; Alkhamis, Obtin; Canoura, Juan; Yang, Kyung-Ae; Xiao, Yi

2018-01-01

Abstract Aptamer-based sensors offer a powerful tool for molecular detection, but the practical implementation of these biosensors is hindered by costly and laborious sequence engineering and chemical modification procedures. We report a simple strategy for directly isolating signal-reporting aptamers in vitro through systematic evolution of ligands by exponential enrichment (SELEX) that transduce binding events into a detectable change of absorbance via target-induced displacement of a small-molecule dye. We first demonstrate that diethylthiatricarbocyanine (Cy7) can stack into DNA three-way junctions (TWJs) in a sequence-independent fashion, greatly altering the dye's absorbance spectrum. We then design a TWJ-containing structured library and isolate an aptamer against 3,4-methylenedioxypyrovalerone (MDPV), a synthetic cathinone that is an emerging drug of abuse. This aptamer intrinsically binds Cy7 within its TWJ domain, but MDPV efficiently displaces the dye, resulting in a change in absorbance within seconds. This assay is label-free, and detects nanomolar concentrations of MDPV. It also recognizes other synthetic cathinones, offering the potential to detect newly-emerging designer drugs, but does not detect structurally-similar non-cathinone compounds or common cutting agents. Moreover, we demonstrate that the Cy7-displacement colorimetric assay is more sensitive than a conventional strand-displacement fluorescence assay. We believe our strategy offers an effective generalized approach for the development of sensitive dye-displacement colorimetric assays for other small-molecule targets. PMID:29361056

CryoEM structure of the human SLC4A4 sodium-coupled acid-base transporter NBCe1.

PubMed

Huynh, Kevin W; Jiang, Jiansen; Abuladze, Natalia; Tsirulnikov, Kirill; Kao, Liyo; Shao, Xuesi; Newman, Debra; Azimov, Rustam; Pushkin, Alexander; Zhou, Z Hong; Kurtz, Ira

2018-03-02

Na + -coupled acid-base transporters play essential roles in human biology. Their dysfunction has been linked to cancer, heart, and brain disease. High-resolution structures of mammalian Na + -coupled acid-base transporters are not available. The sodium-bicarbonate cotransporter NBCe1 functions in multiple organs and its mutations cause blindness, abnormal growth and blood chemistry, migraines, and impaired cognitive function. Here, we have determined the structure of the membrane domain dimer of human NBCe1 at 3.9 Å resolution by cryo electron microscopy. Our atomic model and functional mutagenesis revealed the ion accessibility pathway and the ion coordination site, the latter containing residues involved in human disease-causing mutations. We identified a small number of residues within the ion coordination site whose modification transformed NBCe1 into an anion exchanger. Our data suggest that symporters and exchangers utilize comparable transport machinery and that subtle differences in their substrate-binding regions have very significant effects on their transport mode.

New isoxazolidinone and 3,4-dehydro-β-proline derivatives as antibacterial agents and MAO-inhibitors: A complex balance between two activities.

PubMed

Ferrazzano, Lucia; Viola, Angelo; Lonati, Elena; Bulbarelli, Alessandra; Musumeci, Rosario; Cocuzza, Clementina; Lombardo, Marco; Tolomelli, Alessandra

2016-11-29

Among the different classes of antibiotics, oxazolidinone derivatives represent important drugs, since their unique mechanism of action overcomes commonly diffused multidrug-resistant bacteria. Anyway, the structural similarity of these molecules to monoamino oxidase (MAO) inhibitors, like toloxatone and blefoxatone, induces in many cases loss of selectivity as a major concern. A small library of compounds based on isoxazolidinone and dehydro-β-proline scaffold was designed with the aim to obtain antibacterial agents, evaluating at the same time the potential effects of structural features on MAO inhibitory behaviour. The structural modification introduced in the backbone, starting from Linezolid model, lead to a significant loss in antibiotic activity, while a promising inhibitory effect could be observed on monoamino oxidases. These interesting results are also in agreement with docking experiments suggesting a good binding pose of the synthesized compounds into the pocket of the oxidase enzymes, in particular of MAO-B. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Additive Manufacturing of Composites and Complex Materials

NASA Astrophysics Data System (ADS)

Spowart, Jonathan E.; Gupta, Nikhil; Lehmhus, Dirk

2018-03-01

Advanced composite materials form an important class of high-performance industrial materials used in weight-sensitive applications such as aerospace structures, automotive structures and sports equipment. In many of these applications, parts are made in small production runs, are highly customized and involve long process development times. Developments in additive manufacturing (AM) methods have helped in overcoming many of these limitations. The special topic of Additive Manufacturing of Composites and Complex Materials captures the state of the art in this area by collecting nine papers that present much novel advancement in this field. The studies under this topic show advancement in the area of AM of carbon fiber and graphene-reinforced composites with high thermal and electrical conductivities, development of new hollow glass particle-filled syntactic foam filaments for printing lightweight structures and integration of sensors or actuators during AM of metallic parts. Some of the studies are focused on process optimization or modification to increase the manufacturing speed or tuning manufacturing techniques to enable AM of new materials.

Propagation of electromagnetic waves in a turbulent medium

NASA Technical Reports Server (NTRS)

Canuto, V. M.; Hartke, G. J.

1986-01-01

Theoretical modeling of the wealth of experimental data on propagation of electromagnetic radiation through turbulent media has centered on the use of the Heisenberg-Kolmogorov (HK) model, which is, however, valid only for medium to small sized eddies. Ad hoc modifications of the HK model to encompass the large-scale region of the eddy spectrum have been widely used, but a sound physical basis has been lacking. A model for large-scale turbulence that was recently proposed is applied to the above problem. The spectral density of the temperature field is derived and used to calculate the structure function of the index of refraction N. The result is compared with available data, yielding a reasonably good fit. The variance of N is also in accord with the data. The model is also applied to propagation effects. The phase structure function, covariance of the log amplitude, and variance of the log intensity are calculated. The calculated phase structure function is in excellent agreement with available data.

Epigenomic landscape modified by histone modification correlated with activation of IGF2 gene

USDA-ARS?s Scientific Manuscript database

The links of histone post-translational modifications and chromatin structure to cell cycle progression, DNA replication, and overall chromosome functions are very clear. The modulation of genome expression as a consequence of chromatin structural changes is most likely a basic mechanism. The epige...

Surface modifications of ultra-thin gold films by swift heavy ion irradiation

NASA Astrophysics Data System (ADS)

Dash, P.; Mallick, P.; Rath, H.; Dash, B. N.; Tripathi, A.; Prakash, Jai; Avasthi, D. K.; Satyam, P. V.; Mishra, N. C.

2010-10-01

Gold films of thickness 10 and 20 nm grown on float glass substrate by thermal evaporation technique were irradiated with 107 MeV Ag8+ and 58 MeV Ni5+ ions at different fluences and characterized by Grazing Incidence X-ray Diffraction (GIXRD) and Atomic Force Microscopy (AFM). The pristine films were continuous and no island structures were found even at these small thicknesses. The surface roughness estimated from AFM data did not show either monotonic increase or decrease with ion fluences. Instead, it increased at low fluences and decreased at high fluences for 20 nm thick film. In the 10 nm film roughness first increased with ion fluence, then decreased and again increased at higher fluences. The pattern of variation, however, was identical for Ni and Ag beams. Both the beams led to the formation of cracks on the film surface at intermediate fluences. The observed ion-irradiation induced thickness dependent topographic modification is explained by the spatial confinement of the energy deposited by ions in the reduced dimension of the films.

A plant derived multifunctional tool for nanobiotechnology based on Tomato bushy stunt virus.

PubMed

Grasso, Simone; Lico, Chiara; Imperatori, Francesca; Santi, Luca

2013-06-01

Structure, size, physicochemical properties and production strategies make many plant viruses ideal protein based nanoscaffolds, nanocontainers and nano-building blocks expected to deliver a multitude of applications in different fields such as biomedicine, pharmaceutical chemistry, separation science, catalytic chemistry, crop pest control and biomaterials science. Functionalization of viral nanoparticles through modification by design of their external and internal surfaces is essential to fully exploit the potentiality of these objects. In the present paper we describe the development of a plant derived multifunctional tool for nanobiotechnology based on Tomato bushy stunt virus. We demonstrate the ability of this system to remarkably sustain genetic modifications and in vitro chemical derivatizations of its outer surface, which resulted in the successful display of large chimeric peptides fusions and small chemical molecules, respectively. Moreover, we have defined physicochemical conditions for viral swelling and reversible viral pore gating that we have successfully employed for foreign molecules loading and retention in the inner cavity of this plant virus nanoparticles system. Finally, a production and purification strategy from Nicotiana benthamiana plants has been addressed and optimized.

Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone

PubMed Central

Sheng, Jia; Zhang, Wen; Hassan, Abdalla E. A.; Gan, Jianhua; Soares, Alexei S.; Geng, Song; Ren, Yi; Huang, Zhen

2012-01-01

Natural RNAs, especially tRNAs, are extensively modified to tailor structure and function diversities. Uracil is the most modified nucleobase among all natural nucleobases. Interestingly, >76% of uracil modifications are located on its 5-position. We have investigated the natural 5-methoxy (5-O-CH3) modification of uracil in the context of A-form oligonucleotide duplex. Our X-ray crystal structure indicates first a H-bond formation between the uracil 5-O-CH3 and its 5′-phosphate. This novel H-bond is not observed when the oxygen of 5-O-CH3 is replaced with a larger atom (selenium or sulfur). The 5-O-CH3 modification does not cause significant structure and stability alterations. Moreover, our computational study is consistent with the experimental observation. The investigation on the uracil 5-position demonstrates the importance of this RNA modification at the atomic level. Our finding suggests a general interaction between the nucleobase and backbone and reveals a plausible function of the tRNA 5-O-CH3 modification, which might potentially rigidify the local conformation and facilitates translation. PMID:22641848

The computational nature of memory modification.

PubMed

Gershman, Samuel J; Monfils, Marie-H; Norman, Kenneth A; Niv, Yael

2017-03-15

Retrieving a memory can modify its influence on subsequent behavior. We develop a computational theory of memory modification, according to which modification of a memory trace occurs through classical associative learning, but which memory trace is eligible for modification depends on a structure learning mechanism that discovers the units of association by segmenting the stream of experience into statistically distinct clusters (latent causes). New memories are formed when the structure learning mechanism infers that a new latent cause underlies current sensory observations. By the same token, old memories are modified when old and new sensory observations are inferred to have been generated by the same latent cause. We derive this framework from probabilistic principles, and present a computational implementation. Simulations demonstrate that our model can reproduce the major experimental findings from studies of memory modification in the Pavlovian conditioning literature.

Structure-Function, Stability, and Chemical Modification of the Cyanobacterial Cytochrome b6f Complex from Nostoc sp. PCC 7120*

PubMed Central

Baniulis, Danas; Yamashita, Eiki; Whitelegge, Julian P.; Zatsman, Anna I.; Hendrich, Michael P.; Hasan, S. Saif; Ryan, Christopher M.; Cramer, William A.

2009-01-01

The crystal structure of the cyanobacterial cytochrome b6f complex has previously been solved to 3.0-Å resolution using the thermophilic Mastigocladus laminosus whose genome has not been sequenced. Several unicellular cyanobacteria, whose genomes have been sequenced and are tractable for mutagenesis, do not yield b6f complex in an intact dimeric state with significant electron transport activity. The genome of Nostoc sp. PCC 7120 has been sequenced and is closer phylogenetically to M. laminosus than are unicellular cyanobacteria. The amino acid sequences of the large core subunits and four small peripheral subunits of Nostoc are 88 and 80% identical to those in the M. laminosus b6f complex. Purified b6f complex from Nostoc has a stable dimeric structure, eight subunits with masses similar to those of M. laminosus, and comparable electron transport activity. The crystal structure of the native b6f complex, determined to a resolution of 3.0Å (PDB id: 2ZT9), is almost identical to that of M. laminosus. Two unique aspects of the Nostoc complex are: (i) a dominant conformation of heme bp that is rotated 180° about the α- and γ-meso carbon axis relative to the orientation in the M. laminosus complex and (ii) acetylation of the Rieske iron-sulfur protein (PetC) at the N terminus, a post-translational modification unprecedented in cyanobacterial membrane and electron transport proteins, and in polypeptides of cytochrome bc complexes from any source. The high spin electronic character of the unique heme cn is similar to that previously found in the b6f complex from other sources. PMID:19189962

Composition dependent structural and optical properties of PbF₂-TeO₂-B₂O₃-Eu₂O₃ glasses.

PubMed

Wagh, Akshatha; Raviprakash, Y; Upadhyaya, Vyasa; Kamath, Sudha D

2015-12-05

Boric oxide based quaternary glasses in the system PbF2-TeO2-B2O3-Eu2O3 have been prepared by melt quenching technique. Density, molar volume, FTIR, UV-Vis techniques were used to probe the structural modifications with incorporation of europium ions in the glass network. An increase in glass density & decrease in molar volume (Vm) values proved the structural changes occurring in coordination of boron atom [conversion of BO3 units to BO4]. This resulted in the increase of the compaction of the prepared glasses with increase in Eu2O3 contents. The amorphous natures of the samples were ascertained by XRD and metallization criterion (M) studies. XPS study showed the values of core-level binding energy [O1s, Eu3d, Eu4d, Te3d, Te4d, Pd4f, Pb5d, O1s, and F1s] of (PbF2-TeO2-B2O3-Eu2O3) the glass matrix. The frequency and temperature dependence of dielectric properties of present glasses were investigated in the frequency range of 1 Hz-10 MHz and temperature range of 313-773K. The study of dielectric measurements proved good insulating and thermal stability of the prepared glasses. At room temperature, dielectric loss [tanδ] values were negligibly small for prepared glasses and increased with increase in temperature. FTIR spectroscopy results were in good agreement with optical band energy gap, density, molar volume and hardness values revealing network modifications caused by europium ions in the glass structure. Copyright © 2015 Elsevier B.V. All rights reserved.

Structural control of caspase-generated glutamyl-tRNA synthetase by appended noncatalytic WHEP domains.

PubMed

Halawani, Dalia; Gogonea, Valentin; DiDonato, Joseph A; Pipich, Vitaliy; Yao, Peng; China, Arnab; Topbas, Celalettin; Vasu, Kommireddy; Arif, Abul; Hazen, Stanley L; Fox, Paul L

2018-06-08

Aminoacyl-tRNA synthetases are ubiquitous, evolutionarily conserved enzymes catalyzing the conjugation of amino acids onto cognate tRNAs. During eukaryotic evolution, tRNA synthetases have been the targets of persistent structural modifications. These modifications can be additive, as in the evolutionary acquisition of noncatalytic domains, or subtractive, as in the generation of truncated variants through regulated mechanisms such as proteolytic processing, alternative splicing, or coding region polyadenylation. A unique variant is the human glutamyl-prolyl-tRNA synthetase (EPRS) consisting of two fused synthetases joined by a linker containing three copies of the WHEP domain (termed by its presence in tryptophanyl-, histidyl-, and glutamyl-prolyl-tRNA synthetases). Here, we identify site-selective proteolysis as a mechanism that severs the linkage between the EPRS synthetases in vitro and in vivo Caspase action targeted Asp-929 in the third WHEP domain, thereby separating the two synthetases. Using a neoepitope antibody directed against the newly exposed C terminus, we demonstrate EPRS cleavage at Asp-929 in vitro and in vivo Biochemical and biophysical characterizations of the N-terminally generated EPRS proteoform containing the glutamyl-tRNA synthetase and most of the linker, including two WHEP domains, combined with structural analysis by small-angle neutron scattering, revealed a role for the WHEP domains in modulating conformations of the catalytic core and GSH- S -transferase-C-terminal-like (GST-C) domain. WHEP-driven conformational rearrangement altered GST-C domain interactions and conferred distinct oligomeric states in solution. Collectively, our results reveal long-range conformational changes imposed by the WHEP domains and illustrate how noncatalytic domains can modulate the global structure of tRNA synthetases in complex eukaryotic systems. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Structure-Function, Stability, and Chemical Modification of the Cyanobacterial Cytochrome b[subscript 6]f Complex from Nostoc sp. PCC 7120

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

Baniulis, Danas; Yamashita, Eiki; Whitelegge, Julian P.

2009-06-08

The crystal structure of the cyanobacterial cytochrome b{sub 6}f complex has previously been solved to 3.0-{angstrom} resolution using the thermophilic Mastigocladus laminosus whose genome has not been sequenced. Several unicellular cyanobacteria, whose genomes have been sequenced and are tractable for mutagenesis, do not yield b{sub 6}f complex in an intact dimeric state with significant electron transport activity. The genome of Nostoc sp. PCC 7120 has been sequenced and is closer phylogenetically to M. laminosus than are unicellular cyanobacteria. The amino acid sequences of the large core subunits and four small peripheral subunits of Nostoc are 88 and 80% identical tomore » those in the M. laminosus b{sub 6}f complex. Purified b{sub 6}f complex from Nostoc has a stable dimeric structure, eight subunits with masses similar to those of M. laminosus, and comparable electron transport activity. The crystal structure of the native b{sub 6}f complex, determined to a resolution of 3.0{angstrom} (PDB id: 2ZT9), is almost identical to that of M. laminosus. Two unique aspects of the Nostoc complex are: (i) a dominant conformation of heme b{sub p} that is rotated 180 deg. about the {alpha}- and {gamma}-meso carbon axis relative to the orientation in the M. laminosus complex and (ii) acetylation of the Rieske iron-sulfur protein (PetC) at the N terminus, a post-translational modification unprecedented in cyanobacterial membrane and electron transport proteins, and in polypeptides of cytochrome bc complexes from any source. The high spin electronic character of the unique heme cn is similar to that previously found in the b{sub 6}f complex from other sources.« less

76 FR 37835 - Petitions for Modification of Application of Existing Mandatory Safety Standards

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-28

... small quantity of steel turnings, or other small magnetic particles, will be embedded in the top of the..., Cementation USA, to apply the 500 feet per minute requirement to the man-riding conveyance as well as the...

Chemical Methods for the Direct Detection and Labeling of S-Nitrosothiols

PubMed Central

Bechtold, Erika

2012-01-01

Abstract Significance: Posttranslational modification of proteins through phosphorylation, glycosylation, and oxidation adds complexity to the proteome by reversibly altering the structure and function of target proteins in a highly controlled fashion. Recent Advances: The study of reversible cysteine oxidation highlights a role for this oxidative modification in complex signal transduction pathways. Nitric oxide (NO), and its respective metabolites (including reactive nitrogen species), participates in a variety of these cellular redox processes, including the reversible oxidation of cysteine to S-nitrosothiols (RSNOs). RSNOs act as endogenous transporters of NO, but also possess beneficial effects independent of NO-related signaling, which suggests a complex and versatile biological role. In this review, we highlight the importance of RSNOs as a required posttranslational modification and summarize the current methods available for detecting S-nitrosation. Critical Issues: Given the limitations of these indirect detection methods, the review covers recent developments toward the direct detection of RSNOs by phosphine-based chemical probes. The intrinsic properties that dictate this phosphine/RSNO reactivity are summarized. In general, RSNOs (both small molecule and protein) react with phosphines to yield reactive S-substituted aza-ylides that undergo further reactions leading to stable RSNO-based adducts. Future Directions: This newly explored chemical reactivity forms the basis of a number of exciting potential chemical methods for protein RSNO detection in biological systems. Antioxid. Redox Signal. 17, 981–991. PMID:22356122

Authentication, integrity, and confidentiality in DICOM-structured reporting: concept and implementation

NASA Astrophysics Data System (ADS)

Riesmeier, Joerg; Eichelberg, Marco; Kleber, Klaus; Groenemeyer, Dietrich H.; Oosterwijk, Herman J.; Jensch, Peter F.

2002-05-01

With the release of 'DICOM Structured Reporting' (SR) as an official extension of the standard about two years ago, DICOM has entered a new domain that is only indirectly related to medical imaging. Basically, DICOM SR is a general model allowing to encode medical reports in a structured manner in DICOM's tag-based format. Therefore, the existing DICOM infrastructure can be used to archive and communicate structured reports, with only relatively small changes to existing systems. As a consequence of the introduction of medical reports in a digital form, the relevance of security measures increases significantly. We have developed a prototype implementation of DICOM structured reporting together with the new security extensions for secure transport connections and digital signatures. The application allows to create, read and modify any SR document, to digitally sign an SR document in whole or part and to transmit such documents over a network. While the secure transport connection protects data from modifications or unauthorized access only during transmission, digital signatures provide a lifetime integrity check and, therefore, maintain the legal document status of structured reports. The application has been successfully demonstrated at RSNA 2000 and ECR 2001, and is freely available on the Internet.

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

PubMed Central

Zubradt, Meghan; Gupta, Paromita; Persad, Sitara; Lambowitz, Alan M.; Weissman, Jonathan S.; Rouskin, Silvi

2017-01-01

Coupling structure-specific in vivo chemical modification to next-generation sequencing is transforming RNA secondary structural studies in living cells. The dominant strategy for detecting in vivo chemical modifications uses reverse transcriptase truncation products, which introduces biases and necessitates population-average assessments of RNA structure. Here we present dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase (TGIRT). DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features per molecule, and allows both genome-wide studies and focused in vivo investigations of even low abundance RNAs. We apply DMS-MaPseq for the first analysis of RNA structure within an animal tissue and to identify a functional structure involved in non-canonical translation initiation. Additionally, we use DMS-MaPseq to compare the in vivo structure of pre-mRNAs to their mature isoforms. These applications illustrate DMS-MaPseq’s capacity to dramatically expand in vivo analysis of RNA structure. PMID:27819661

Surface modification of paper on a continuous atmospheric-pressure-plasma system

NASA Astrophysics Data System (ADS)

Cruz-Barba, Luis Emilio

Plasma technologies for the continuous modification of materials in atmospheric-pressure-plasma conditions were used to evaluate the surface modification of paper under different plasma conditions. The generation of hydrophobic layers was used to characterize the efficiency of the originally designed system for future application in the paper industry. Generation of hydrophobic layers was carried out by deposition of thin layers from fluorine containing gases, as well as cross-linking of pre-deposited thin layers of hydrophobic materials, such as fluoropolymers and silicones, in a continuous system plasma reactor (CSPR). Physical and chemical characterization of these layers was carried out by X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), scanning electron microscopy (SEM), contact angle goniometry, and water absorption evaluations. Pure gaseous CF4 and a CF4/CH4 mixture were used to deposit fluorinated layers, rendering paper surfaces with low to moderate relative surface atomic contents of fluorine (2.5 to 16.3%). Morphological characterization revealed that the deposition consists of small clusters of fluorinated species scattered on the surface. Contact angle evaluations (50°--70°) indicated a reduction in the water affinity of the paper. Thin layers of fluoropolymer pre-deposited on paper surfaces were cross-linked in the presence of CF4, CF4/CH4, and NH 3 plasmas. All of the gases proved to be effective for the cross-linking under different conditions. These cross-linked layers were determined to maintain the original polymer structure, consisting mainly of CF2-CF 2 and small quantities of CFx. Surface characterization by AFM indicated lower roughness values compared to the untreated additive-free paper (45.1 vs 67.1 nm). Paper samples treated by this approach showed a highly hydrophobic character with up to 160° contact angles, and water absorption was reduced by as much as 61.6%. Silicone layers were cross-linked in the presence of argon and oxygen plasmas. Characterization of the silicone-coated paper indicated, as in the case of fluoropolymers, the retention of the original chemical structure. Surface roughness values (AFM) were in the range of 11.8 to 18.2 nm, evidence of a very smooth surface. High hydrophobicity levels were reached, as shown by contact angles of up to 126°, and water absorption showed a maximum reduction of 76.8%.

Structural evolution of zirconium carbide under ion irradiation

NASA Astrophysics Data System (ADS)

Gosset, D.; Dollé, M.; Simeone, D.; Baldinozzi, G.; Thomé, L.

2008-02-01

Zirconium carbide is one of the candidate materials to be used for some fuel components of the high temperature nuclear reactors planned in the frame of the Gen-IV project. Few data exist regarding its behaviour under irradiation. We have irradiated ZrC samples at room temperature with slow heavy ions (4 MeV Au, fluence from 10 11 to 5 × 10 15 cm -2) in order to simulate neutron irradiations. Grazing incidence X-Ray diffraction (GIXRD) and transmission electron microscopy (TEM) analysis have been performed in order to study the microstructural evolution of the material versus ion fluence. A high sensitivity to oxidation is observed with the formation of zirconia precipitates during the ion irradiations. Three damage stages are observed. At low fluence (<10 12 cm -2), low modifications are observed. At intermediate fluence, high micro-strains appear together with small faulted dislocation loops. At the highest fluence (>10 14 cm -2), the micro-strains saturate and the loops coalesce to form a dense dislocation network. No other structural modification is observed. The material shows a moderate cell parameter increase, corresponding to a 0.6 vol.% swelling, which saturates around 10 14 ions/cm 2, i.e., a few Zr dpa. As a result, in spite of a strong covalent bonding component, ZrC seems to have a behaviour under irradiation close to cubic metals.

Prenylated flavonoids as potent phosphodiesterase-4 inhibitors from Morus alba: Isolation, modification, and structure-activity relationship study.

PubMed

Guo, Yan-Qiong; Tang, Gui-Hua; Lou, Lan-Lan; Li, Wei; Zhang, Bei; Liu, Bo; Yin, Sheng

2018-01-20

The bioassay-guided phytochemical study of a traditional Chinese medicine Morus alba led to the isolation of 18 prenylated flavonoids (1-18), of which (±)-cyclomorusin (1/2), a pair of enantiomers, and 14-methoxy-dihydromorusin (3) are the new ones. Subsequent structural modification of the selected components by methylation, esterification, hydrogenation, and oxidative cyclization led to 14 more derivatives (19-32). The small library was screened for its inhibition against phosphodiesterase-4 (PDE4), which is a drug target for the treatment of asthma and chronic obstructive pulmonary disease (COPD). Among them, nine compounds (1-5, 8, 10, 16, and 17) exhibited remarkable activities with IC 50 values ranging from 0.0054 to 0.40 μM, being more active than the positive control rolipram (IC 50  = 0.62 μM). (+)-Cyclomorusin (1), the most active natural PDE4 inhibitor reported so far, also showed a high selectivity across other PDE members with the selective fold greater than 55. The SAR study revealed that the presence of prenyls at C-3 and/or C-8, 2H-pyran ring D, and the phenolic hydroxyl groups were important to the activity, which was further supported by the recognition mechanism study of the inhibitors with PDE4 by using molecular modeling. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Illuminating structure and acyl donor sites of a physiological transglutaminase substrate from Streptomyces mobaraensis.

PubMed

Juettner, Norbert E; Schmelz, Stefan; Bogen, Jan P; Happel, Dominic; Fessner, Wolf-Dieter; Pfeifer, Felicitas; Fuchsbauer, Hans-Lothar; Scrima, Andrea

2018-05-01

Transglutaminase from Streptomyces mobaraensis (MTG) has become a powerful tool to covalently and highly specifically link functional amines to glutamine donor sites of therapeutic proteins. However, details regarding the mechanism of substrate recognition and interaction of the enzyme with proteinaceous substrates still remain mostly elusive. We have determined the crystal structure of the Streptomyces papain inhibitory protein (SPI p ), a substrate of MTG, to study the influence of various substrate amino acids on positioning glutamine to the active site of MTG. SPI p exhibits a rigid, thermo-resistant double-psi-beta-barrel fold that is stabilized by two cysteine bridges. Incorporation of biotin cadaverine identified Gln-6 as the only amine acceptor site on SPI p accessible for MTG. Substitution of Lys-7 demonstrated that small and hydrophobic residues in close proximity to Gln-6 favor MTG-mediated modification and are likely to facilitate introduction of the substrate into the front vestibule of MTG. Moreover, exchange of various surface residues of SPI p for arginine and glutamate/aspartate outside the glutamine donor region influences the efficiency of modification by MTG. These results suggest the occurrence of charged contact areas between MTG and the acyl donor substrates beyond the front vestibule, and pave the way for protein engineering approaches to improve the properties of artificial MTG-substrates used in biomedical applications. © 2018 The Protein Society.

The helical domain of the EcoR124I motor subunit participates in ATPase activity and dsDNA translocation

PubMed Central

Shamayeva, Katsiaryna; Guzanova, Alena; Řeha, David; Csefalvay, Eva; Carey, Jannette; Weiserova, Marie

2017-01-01

Type I restriction-modification enzymes are multisubunit, multifunctional molecular machines that recognize specific DNA target sequences, and their multisubunit organization underlies their multifunctionality. EcoR124I is the archetype of Type I restriction-modification family IC and is composed of three subunit types: HsdS, HsdM, and HsdR. DNA cleavage and ATP-dependent DNA translocation activities are housed in the distinct domains of the endonuclease/motor subunit HsdR. Because the multiple functions are integrated in this large subunit of 1,038 residues, a large number of interdomain contacts might be expected. The crystal structure of EcoR124I HsdR reveals a surprisingly sparse number of contacts between helicase domain 2 and the C-terminal helical domain that is thought to be involved in assembly with HsdM. Only two potential hydrogen-bonding contacts are found in a very small contact region. In the present work, the relevance of these two potential hydrogen-bonding interactions for the multiple activities of EcoR124I is evaluated by analysing mutant enzymes using in vivo and in vitro experiments. Molecular dynamics simulations are employed to provide structural interpretation of the functional data. The results indicate that the helical C-terminal domain is involved in the DNA translocation, cleavage, and ATPase activities of HsdR, and a role in controlling those activities is suggested. PMID:28133570

Structural and theoretical basis for ligand exchange on thiolate monolayer protected gold nanoclusters.

PubMed

Heinecke, Christine L; Ni, Thomas W; Malola, Sami; Mäkinen, Ville; Wong, O Andrea; Häkkinen, Hannu; Ackerson, Christopher J

2012-08-15

Ligand exchange reactions are widely used for imparting new functionality on or integrating nanoparticles into devices. Thiolate-for-thiolate ligand exchange in monolayer protected gold nanoclusters has been used for over a decade; however, a firm structural basis of this reaction has been lacking. Herein, we present the first single-crystal X-ray structure of a partially exchanged Au(102)(p-MBA)(40)(p-BBT)(4) (p-MBA = para-mercaptobenzoic acid, p-BBT = para-bromobenzene thiol) with p-BBT as the incoming ligand. The crystal structure shows that 2 of the 22 symmetry-unique p-MBA ligand sites are partially exchanged to p-BBT under the initial fast kinetics in a 5 min timescale exchange reaction. Each of these ligand-binding sites is bonded to a different solvent-exposed Au atom, suggesting an associative mechanism for the initial ligand exchange. Density functional theory calculations modeling both thiol and thiolate incoming ligands postulate a mechanistic pathway for thiol-based ligand exchange. The discrete modification of a small set of ligand binding sites suggests Au(102)(p-MBA)(44) as a powerful platform for surface chemical engineering.

Nd and Ru co-doped bismuth titanate polycrystalline thin films with improved ferroelectric properties

NASA Astrophysics Data System (ADS)

Sahoo, Kishor Kumar; Singh Rajput, Shailendra; Gupta, Rajeev; Roy, Amritendu; Garg, Ashish

2018-02-01

We report the ferroelectric properties of pulsed laser deposited thin films of Nd and Ru co-doped bismuth titanate (Bi4-x Nd x Ti3-y Ru y O12). Structural analysis of the as-grown films, using x-ray diffraction, showed a single-phase formation with a polycrystalline structure. In comparison to un-doped and Nd-doped films, ferroelectric measurements on co-doped films demonstrated improved properties with remnant polarization (P r) ~ 12.5 µC cm-2 and an enhanced electrical fatigue life for Bi3.25Nd0.75Ti2.8Ru0.20O12 films. The enhancement in remanent polarization is attributed to microscopic changes, such as local structural distortion and the modification of the dynamical/effective charges on constituent ions due to chemical strain upon simultaneous Bi- (A) and Ti- (B) site doping with Nd and Ru, which has a far stronger effect than only A-site doping with Nd. Piezoresponse force microscopy further confirmed the polar structure and domain switching at nanoscale. The films exhibit small yet finite magnetization at 10 K resulting from strain.

Multifunctional Nanotube Polymer Nanocomposites for Aerospace Applications: Adhesion between SWCNT and Polymer Matrix

NASA Technical Reports Server (NTRS)

Park, Cheol; Wise, Kristopher E.; Kang, Jin Ho; Kim, Jae-Woo; Sauti, Godfrey; Lowther, Sharon E.; Lillehei, Peter T.; Smith, Michael W.; Siochi, Emilie J.; Harrison, Joycelyn S.;

Synthesis and structure-activity relationship of the first nonpeptidergic inverse agonists for the human cytomegalovirus encoded chemokine receptor US28.

PubMed

Hulshof, Janneke W; Casarosa, Paola; Menge, Wiro M P B; Kuusisto, Leena M S; van der Goot, Henk; Smit, Martine J; de Esch, Iwan J P; Leurs, Rob

2005-10-06

US28 is a human cytomegalovirus (HCMV) encoded G-protein-coupled receptor that signals in a constitutively active manner. Recently, we identified 1 [5-(4-(4-chlorophenyl)-4-hydroxypiperidin-1-yl)-2,2-diphenylpentanenitrile] as the first reported nonpeptidergic inverse agonist for a viral-encoded chemokine receptor. Interestingly, this compound is able to partially inhibit the viral entry of HIV-1. In this study we describe the synthesis of 1 and several of its analogues and unique structure-activity relationships for this first class of small-molecule ligands for the chemokine receptor US28. Moreover, the compounds have been pharmacologically characterized as inverse agonists on US28. By modification of lead structure 1, it is shown that a 4-phenylpiperidine moiety is essential for affinity and activity. Other structural features of 1 are shown to be of less importance. These compounds define the first SAR of ligands on a viral GPCR (US28) and may therefore serve as important tools to investigate the significance of US28-mediated constitutive activity during viral infection.

A review on the application of inorganic nano-structured materials in the modification of textiles: focus on anti-microbial properties.

PubMed

Dastjerdi, Roya; Montazer, Majid

2010-08-01

Textiles can provide a suitable substrate to grow micro-organisms especially at appropriate humidity and temperature in contact to human body. Recently, increasing public concern about hygiene has been driving many investigations for anti-microbial modification of textiles. However, using many anti-microbial agents has been avoided because of their possible harmful or toxic effects. Application of inorganic nano-particles and their nano-composites would be a good alternative. This review paper has focused on the properties and applications of inorganic nano-structured materials with good anti-microbial activity potential for textile modification. The discussed nano-structured anti-microbial agents include TiO(2) nano-particles, metallic and non-metallic TiO(2) nano-composites, titania nanotubes (TNTs), silver nano-particles, silver-based nano-structured materials, gold nano-particles, zinc oxide nano-particles and nano-rods, copper nano-particles, carbon nanotubes (CNTs), nano-clay and its modified forms, gallium, liposomes loaded nano-particles, metallic and inorganic dendrimers nano-composite, nano-capsules and cyclodextrins containing nano-particles. This review is also concerned with the application methods for the modification of textiles using nano-structured materials. Copyright 2010 Elsevier B.V. All rights reserved.

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard.

PubMed

Terwilliger, Thomas C; Grosse-Kunstleve, Ralf W; Afonine, Pavel V; Moriarty, Nigel W; Zwart, Peter H; Hung, Li Wei; Read, Randy J; Adams, Paul D

2008-01-01

The PHENIX AutoBuild wizard is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE model building, RESOLVE statistical density modification and phenix.refine structure refinement. Recent advances in the AutoBuild wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model-completion algorithms and automated solvent-molecule picking. Model-completion algorithms in the AutoBuild wizard include loop building, crossovers between chains in different models of a structure and side-chain optimization. The AutoBuild wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 to 3.2 A, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29. The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution.

MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction.

PubMed

Li, Nan; Ainsworth, Richard I; Wu, Meixin; Ding, Bo; Wang, Wei

2016-03-15

MIEC-SVM is a structure-based method for predicting protein recognition specificity. Here, we present an automated MIEC-SVM pipeline providing an integrated and user-friendly workflow for construction and application of the MIEC-SVM models. This pipeline can handle standard amino acids and those with post-translational modifications (PTMs) or small molecules. Moreover, multi-threading and support to Sun Grid Engine (SGE) are implemented to significantly boost the computational efficiency. The program is available at http://wanglab.ucsd.edu/MIEC-SVM CONTACT: : wei-wang@ucsd.edu Supplementary data available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

High-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics

PubMed Central

Kuster, Daniel J.; Liu, Chengyu; Fang, Zheng; Ponder, Jay W.; Marshall, Garland R.

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.613 α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.613/10-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding. PMID:25894612

High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

PubMed

Kuster, Daniel J; Liu, Chengyu; Fang, Zheng; Ponder, Jay W; Marshall, Garland R

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.6(13) α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.6(13/10)-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding.

Simple Sugars to Complex Disease—Mucin-Type O-Glycans in Cancer

PubMed Central

Kudelka, Matthew R.; Ju, Tongzhong; Heimburg-Molinaro, Jamie; Cummings, Richard D.

2017-01-01

Mucin-type O-glycans are a class of glycans initiated with N-acetylgalactosamine (GalNAc) α-linked primarily to Ser/Thr residues within glycoproteins and often extended or branched by sugars or saccharides. Most secretory and membrane-bound proteins receive this modification, which is important in regulating many biological processes. Alterations in mucin-type O-glycans have been described across tumor types and include expression of relatively small-sized, truncated O-glycans and altered terminal structures, both of which are associated with patient prognosis. New discoveries in the identity and expression of tumor-associated O-glycans are providing new avenues for tumor detection and treatment. This chapter describes mucin-type O-glycan biosynthesis, altered mucin-type O-glycans in primary tumors, including mechanisms for structural changes and contributions to the tumor phenotype, and clinical approaches to detect and target altered O-glycans for cancer treatment and management. PMID:25727146

Experimental methods of post-growth tuning of the excitonic fine structure splitting in semiconductor quantum dots

PubMed Central

2012-01-01

Deterministic sources of polarization entangled photon pairs on demand are considered as important building blocks for quantum communication technology. It has been demonstrated that semiconductor quantum dots (QDs), which exhibit a sufficiently small excitonic fine structure splitting (FSS) can be used as triggered, on-chip sources of polarization entangled photon pairs. As-grown QDs usually do not have the required values of the FSS, making the availability of post-growth tuning techniques highly desired. This article reviews the effect of different post-growth treatments and external fields on the FSS such as thermal annealing, magnetic fields, the optical Stark effect, electric fields, and anisotropic stress. As a consequence of the tuning of the FSS, for some tuning techniques a rotation of the polarization of the emitted light is observed. The joint modification of polarization orientation and FSS can be described by an anticrossing of the bright excitonic states. PMID:22726724

Regulation of the mammalian heat shock factor 1.

PubMed

Dayalan Naidu, Sharadha; Dinkova-Kostova, Albena T

2017-06-01

Living organisms are endowed with the capability to tackle various forms of cellular stress due to the presence of molecular chaperone machinery complexes that are ubiquitous throughout the cell. During conditions of proteotoxic stress, the transcription factor heat shock factor 1 (HSF1) mediates the elevation of heat shock proteins, which are crucial components of the chaperone complex machinery and function to ameliorate protein misfolding and aggregation and restore protein homeostasis. In addition, HSF1 orchestrates a versatile transcriptional programme that includes genes involved in repair and clearance of damaged macromolecules and maintenance of cell structure and metabolism, and provides protection against a broad range of cellular stress mediators, beyond heat shock. Here, we discuss the structure and function of the mammalian HSF1 and its regulation by post-translational modifications (phosphorylation, sumoylation and acetylation), proteasomal degradation, and small-molecule activators and inhibitors. © 2017 Federation of European Biochemical Societies.

Wind turbine blades: A study of prototypes in a steady regime - Unsteady considerations

NASA Astrophysics Data System (ADS)

Leblanc, R.; Goethals, R.; de Saint Louvent, B.

1981-11-01

The results of comparisons of numerical models with experimental results for the performance of prototype wind turbines in steady flows are presented, along with preliminary results on behavior in unsteady flows. The numerical models are based on previous schemes devised for propellers, with modifications for small perturbations, significant radial velocity effects from the wake, and the fact that the speed is induced. Two computational methods are currently used, one a method of short blades, the other the Prandtl lifting line theory. Trials have been run in the T4 wind tunnel using a 3 m horizontal axis machine and a 2.5 m Darrieus. Attention is given to modeling the structural dynamics and turbulent flow structures encountered by wind turbines. Experimental results relating windspeed, angle of attack, and output are presented. Optimization studies have indicated that wind farms will require a 6-7 blade diameter unit spacing to maintain satisfactory group output efficiencies.

Controlled Shape Memory Behavior of a Smectic Main-Chain Liquid Crystalline Elastomer

DOE PAGES

Li, Yuzhan; Pruitt, Cole; Rios, Orlando; ...

2015-04-10

Here, we describe how a smectic main-chain liquid crystalline elastomer (LCE), with controlled shape memory behavior, is synthesized by polymerizing a biphenyl-based epoxy monomer with an aliphatic carboxylic acid curing agent. Microstructures of the LCEs, including their liquid crystallinity and cross-linking density, are modified by adjusting the stoichiometric ratio of the reactants to tailor the thermomechanical properties and shape memory behavior of the material. Thermal and liquid crystalline properties of the LCEs, characterized using differential scanning calorimetry and dynamic mechanical analysis, and structural analysis, performed using small-angle and wide-angle X-ray scattering, show that liquid crystallinity, cross-linking density, and network rigiditymore » are strongly affected by the stoichiometry of the curing reaction. With appropriate structural modifications it is possible to tune the thermal, dynamic mechanical, and thermomechanical properties as well as the shape memory and thermal degradation behavior of LCEs.« less

Controlled Shape Memory Behavior of a Smectic Main-Chain Liquid Crystalline Elastomer

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

Li, Yuzhan; Pruitt, Cole; Rios, Orlando

Here, we describe how a smectic main-chain liquid crystalline elastomer (LCE), with controlled shape memory behavior, is synthesized by polymerizing a biphenyl-based epoxy monomer with an aliphatic carboxylic acid curing agent. Microstructures of the LCEs, including their liquid crystallinity and cross-linking density, are modified by adjusting the stoichiometric ratio of the reactants to tailor the thermomechanical properties and shape memory behavior of the material. Thermal and liquid crystalline properties of the LCEs, characterized using differential scanning calorimetry and dynamic mechanical analysis, and structural analysis, performed using small-angle and wide-angle X-ray scattering, show that liquid crystallinity, cross-linking density, and network rigiditymore » are strongly affected by the stoichiometry of the curing reaction. With appropriate structural modifications it is possible to tune the thermal, dynamic mechanical, and thermomechanical properties as well as the shape memory and thermal degradation behavior of LCEs.« less

Bromodomain inhibitors and cancer therapy: From structures to applications

PubMed Central

Pérez-Salvia, Montserrat; Esteller, Manel

2017-01-01

ABSTRACT Aberrations in the epigenetic landscape are a hallmark of cancer. Alterations in enzymes that are “writers,” “erasers,” or “readers” of histone modification marks are common. Bromodomains are “readers” that bind acetylated lysines in histone tails. Their most important function is the regulation of gene transcription by the recruitment of different molecular partners. Moreover, proteins containing bromodomains are also epigenetic regulators, although little is known about the specific function of these domains. In recent years, there has been increasing interest in developing small molecules that can target specific bromodomains. First, this has helped clarify biological functions of bromodomain-containing proteins. Secondly, it opens a new front for combatting cancer. In this review we will describe the structures and mechanisms associated with Bromodomain and Extra-Terminal motif (BET) inhibitors and non-BET inhibitors, their current status of development, and their promising role as anti-cancer agents. PMID:27911230

Organizational structure and communication strategies of the bypass angioplasty revascularization investigation: a multicenter clinical trial.

PubMed

Naydeck, B L; Sutton-Tyrrell, K; Burek, K; Sopko, G S

1996-06-01

Efficient communication is a challenge for the many operating components of a multicenter randomized clinical trial. Traditional management theory states that communications generally flow along a path established by a hierarchical organizational structure. A multicenter clinical trial does not fit traditional organizational models well and requires modification of traditional communication techniques. While the scientific community typically views a clinical trial as one large and cohesive enterprise, at each site the trial may actually be conducted as a small project related to the medical specialty of the investigator. Therefore overall trial management must be accomplished through collaboration rather than through direct management. In the Bypass Angioplasty Revascularization Investigation (BARI), the BARI clinical coordinating center has designed and utilized several mechanisms that facilitate effective communication and administrative control of a multicenter clinical trial. These mechanisms provide a framework of communication techniques that accommodate the specific needs of a complex organization.

Eukaryotic DNA polymerase ζ

PubMed Central

Makarova, Alena V.; Burgers, Peter M.

2015-01-01

This review focuses on eukaryotic DNA polymerase ζ (Pol ζ), the enzyme responsible for the bulk of mutagenesis in eukaryotic cells in response to DNA damage. Pol ζ is also responsible for a large portion of mutagenesis during normal cell growth, in response to spontaneous damage or to certain DNA structures and other blocks that stall DNA replication forks. Novel insights in mutagenesis have been derived from recent advances in the elucidation of the subunit structure of Pol ζ. The lagging strand DNA polymerase δ shares the small Pol31 and Pol32 subunits with the Rev3-Rev7 core assembly giving a four subunit Pol ζ complex that is the active form in mutagenesis. Furthermore, Pol ζ forms essential interactions with the mutasome assembly factor Rev1 and with proliferating cell nuclear antigen (PCNA). These interactions are modulated by posttranslational modifications such as ubiquitination and phosphorylation that enhance translesion synthesis (TLS) and mutagenesis. PMID:25737057

Subtractive Structural Modification of Morpho Butterfly Wings.

PubMed

Shen, Qingchen; He, Jiaqing; Ni, Mengtian; Song, Chengyi; Zhou, Lingye; Hu, Hang; Zhang, Ruoxi; Luo, Zhen; Wang, Ge; Tao, Peng; Deng, Tao; Shang, Wen

2015-11-11

Different from studies of butterfly wings through additive modification, this work for the first time studies the property change of butterfly wings through subtractive modification using oxygen plasma etching. The controlled modification of butterfly wings through such subtractive process results in gradual change of the optical properties, and helps the further understanding of structural optimization through natural evolution. The brilliant color of Morpho butterfly wings is originated from the hierarchical nanostructure on the wing scales. Such nanoarchitecture has attracted a lot of research effort, including the study of its optical properties, its potential use in sensing and infrared imaging, and also the use of such structure as template for the fabrication of high-performance photocatalytic materials. The controlled subtractive processes provide a new path to modify such nanoarchitecture and its optical property. Distinct from previous studies on the optical property of the Morpho wing structure, this study provides additional experimental evidence for the origination of the optical property of the natural butterfly wing scales. The study also offers a facile approach to generate new 3D nanostructures using butterfly wings as the templates and may lead to simpler structure models for large-scale man-made structures than those offered by original butterfly wings. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development of Multiple Cell-Based Assays for the Detection of Histone H3 Lys27 Trimethylation (H3K27me3)

PubMed Central

Lu, Lihui; Wu, Jianghong

2013-01-01

Abstract Posttranslational modification of histone proteins in eukaryotes plays an important role in gene transcription and chromatin structure. Dysregulation of the enzymes involved in histone modification has been linked to many cancer forms, making this target class a potential new area for therapeutics. A reliable assay to monitor small-molecule inhibition of various epigenetic enzymes should play a critical role in drug discovery to fight cancer. However, it has been challenging to develop cell-based assays for high-throughput screening (HTS) and compound profiling. Recently, two homogeneous cell-based assay kits using the AlphaLISA® and LanthaScreen® technologies to detect trimethyl histone H3 Lysine 27 have become commercially available, and a heterogeneous cell assay with modified dissociation-enhanced lanthanide fluorescence immunoassay (DELFIA®) format has been reported. To compare their pros and cons, we evaluated, optimized, and validated these three assay formats in three different cell lines and compared their activities with traditional Western blot detection of histone methylation inhibition by using commercial and in-house small-molecule inhibitors. Our data indicate that, although all four formats produced acceptable results, the homogeneous AlphaLISA assay was best suited for HTS and compound profiling due to its wider window and ease of automation. The DELFIA and Western blot assays were useful as validation tools to confirm the cell activities and eliminate potential false-positive compounds. PMID:23992119

Complete Genomic Structure of the Bloom-forming Toxic Cyanobacterium Microcystis aeruginosa NIES-843

PubMed Central

Kaneko, Takakazu; Nakajima, Nobuyoshi; Okamoto, Shinobu; Suzuki, Iwane; Tanabe, Yuuhiko; Tamaoki, Masanori; Nakamura, Yasukazu; Kasai, Fumie; Watanabe, Akiko; Kawashima, Kumiko; Kishida, Yoshie; Ono, Akiko; Shimizu, Yoshimi; Takahashi, Chika; Minami, Chiharu; Fujishiro, Tsunakazu; Kohara, Mitsuyo; Katoh, Midori; Nakazaki, Naomi; Nakayama, Shinobu; Yamada, Manabu; Tabata, Satoshi; Watanabe, Makoto M.

2007-01-01

Abstract The nucleotide sequence of the complete genome of a cyanobacterium, Microcystis aeruginosa NIES-843, was determined. The genome of M. aeruginosa is a single, circular chromosome of 5 842 795 base pairs (bp) in length, with an average GC content of 42.3%. The chromosome comprises 6312 putative protein-encoding genes, two sets of rRNA genes, 42 tRNA genes representing 41 tRNA species, and genes for tmRNA, the B subunit of RNase P, SRP RNA, and 6Sa RNA. Forty-five percent of the putative protein-encoding sequences showed sequence similarity to genes of known function, 32% were similar to hypothetical genes, and the remaining 23% had no apparent similarity to reported genes. A total of 688 kb of the genome, equivalent to 11.8% of the entire genome, were composed of both insertion sequences and miniature inverted-repeat transposable elements. This is indicative of a plasticity of the M. aeruginosa genome, through a mechanism that involves homologous recombination mediated by repetitive DNA elements. In addition to known gene clusters related to the synthesis of microcystin and cyanopeptolin, novel gene clusters that may be involved in the synthesis and modification of toxic small polypeptides were identified. Compared with other cyanobacteria, a relatively small number of genes for two component systems and a large number of genes for restriction-modification systems were notable characteristics of the M. aeruginosa genome. PMID:18192279

Epigenetic modification in neurons of the mollusc Pomacea canaliculata after immune challenge.

PubMed

Ottaviani, Enzo; Accorsi, Alice; Rigillo, Giovanna; Malagoli, Davide; Blom, Joan M C; Tascedda, Fabio

2013-11-06

In human and rodents, the transcriptional response of neurons to stress is related to epigenetic modifications of both DNA and histone proteins. To assess the suitability of simple invertebrate models in studying the basic mechanisms of stress-related epigenetic modifications, we analyzed epigenetic modifications in neurons of the freshwater snail Pomacea canaliculata after the injection of Escherichia coli-derived lipopolysaccharide (LPS). The phospho-acetylation of histone H3, together with the induction of stress-related factors, c-Fos and HSP70, were evaluated in large and small neurons of the pedal ganglia of sham- and LPS-injected snails. Immunocytochemical investigations showed that after LPS injection, the immunopositivity towards phospho (Ser10)-acetyl (Lys14)-histone H3 and c-Fos increases in the nuclei of small gangliar neurons. Western blot analysis confirmed a significant increase of phospho (Ser10)-acetyl (Lys14)-histone H3 in nuclear extracts from 2h LPS-injected animals. c-Fos protein levels were significantly augmented 6h after LPS injection. Immunocytochemistry and western blot indicated that no changes occurred in HSP70 distribution and protein levels. To our knowledge this is the first demonstration of epigenetic changes in molluscan neurons after an immune challenge and indicate the gastropod P. canaliculata as a suitable model for evolutionary and translational studies on stress-related epigenetic modifications. © 2013 Published by Elsevier B.V.

Novel roles for biogenic monoamines: from monoamines in transglutaminase-mediated post-translational protein modification to monoaminylation deregulation diseases.

PubMed

Walther, Diego J; Stahlberg, Silke; Vowinckel, Jakob

2011-12-01

Functional protein serotonylation is a newly recognized post-translational modification with the primary biogenic monoamine (PBMA) serotonin (5-HT). This covalent protein modification is catalyzed by transglutaminases (TGs) and, for example, acts in the constitutive activation of small GTPases. Multiple physiological roles have been identified since its description in 2003 and, importantly, deregulated serotonylation was shown in the etiology of bleeding disorders, primary pulmonary hypertension and diabetes. The PBMAs 5-HT, histamine, dopamine, and norepinephrine all act as neurotransmitters in the nervous system and as hormones in non-neuronal tissues, which points out their physiological importance. In analogy to serotonylation we have found that also the other PBMAs act through the TG-catalyzed mechanisms of 'histaminylation', 'dopaminylation' and 'norepinephrinylation'. Therefore, PBMAs deploy a considerable portion of their effects via protein monoaminylation in addition to their canonical receptor-mediated signaling. Here, the implications of these newly identified post-translational modifications are presented and discussed. Furthermore, the potential regulatory roles of protein monoaminylation in small GTPase, heterotrimeric G-protein and lipid signaling, as well as in modulating metabolic enzymes and nuclear processes, are critically assessed. © 2011 The Authors Journal compilation © 2011 FEBS.

Changes in leptospirosis etiology in animals and humans.

PubMed

Vasylieva, Natalia; Andreychyn, Mykhaylo; Kravchuk, Yulia; Chervinska, Оlena; Iosyk, Iaryna

2017-12-23

Leptospirosis is endemic in Ternopil region. In Ukraine, the disease is registered in almost all regions, including the Ternopil region. The aim of the research is to study the regularities of epidemic and epizootic processes of leptospirosis, and the circulation of its pathogens among different sources (small mammals, animals) and humans. Etiologic spectrum of leptospirosis registered in Ternopil region in 1972-2016 among small mammals, farm animals and sick people was studied. Due to the analysis of pathogens circulation among different sources (small mammals, animals), as well as the annual morbidity in humans, it was proved that new leptospira serovars are endemic and brought into the regions mostly by farm animals. Farm animals introduce the infection to humans through the environment, sometimes within 3-5-years. The spread was observed of pathogen serovars, which are new in certain areas, among all types of mouse-like small mammals and rats. It was established that livestock and small mammals are parallel reservoirs. In the regions with endemic species, the structural modification in the etiology of leptospirosis in humans is caused by additional reservoirs among animals, as well as the circulation of other pathogen serovars that were absent in the main natural reservoir, i.e. mouse-like small mammals and rats. The constant monitoring of the population, contamination and carrier state of mouse-like small mammals, rats and farm animals, is required In order to predict the future epidemiological situation on leptospirosis among the population and to improve leptospirosis diagnosis.

Anomalous uptake and circulatory characteristics of the plant-based small RNA MIR2911.

PubMed

Yang, Jian; Hotz, Tremearne; Broadnax, LaCassidy; Yarmarkovich, Mark; Elbaz-Younes, Ismail; Hirschi, Kendal D

2016-06-02

Inconsistent detection of plant-based dietary small RNAs in circulation has thwarted the use of dietary RNA therapeutics. Here we demonstrate mice consuming diets rich in vegetables displayed enhanced serum levels of the plant specific small RNA MIR2911. Differential centrifugation, size-exclusion chromatography, and proteinase K treatment of plant extracts suggest this RNA resides within a proteinase K-sensitive complex. Plant derived MIR2911 was more bioavailable than the synthetic RNA. Furthermore, MIR2911 exhibited unusual digestive stability compared with other synthetic plant microRNAs. The characteristics of circulating MIR2911 were also unusual as it was not associated with exosomes and fractionated as a soluble complex that was insensitive to proteinase K treatment, consistent with MIR2911 being stabilized by modifications conferred by the host. These results indicate that intrinsic stability and plant-based modifications orchestrate consumer uptake of this anomalous plant based small RNA and invite revisiting plant-based microRNA therapeutic approaches.

Anomalous uptake and circulatory characteristics of the plant-based small RNA MIR2911

PubMed Central

Yang, Jian; Hotz, Tremearne; Broadnax, LaCassidy; Yarmarkovich, Mark; Elbaz-Younes, Ismail; Hirschi, Kendal D.

2016-01-01

Inconsistent detection of plant-based dietary small RNAs in circulation has thwarted the use of dietary RNA therapeutics. Here we demonstrate mice consuming diets rich in vegetables displayed enhanced serum levels of the plant specific small RNA MIR2911. Differential centrifugation, size-exclusion chromatography, and proteinase K treatment of plant extracts suggest this RNA resides within a proteinase K-sensitive complex. Plant derived MIR2911 was more bioavailable than the synthetic RNA. Furthermore, MIR2911 exhibited unusual digestive stability compared with other synthetic plant microRNAs. The characteristics of circulating MIR2911 were also unusual as it was not associated with exosomes and fractionated as a soluble complex that was insensitive to proteinase K treatment, consistent with MIR2911 being stabilized by modifications conferred by the host. These results indicate that intrinsic stability and plant-based modifications orchestrate consumer uptake of this anomalous plant based small RNA and invite revisiting plant-based microRNA therapeutic approaches. PMID:27251858

30 CFR 77.216-2 - Water, sediment, or slurry impoundments and impounding structures; minimum plan requirements...

Code of Federal Regulations, 2013 CFR

2013-07-01

... the District Manager. (b) Any changes or modifications to plans for water, sediment, or slurry... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Water, sediment, or slurry impoundments and impounding structures; minimum plan requirements; changes or modifications; certification. 77.216-2 Section...

30 CFR 77.216-2 - Water, sediment, or slurry impoundments and impounding structures; minimum plan requirements...

Code of Federal Regulations, 2012 CFR

2012-07-01

... the District Manager. (b) Any changes or modifications to plans for water, sediment, or slurry... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Water, sediment, or slurry impoundments and impounding structures; minimum plan requirements; changes or modifications; certification. 77.216-2 Section...

30 CFR 77.216-2 - Water, sediment, or slurry impoundments and impounding structures; minimum plan requirements...

Code of Federal Regulations, 2011 CFR

2011-07-01

... the District Manager. (b) Any changes or modifications to plans for water, sediment, or slurry... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Water, sediment, or slurry impoundments and impounding structures; minimum plan requirements; changes or modifications; certification. 77.216-2 Section...

30 CFR 77.216-2 - Water, sediment, or slurry impoundments and impounding structures; minimum plan requirements...

Code of Federal Regulations, 2014 CFR

2014-07-01

... the District Manager. (b) Any changes or modifications to plans for water, sediment, or slurry... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Water, sediment, or slurry impoundments and impounding structures; minimum plan requirements; changes or modifications; certification. 77.216-2 Section...

Fitting Meta-Analytic Structural Equation Models with Complex Datasets

ERIC Educational Resources Information Center

Wilson, Sandra Jo; Polanin, Joshua R.; Lipsey, Mark W.

2016-01-01

A modification of the first stage of the standard procedure for two-stage meta-analytic structural equation modeling for use with large complex datasets is presented. This modification addresses two common problems that arise in such meta-analyses: (a) primary studies that provide multiple measures of the same construct and (b) the correlation…

Speckle contrast techniques in the study of tissue thermal modification and denaturation

NASA Astrophysics Data System (ADS)

Agafonov, Dmitry N.; Kuznetsova, Liana V.; Zimnyakov, Dmitry A.; Sviridov, Alexander P.; Omelchenko, Alexander I.

2002-05-01

Results of the contrast analysis of time-averaged dynamic speckle patterns in application to monitoring of the structure modification of the thermally treated collagenous tissue such as cartilage are presented. The modification presumably induced by the bound to free water phase transition in the matrix of the treated tissue cause the specific feature of evolution of the time-averaged speckle contrast with the change of the current temperature of modified collagen tissue. This evolution appears as hysteresis associated with irreversible changes in tissue structure.

[Genotoxic modification of nucleic acid bases and biological consequences of it. Review and prospects of experimental and computational investigations

NASA Technical Reports Server (NTRS)

Poltev, V. I.; Bruskov, V. I.; Shuliupina, N. V.; Rein, R.; Shibata, M.; Ornstein, R.; Miller, J.

1993-01-01

The review is presented of experimental and computational data on the influence of genotoxic modification of bases (deamination, alkylation, oxidation) on the structure and biological functioning of nucleic acids. Pathways are discussed for the influence of modification on coding properties of bases, on possible errors of nucleic acid biosynthesis, and on configurations of nucleotide mispairs. The atomic structure of nucleic acid fragments with modified bases and the role of base damages in mutagenesis and carcinogenesis are considered.

High-pressure polymorphism of As2S3 and new AsS2 modification with layered structure

NASA Astrophysics Data System (ADS)

Bolotina, N. B.; Brazhkin, V. V.; Dyuzheva, T. I.; Katayama, Y.; Kulikova, L. F.; Lityagina, L. V.; Nikolaev, N. A.

2014-01-01

At normal pressure, the As2S3 compound is the most stable equilibrium modification with unique layered structure. The possibility of high-pressure polymorphism of this substance remains questionable. Our research showed that the As2S3 substance was metastable under pressures P > 6 GPa decomposing into two high-pressure phases: As2S3 → AsS2 + AsS. New AsS2 phase can be conserved in the single crystalline form in metastable state at room pressure up to its melting temperature (470 K). This modification has the layered structure with P1211 monoclinic symmetry group; the unit-cell values are a = 7.916(2) Å, b = 9.937(2) Å, c = 7.118(1) Å, β = 106.41° ( Z = 8, density 3.44 g/cm3). Along with the recently studied AsS high-pressure modification, the new AsS2 phase suggests that high pressure polymorphism is a very powerful tool to create new layered-structure phases with "wrong" stoichiometry.

Multifunctional Pt(II) Reagents: Covalent Modifications of Pt Complexes Enable Diverse Structural Variation and In-Cell Detection.

PubMed

White, Jonathan D; Haley, Michael M; DeRose, Victoria J

2016-01-19

To enhance the functionality of Pt-based reagents, several strategies have been developed that utilize Pt compounds modified with small, reactive handles. This Account encapsulates work done by us and other groups regarding the use of Pt(II) compounds with reactive handles for subsequent elaboration with fluorophores or other functional moieties. Described strategies include the incorporation of substituents for well-known condensation or nucleophilic displacement-type reactions and their use, for example, to tether spectroscopic handles to Pt reagents for in vivo investigation. Other chief uses of displacement-type reactions have included tethering various small molecules exhibiting pharmacological activity directly to Pt, thus adding synergistic effects. Click chemistry-based ligation techniques have also been applied, primarily with azide- and alkyne-appended Pt complexes. Orthogonally reactive click chemistry reactions have proven invaluable when more traditional nucleophilic displacement reactions induce side-reactivity with the Pt center or when systematic functionalization of a larger number of Pt complexes is desired. Additionally, a diverse assortment of Pt-fluorophore conjugates have been tethered via click chemistry conjugation. In addition to providing a convenient synthetic path for diversifying Pt compounds, the use of click-capable Pt complexes has proved a powerful strategy for postbinding covalent modification and detection with fluorescent probes. This strategy bypasses undesirable influences of the fluorophore camouflaged as reactivity due to Pt that may be present when detecting preattached Pt-fluorophore conjugates. Using postbinding strategies, Pt reagent distributions in HeLa and lung carcinoma (NCI-H460) cell cultures were observed with two different azide-modified Pt compounds, a monofunctional Pt(II)-acridine type and a difunctional Pt(II)-neutral complex. In addition, cellular distribution was observed with an alkyne-appended difunctional Pt(II)-neutral complex analogous in structure to the aforementioned difunctional azide-Pt(II) reagent. In all cases, significant accumulation of Pt in the nucleolus of cells was observed, in addition to broader localization in the nucleus and cytoplasm of the cell. Using the same strategy of postbinding click modification with fluorescent probes, Pt adducts were detected and roughly quantified on rRNA and tRNA from Pt-treated Saccharomyces cerevisiae; rRNA adducts were found to be relatively long-lived and not targeted for immediate degradation. Finally, the utility and feasibility of the alkyne-appended Pt(II) compound has been further demonstrated with a turn-on fluorophore, dansyl azide, in fluorescent detection of DNA in vitro. In all, these modifications utilizing reactive handles have allowed for the diversification of new Pt reagents, as well as providing cellular localization information on the modified Pt compounds.

Hydrophobic ultrathin films formed by fluorofunctional cage silsesquioxanes

NASA Astrophysics Data System (ADS)

Wamke, Anna; Makowiecki, Jaroslaw; Dopierała, Katarzyna; Karasiewicz, Joanna; Prochaska, Krystyna

2018-06-01

The usefulness of fluorofunctional cage silsesquioxanes (POSS) as coating materials effectively changing the surface properties of model substrates was analyzed. Five fully condensed silsesquioxanes (containing two types of organic groups attached to the Si-O cage: octafluoropentyloxypropyl (OFP) and trimethoxysilylethyl (TMS) at different ratios, one monofunctional derivative with OFP groups only and one open cage POSS derivative with three OFP and seven isobutyl groups as organic substituents were investigated. All POSS derivatives were applied to enhance hydrophobicity of quartz or glass plates by deposition of thin LB film transferred from the water subphase. Then, by comparison of water contact angles (WCA) on modified surfaces the effect of silsesquioxane structure (i.e. the TMS and fluoroalkyl group contents as well as the structure of silicon-oxygen cage) on hydrophobic properties was determined. Moreover, the texture of LB films formed by POSS considered was analyzed using the AFM technique. It has been established that the hydrophobizing properties of silsesquioxanes are considerably influenced not only by the number of OFP groups, but also by the silsesquioxane structure. The most effective appeared to be the open cage OFP-POSS derivative which produced coatings with water contact angles (WCA) equal to about 100 deg. Additionally the POSS derivatives studied were also used for dip-coating and spin-coating surface modification. The study has shown that fluorofunctional POSS derivatives can be effective hydrophobizing agents. Additionally applying the LB technique for surface modification allows obtaining substrate of enhanced hydrophobicity by using vanishingly small amount of the modifying substance in comparison to the dip-coating and spin-coating method, which is especially important from the economic viewpoint.

Structural characterization of ribosome recruitment and translocation by type IV IRES.

PubMed

Murray, Jason; Savva, Christos G; Shin, Byung-Sik; Dever, Thomas E; Ramakrishnan, V; Fernández, Israel S

2016-05-09

Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps before the first peptidyl transfer are essential for the initiation of translation by these mRNAs. Using electron cryomicroscopy (cryo-EM) we have structurally characterized at high resolution how the Cricket Paralysis Virus Internal Ribosomal Entry Site (CrPV-IRES) binds the small ribosomal subunit (40S) and the translocation intermediate stabilized by elongation factor 2 (eEF2). The CrPV-IRES restricts tvhe otherwise flexible 40S head to a conformation compatible with binding the large ribosomal subunit (60S). Once the 60S is recruited, the binary CrPV-IRES/80S complex oscillates between canonical and rotated states (Fernández et al., 2014; Koh et al., 2014), as seen for pre-translocation complexes with tRNAs. Elongation factor eEF2 with a GTP analog stabilizes the ribosome-IRES complex in a rotated state with an extra ~3 degrees of rotation. Key residues in domain IV of eEF2 interact with pseudoknot I (PKI) of the CrPV-IRES stabilizing it in a conformation reminiscent of a hybrid tRNA state. The structure explains how diphthamide, a eukaryotic and archaeal specific post-translational modification of a histidine residue of eEF2, is involved in translocation.

Quaternary Structure Heterogeneity of Oligomeric Proteins: A SAXS and SANS Study of the Dissociation Products of Octopus vulgaris Hemocyanin

PubMed Central

Spinozzi, Francesco; Mariani, Paolo; Mičetić, Ivan; Ferrero, Claudio; Pontoni, Diego; Beltramini, Mariano

2012-01-01

Octopus vulgaris hemocyanin shows a particular self-assembling pattern, characterized by a hierarchical organization of monomers. The highest molecular weight aggregate is a decamer, the stability of which in solution depends on several parameters. Different pH values, buffer compositions, H2O/D2O ratios and Hofmeister’s salts result in modifications of the aggregation state of Octopus vulgaris hemocyanin. The new QUAFIT method, recently applied to derive the structure of the decameric and the monomeric assembly from small-angle scattering data, is used here to model the polydisperse system that results from changing the solution conditions. A dataset of small-angle X-rays and neutron scattering curves is analysed by QUAFIT to derive structure, composition and concentration of different assemblies present in solution. According to the hierarchy of the association/dissociation processes and the possible number of different aggregation products in solution, each sample has been considered as a heterogeneous mixture composed of the entire decamer, the dissociated “loose” monomer and all the intermediate dissociation products. Scattering curves corresponding to given experimental conditions are well fitted by using a linear combination of single particle form factors. QUAFIT has proved to be a method of general validity to describe solutions of proteins that, even after purification processes, result to be intrinsically heterogeneous. PMID:23166737

Biological impacts of local vs. regional land use on a small tributary of the Seine River (France): insights from a food web approach based on stable isotopes.

PubMed

Hette-Tronquart, Nicolas; Oberdorff, Thierry; Tales, Evelyne; Zahm, Amandine; Belliard, Jérôme

2017-03-23

As part of the landscape, streams are influenced by land use. Here, we contributed to the understanding of the biological impacts of land use on streams, investigating how landscape effects vary with spatial scales (local vs. regional). We adopted a food web approach integrating both biological structure and functioning, to focus on the overall effect of land use on stream biocœnosis. We selected 17 sites of a small tributary of the Seine River (France) for their contrasted land use, and conducted a natural experiment by sampling three organic matter sources, three macroinvertebrate taxa, and most of the fish community. Using stable isotope analysis, we calculated three food web metrics evaluating two major dimensions of the trophic diversity displayed by the fish community: (i) the diversity of exploited resources and (ii) the trophic level richness. The idea was to examine whether (1) land-use effects varied according to spatial scales, (2) land use affected food webs through an effect on community structure and (3) land use affected food webs through an effect on available resources. Beside an increase in trophic diversity from upstream to downstream, our empirical data showed that food webs were influenced by land use in the riparian corridors (local scale). The effect was complex, and depended on site's position along the upstream-downstream gradient. By contrast, land use in the catchment (regional scale) did not influence stream biocœnosis. At the local scale, community structure was weakly influenced by land use, and thus played a minor role in explaining food web modifications. Our results suggested that the amount of available resources at the base of the food web was partly responsible for food web modifications. In addition, changes in biological functioning (i.e. feeding interactions) can also explain another part of the land-use effect. These results highlight the role played by the riparian corridors as a buffer zone, and advocate that riparian corridor should be at the centre of water management attention.

The computational nature of memory modification

PubMed Central

Gershman, Samuel J; Monfils, Marie-H; Norman, Kenneth A; Niv, Yael

2017-01-01

Retrieving a memory can modify its influence on subsequent behavior. We develop a computational theory of memory modification, according to which modification of a memory trace occurs through classical associative learning, but which memory trace is eligible for modification depends on a structure learning mechanism that discovers the units of association by segmenting the stream of experience into statistically distinct clusters (latent causes). New memories are formed when the structure learning mechanism infers that a new latent cause underlies current sensory observations. By the same token, old memories are modified when old and new sensory observations are inferred to have been generated by the same latent cause. We derive this framework from probabilistic principles, and present a computational implementation. Simulations demonstrate that our model can reproduce the major experimental findings from studies of memory modification in the Pavlovian conditioning literature. DOI: http://dx.doi.org/10.7554/eLife.23763.001 PMID:28294944

Modification of transparent materials with ultrashort laser pulses: What is energetically and mechanically meaningful?

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

Bulgakova, Nadezhda M., E-mail: nadezhda.bulgakova@hilase.cz; Institute of Thermophysics SB RAS, 1 Lavrentyev Ave., 630090 Novosibirsk; Zhukov, Vladimir P.

A comprehensive analysis of laser-induced modification of bulk glass by single ultrashort laser pulses is presented which is based on combination of optical Maxwell-based modeling with thermoelastoplastic simulations of post-irradiation behavior of matter. A controversial question on free electron density generated inside bulk glass by ultrashort laser pulses in modification regimes is addressed on energy balance grounds. Spatiotemporal dynamics of laser beam propagation in fused silica have been elucidated for the regimes used for direct laser writing in bulk glass. 3D thermoelastoplastic modeling of material relocation dynamics under laser-induced stresses has been performed up to the microsecond timescale when allmore » motions in the material decay. The final modification structure is found to be imprinted into material matrix already at sub-nanosecond timescale. Modeling results agree well with available experimental data on laser light transmission through the sample and the final modification structure.« less

Re-connecting Urban Ecohydrology to Improve Ecosystem Functioning: The Role of Local-scale Green Infrastructure

NASA Astrophysics Data System (ADS)

Pavao-Zuckerman, M.

2010-12-01

As rates of urbanization continue to rise and a greater proportion of the population lives in urban and suburban areas, the provision of ecological services and functions become increasingly important to sustain human and environmental health in urban ecosystems. Soils play a primary role in the healthy functioning of ecosystems that provide supporting, provisioning, regulating, preserving, and cultural ecosystem services, yet developing our understanding of how urban soils function to provide these services within an ecological context is just getting underway. Soils in urban ecosytems are highly heterogeneous, and are affected by both direct and indirect influences and local modifications which alter their functioning relative to non-urbanized local soils. Here I discuss the functioning of rain gardens in and around Tucson, AZ, that have been installed in the urban landscape with the purpose of providing various ecosystem services to local residents and the greater urban ecosystem. This reconnection of ecohydrologic flows in the city has the potential to alter the structure and function of urban ecosystems in positive (through the increase in water availability) and negative (through the import of pollutants to soils) ways. This study compares soil properties, microbial function, and ecosystem functions within the urban ecosystem to determine how urbanization alters soils in semi-arid environments, and to determine if green urban modifications in desert cities can improve soils and ecosystem services. Soils in rain gardens have nearly twice the organic matter contents of native and urban soils, and correspondingly, greater microbial function (as indicated through respiration potential), higher abundance (through substrate induced respiration), and community complexity (indicated by a 3x increase in metabolic diversity) in these green design modifications. Net N-mineralization rates are almost 1.5 times faster in the rain garden basins than urban soils in general. This study also includes the comparison of different approaches to installing rain gardens to illustrate the effects of different management strategies on biogeochemical cycling. The inclusion of mulch in the garden design increases microbial biomass and reduces the rate of N-mineralization. These data indicate that soil quality is improved in arid system rain gardens. Such urban modifications both improve soils and reconnect ecohydrologic flows in Tucson neighborhoods, suggesting that the provision of ecosystem services in cities can be assisted with small scale green infrastructure modifications. In fact, such small scale improvements in ecosystem functioning may contribute to broader scale resilience of the urban ecosystem.

Spatio-temporal neighborhood impacts on internalizing and externalizing behaviors in U.S. elementary school children: Effect modification by child and family socio-demographics.

PubMed

Humphrey, Jamie L; Root, Elisabeth D

2017-05-01

Increasing evidence from experimental and non-experimental research has shown that children residing in disadvantaged neighborhoods exhibit greater levels of internalizing and externalizing behaviors, above and beyond individual characteristics, and family or school contexts. Using the ECLS-K, a nationally representative, longitudinal survey of U.S. school children, this study examined direct neighborhood effects on internalizing (N = 14,870; N = 10,610) and externalizing (N = 14,960; N = 10,730) behaviors at the beginning and end of elementary school. Using IPTW propensity scores to mitigate selection bias and ordinary least squares regression, we examined direct neighborhood effects when children were 7 years old (1st grade) and when they were 11 years old (5th grade). We also examined neighborhood effect modification by child child race/ethnicity, sex, family structure, and family SES. Both the direct effect and effect modification models indicated that living in disadvantaged neighborhoods had no impact on either internalizing or externalizing behaviors at the beginning of elementary school (age 7). At the end of elementary school (age 11), we found small, yet significant direct neighborhood associations with effect sizes ranging from 0.12 to 0.18 standard deviations. The effect modification analysis revealed that being black (relative to white) was the strongest moderator of the relationship between neighborhood context and internalizing and externalizing behaviors in 5th grade, with effect sizes ranging from 0.27 to 0.59 standard deviations. Being Hispanic in high poverty neighborhoods was found to be protective for externalizing behaviors, suggesting the presence of the Hispanic health paradox. We also found, that in some neighborhood contexts, child sex, family structure, and family socioeconomic status amplified or dampened the effect of neighborhood, but only for externalizing behaviors. These results demonstrate the importance of age-dependent neighborhood effects and that children with different demographic profiles respond differently to the social contexts in which they are exposed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Synthesis and Crystal Structure of 2’-Se-modified guanosine Containing DNA

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

Salon, J.; Sheng, J; Gan, J

Selenium modification of nucleic acids is of great importance in X-ray crystal structure determination and functional study of nucleic acids. Herein, we describe a convenient synthesis of a new building block, the 2{prime}-SeMe-modified guanosine (G{sub Se}) phosphoramidite, and report the first incorporation of the 2{prime}-Se-G moiety into DNA. The X-ray crystal structure of the 2{prime}-Se-modified octamer DNA (5{prime}-GTG{sub Se}TACAC-3{prime}) was determined at a resolution of 1.20 {angstrom}. We also found that the 2{prime}-Se modification points to the minor groove and that the modified and native structures are virtually identical. Furthermore, we observed that the 2{prime}-Se-G modification can significantly facilitate themore » crystal growth with respect to the corresponding native DNA.« less

48 CFR 1815.208 - Submission, modification, revision, and withdrawal of proposals. (NASA supplements paragraph (b))

Code of Federal Regulations, 2010 CFR

2010-10-01

... late proposal criteria do not apply to Announcements of Opportunity, NASA Research Announcements, and Small Business Innovative Research (SBIR) Phase I and Phase II solicitations, and Small Business... Acquisition Regulations System NATIONAL AERONAUTICS AND SPACE ADMINISTRATION CONTRACTING METHODS AND CONTRACT...

76 FR 43957 - Modifications of Certain Derivative Contracts

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-22

... rulemaking has been submitted to the Chief Counsel for Advocacy of the Small Business Administration for comment on its impact on small businesses. Comments and Public Hearing Before these proposed regulations... made easier to understand. All comments will be available for public inspection and copying. A public...

tRNA modification profiles of the fast-proliferating cancer cells

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

Dong, Chao; Niu, Leilei; Song, Wei

Despite the recent progress in RNA modification study, a comprehensive modification profile is still lacking for mammalian cells. Using a quantitative HPLC/MS/MS assay, we present here a study where RNA modifications are examined in term of the major RNA species. With paired slow- and fast-proliferating cell lines, distinct RNA modification profiles are first revealed for diverse RNA species. Compared to mRNAs, increased ribose and nucleobase modifications are shown for the highly-structured tRNAs and rRNAs, lending support to their contribution to the formation of high-order structures. This study also reveals a dynamic tRNA modification profile in the fast-proliferating cells. In additionmore » to cultured cells, this unique tRNA profile has been further confirmed with endometrial cancers and their adjacent normal tissues. Taken together, the results indicate that tRNA is a actively regulated RNA species in the fast-proliferating cancer cells, and suggest that they may play a more active role in biological process than expected. -- Highlights: •RNA modifications were first examined in term of the major RNA species. •A dynamic tRNA modifications was characterized for the fast-proliferating cells. •The unique tRNA profile was confirmed with endometrial cancers and their adjacent normal tissues. •tRNA was predicted as an actively regulated RNA species in the fast-proliferating cancer cells.« less

m1A Post-Transcriptional Modification in tRNAs.

PubMed

Oerum, Stephanie; Dégut, Clément; Barraud, Pierre; Tisné, Carine

2017-02-21

To date, about 90 post-transcriptional modifications have been reported in tRNA expanding their chemical and functional diversity. Methylation is the most frequent post-transcriptional tRNA modification that can occur on almost all nitrogen sites of the nucleobases, on the C5 atom of pyrimidines, on the C2 and C8 atoms of adenosine and, additionally, on the oxygen of the ribose 2'-OH. The methylation on the N1 atom of adenosine to form 1-methyladenosine (m1A) has been identified at nucleotide position 9, 14, 22, 57, and 58 in different tRNAs. In some cases, these modifications have been shown to increase tRNA structural stability and induce correct tRNA folding. This review provides an overview of the currently known m1A modifications, the different m1A modification sites, the biological role of each modification, and the enzyme responsible for each methylation in different species. The review further describes, in detail, two enzyme families responsible for formation of m1A at nucleotide position 9 and 58 in tRNA with a focus on the tRNA binding, m1A mechanism, protein domain organisation and overall structures.

An albumin-mediated cholesterol design-based strategy for tuning siRNA pharmacokinetics and gene silencing.

PubMed

Bienk, Konrad; Hvam, Michael Lykke; Pakula, Malgorzata Maria; Dagnæs-Hansen, Frederik; Wengel, Jesper; Malle, Birgitte Mølholm; Kragh-Hansen, Ulrich; Cameron, Jason; Bukrinski, Jens Thostrup; Howard, Kenneth A

2016-06-28

Major challenges for the clinical translation of small interfering RNA (siRNA) include overcoming the poor plasma half-life, site-specific delivery and modulation of gene silencing. In this work, we exploit the intrinsic transport properties of human serum albumin to tune the blood circulatory half-life, hepatic accumulation and gene silencing; based on the number of siRNA cholesteryl modifications. We demonstrate by a gel shift assay a strong and specific affinity of recombinant human serum albumin (rHSA) towards cholesteryl-modified siRNA (Kd>1×10(-7)M) dependent on number of modifications. The rHSA/siRNA complex exhibited reduced nuclease degradation and reduced induction of TNF-α production by human peripheral blood mononuclear cells. The increased solubility of heavily cholesteryl modified siRNA in the presence of rHSA facilitated duplex annealing and consequent interaction that allowed in vivo studies using multiple cholesteryl modifications. A structural-activity-based screen of in vitro EGFP-silencing was used to select optimal siRNA designs containing cholesteryl modifications within the sense strand that were used for in vivo studies. We demonstrate plasma half-life extension in NMRI mice from t1/2 12min (naked) to t1/2 45min (single cholesteryl) and t1/2 71min (double cholesteryl) using fluorescent live bioimaging. The biodistribution showed increased accumulation in the liver for the double cholesteryl modified siRNA that correlated with an increase in hepatic Factor VII gene silencing of 28% (rHSA/siRNA) compared to 4% (naked siRNA) 6days post-injection. This work presents a novel albumin-mediated cholesteryl design-based strategy for tuning pharmacokinetics and systemic gene silencing. Copyright © 2016 Elsevier B.V. All rights reserved.

A simple ion implanter for material modifications in agriculture and gemmology

NASA Astrophysics Data System (ADS)

Singkarat, S.; Wijaikhum, A.; Suwannakachorn, D.; Tippawan, U.; Intarasiri, S.; Bootkul, D.; Phanchaisri, B.; Techarung, J.; Rhodes, M. W.; Suwankosum, R.; Rattanarin, S.; Yu, L. D.

2015-12-01

In our efforts in developing ion beam technology for novel applications in biology and gemmology, an economic simple compact ion implanter especially for the purpose was constructed. The designing of the machine was aimed at providing our users with a simple, economic, user friendly, convenient and easily operateable ion implanter for ion implantation of biological living materials and gemstones for biotechnological applications and modification of gemstones, which would eventually contribute to the national agriculture, biomedicine and gem-industry developments. The machine was in a vertical setup so that the samples could be placed horizontally and even without fixing; in a non-mass-analyzing ion implanter style using mixed molecular and atomic nitrogen (N) ions so that material modifications could be more effective; equipped with a focusing/defocusing lens and an X-Y beam scanner so that a broad beam could be possible; and also equipped with a relatively small target chamber so that living biological samples could survive from the vacuum period during ion implantation. To save equipment materials and costs, most of the components of the machine were taken from decommissioned ion beam facilities. The maximum accelerating voltage of the accelerator was 100 kV, ideally necessary for crop mutation induction and gem modification by ion beams from our experience. N-ion implantation of local rice seeds and cut gemstones was carried out. Various phenotype changes of grown rice from the ion-implanted seeds and improvements in gemmological quality of the ion-bombarded gemstones were observed. The success in development of such a low-cost and simple-structured ion implanter provides developing countries with a model of utilizing our limited resources to develop novel accelerator-based technologies and applications.

Structural and physico-chemical properties of insoluble rice bran fiber: effect of acid–base induced modifications

USDA-ARS?s Scientific Manuscript database

The structural modifications of insoluble rice bran fiber (IRBF) by sequential regimes of sulphuric acid (H2SO4) and their effects on the physicochemical attributes were studied. The increment of H2SO4 concentration resulted in decreased water holding capacity that ultimately enhanced the oil bindin...

Effect of Sr Additive Amount and Holding Time on Microstructure of A390 Aluminum Alloy

NASA Astrophysics Data System (ADS)

Zhang, J. H.; Xing, S. M.; Han, Q. Y.; Guo, Q.; Wang, R. F.

2017-11-01

The microstructure of A390 alloy under different Sr additive amounts and holding times was studied by means of direct reading spectrum analysis, energy spectrum analysis, optical microscope and electron microscope. The results show that Sr has a good modification to eutectic Si, while it has a negative effect on primary silicon. The Sr addition will increase the size of primary silicon. When the addition amount of Al-10Sr alloy is 0.6%, the modification of eutectic silicon is the optimum. The Sr has a short incubation period and a fine modification at 10min, but it is more serious burning rate in small furnace smelting, and the modification effect disappears basically after 100min.

Structural basis of ubiquitin modification by the Legionella effector SdeA.

PubMed

Dong, Yanan; Mu, Yajuan; Xie, Yongchao; Zhang, Yupeng; Han, Youyou; Zhou, Yu; Wang, Wenhe; Liu, Zihe; Wu, Mei; Wang, Hao; Pan, Man; Xu, Ning; Xu, Cong-Qiao; Yang, Maojun; Fan, Shilong; Deng, Haiteng; Tan, Tianwei; Liu, Xiaoyun; Liu, Lei; Li, Jun; Wang, Jiawei; Fang, Xianyang; Feng, Yue

2018-05-01

Protein ubiquitination is a multifaceted post-translational modification that controls almost every process in eukaryotic cells. Recently, the Legionella effector SdeA was reported to mediate a unique phosphoribosyl-linked ubiquitination through successive modifications of the Arg42 of ubiquitin (Ub) by its mono-ADP-ribosyltransferase (mART) and phosphodiesterase (PDE) domains. However, the mechanisms of SdeA-mediated Ub modification and phosphoribosyl-linked ubiquitination remain unknown. Here we report the structures of SdeA in its ligand-free, Ub-bound and Ub-NADH-bound states. The structures reveal that the mART and PDE domains of SdeA form a catalytic domain over its C-terminal region. Upon Ub binding, the canonical ADP-ribosyltransferase toxin turn-turn (ARTT) and phosphate-nicotinamide (PN) loops in the mART domain of SdeA undergo marked conformational changes. The Ub Arg72 might act as a 'probe' that interacts with the mART domain first, and then movements may occur in the side chains of Arg72 and Arg42 during the ADP-ribosylation of Ub. Our study reveals the mechanism of SdeA-mediated Ub modification and provides a framework for further investigations into the phosphoribosyl-linked ubiquitination process.

Structure of human POFUT2: insights into thrombospondin type 1 repeat fold and O-fucosylation

PubMed Central

Chen, Chun-I; Keusch, Jeremy J; Klein, Dominique; Hess, Daniel; Hofsteenge, Jan; Gut, Heinz

2012-01-01

Protein O-fucosylation is a post-translational modification found on serine/threonine residues of thrombospondin type 1 repeats (TSR). The fucose transfer is catalysed by the enzyme protein O-fucosyltransferase 2 (POFUT2) and >40 human proteins contain the TSR consensus sequence for POFUT2-dependent fucosylation. To better understand O-fucosylation on TSR, we carried out a structural and functional analysis of human POFUT2 and its TSR substrate. Crystal structures of POFUT2 reveal a variation of the classical GT-B fold and identify sugar donor and TSR acceptor binding sites. Structural findings are correlated with steady-state kinetic measurements of wild-type and mutant POFUT2 and TSR and give insight into the catalytic mechanism and substrate specificity. By using an artificial mini-TSR substrate, we show that specificity is not primarily encoded in the TSR protein sequence but rather in the unusual 3D structure of a small part of the TSR. Our findings uncover that recognition of distinct conserved 3D fold motifs can be used as a mechanism to achieve substrate specificity by enzymes modifying completely folded proteins of very wide sequence diversity and biological function. PMID:22588082

Identifying Novel Molecular Structures for Advanced Melanoma by Ligand-Based Virtual Screening

PubMed Central

Wang, Zhao; Lu, Yan; Seibel, William; Miller, Duane D.; Li, Wei

2009-01-01

We recently discovered a new class of thiazole analogs that are highly potent against melanoma cells. To expand the structure-activity relationship study and to explore potential new molecular scaffolds, we performed extensive ligand-based virtual screening against a compound library containing 342,910 small molecules. Two different approaches of virtual screening were carried out using the structure of our lead molecule: 1) connectivity-based search using Scitegic Pipeline Pilot from Accelerys and 2) molecular shape similarity search using Schrodinger software. Using a testing compound library, both approaches can rank similar compounds very high and rank dissimilar compounds very low, thus validating our screening methods. Structures identified from these searches were analyzed, and selected compounds were tested in vitro to assess their activity against melanoma cancer cell lines. Several molecules showed good anticancer activity. While none of the identified compounds showed better activity than our lead compound, they provided important insight into structural modifications for our lead compound and also provided novel platforms on which we can optimize new classes of anticancer compounds. One of the newly synthesized analogs based on this virtual screening has improved potency and selectivity against melanoma. PMID:19445498

DNA-controlled assembly of a NaTl lattice structure from gold nanoparticles and protein nanoparticles

NASA Astrophysics Data System (ADS)

Cigler, Petr; Lytton-Jean, Abigail K. R.; Anderson, Daniel G.; Finn, M. G.; Park, Sung Yong

2010-11-01

The formation of diamond structures from tailorable building blocks is an important goal in colloidal crystallization because the non-compact diamond lattice is an essential component of photonic crystals for the visible-light range. However, designing nanoparticle systems that self-assemble into non-compact structures has proved difficult. Although several methods have been proposed, single-component nanoparticle assembly of a diamond structure has not been reported. Binary systems, in which at least one component is arranged in a diamond lattice, provide alternatives, but control of interparticle interactions is critical to this approach. DNA has been used for this purpose in a number of systems. Here we show the creation of a non-compact lattice by DNA-programmed crystallization using surface-modified Qβ phage capsid particles and gold nanoparticles, engineered to have similar effective radii. When combined with the proper connecting oligonucleotides, these components form NaTl-type colloidal crystalline structures containing interpenetrating organic and inorganic diamond lattices, as determined by small-angle X-ray scattering. DNA control of assembly is therefore shown to be compatible with particles possessing very different properties, as long as they are amenable to surface modification.

Ferritin-Polymer Conjugates: Grafting Chemistry and Self-Assembly

DTIC Science & Technology

2009-10-26

a collection of information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. a...Chemoselective modification of M13 bacteriophage and cell imaging We systematically investigated the chemical modification of three kinds of reactive...tyrosine residues, on M13 surface. The reactivity for each group was identified by conjugation with small fluorescent molecules. Furthermore, the

Game-Based Approaches, Pedagogical Principles and Tactical Constraints: Examining Games Modification

ERIC Educational Resources Information Center

Serra-Olivares, Jaime; García-López, Luis M.; Calderón, Antonio

2016-01-01

The purpose of this study was to analyze the effect of modification strategies based on the pedagogical principles of the Teaching Games for Understanding approach on tactical constraints of four 3v3 soccer small-sided games. The Game performance of 21 U-10 players was analyzed in a game similar to the adult game; one based on keeping-the-ball;…

Community composition of lacustrine small eukaryotes in hyper-eutrophic conditions in relation to top-down and bottom-up factors.

PubMed

Lepère, Cécile; Domaizon, Isabelle; Debroas, Didier

2007-09-01

Small eukaryotes (0.2-5 microm) in hyper-eutrophic conditions were described using terminal restriction fragment length polymorphism and cloning-sequencing, and were related to environmental variables both by an experimental approach and by a temporal field study. In situ analysis showed marked temporal variations in the dominant terminal restriction fragments (T-RFs), which were related to environmental variables such as nutrient concentrations and metazooplankton composition. To monitor the responses of the small-eukaryote community to top-down (absence or presence of planktivorous fish) and bottom-up (low or high nitrogen and phosphorus addition) effects, a cross-classified design mesocosm experiment was used. Depending on the type of treatment, we recorded changes in the diversity of T-RFs, as well as modifications in phylogenetic composition. Centroheliozoa and Cryptophyta were found in all types of treatment, whereas Chlorophyta were specific to enclosures receiving high nutrient loadings, and were associated either with LKM11 and 'environmental sequences'. Cercozoa and Fungi were not detected in enclosures receiving high nutrient loadings and fishes. Our results showed that resources and top-down factors are both clearly involved in shaping the structure of small eukaryotes, not only autotrophs but also heterotrophs, via complex interactions and trophic cascades within a microbial loop, notably in response to nutrient loading.

Chemical methodology as a source of small-molecule checkpoint inhibitors and heat shock protein 70 (Hsp70) modulators.

PubMed

Huryn, Donna M; Brodsky, Jeffrey L; Brummond, Kay M; Chambers, Peter G; Eyer, Benjamin; Ireland, Alex W; Kawasumi, Masaoki; Laporte, Matthew G; Lloyd, Kayla; Manteau, Baptiste; Nghiem, Paul; Quade, Bettina; Seguin, Sandlin P; Wipf, Peter

2011-04-26

Unique chemical methodology enables the synthesis of innovative and diverse scaffolds and chemotypes and allows access to previously unexplored "chemical space." Compound collections based on such new synthetic methods can provide small-molecule probes of proteins and/or pathways whose functions are not fully understood. We describe the identification, characterization, and evolution of two such probes. In one example, a pathway-based screen for DNA damage checkpoint inhibitors identified a compound, MARPIN (ATM and ATR pathway inhibitor) that sensitizes p53-deficient cells to DNA-damaging agents. Modification of the small molecule and generation of an immobilized probe were used to selectively bind putative protein target(s) responsible for the observed activity. The second example describes a focused library approach that relied on tandem multicomponent reaction methodologies to afford a series of modulators of the heat shock protein 70 (Hsp70) molecular chaperone. The synthesis of libraries based on the structure of MAL3-101 generated a collection of chemotypes, each modulating Hsp70 function, but exhibiting divergent pharmacological activities. For example, probes that compromise the replication of a disease-associated polyomavirus were identified. These projects highlight the importance of chemical methodology development as a source of small-molecule probes and as a drug discovery starting point.

Chemical methodology as a source of small-molecule checkpoint inhibitors and heat shock protein 70 (Hsp70) modulators

PubMed Central

Huryn, Donna M.; Brodsky, Jeffrey L.; Brummond, Kay M.; Chambers, Peter G.; Eyer, Benjamin; Ireland, Alex W.; Kawasumi, Masaoki; LaPorte, Matthew G.; Lloyd, Kayla; Manteau, Baptiste; Nghiem, Paul; Quade, Bettina; Seguin, Sandlin P.; Wipf, Peter

2011-01-01

Unique chemical methodology enables the synthesis of innovative and diverse scaffolds and chemotypes and allows access to previously unexplored “chemical space.” Compound collections based on such new synthetic methods can provide small-molecule probes of proteins and/or pathways whose functions are not fully understood. We describe the identification, characterization, and evolution of two such probes. In one example, a pathway-based screen for DNA damage checkpoint inhibitors identified a compound, MARPIN (ATM and ATR pathway inhibitor) that sensitizes p53-deficient cells to DNA-damaging agents. Modification of the small molecule and generation of an immobilized probe were used to selectively bind putative protein target(s) responsible for the observed activity. The second example describes a focused library approach that relied on tandem multicomponent reaction methodologies to afford a series of modulators of the heat shock protein 70 (Hsp70) molecular chaperone. The synthesis of libraries based on the structure of MAL3-101 generated a collection of chemotypes, each modulating Hsp70 function, but exhibiting divergent pharmacological activities. For example, probes that compromise the replication of a disease-associated polyomavirus were identified. These projects highlight the importance of chemical methodology development as a source of small-molecule probes and as a drug discovery starting point. PMID:21502524

Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli

PubMed Central

Kim, Sang Hyon; Spensley, Mark; Choi, Seung Kook; Calixto, Cristiane P. G.; Pendle, Ali F.; Koroleva, Olga; Shaw, Peter J.; Brown, John W. S.

2010-01-01

Small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs (scaRNAs) are non-coding RNAs whose main function in eukaryotes is to guide the modification of nucleotides in ribosomal and spliceosomal small nuclear RNAs, respectively. Full-length sequences of Arabidopsis snoRNAs and scaRNAs have been obtained from cDNA libraries of capped and uncapped small RNAs using RNA from isolated nucleoli from Arabidopsis cell cultures. We have identified 31 novel snoRNA genes (9 box C/D and 22 box H/ACA) and 15 new variants of previously described snoRNAs. Three related capped snoRNAs with a distinct gene organization and structure were identified as orthologues of animal U13snoRNAs. In addition, eight of the novel genes had no complementarity to rRNAs or snRNAs and are therefore putative orphan snoRNAs potentially reflecting wider functions for these RNAs. The nucleolar localization of a number of the snoRNAs and the localization to nuclear bodies of two putative scaRNAs was confirmed by in situ hybridization. The majority of the novel snoRNA genes were found in new gene clusters or as part of previously described clusters. These results expand the repertoire of Arabidopsis snoRNAs to 188 snoRNA genes with 294 gene variants. PMID:20081206

Treating Sample Covariances for Use in Strongly Coupled Atmosphere-Ocean Data Assimilation

NASA Astrophysics Data System (ADS)

Smith, Polly J.; Lawless, Amos S.; Nichols, Nancy K.

2018-01-01

Strongly coupled data assimilation requires cross-domain forecast error covariances; information from ensembles can be used, but limited sampling means that ensemble derived error covariances are routinely rank deficient and/or ill-conditioned and marred by noise. Thus, they require modification before they can be incorporated into a standard assimilation framework. Here we compare methods for improving the rank and conditioning of multivariate sample error covariance matrices for coupled atmosphere-ocean data assimilation. The first method, reconditioning, alters the matrix eigenvalues directly; this preserves the correlation structures but does not remove sampling noise. We show that it is better to recondition the correlation matrix rather than the covariance matrix as this prevents small but dynamically important modes from being lost. The second method, model state-space localization via the Schur product, effectively removes sample noise but can dampen small cross-correlation signals. A combination that exploits the merits of each is found to offer an effective alternative.

Limited impact of beach nourishment on macrofaunal recruitment/settlement in a site of community interest in coastal area of the Adriatic Sea (Mediterranean Sea).

PubMed

Danovaro, Roberto; Nepote, Ettore; Martire, Marco Lo; Ciotti, Claudia; De Grandis, Gianluca; Corinaldesi, Cinzia; Carugati, Laura; Cerrano, Carlo; Pica, Daniela; Di Camillo, Cristina Gioia; Dell'Anno, Antonio

2018-03-01

Beach nourishment is a widely utilized solution to counteract the erosion of shorelines, and there is an active discussion on its possible consequences on coastal marine assemblages. We investigated the impact caused by a small-scale beach nourishment carried out in the Western Adriatic Sea on macrofaunal recruitment and post-settlement events. Artificial substrates were deployed in proximity of nourished and non-manipulated beaches and turbidity and sedimentation rates were measured. Our results indicate that sedimentation rates in the impacted site showed a different temporal change compared to the control sites, suggesting potential modifications due to the beach nourishment. The impact site was characterized by subtle changes in terms of polychaete abundance and community structure when compared to controls, possibly due to beach nourishment, although the role of other factors cannot be ruled out. We conclude that small-scale beach nourishments appear to be an eco-sustainable approach to contrast coastal erosion. Copyright © 2018. Published by Elsevier Ltd.

Modification of the Atmospheric Boundary Layer by a Small Island: Observations from Nauru

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

Matthews, Stuart; Hacker, Jorg M.; Cole, Jason N.

2007-03-01

Nauru, a small island in the tropical pacific, generates plumes of clouds that may grow to several hundred km length. This study uses observations to examine the mesoscale disturbance of the marine atmospheric boundary layer by the island that produces these cloud streets. Observations of the surface layer were made from two ships in the vicinity of Nauru and from instruments on the island. The structure of the atmospheric boundary layer over the island was investigated using aircraft flights. Cloud production over Nauru was examined using remote sensing instruments. During the day the island surface layer was warmer than themore » marine surface layer and wind speed was lower than over the ocean. Surface heating forced the growth of a thermal internal boundary layer, above which a street of cumulus clouds formed. The production of clouds resulted in reduced downwelling shortwave irradiance at the island surface. A plume of warm-dry air was observed over the island which extended 15 – 20 km downwind.« less

Drainage Behavior in Soap Films Above and Below the CMC

NASA Astrophysics Data System (ADS)

Berg, S.; Adelizzi, E. A.; Troian, S. M.

2003-11-01

We investigate through laser interferometry the drainage behavior of Newtonian soap films initially entrained on a fiber frame at small and constant capillary number. The initial film thickness is sufficiently small that gravitational drainage is presumed minimal. The drainage of rigid soap films by capillary forces alone should proceed according to h(t) ˜ t^- 1/2. Our experimental results show much more rapid drainage with exponents as large as -2, especially for those solutions whose surfactant concentrations are below the CMC. Video recordings of the entire film surface reveal a variety of structures during the drainage process, some attributable to marginal regeneration. Though still a controversial issue, this regeneration process is believed to be caused by surfactant accumulation in the meniscus region (1). We show that modification of the relevant capillary drainage equation to account for Marangoni effects through a course-grained slip condition at the air-liquid interface produces exponents in better agreement with experimental findings. (1) V. A. Nierstrasz and G. Frens, JCIS 215, 28 (1999).

Strain-Mediated Modification of Phagraphene Dirac Cones

DOE PAGES

Lopez-Bezanilla, Alejandro

2016-07-07

We present a first-principles study on the electronic and dynamical properties of phagraphene [Nano Lett., 2015, 15 (9), pp 6182]. This carbon allotrope exhibits a square unit cell, Dirac cones, and robustness against uniaxial deformation. By analyzing the contribution of each carbon atom orbital in the formation of the electronic states, we conclude that only the pz orbitals of eight out of the twenty atoms in the square unit cell are responsible of the formation of the nano-structure Dirac cones. Spatial symmetry breaking of the underlying honeycomb-like network upon shear stress application leads to a band gap opening. The analysismore » of the phonon spectra demonstrates that the dynamical stability of phagraphene is guaranteed for small distortion angles. Phagraphene is identified here as the first all-C graphitic monolayer with Dirac cones modifiable by a small and realistic physical deformation. The analysis and conclusions of this study can be applied to other monolayered materials exhibiting Dirac cones in square lattices.« less

Elevation and igneous crater modification on Venus: Implications for magmatic volatile content

NASA Technical Reports Server (NTRS)

Wichman, R. W.

1993-01-01

Although most impact craters on Venus preserve nearly pristine crater rim and ejecta features, a small number of craters have been identified showing clear evidence of either igneous intrusion emplacement (floor-fracturing) beneath the crater floor or of volcanically embayed exterior ejecta deposits. Since the volcanically embayed craters consistently occur at higher elevations than the identified floor-fractured craters, this report proposes that igneous crater modification on Venus is elevation dependent. This report describes how regional variations in magmatic neutral buoyancy could produce such elevation dependent crater modification and considers the implications for typical magmatic volatile contents on Venus.

Apparatus and method for electrochemical modification of liquids

DOEpatents

James, Patrick I

2015-04-21

An apparatus for electrochemical modification of liquid streams employing an electrolytic cell which includes an anode compartment defined by an anode structure where oxidation is effected, containing a liquid electrolyte anolyte, and a cathode compartment defined by a cathode structure where reduction is effected containing a liquid electrolyte catholyte. In addition, the electrolytic cell includes at least one additional compartment arranged at least partially between the anode compartment and the cathode compartment and separated from the anode compartment and the cathode compartment by a separator structure arranged to supports ionic conduction of current between the anode structure and the cathode structure.

Molecular modification of native coffee polysaccharide using subcritical water treatment: Structural characterization, antioxidant, and DNA protecting activities.

PubMed

Getachew, Adane Tilahun; Chun, Byung Soo

2017-06-01

Polysaccharides are an abundant resource in coffee beans and have proved to show numerous bioactivities. Despite their abundance, their activities are not always satisfactory mostly due to their structure and large molecular size. Molecular modifications of native polysaccharides can overcome this problem. In this study, we used a novel and green method to modify native coffee polysaccharides using subcritical water (SCW) treatment. The SCW treatment was used at the temperature of 180°C-220°C and pressure of 30-60bar. The molecular and structural modification of the polysaccharides was confirmed using several techniques such as FT-IR, UV spectroscopy, XRD, and TGA. The antioxidant activity of the modified polysaccharides was evaluated using several chemical and Saccharomyces cerevisiae-based high throughput assays. The modified polysaccharides showed high antioxidant activities in all tested assays. Moreover, the polysaccharides showed high DNA protection activities. Therefore, SCW could be employed as a green solvent for molecular modification of polysaccharides. Copyright © 2017 Elsevier B.V. All rights reserved.

37 CFR 401.5 - Modification and tailoring of clauses.

Code of Federal Regulations, 2010 CFR

2010-07-01

... clauses. 401.5 Section 401.5 Patents, Trademarks, and Copyrights ASSISTANT SECRETARY FOR TECHNOLOGY POLICY, DEPARTMENT OF COMMERCE RIGHTS TO INVENTIONS MADE BY NONPROFIT ORGANIZATIONS AND SMALL BUSINESS FIRMS UNDER... may delete paragraph (g)(2) of the clause and delete the words “to be performed by a small business...

78 FR 77377 - Small Business Investment Companies-Investments in Passive Businesses

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-23

..., each of which must be a non-passive small business. The proposed rule would modify this exception to.... This modification would place SBICs on an equal footing with their non-SBIC counterparts in the venture... their equivalents under the North American Industrial Classification System (NAICS); correct erroneous...

Rutile TiO2 Flocculent Ripples with High Antireflectivity and Superhydrophobicity on the Surface of Titanium under 10 ns Laser Irradiation without Focusing.

PubMed

Pan, Aifei; Wang, Wenjun; Mei, Xuesong; Wang, Kedian; Yang, Xianbin

2017-09-26

We report on the formation of rutile TiO 2 flocculent laser-induced periodic surface structures (LIPSSs) with high antireflectivity and superhydrophobicity on the surface of titanium under 10 ns 1064 nm laser irradiation without focusing. The center part of the Gaussian laser beam is used to deposit flocculent structure and the edge part used to produce LIPSSs. The melt and modification thresholds of titanium were determined first, and then, the melt and modification spot-overlap numbers, several responsible for the formation of flocculent structure and LIPSSs, were introduced. It is found that both the melt and modification spot-overlap numbers increase with an increase in laser fluence and spot-overlap number, contributing to the production of flocculent LIPSSs. LIPSSs are obtained with the modification spot-overlap number above 300, and the amount of flocculent structures increases with an increase in the peak laser fluence and spot-overlap number. Then, considering that the fine adjustment of the melt and modification spot-overlop numbers in one-time line scanning is quite difficult, the composite structure, of which both LIPSSs and flocculent structures are distinct, was optimized using laser line scanning twice. On this basis, a characterization test shows the sample full of the flocculent LIPSSs represents best antireflectivity with the value around 10% in the waveband between 260 and 2600 nm (advance 5 times in infrared wavelengths compared to the initial titanium surface), and shows the no-stick hydrophobicity with the contact angle of 160° and roll-off angle of 25° because of the pure rutile phase of TiO 2 .

Mass spectrometry-based carboxyl footprinting of proteins: Method evaluation

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

Zhang, Hao; Wen, Jianzhong; Huang, Richard Y-C.

2012-02-01

Protein structure determines function in biology, and a variety of approaches have been employed to obtain structural information about proteins. Mass spectrometry-based protein footprinting is one fast-growing approach. One labeling-based footprinting approach is the use of a water-soluble carbodiimide, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and glycine ethyl ester (GEE) to modify solvent-accessible carboxyl groups on glutamate (E) and aspartate (D). This paper describes method development of carboxyl-group modification in protein footprinting. The modification protocol was evaluated by using the protein calmodulin as a model. Because carboxyl-group modification is a slow reaction relative to protein folding and unfolding, there is an issue that modificationsmore » at certain sites may induce protein unfolding and lead to additional modification at sites that are not solvent-accessible in the wild-type protein. We investigated this possibility by using hydrogen deuterium amide exchange (H/DX). The study demonstrated that application of carboxyl group modification in probing conformational changes in calmodulin induced by Ca{sup 2+} binding provides useful information that is not compromised by modification-induced protein unfolding.« less

Influence of 5-N-carboxamide modifications on the thermodynamic stability of oligonucleotides

PubMed Central

Wolk, Steven K.; Shoemaker, Richard K.; Mayfield, Wes S.; Mestdagh, Andrew L.; Janjic, Nebojsa

2015-01-01

We have recently shown that the incorporation of modified nucleotides such as 5-N-carboxamide-deoxyuridines into random nucleic acid libraries improves success rates in SELEX experiments and facilitates the identification of ligands with slow off-rates. Here we report the impact of these modifications on the thermodynamic stability of both duplexes and intramolecular ‘single-stranded’ structures. Within duplexes, large, hydrophobic naphthyl groups were destabilizing relative to the all natural DNA duplex, while the hydrophilic groups exhibited somewhat improved duplex stability. All of the significant changes in stability were driven by opposing contributions from the enthalpic and entropic terms. In contrast, both benzyl and naphthyl modifications stabilized intramolecular single-stranded structures relative to their natural DNA analogs, consistent with the notion that intramolecular folding allows formation of novel, stabilizing hydrophobic interactions. Imino proton NMR data provided evidence that elements of the folded structure form at temperatures well below the Tm, with a melting transition that is distinctly less cooperative when compared to duplex DNA. Although there are no data to suggest that the unmodified DNA sequences fold into structures similar to their modified analogs, this still represents clear evidence that these modifications impart thermodynamic stability to the folded structure not achievable with unmodified DNA. PMID:26438535

Enzymatic synthesis of structured lipids.

PubMed

Iwasaki, Yugo; Yamane, Tsuneo

2004-01-01

Structured lipids (SLs) are defined as lipids that are modified chemically or enzymatically in order to change their structure. This review deals with structured triacylglycerols (STGs) and structured phospholipids (SPLs). The most typical STGs are MLM-type STGs, having medium chain fatty acids (FAs) at the 1- and 3-positions and a long chain fatty acid at the 2- position. MLM-type STGs are synthesized by: 1) 1,3-position-specific lipase-catalyzed acyl exchange of TG with FA or with FA ethylester (FAEt); 2) 1,3-position-specific lipase-catalyzed acylation of glycerol with FA, giving symmetric 1,3-diacyl-sn-glycerol, followed by chemical acylation at the sn-2 position, and; 3) 1,3-position-specific lipase-catalyzed deacylation of TG, giving 2-monoacylglycerol, followed by reacylation at the 1- and 3-positions with FA or with (FAEt). Enzymatic preparation of SPLs requires: 1) acyl group modification, and 2) head group modification of phospholipids. Acyl group modification is performed using lipases or phospholipase A2-mediated transesterification or ester synthesis to introduce arbitrary fatty acid to phospholipids. Head group modification is carried out by phospholipase D-catalyzed transphosphatidylation. A wide range of compounds can be introduced into the polar head of phospholipids, making it possible to prepare various SPLs.

Synthesis of (-)-pseudotabersonine, (-)-pseudovincadifformine, and (+)-coronaridine enabled by photoredox catalysis in flow.

PubMed

Beatty, Joel W; Stephenson, Corey R J

2014-07-23

Natural product modification with photoredox catalysis allows for mild, chemoselective access to a wide array of related structures in complex areas of chemical space, providing the possibility for novel structural motifs as well as useful quantities of less abundant congeners. While amine additives have been used extensively as stoichiometric electron donors for photocatalysis, the controlled modification of amine substrates through single-electron oxidation is ideal for the synthesis and modification of alkaloids. Here, we report the conversion of the amine (+)-catharanthine into the natural products (-)-pseudotabersonine, (-)-pseudovincadifformine, and (+)-coronaridine utilizing visible light photoredox catalysis.

Preparation of sumoylated substrates for biochemical analysis.

PubMed

Knipscheer, Puck; Klug, Helene; Sixma, Titia K; Pichler, Andrea

2009-01-01

Covalent modification of proteins with SUMO (small ubiquitin related modifier) affects many cellular processes like transcription, nuclear transport, DNA repair and cell cycle progression. Although hundreds of SUMO targets have been identified, for several of them the function remains obscure. In the majority of cases sumoylation is investigated via "loss of modification" analysis by mutating the relevant target lysine. However, in other cases this approach is not successful since mapping of the modification site is problematic or mutation does not cause an obvious phenotype. These latter cases ask for different approaches to investigate the target modification. One possibility is to choose the opposite approach, a "gain in modification" analysis by producing both SUMO modified and unmodified protein in vitro and comparing them in functional assays. Here, we describe the purification of the ubiquitin conjugating enzyme E2-25K, its in vitro sumoylation with recombinant enzymes and the subsequent separation and purification of the modified and the unmodified forms.

2-Guanidino-quinazolines as a novel class of translation inhibitors.

PubMed

Komarova Andreyanova, E S; Osterman, I A; Pletnev, P I; Ivanenkov, Y A; Majouga, A G; Bogdanov, A A; Sergiev, P V

2017-02-01

A variety of structurally unrelated organic compounds has been reported to have antibacterial activity. Among these, certain small-molecule translation inhibitors have attracted a great deal of attention, due to their relatively high selectivity against prokaryotes, and an appropriate therapeutic index with minor "off target" effects. However, ribosomes are being considered as poorly druggable biological targets, thereby making some routine computational-based approaches to rational drug design and its development rather ineffective. Taking this into account, diversity-oriented biological screening can reasonably be considered as the most advantageous strategy. Thus, using a high-throughput screening (HTS) platform, we applied a unique biological assay for in vitro evaluation of thousands of organic molecules, especially targeted against bacterial ribosomes and translation. As a result, we have identified a series of structurally diverse small-molecule compounds that induce a reporter strain sensitive to translation and DNA biosynthesis inhibitors. In a cell free system, several molecules were found to strongly inhibit protein biosynthesis. Among them, compounds bearing a 2-guanidino-quinazoline core demonstrated the most promising antibacterial activity. With regard to the preliminary structure-activity relationship (SAR) study, we revealed that relatively small substituents at positions 4, 6 and 8 of the quinazoline ring significantly enhance the target activity whereas modification of the guanidine group leads to decrease or loss of antibacterial potency. This novel class of translation inhibitors can properly be regarded as a promising starting point for the development of novel antibacterial therapeutic or screening tools. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Geophysics of Small Planetary Bodies

NASA Technical Reports Server (NTRS)

Asphaug, Erik I.

1998-01-01

As a SETI Institute PI from 1996-1998, Erik Asphaug studied impact and tidal physics and other geophysical processes associated with small (low-gravity) planetary bodies. This work included: a numerical impact simulation linking basaltic achondrite meteorites to asteroid 4 Vesta (Asphaug 1997), which laid the groundwork for an ongoing study of Martian meteorite ejection; cratering and catastrophic evolution of small bodies (with implications for their internal structure; Asphaug et al. 1996); genesis of grooved and degraded terrains in response to impact; maturation of regolith (Asphaug et al. 1997a); and the variation of crater outcome with impact angle, speed, and target structure. Research of impacts into porous, layered and prefractured targets (Asphaug et al. 1997b, 1998a) showed how shape, rheology and structure dramatically affects sizes and velocities of ejecta, and the survivability and impact-modification of comets and asteroids (Asphaug et al. 1998a). As an affiliate of the Galileo SSI Team, the PI studied problems related to cratering, tectonics, and regolith evolution, including an estimate of the impactor flux around Jupiter and the effect of impact on local and regional tectonics (Asphaug et al. 1998b). Other research included tidal breakup modeling (Asphaug and Benz 1996; Schenk et al. 1996), which is leading to a general understanding of the role of tides in planetesimal evolution. As a Guest Computational Investigator for NASA's BPCC/ESS supercomputer testbed, helped graft SPH3D onto an existing tree code tuned for the massively parallel Cray T3E (Olson and Asphaug, in preparation), obtaining a factor xIO00 speedup in code execution time (on 512 cpus). Runs which once took months are now completed in hours.

Understanding the structural and dynamic consequences of DNA epigenetic modifications: Computational insights into cytosine methylation and hydroxymethylation

PubMed Central

Carvalho, Alexandra T P; Gouveia, Leonor; Kanna, Charan Raju; Wärmländer, Sebastian K T S; Platts, Jamie A; Kamerlin, Shina Caroline Lynn

2014-01-01

We report a series of molecular dynamics (MD) simulations of up to a microsecond combined simulation time designed to probe epigenetically modified DNA sequences. More specifically, by monitoring the effects of methylation and hydroxymethylation of cytosine in different DNA sequences, we show, for the first time, that DNA epigenetic modifications change the molecule's dynamical landscape, increasing the propensity of DNA toward different values of twist and/or roll/tilt angles (in relation to the unmodified DNA) at the modification sites. Moreover, both the extent and position of different modifications have significant effects on the amount of structural variation observed. We propose that these conformational differences, which are dependent on the sequence environment, can provide specificity for protein binding. PMID:25625845

Plant Sterols: Chemical and Enzymatic Structural Modifications and Effects on Their Cholesterol-Lowering Activity.

PubMed

He, Wen-Sen; Zhu, Hanyue; Chen, Zhen-Yu

2018-03-28

Plant sterols have attracted increasing attention due to their excellent cholesterol-lowering activity. However, free plant sterols have some characteristics of low oil solubility, water insolubility, high melting point, and low bioavailability, which greatly limit their application in foods. Numerous studies have been undertaken to modify their chemical structures to improve their chemical and physical properties in meeting the needs of various applications. The present review is to summarize the literature and update the progress on structural modifications of plant sterols in the following aspects: (i) synthesis of plant sterol esters by esterification and transesterification with hydrophobic fatty acids and triacylglycerols to improve their oil solubility, (ii) synthesis of plant sterol derivatives by coupling with various hydrophilic moieties to enhance their water solubility, and (iii) mechanisms by which plant sterols reduce plasma cholesterol and the effect of structural modifications on plasma cholesterol-lowering activity of plant sterols.

Nitroxide free radicals protect macular carotenoids against chemical destruction (bleaching) during lipid peroxidation

PubMed Central

Zareba, M.; Widomska, J.; Burke, J. M.; Subczynski, W. K.

2016-01-01

Macular xanthophylls (MXs) lutein and zeaxanthin are dietary carotenoids that are selectively concentrated in the human eye retina, where they are thought to protect against age-related macular degeneration (AMD) by multiple mechanisms, including filtration of phototoxic blue light and quenching of singlet oxygen and triplet states of photosensitizers. These physical protective mechanisms require that MXs be in their intact structure. Here, we investigated the protection of the intact structure of zeaxanthin incorporated into model membranes subjected to oxidative modification by water- and/or membrane-soluble small nitroxide free radicals. Model membranes were formed from saturated, monounsaturated, and polyunsaturated phosphatidylcholines (PCs). Oxidative modification involved autoxidation, iron-mediated, and singlet oxygen-mediated lipid peroxidation. The extent of chemical destruction (bleaching) of zeaxanthin was evaluated from its absorption spectra and compared with the extent of lipid peroxidation evaluated using the thiobarbituric acid assay. Nitroxide free radicals with different polarity (membrane/water partition coefficients) were used. The extent of zeaxanthin bleaching increased with membrane unsaturation and correlated with the rate of PC oxidation. Protection of the intact structure of zeaxanthin by membrane-soluble nitroxides was much stronger than that by water-soluble nitroxides. The combination of zeaxanthin and lipid-soluble nitroxides exerted strong synergistic protection against singlet oxygen-induced lipid peroxidation. The synergistic effect may be explained in terms of protection of the intact zeaxanthin structure by effective scavenging of free radicals by nitroxides, therefore allowing zeaxanthin to quench the primary oxidant, singlet oxygen, effectively by the physical protective mechanism. The redox state of nitroxides was monitored using electron paramagnetic resonance spectroscopy. Both nitroxide free radicals and their reduced form, hydroxylamines, were equally effective. Obtained data were compared with the protective effects of α-tocopherol, which is the natural antioxidant and protector of MXs within the retina. The new strategies employed here to maintain the intact structure of MXs may enhance their protective potential against AMD. PMID:27840316

Nitroxide free radicals protect macular carotenoids against chemical destruction (bleaching) during lipid peroxidation.

PubMed

Zareba, M; Widomska, J; Burke, J M; Subczynski, W K

2016-12-01

Macular xanthophylls (MXs) lutein and zeaxanthin are dietary carotenoids that are selectively concentrated in the human eye retina, where they are thought to protect against age-related macular degeneration (AMD) by multiple mechanisms, including filtration of phototoxic blue light and quenching of singlet oxygen and triplet states of photosensitizers. These physical protective mechanisms require that MXs be in their intact structure. Here, we investigated the protection of the intact structure of zeaxanthin incorporated into model membranes subjected to oxidative modification by water- and/or membrane-soluble small nitroxide free radicals. Model membranes were formed from saturated, monounsaturated, and polyunsaturated phosphatidylcholines (PCs). Oxidative modification involved autoxidation, iron-mediated, and singlet oxygen-mediated lipid peroxidation. The extent of chemical destruction (bleaching) of zeaxanthin was evaluated from its absorption spectra and compared with the extent of lipid peroxidation evaluated using the thiobarbituric acid assay. Nitroxide free radicals with different polarity (membrane/water partition coefficients) were used. The extent of zeaxanthin bleaching increased with membrane unsaturation and correlated with the rate of PC oxidation. Protection of the intact structure of zeaxanthin by membrane-soluble nitroxides was much stronger than that by water-soluble nitroxides. The combination of zeaxanthin and lipid-soluble nitroxides exerted strong synergistic protection against singlet oxygen-induced lipid peroxidation. The synergistic effect may be explained in terms of protection of the intact zeaxanthin structure by effective scavenging of free radicals by nitroxides, therefore allowing zeaxanthin to quench the primary oxidant, singlet oxygen, effectively by the physical protective mechanism. The redox state of nitroxides was monitored using electron paramagnetic resonance spectroscopy. Both nitroxide free radicals and their reduced form, hydroxylamines, were equally effective. Obtained data were compared with the protective effects of α-tocopherol, which is the natural antioxidant and protector of MXs within the retina. The new strategies employed here to maintain the intact structure of MXs may enhance their protective potential against AMD. Copyright © 2016 Elsevier Inc. All rights reserved.

Convergent evolution of chromatin modification by structurally distinct enzymes: comparative enzymology of histone H3 Lys²⁷ methylation by human polycomb repressive complex 2 and vSET.

PubMed

Swalm, Brooke M; Hallenbeck, Kenneth K; Majer, Christina R; Jin, Lei; Scott, Margaret Porter; Moyer, Mikel P; Copeland, Robert A; Wigle, Tim J

2013-07-15

H3K27 (histone H3 Lys27) methylation is an important epigenetic modification that regulates gene transcription. In humans, EZH (enhancer of zeste homologue) 1 and EZH2 are the only enzymes capable of catalysing methylation of H3K27. There is great interest in understanding structure-function relationships for EZH2, as genetic alterations in this enzyme are thought to play a causal role in a number of human cancers. EZH2 is challenging to study because it is only active in the context of the multi-subunit PRC2 (polycomb repressive complex 2). vSET is a viral lysine methyltransferase that represents the smallest protein unit capable of catalysing H3K27 methylation. The crystal structure of this minimal catalytic protein has been solved and researchers have suggested that vSET might prove useful as an EZH2 surrogate for the development of active site-directed inhibitors. To test this proposition, we conducted comparative enzymatic analysis of human EZH2 and vSET and report that, although both enzymes share similar preferences for methylation of H3K27, they diverge in terms of their permissiveness for catalysing methylation of alternative histone lysine sites, their relative preferences for utilization of multimeric macromolecular substrates, their active site primary sequences and, most importantly, their sensitivity to inhibition by drug-like small molecules. The cumulative data led us to suggest that EZH2 and vSET have very distinct active site structures, despite the commonality of the reaction catalysed by the two enzymes. Hence, the EZH2 and vSET pair of enzymes represent an example of convergent evolution in which distinct structural solutions have developed to solve a common catalytic need.

Divergent actions of the pyrethroid insecticides S-bioallethrin, tefluthrin, and deltamethrin on rat Na{sub v}1.6 sodium channels

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

Tan Jianguo; Soderlund, David M., E-mail: dms6@cornell.ed

2010-09-15

We expressed rat Na{sub v}1.6 sodium channels in combination with the rat {beta}{sub 1} and {beta}{sub 2} auxiliary subunits in Xenopus laevis oocytes and evaluated the effects of the pyrethroid insecticides S-bioallethrin, deltamethrin, and tefluthrin on expressed sodium currents using the two-electrode voltage clamp technique. S-Bioallethrin, a type I structure, produced transient modification evident in the induction of rapidly decaying sodium tail currents, weak resting modification (5.7% modification at 100 {mu}M), and no further enhancement of modification upon repetitive activation by high-frequency trains of depolarizing pulses. By contrast deltamethrin, a type II structure, produced sodium tail currents that were {approx}more » 9-fold more persistent than those caused by S-bioallethrin, barely detectable resting modification (2.5% modification at 100 {mu}M), and 3.7-fold enhancement of modification upon repetitive activation. Tefluthrin, a type I structure with high mammalian toxicity, exhibited properties intermediate between S-bioallethrin and deltamethrin: intermediate tail current decay kinetics, much greater resting modification (14.1% at 100 {mu}M), and 2.8-fold enhancement of resting modification upon repetitive activation. Comparison of concentration-effect data showed that repetitive depolarization increased the potency of tefluthrin {approx} 15-fold and that tefluthrin was {approx} 10-fold more potent than deltamethrin as a use-dependent modifier of Na{sub v}1.6 sodium channels. Concentration-effect data from parallel experiments with the rat Na{sub v}1.2 sodium channel coexpressed with the rat {beta}{sub 1} and {beta}{sub 2} subunits in oocytes showed that the Na{sub v}1.6 isoform was at least 15-fold more sensitive to tefluthrin and deltamethrin than the Na{sub v}1.2 isoform. These results implicate sodium channels containing the Na{sub v}1.6 isoform as potential targets for the central neurotoxic effects of pyrethroids.« less

Chemical Approaches for Structure and Function of RNA in Postgenomic Era

PubMed Central

Ro-Choi, Tae Suk; Choi, Yong Chun

2012-01-01

In the study of cellular RNA chemistry, a major thrust of research focused upon sequence determinations for decades. Structures of snRNAs (4.5S RNA I (Alu), U1, U2, U3, U4, U5, and U6) were determined at Baylor College of Medicine, Houston, Tex, in an earlier time of pregenomic era. They show novel modifications including base methylation, sugar methylation, 5′-cap structures (types 0–III) and sequence heterogeneity. This work offered an exciting problem of posttranscriptional modification and underwent numerous significant advances through technological revolutions during pregenomic, genomic, and postgenomic eras. Presently, snRNA research is making progresses involved in enzymology of snRNA modifications, molecular evolution, mechanism of spliceosome assembly, chemical mechanism of intron removal, high-order structure of snRNA in spliceosome, and pathology of splicing. These works are destined to reach final pathway of work “Function and Structure of Spliceosome” in addition to exciting new exploitation of other noncoding RNAs in all aspects of regulatory functions. PMID:22347623

Structural characterization of thioether-bridged bacteriocins.

PubMed

Lohans, Christopher T; Vederas, John C

2014-01-01

Bacteriocins are a group of ribosomally synthesized antimicrobial peptides produced by bacteria, some of which are extensively post-translationally modified. Some bacteriocins, namely the lantibiotics and sactibiotics, contain one or more thioether bridges. However, these modifications complicate the structural elucidation of these bacteriocins using conventional techniques. This review will discuss the techniques and strategies that have been applied to determine the primary structures of lantibiotics and sactibiotics. A major challenge is to identify the topology of thioether bridges in these peptides (i.e., which amino-acid residues are involved in which bridges). Edman degradation, NMR spectroscopy and tandem MS have all been commonly applied to characterize these bacteriocins, but can be incompatible with the post-translational modifications present. Chemical modifications to the modified residues, such as desulfurization and reduction, make the treated bacteriocins more compatible to analysis by these standard peptide analytical techniques. Despite their differences in structure, similar strategies have proved useful to study the structures of both lantibiotics and sactibiotics.

Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard

PubMed Central

Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V.; Moriarty, Nigel W.; Zwart, Peter H.; Hung, Li-Wei; Read, Randy J.; Adams, Paul D.

2008-01-01

The PHENIX AutoBuild wizard is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE model building, RESOLVE statistical density modification and phenix.refine structure refinement. Recent advances in the AutoBuild wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model-completion algorithms and automated solvent-molecule picking. Model-completion algorithms in the AutoBuild wizard include loop building, crossovers between chains in different models of a structure and side-chain optimization. The AutoBuild wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 to 3.2 Å, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29. The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution. PMID:18094468

Two-track virtual screening approach to identify both competitive and allosteric inhibitors of human small C-terminal domain phosphatase 1

NASA Astrophysics Data System (ADS)

Park, Hwangseo; Lee, Hye Seon; Ku, Bonsu; Lee, Sang-Rae; Kim, Seung Jun

2017-08-01

Despite a wealth of persuasive evidence for the involvement of human small C-terminal domain phosphatase 1 (Scp1) in the impairment of neuronal differentiation and in Huntington's disease, small-molecule inhibitors of Scp1 have been rarely reported so far. This study aims to the discovery of both competitive and allosteric Scp1 inhibitors through the two-track virtual screening procedure. By virtue of the improvement of the scoring function by implementing a new molecular solvation energy term and by reoptimizing the atomic charges for the active-site Mg2+ ion cluster, we have been able to identify three allosteric and five competitive Scp1 inhibitors with low-micromolar inhibitory activity. Consistent with the results of kinetic studies on the inhibitory mechanisms, the allosteric inhibitors appear to be accommodated in the peripheral binding pocket through the hydrophobic interactions with the nonpolar residues whereas the competitive ones bind tightly in the active site with a direct coordination to the central Mg2+ ion. Some structural modifications to improve the biochemical potency of the newly identified inhibitors are proposed based on the binding modes estimated with docking simulations.

Uptake and transfection with polymeric nanoparticles are dependent on polymer end-group structure, but largely independent of nanoparticle physical and chemical properties

PubMed Central

Sunshine, Joel C.; Peng, Daniel Y.; Green, Jordan J.

2012-01-01

Development of non-viral particles for gene delivery requires a greater understanding of the properties that enable gene delivery particles to overcome the numerous barriers to intracellular DNA delivery. Linear poly(beta-amino) esters (PBAE) have shown substantial promise for gene delivery, but the mechanism behind their effectiveness is not well quantified with respect to these barriers. In this study, we synthesized, characterized, and evaluated for gene delivery an array of linear PBAEs that differed by small changes along the backbone, side chain, and end-group of the polymers. We examined particle size and surface charge, polymer molecular weight, polymer degradation rate, buffering capacity, cellular uptake, transfection, and cytotoxicity of nanoparticles formulated with these polymers. Significantly, this is the first study that has quantified how small differential structural changes to polymers of this class modulate buffering capacity and polymer degradation rate and relates these findings to gene delivery efficacy. All polymers formed positively charged (zeta potential 21–29 mV) nanosized articles (~ 150 nm). The polymers hydrolytically degraded quickly in physiological conditions, with half-lives ranging from 90 minutes to 6 hours depending on polymer structure. The PBAE buffering capacities in the relevant pH range (pH 5.1 – 7.4) varied from 34% to 95% protonable amines, and on a per mass basis, PBAEs buffered 1.4–4.6 mmol H+/g. When compared to 25 kDa branched polyethyleneimine (PEI), PBAEs buffer significantly fewer protons/mass, as PEI buffers 6.2 mmol H+/g over the same range. However, due to the relatively low cytotoxicity of PBAEs, higher polymer mass can be used to form particles than with PEI and total buffering capacity of PBAE-based particles significantly exceeds that of PEI. Uptake into COS-7 cells ranged from 0% to 95% of cells and transfection ranged from 0% to 93% of cells, depending on the base polymer structure and the end-modifications examined. Five polymers achieved higher uptake and transfection efficacy with less toxicity than branched-PEI control. Surprisingly, acrylate-terminated base polymers were dramatically less efficacious than their end-capped versions, both in terms of uptake (1–3% for acrylate, 75–94% for end-capped) and transfection efficacy (0–1% vs. 20–89%), even though there are minimal differences between acrylate and end-capped polymers in terms of DNA retardation in gel electrophoresis, particle size, zeta potential, and cytotoxicity. These studies further elucidate the role of polymer structure for gene delivery and highlight that small molecule end-group modification of a linear polymer can be critical for cellular uptake in a manner that is largely independent of polymer/DNA binding, particle size, and particle surface charge. PMID:22970908

Centromere inactivation and epigenetic modifications of a plant chromosome with three functional centromeres.

PubMed

Zhang, Wenli; Friebe, Bernd; Gill, Bikram S; Jiang, Jiming

2010-10-01

A chromosome with two functional centromeres is cytologically unstable and can only be stabilized when one of the two centromeres becomes inactivated via poorly understood mechanisms. Here, we report a transmissible chromosome with multiple centromeres in wheat. This chromosome encompassed one large and two small domains containing the centromeric histone CENH3. The two small centromeres are in a close vicinity and often fused as a single centromere on metaphase chromosomes. This fused centromere contained approximately 30% of the CENH3 compared to the large centromere. An intact tricentric chromosome was transmitted to about 70% of the progenies, which was likely a consequence of the dominating pulling capacity of the large centromere during anaphases of meiosis. The tricentric chromosome showed characteristics typical to dicentric chromosomes, including chromosome breaks and centromere inactivation. Remarkably, inactivation was always associated with the small centromeres, indicating that small centromeres are less likely to survive than large ones in dicentric chromosomes. The inactivation of the small centromeres also coincided with changes of specific histone modifications, including H3K27me2 and H3K27me3, of the pericentromeric chromatin.

75 FR 47880 - Notice of Application for Approval of Discontinuance or Modification of a Railroad Signal System...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-09

... Discontinuance or Modification of a Railroad Signal System or Relief Pursuant to Title 49 Code of Federal... Administration (FRA) seeking approval for the discontinuance or modification of the signal system or relief from... & Louisville Railway, Inc., Mr. C. D. Edwards, General Supervisor of Signals & Structures, 1500 Kentucky Avenue...

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

Tripathi, S., E-mail: shilpatr3@gmail.com; Shripathi, T.; Tripathi, J.

The results are reported on solution cast PMMA-PCTFE blend films characterized using x-ray diffraction and FTIR. The nanocrystalline nature of PMMA is still seen in the blends, however, the bond modifications are clearly observed. The addition of PCTFE results in the modification in structural properties, as reflected in the XRD and FTIR spectra showing modifications in bonding as a function of PCTFE percentage.

The Stability of Post Hoc Model Modifications in Covariance Structure Models.

ERIC Educational Resources Information Center

Hutchinson, Susan R.

The work of R. MacCallum et al. (1992) was extended by examining chance modifications through a Monte Carlo simulation. The stability of post hoc model modifications was examined under varying sample size, model complexity, and severity of misspecification using 2- and 4-factor oblique confirmatory factor analysis (CFA) models with four and eight…

Generation of siRNA Nanosheets for Efficient RNA Interference

NASA Astrophysics Data System (ADS)

Kim, Hyejin; Lee, Jae Sung; Lee, Jong Bum

2016-04-01

After the discovery of small interference RNA (siRNA), nanostructured siRNA delivery systems have been introduced to achieve an efficient regulation of the target gene expression. Here we report a new siRNA-generating two dimensional nanostructure in a formation of nanosized sheet. Inspired by tunable mechanical and functional properties of the previously reported RNA membrane, siRNA nanosized sheets (siRNA-NS) with multiple Dicer cleavage sites were prepared. The siRNA-NS has two dimensional structure, providing a large surface area for Dicer to cleave the siRNA-NS for the generation of functional siRNAs. Furthermore, downregulation of the cellular target gene expression was achieved by delivery of siRNA-NS without chemical modification of RNA strands or conjugation to other substances.

Recombinant organisms for production of industrial products

PubMed Central

Adrio, Jose-Luis

2010-01-01

A revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of DNA and the development of recombinant DNA technology. Traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. Novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding techniques and their modifications are contributing greatly to the development of improved industrial processes. In addition, functional genomics, proteomics and metabolomics are being exploited for the discovery of novel valuable small molecules for medicine as well as enzymes for catalysis. The sequencing of industrial microbal genomes is being carried out which bodes well for future process improvement and discovery of new industrial products. PMID:21326937

Deuterium retention and surface modification of tungsten macrobrush samples exposed in FTU Tokamak

NASA Astrophysics Data System (ADS)

Maddaluno, G.; Giacomi, G.; Rufoloni, A.; Verdini, L.

2007-06-01

The effect of discrete structures such as macrobrush or castellated surfaces on power handling and deuterium retention of plasma facing components is to be assessed since such geometrical configurations are needed for increasing the lifetime of the armour to heat-sink joint. Four small macrobrush W and W + 1%La2O3 samples have been exposed in the Frascati Tokamak Upgrade (FTU) scrape-off layer up to the last closed flux surface by means of the Sample Introduction System. FTU is an all metal machine with no carbon source inside vacuum vessel; it exhibits ITER relevant energy and particle fluxes on the plasma facing components. Here, results on morphological surface changes (SEM), chemical composition (EDX) and deuterium retention (TDS) are reported.

Shape control of an adaptive wing for transonic drag reduction

NASA Astrophysics Data System (ADS)

Austin, Fred; Van Nostrand, William C.

1995-05-01

Theory and experiments to control the static shape of flexible structures by employing internal translational actuators are summarized and plants to extend the work to adaptive wings are presented. Significant reductions in the shock-induced drag are achievable during transonic- cruise by small adaptive modifications to the wing cross-sectional profile. Actuators are employed as truss elements of active ribs to deform the wing cross section. An adaptive-rib model was constructed, and experiments validated the shape-control theory. Plans for future development under an ARPA/AFWAL contract include payoff assessments of the method on an actual aircraft, the development of inchworm TERFENOL-D actuators, and the development of a method to optimize the wing cross-sectional shapes by direct-drag measurements.

All roads lead to PP2A: Exploiting the therapeutic potential of this phosphatase

PubMed Central

Sangodkar, Jaya; Farrington, Caroline; McClinch, Kimberly; Galsky, Matthew D.; Kastrinsky, David B.; Narla, Goutham

2015-01-01

Protein phosphatase 2A is a serine/threonine phosphatase involved in the regulation of many cellular processes. A confirmed tumor suppressor protein, PP2A is genetically altered or functionally inactivated in many cancers highlighting a need for its therapeutic reactivation. In this review we will discuss recent literature on PP2A: the elucidation of its structure and the functions of its subunits, and the identification of molecular lesions and post-translational modifications leading to its dysregulation in cancer. A final section will discuss the proteins and small molecules that modulate PP2A and how these might be used to target dysregulated forms of PP2A to treat cancers and other diseases. PMID:26507691

An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes.

PubMed

Taoka, Masato; Yamauchi, Yoshio; Nobe, Yuko; Masaki, Shunpei; Nakayama, Hiroshi; Ishikawa, Hideaki; Takahashi, Nobuhiro; Isobe, Toshiaki

2009-11-01

We describe here a mass spectrometry (MS)-based analytical platform of RNA, which combines direct nano-flow reversed-phase liquid chromatography (RPLC) on a spray tip column and a high-resolution LTQ-Orbitrap mass spectrometer. Operating RPLC under a very low flow rate with volatile solvents and MS in the negative mode, we could estimate highly accurate mass values sufficient to predict the nucleotide composition of a approximately 21-nucleotide small interfering RNA, detect post-transcriptional modifications in yeast tRNA, and perform collision-induced dissociation/tandem MS-based structural analysis of nucleolytic fragments of RNA at a sub-femtomole level. Importantly, the method allowed the identification and chemical analysis of small RNAs in ribonucleoprotein (RNP) complex, such as the pre-spliceosomal RNP complex, which was pulled down from cultured cells with a tagged protein cofactor as bait. We have recently developed a unique genome-oriented database search engine, Ariadne, which allows tandem MS-based identification of RNAs in biological samples. Thus, the method presented here has broad potential for automated analysis of RNA; it complements conventional molecular biology-based techniques and is particularly suited for simultaneous analysis of the composition, structure, interaction, and dynamics of RNA and protein components in various cellular RNP complexes.

Modification of the Sandwich Estimator in Generalized Estimating Equations with Correlated Binary Outcomes in Rare Event and Small Sample Settings

PubMed Central

Rogers, Paul; Stoner, Julie

2016-01-01

Regression models for correlated binary outcomes are commonly fit using a Generalized Estimating Equations (GEE) methodology. GEE uses the Liang and Zeger sandwich estimator to produce unbiased standard error estimators for regression coefficients in large sample settings even when the covariance structure is misspecified. The sandwich estimator performs optimally in balanced designs when the number of participants is large, and there are few repeated measurements. The sandwich estimator is not without drawbacks; its asymptotic properties do not hold in small sample settings. In these situations, the sandwich estimator is biased downwards, underestimating the variances. In this project, a modified form for the sandwich estimator is proposed to correct this deficiency. The performance of this new sandwich estimator is compared to the traditional Liang and Zeger estimator as well as alternative forms proposed by Morel, Pan and Mancl and DeRouen. The performance of each estimator was assessed with 95% coverage probabilities for the regression coefficient estimators using simulated data under various combinations of sample sizes and outcome prevalence values with an Independence (IND), Autoregressive (AR) and Compound Symmetry (CS) correlation structure. This research is motivated by investigations involving rare-event outcomes in aviation data. PMID:26998504

The solvent component of macromolecular crystals

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

Weichenberger, Christian X.; Afonine, Pavel V.; Kantardjieff, Katherine

2015-04-30

On average, the mother liquor or solvent and its constituents occupy about 50% of a macromolecular crystal. Ordered as well as disordered solvent components need to be accurately accounted for in modelling and refinement, often with considerable complexity. The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initialmore » phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.« less

Increased Tensile Strength of Carbon Nanotube Yarns and Sheets through Chemical Modification and Electron Beam Irradiation

NASA Technical Reports Server (NTRS)

Miller, Sandi G.; Williams, Tiffany S.; Baker, James S.; Sola, Francisco; Lebron-Colon, Marisabel; McCorkle, Linda S.; Wilmoth, Nathan G.; Gaier, James; Chen, Michelle; Meador, Michael A.

2014-01-01

The inherent strength of individual carbon nanotubes offers considerable opportunity for the development of advanced, lightweight composite structures. Recent work in the fabrication and application of carbon nanotube (CNT) forms such as yarns and sheets has addressed early nanocomposite limitations with respect to nanotube dispersion and loading; and has pushed the technology toward structural composite applications. However, the high tensile strength of an individual CNT has not directly translated to macro-scale CNT forms where bulk material strength is limited by inter-tube electrostatic attraction and slippage. The focus of this work was to assess post processing of CNT sheet and yarn to improve the macro-scale strength of these material forms. Both small molecule functionalization and e-beam irradiation was evaluated as a means to enhance tensile strength and Youngs modulus of the bulk CNT material. Mechanical testing results revealed a tensile strength increase in CNT sheets by 57 when functionalized, while an additional 48 increase in tensile strength was observed when functionalized sheets were irradiated; compared to unfunctionalized sheets. Similarly, small molecule functionalization increased yarn tensile strength up to 25, whereas irradiation of the functionalized yarns pushed the tensile strength to 88 beyond that of the baseline yarn.

Modifications to toxic CUG RNAs induce structural stability, rescue mis-splicing in a myotonic dystrophy cell model and reduce toxicity in a myotonic dystrophy zebrafish model

DOE PAGES

deLorimier, Elaine; Coonrod, Leslie A.; Copperman, Jeremy; ...

2014-10-10

In this study, CUG repeat expansions in the 3' UTR of dystrophia myotonica protein kinase ( DMPK) cause myotonic dystrophy type 1 (DM1). As RNA, these repeats elicit toxicity by sequestering splicing proteins, such as MBNL1, into protein–RNA aggregates. Structural studies demonstrate that CUG repeats can form A-form helices, suggesting that repeat secondary structure could be important in pathogenicity. To evaluate this hypothesis, we utilized structure-stabilizing RNA modifications pseudouridine (Ψ) and 2'-O-methylation to determine if stabilization of CUG helical conformations affected toxicity. CUG repeats modified with Ψ or 2'-O-methyl groups exhibited enhanced structural stability and reduced affinity for MBNL1. Molecularmore » dynamics and X-ray crystallography suggest a potential water-bridging mechanism for Ψ-mediated CUG repeat stabilization. Ψ modification of CUG repeats rescued mis-splicing in a DM1 cell model and prevented CUG repeat toxicity in zebrafish embryos. This study indicates that the structure of toxic RNAs has a significant role in controlling the onset of neuromuscular diseases.« less

Reactive modification of polyesters and their blends

NASA Astrophysics Data System (ADS)

Wan, Chen

2004-12-01

As part of a broader research effort to investigate the chemical modification of polyesters by reactive processing a low molecular weight (MW) unsaturated polyester (UP) and a higher MW saturated polyester, polyethylene terephthalate (PET), alone or blended with polypropylene (PP) were melt processed in a batch mixer and continuous twin screw extruders. Modification was monitored by on-line rheology and the products were characterized primarily by off-line rheology, morphology and thermal analysis. Efforts were made to establish processing/property relationships and provide an insight of the accompanying structural changes. The overall response of the reactively modified systems was found to be strongly dependent on the component characteristics, blend composition, type and concentrations of reactive additives and processing conditions. The work concluded that UP can be effectively modified through reactive melt processing. Its melt viscosity and MW can be increased through chemical reactions between organic peroxides (POX) and chain unsaturation or between MgO and carboxyl/hydroxyl end groups. Reactive blending of PP/UP blends through peroxide modification gave finer and more uniform morphology than unreacted blends and at a given PP/UP weight ratio more thermoplastic elastomers-like rheological behavior. This is due to the continuously decreasing viscosity ratio of PP/UP towards unity by the competing reactions between POX and the blend components and formation of PP-UP copolymers which serve as in-situ compatibilizers to promote better interfacial adhesion. Kinetics of the competing reactions were analyzed through a developed model. In addition to POX concentration and mixing efficiency, rheology and morphology of UP/PP bends were significantly affected by the addition of inorganic and organic coagents. Addition of coagents such as a difunctional maleimide, MgO and/or an anhydride functionalized PP during reactive blending offers effective means for tailoring the desired rheological and structural characteristics of the final products for potential applications such as low density extrusion foaming or compatibilization of immiscible polymer blends. Important modification conditions through coagents are identified and reaction mechanisms are proposed. A high MW saturated polyester, PET, can also be rheologically modified in extruders through low MW multifunctional anhydride and epoxy compounds by chain extension/branching. Several such modifiers were successfully screened in terms of their reactivity towards PET under controlled reactive extrusion conditions. A dianhydride with medium reactivity was then successfully used in a one-step reactive modification/extrusion foaming process to produce low density foams. A similar process was successfully used to produce small cell size foams from a four component system containing PET, PP and lesser amounts of a low molecular weight multifunctional epoxy compound and an acid functionalized polyolefin, the latter acting as compatibilizers.

Frequency band enlargement of the penetrator seismometer and its application to moonquake observation

NASA Astrophysics Data System (ADS)

Yamada, Ryuhei; Nébut, Tanguy; Shiraishi, Hiroaki; Lognonné, Philippe; Kobayashi, Naoki; Tanaka, Satoshi

2015-07-01

Seismic data obtained over a broad frequency range are very useful in investigation of the internal structures of the Earth and other planetary bodies. However, planetary seismic data acquired through the NASA Apollo and Viking programs were obtained only over a very limited frequency range. To obtain effective seismic data over a broader frequency range on planetary surfaces, broadband seismometers suitable for planetary seismology must be developed. In this study, we have designed a new broadband seismometer based on a short-period seismometer whose resonant frequency is 1 Hz for future geophysical missions. The seismometer is of an electromagnetic type, light weight, small size and has good shock-durability, making it suitable for being loaded onto a penetrator, which is a small, hard-landing probe developed in the LUNAR-A Project, a previous canceled mission. We modified the short-period seismometer so as to have a flat frequency response above about 0.1 Hz and the detection limit could be lowered to cover frequencies below the frequency. This enlargement of the frequency band will allow us to investigate moonquakes for lower frequency components in which waveforms are less distorted because strong scattering due to fractured structures near the lunar surface is likely to be suppressed. The modification was achieved simply by connecting a feedback circuit to the seismometer, without making any mechanical changes to the short-period sensor. We have confirmed that the broadband seismometer exhibits the frequency response as designed and allows us to observe long-period components of small ground motions. Methods to improve the performance of the broadband seismometer from the current design are also discussed. These developments should promise to increase the opportunity for application of this small and tough seismometer in various planetary seismological missions.

THE DEVELOPMENT OF A STANDARDIZED ACHIEVEMENT TEST FOR SMALL GASOLINE ENGINE INSTRUCTION.

ERIC Educational Resources Information Center

EBBERT, J. MARVIN

THE PURPOSE OF THE STUDY WAS TO DEVELOP A STANDARDIZED, MULTIPLE-CHOICE ACHIEVEMENT TEST ON THE OPERATION, CARE, AND MAINTENANCE OF SMALL GASOLINE ENGINES. OBJECTIVES AND A UNIT OUTLINE WERE DEVELOPED WITH THE COOPERATION OF 75 INDIANA VOCATIONAL AGRICULTURE TEACHERS. A PANEL SUGGESTED MODIFICATIONS, AND THE REFINED OBJECTIVES AND OUTLINE WERE…

The Utility of IRT in Small-Sample Testing Applications.

ERIC Educational Resources Information Center

Sireci, Stephen G.

The utility of modified item response theory (IRT) models in small sample testing applications was studied. The modified IRT models were modifications of the one- and two-parameter logistic models. One-, two-, and three-parameter models were also studied. Test data were from 4 years of a national certification examination for persons desiring…

Correct folding of an α-helix and a β-hairpin using a polarized 2D torsional potential

PubMed Central

Gao, Ya; Li, Yongxiu; Mou, Lirong; Lin, Bingbing; Zhang, John Z. H.; Mei, Ye

2015-01-01

A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER032D), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by high-level quantum mechanical calculations of small peptides in solution. Molecular dynamics simulations are performed to study the folding of two model peptides adopting either α-helix or β-hairpin structures. Both peptides are successfully folded into their native structures using an AMBER032D force field with the implementation of a polarization scheme (AMBER032Dp). For comparison, simulations using a standard AMBER03 force field with and without polarization, as well as AMBER032D without polarization, fail to fold both peptides successfully. The correction to secondary structure propensity in the AMBER03 force field and the polarization effect are critical to folding Trpzip2; without these factors, a helical structure is obtained. This study strongly suggests that this new force field is capable of providing a more balanced preference for helical and extended conformations. The electrostatic polarization effect is shown to be indispensable to the growth of secondary structures. PMID:26039188

Biophysical analysis of the effect of chemical modification by 4-oxononenal on the structure, stability, and function of binding immunoglobulin protein (BiP)

PubMed Central

Shah, Dinen D.; Singh, Surinder M.; Dzieciatkowska, Monika

2017-01-01

Binding immunoglobulin protein (BiP) is a molecular chaperone important for the folding of numerous proteins, which include millions of immunoglobulins in human body. It also plays a key role in the unfolded protein response (UPR) in the endoplasmic reticulum. Free radical generation is a common phenomenon that occurs in cells under healthy as well as under stress conditions such as ageing, inflammation, alcohol consumption, and smoking. These free radicals attack the cell membranes and generate highly reactive lipid peroxidation products such as 4-oxononenal (4-ONE). BiP is a key protein that is modified by 4-ONE. In this study, we probed how such chemical modification affects the biophysical properties of BiP. Upon modification, BiP shows significant tertiary structural changes with no changes in its secondary structure. The protein loses its thermodynamic stability, particularly, that of the nucleotide binding domain (NBD) where ATP binds. In terms of function, the modified BiP completely loses its ATPase activity with decreased ATP binding affinity. However, modified BiP retains its immunoglobulin binding function and its chaperone activity of suppressing non-specific protein aggregation. These results indicate that 4-ONE modification can significantly affect the structure-function of key proteins such as BiP involved in cellular pathways, and provide a molecular basis for how chemical modifications can result in the failure of quality control mechanisms inside the cell. PMID:28886061

Structure of the CFA/III major pilin subunit CofA from human enterotoxigenic Escherichia coli determined at 0.90 Å resolution by sulfur-SAD phasing.

PubMed

Fukakusa, Shunsuke; Kawahara, Kazuki; Nakamura, Shota; Iwashita, Takaki; Baba, Seiki; Nishimura, Mitsuhiro; Kobayashi, Yuji; Honda, Takeshi; Iida, Tetsuya; Taniguchi, Tooru; Ohkubo, Tadayasu

2012-10-01

CofA, a major pilin subunit of colonization factor antigen III (CFA/III), forms pili that mediate small-intestinal colonization by enterotoxigenic Escherichia coli (ETEC). In this study, the crystal structure of an N-terminally truncated version of CofA was determined by single-wavelength anomalous diffraction (SAD) phasing using five sulfurs in the protein. Given the counterbalance between anomalous signal strength and the undesired X-ray absorption of the solvent, diffraction data were collected at 1.5 Å resolution using synchrotron radiation. These data were sufficient to elucidate the sulfur substructure at 1.38 Å resolution. The low solvent content (29%) of the crystal necessitated that density modification be performed with an additional 0.9 Å resolution data set to reduce the phase error caused by the small sulfur anomalous signal. The CofA structure showed the αβ-fold typical of type IVb pilins and showed high structural homology to that of TcpA for toxin-coregulated pili of Vibrio cholerae, including spatial distribution of key residues critical for pilin self-assembly. A pilus-filament model of CofA was built by computational docking and molecular-dynamics simulation using the previously reported filament model of TcpA as a structural template. This model revealed that the CofA filament surface was highly negatively charged and that a 23-residue-long loop between the α1 and α2 helices filled the gap between the pilin subunits. These characteristics could provide a unique binding epitope for the CFA/III pili of ETEC compared with other type IVb pili.

On The Cloud Processing of Aerosol Particles: An Entraining Air Parcel Model With Two-dimensional Spectral Cloud Microphysics and A New Formulation of The Collection Kernel

NASA Astrophysics Data System (ADS)

Bott, Andreas; Kerkweg, Astrid; Wurzler, Sabine

A study has been made of the modification of aerosol spectra due to cloud pro- cesses and the impact of the modified aerosols on the microphysical structure of future clouds. For this purpose an entraining air parcel model with two-dimensional spectral cloud microphysics has been used. In order to treat collision/coalescence processes in the two-dimensional microphysical module, a new realistic and continuous formu- lation of the collection kernel has been developed. Based on experimental data, the kernel covers the entire investigated size range of aerosols, cloud and rain drops, that is the kernel combines all important coalescence processes such as the collision of cloud drops as well as the impaction scavenging of small aerosols by big raindrops. Since chemical reactions in the gas phase and in cloud drops have an important impact on the physico-chemical properties of aerosol particles, the parcel model has been extended by a chemical module describing gas phase and aqueous phase chemical reactions. However, it will be shown that in the numerical case studies presented in this paper the modification of aerosols by chemical reactions has a minor influence on the microphysical structure of future clouds. The major process yielding in a second cloud event an enhanced formation of rain is the production of large aerosol particles by collision/coalescence processes in the first cloud.

Modifications of structural, chemical, and electrical characteristics of Er2O3/Si interface under Co-60 gamma irradiation

NASA Astrophysics Data System (ADS)

Kaya, Senol; Yilmaz, Ercan

2018-03-01

This paper reports the influences of gamma radiation on the structural, electrical, and chemical characteristics of erbium oxide (Er2O3) thin films and the possible mechanisms underlying these irradiation-induced effects. The crystallographic and morphological modifications under gamma irradiation were characterized by X-ray diffraction (XRD) and atomic force microscopy (AFM), respectively, while radiation influences on electrochemical characteristics were analyzed by X-ray photoelectron spectroscopy (XPS). Furthermore, changes in electrical characteristics were analyzed on the basis of capacitance-voltage (C-V) and conductance-voltage (G/ω-V) measurements. The XRD results demonstrated that small atomic displacement was observed and that the grain size of the nanostructure slightly increased. Improvements in surface roughness were observed in AFM measurements. The observed variations in the XRD and AFM measurements can be attributed to the radiation-induced local heating and microscopic atomic mobility. In addition, the XPS analysis obviously demonstrated that the oxygen vacancies increased with irradiation dose because of the breaking of Er2O3 and ErxOy bonds. Significant influences of the generated oxygen vacancies on the electrical measurements were observed, and the radiation-induced hole traps, which caused large flat band shifts, can be attributed to the generated oxygen vacancies. The results show that radiation does not degrade the physical characteristics significantly, but the generation of oxygen vacancies considerably increases the electrical sensitivity of the Er2O3 dielectric.

Chemical modification of citrus pectin: Structural, physical and rheologial implications.

PubMed

Fracasso, Aline Francielle; Perussello, Camila Augusto; Carpiné, Danielle; Petkowicz, Carmen Lúcia de Oliveira; Haminiuk, Charles Windson Isidoro

2018-04-01

The present study aimed to investigate the physical, structural and rheological modifications caused by the chemical modification process of citrus pectin. Therefore, three commercial citrus pectins with different degree of esterification were chemically modified by sequential alkali and acidic hydrolytic process to produce modified citrus pectins (MCP) with special properties. The molar mass (M w ), degree of esterification (DE), monosaccharide composition, 13 C NMR spectra, homogeneity, morphology (SEM) and rheological behavior of both native and modified citrus pectins (MCP) were investigated. The chemical modification reduced the acid uronic content (up to 28.3%) and molar mass (up to 29.98%), however, showed little influence on the degree of esterification of native pectins. Modified citrus pectins presented higher amounts of neutral monosaccharides, mainly galactose, arabinose and rhamnose, typical of the Ramnogalacturonana-I (RG-I) region. Rheological tests indicated that the native and modified citrus pectins presented pseudoplastic behavior, however, the MCP samples were less viscous, compared to the native ones. Modified samples presented better dissolution in water and less strong gels, with good stability during oscillatory shearing at 25°C. This study aims to better understand the implications that chemical modifications may impose on the structure of citrus pectins. Copyright © 2017 Elsevier B.V. All rights reserved.

Introduction to the thematic minireview series on redox-active protein modifications and signaling.

PubMed

Banerjee, Ruma

2013-09-13

The dynamics of redox metabolism necessitate cellular strategies for sensing redox changes and for responding to them. A common mechanism for receiving and transmitting redox changes is via reversible modifications of protein cysteine residues. A plethora of cysteine modifications have been described, including sulfenylation, glutathionylation, and disulfide formation. These post-translational modifications have the potential to alter protein structure and/or function and to modulate cellular processes ranging from division to death and from circadian rhythms to secretion. The focus of this thematic minireview series is cysteine modifications in response to reactive oxygen and nitrogen species.

Ionospheric modification using relativistic electron beams

NASA Technical Reports Server (NTRS)

Banks, Peter M.; Fraser-Smith, Anthony C.; Gilchrist, B. E.

1990-01-01

The recent development of comparatively small electron linear accelerators (linacs) now makes possible a new class of ionospheric modification experiments using beams of relativistic electrons. These experiments can potentially provide much new information about the interactions of natural relativistic electrons with other particles in the upper atmosphere, and it may also make possible new forms of ionization structures extending down from the lower ionosphere into the largely un-ionized upper atmosphere. The consequences of firing a pulsed 1 A, 5 Mev electron beam downwards into the upper atmosphere are investigated. If a small pitch angle with respect to the ambient geomagnetic field is selected, the beam produces a narrow column of substantial ionization extending down from the source altitude to altitudes of approximately 40 to 45 km. This column is immediately polarized by the natural middle atmosphere fair weather electric field and an increasingly large potential difference is established between the column and the surrounding atmosphere. In the regions between 40 to 60 km, this potential can amount to many tens of kilovolts and the associated electric field can be greater than the field required for breakdown and discharge. Under these conditions, it may be possible to initiate lightning discharges along the initial ionization channel. Filamentation may also occur at the lower end to drive further currents in the partially ionized gases of the stratosphere. Such discharges would derive their energy from the earth-ionosphere electrical system and would be sustained until plasma depletion and/or electric field reduction brought the discharge under control. It is likely that this artificially-triggered lightning would produce measurable low-frequency radiation.

Chromatin immunoprecipitation with fixed animal tissues and preparation for high-throughput sequencing.

PubMed

Cotney, Justin L; Noonan, James P

2015-02-02

Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) is a powerful method used to identify genome-wide binding patterns of transcription factors and distribution of various histone modifications associated with different chromatin states. In most published studies, ChIP-Seq has been performed on cultured cells grown under controlled conditions, allowing generation of large amounts of material in a homogeneous biological state. Although such studies have provided great insight into the dynamic landscapes of animal genomes, they do not allow the examination of transcription factor binding and chromatin states in adult tissues, developing embryonic structures, or tumors. Such knowledge is critical to understanding the information required to create and maintain a complex biological tissue and to identify noncoding regions of the genome directly involved in tissues affected by complex diseases such as autism. Studying these tissue types with ChIP-Seq can be challenging due to the limited availability of tissues and the lack of complex biological states able to be achieved in culture. These inherent differences require alterations of standard cross-linking and chromatin extraction typically used in cell culture. Here we describe a general approach for using small amounts of animal tissue to perform ChIP-Seq directed at histone modifications and transcription factors. Tissue is homogenized before treatment with formaldehyde to ensure proper cross-linking, and a two-step nuclear isolation is performed to increase extraction of soluble chromatin. Small amounts of soluble chromatin are then used for immunoprecipitation (IP) and prepared for multiplexed high-throughput sequencing. © 2015 Cold Spring Harbor Laboratory Press.

Protein C-Terminal Labeling and Biotinylation Using Synthetic Peptide and Split-Intein

PubMed Central

Volkmann, Gerrit; Liu, Xiang-Qin

2009-01-01

Background Site-specific protein labeling or modification can facilitate the characterization of proteins with respect to their structure, folding, and interaction with other proteins. However, current methods of site-specific protein labeling are few and with limitations, therefore new methods are needed to satisfy the increasing need and sophistications of protein labeling. Methodology A method of protein C-terminal labeling was developed using a non-canonical split-intein, through an intein-catalyzed trans-splicing reaction between a protein and a small synthetic peptide carrying the desired labeling groups. As demonstrations of this method, three different proteins were efficiently labeled at their C-termini with two different labels (fluorescein and biotin) either in solution or on a solid surface, and a transferrin receptor protein was labeled on the membrane surface of live mammalian cells. Protein biotinylation and immobilization on a streptavidin-coated surface were also achieved in a cell lysate without prior purification of the target protein. Conclusions We have produced a method of site-specific labeling or modification at the C-termini of recombinant proteins. This method compares favorably with previous protein labeling methods and has several unique advantages. It is expected to have many potential applications in protein engineering and research, which include fluorescent labeling for monitoring protein folding, location, and trafficking in cells, and biotinylation for protein immobilization on streptavidin-coated surfaces including protein microchips. The types of chemical labeling may be limited only by the ability of chemical synthesis to produce the small C-intein peptide containing the desired chemical groups. PMID:20027230

Effect of ion-beam treatment on structure and fracture resistance of 12Cr1MoV steel under static, cyclic and dynamic loading

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

Panin, S. V., E-mail: svp@ispms.tsc.ru; Vlasov, I. V., E-mail: good0@yandex.ru; Sergeev, V. P., E-mail: retc@ispms.tsc.ru

2015-10-27

Features of the structure and properties modification of 12Cr1MoV steel subjected to irradiation by zirconium ion beam have been investigated with the use of optical and electron microscopy as well as microhardness measurement. It has been shown that upon treatment the structure modification occurred across the entire cross-section of specimens with the thickness of 1 mm. Changes in the mechanical properties of these specimens under static, cyclic and impact loading are interpreted in terms of identified structure changes.

Effects of sea lamprey substrate modification and carcass nutrients on macroinvertebrate assemblages in a small Atlantic coastal stream

USGS Publications Warehouse

Weaver, Daniel M.; Coghlan, Stephen M.; Zydlewski, Joseph D.

2018-01-01

Aquatic macroinvertebrates respond to patch dynamics arising from interactions of physical and chemical disturbances across space and time. Anadromous fish, such as sea lamprey, Petromyzon marinus, migrate from the ocean and alter physical and chemical properties of recipient spawning streams. Sea lamprey disturb stream benthos physically through nest construction and spawning, and enrich food webs through nutrient deposition from decomposing carcasses. Sea lamprey spawning nests support greater macroinvertebrate abundance than adjacent reference areas, but concurrent effects of stream bed modification and nutrient supplementation have not been examined sequentially. We added carcasses and cleared substrate experimentally to mimic the physical disturbance and nutrient enrichment associated with lamprey spawning, and characterized effects on macroinvertebrate assemblage structure. We found that areas receiving cleared substrate and carcass nutrients were colonized largely by Simuliidae compared to upstream and downstream control areas that were colonized largely by Hydropsychidae, Philopotamidae, and Chironomidae. Environmental factors such as stream flow likely shape assemblages by physically constraining macroinvertebrate establishment and feeding. Our results indicate potential changes in macroinvertebrate assemblages from the physical and chemical changes to streams brought by spawning populations of sea lamprey.

M13 bacteriophage display framework that allows sortase-mediated modification of surface-accessible phage proteins.

PubMed

Hess, Gaelen T; Cragnolini, Juan J; Popp, Maximilian W; Allen, Mark A; Dougan, Stephanie K; Spooner, Eric; Ploegh, Hidde L; Belcher, Angela M; Guimaraes, Carla P

2012-07-18

We exploit bacterial sortases to attach a variety of moieties to the capsid proteins of M13 bacteriophage. We show that pIII, pIX, and pVIII can be functionalized with entities ranging from small molecules (e.g., fluorophores, biotin) to correctly folded proteins (e.g., GFP, antibodies, streptavidin) in a site-specific manner, and with yields that surpass those of any reported using phage display technology. A case in point is modification of pVIII. While a phage vector limits the size of the insert into pVIII to a few amino acids, a phagemid system limits the number of copies actually displayed at the surface of M13. Using sortase-based reactions, a 100-fold increase in the efficiency of display of GFP onto pVIII is achieved. Taking advantage of orthogonal sortases, we can simultaneously target two distinct capsid proteins in the same phage particle and maintain excellent specificity of labeling. As demonstrated in this work, this is a simple and effective method for creating a variety of structures, thus expanding the use of M13 for materials science applications and as a biological tool.

An M13 bacteriophage display framework that allows sortase-mediated modification of surface-accessible phage proteins

PubMed Central

Hess, Gaelen T.; Cragnolini, Juan J.; Popp, Maximilian W.; Allen, Mark A.; Dougan, Stephanie K.; Spooner, Eric; Ploegh, Hidde L.; Belcher, Angela M.; Guimaraes, Carla P.

2013-01-01

We exploit bacterial sortases to attach a variety of moieties to the capsid proteins of M13 bacteriophage. We show that pIII, pIX, and pVIII can be functionalized with entities ranging from small molecules (e.g., fluorophores, biotin) to correctly folded proteins (e.g., GFP, antibodies, streptavidin) in a site-specific manner, and with yields that surpass those of any reported using phage display technology. A case in point is modification of pVIII. While a phage vector limits the size of the insert into pVIII to a few amino acids, a phagemid system limits the number of copies actually displayed at the surface of M13. Using sortase-based reactions, a 100-fold increase in the efficiency of display of GFP onto pVIII is achieved. Taking advantage of orthogonal sortases, we can simultaneously target two distinct capsid proteins in the same phage particle and maintain excellent specificity of labeling. As demonstrated in this work, this is a simple and effective method for creating a variety of structures, thus expanding the use of M13 for materials science applications and as a biological tool. PMID:22759232

Novel small molecule epithelial sodium channel inhibitors as potential therapeutics in cystic fibrosis - a patent evaluation.

PubMed

Schoenberger, Matthias; Althaus, Mike

2013-10-01

Novel molecular platforms for epithelial sodium channel (ENaC) modulators are claimed in the following six patents: WO2012035158(A1); WO2009074575(A2); WO2011028740(A1); WO2009150137(A2); WO2011079087(A1); WO2008135557(A1). These ENaC inhibitors may be used in blocking transepithelial sodium and consequently water absorption across airway epithelia. This may result in airway rehydration and enhanced mucociliary clearance in patients with cystic fibrosis (CF) lung disease. All inhibitors resemble the classical ENaC blocker amiloride but follow different strategies to increase structural diversity in a sterically tolerant region. These substitutions can be modified to i) enhance potency of ENaC inhibition; ii) reduce epithelial permeability; and iii) broaden applicability in order to be used as potential drugs for CF therapy. Most of the claims and patent data are supported by the currently available literature. The patents deliver a solid chemical basis for a variety of chemical modifications of the ENaC inhibitor amiloride. These modifications may result in the development of a novel, applicable ENaC inhibitors which may have lasting effects on diseased airways and may achieve airway rehydration and enhanced mucociliary clearance in CF lung disease.

Studies on high electronic energy deposition in transparent conducting indium tin oxide thin films

NASA Astrophysics Data System (ADS)

Deshpande, N. G.; Gudage, Y. G.; Ghosh, A.; Vyas, J. C.; Singh, F.; Tripathi, A.; Sharma, Ramphal

2008-02-01

We have examined the effect of swift heavy ions using 100 MeV Au8+ ions on the electrical properties of transparent, conducting indium tin oxide polycrystalline films with resistivity of 0.58 × 10-4 Ω cm and optical transmission greater than 78% (pristine). We report on the modifications occurring after high electronic energy deposition. With the increase in fluency, x-ray line intensity of the peaks corresponding to the planes (1 1 0), (4 0 0), (4 4 1) increased, while (3 3 1) remained constant. Surface morphological studies showed a pomegranate structure of pristine samples, which was highly disturbed with a high dose of irradiation. For the high dose, there was a formation of small spherical domes uniformly distributed over the entire surface. The transmittance was seen to be decreasing with the increase in ion fluency. At higher doses, the resistivity and photoluminescence intensity was seen to be decreased. In addition, the carrier concentration was seen to be increased, which was in accordance with the decrease in resistivity. The observed modifications after high electronic energy deposition in these films may lead to fruitful device applications.

Influence of magnetic field configuration on magnetohydrodynamic waves in Earth's core

NASA Astrophysics Data System (ADS)

Knezek, Nicholas; Buffett, Bruce

2018-04-01

We develop a numerical model to study magnetohydrodynamic waves in a thin layer of stratified fluid near the surface of Earth's core. Past studies have been limited to using simple background magnetic field configurations. However, the choice of field distribution can dramatically affect the structure and frequency of the waves. To permit a more general treatment of background magnetic field and layer stratification, we combine finite volume and Fourier methods to describe the wave motions. We validate our model by comparisons to previous studies and examine the influence of background magnetic field configuration on two types of magnetohydrodynamic waves. We show that the structure of zonal Magnetic-Archimedes-Coriolis (MAC) waves for a dipole background field is unstable to small perturbations of the field strength in the equatorial region. Modifications to the wave structures are computed for a range of field configurations. In addition, we show that non-zonal MAC waves are trapped near the equator for realistic magnetic field distributions, and that their latitudinal extent depends upon the distribution of magnetic field strength at the CMB.

Seismic Velocity Measurements at Expanded Seismic Network Sites

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

Woolery, Edward W; Wang, Zhenming

2005-01-01

Structures at the Paducah Gaseous Diffusion Plant (PGDP), as well as at other locations in the northern Jackson Purchase of western Kentucky may be subjected to large far-field earthquake ground motions from the New Madrid seismic zone, as well as those from small and moderate-sized local events. The resultant ground motion a particular structure is exposed from such event will be a consequence of the earthquake magnitude, the structures' proximity to the event, and the dynamic and geometrical characteristics of the thick soils upon which they are, of necessity, constructed. This investigation evaluated the latter. Downhole and surface (i.e., refractionmore » and reflection) seismic velocity data were collected at the Kentucky Seismic and Strong-Motion Network expansion sites in the vicinity of the Paducah Gaseous Diffusion Plant (PGDP) to define the dynamic properties of the deep sediment overburden that can produce modifying effects on earthquake waves. These effects are manifested as modifications of the earthquake waves' amplitude, frequency, and duration. Each of these three ground motion manifestations is also fundamental to the assessment of secondary earthquake engineering hazards such as liquefaction.« less

Structure and short time degradation studies of sodium zirconium phosphate ceramics loaded with simulated fast breeder (FBR) waste

NASA Astrophysics Data System (ADS)

Ananthanarayanan, A.; Ambashta, R. D.; Sudarsan, V.; Ajithkumar, T.; Sen, D.; Mazumder, S.; Wattal, P. K.

2017-04-01

Sodium zirconium phosphate (NZP) ceramics have been prepared using conventional sintering and hot isostatic pressing (HIP) routes. The structure of NZP ceramics, prepared using the HIP route, has been compared with conventionally sintered NZP using a combination of X-ray diffraction (XRD) and (31P and 23Na) nuclear magnetic resonance (NMR) spectroscopy techniques. It is observed that NZP with no waste loading is aggressive toward the steel HIP-can during hot isostatic compaction and significant fraction of cations from the steel enter the ceramic material. Waste loaded NZP samples (10 wt% simulated FBR waste) show significantly low can-interaction and primary NZP phase is evident in this material. Upon exposure of can-interacted and waste loaded NZP to boiling water and steam, 31P NMR does not detect any major modifications in the network structure. However, the 23Na NMR spectra indicate migration of Na+ ions from the surface and possible re-crystallization. This is corroborated by Small-Angle Neutron Scattering (SANS) data and Scanning Electron Microscopy (SEM) measurements carried out on these samples.

Act-and-wait time-delayed feedback control of autonomous systems

NASA Astrophysics Data System (ADS)

Pyragas, Viktoras; Pyragas, Kestutis

2018-02-01

Recently an act-and-wait modification of time-delayed feedback control has been proposed for the stabilization of unstable periodic orbits in nonautonomous dynamical systems (Pyragas and Pyragas, 2016 [30]). The modification implies a periodic switching of the feedback gain and makes the closed-loop system finite-dimensional. Here we extend this modification to autonomous systems. In order to keep constant the phase difference between the controlled orbit and the act-and-wait switching function an additional small-amplitude periodic perturbation is introduced. The algorithm can stabilize periodic orbits with an odd number of real unstable Floquet exponents using a simple single-input single-output constraint control.

Synthesis of (−)-Pseudotabersonine, (−)-Pseudovincadifformine, and (+)-Coronaridine Enabled by Photoredox Catalysis in Flow

PubMed Central

2015-01-01

Natural product modification with photoredox catalysis allows for mild, chemoselective access to a wide array of related structures in complex areas of chemical space, providing the possibility for novel structural motifs as well as useful quantities of less abundant congeners. While amine additives have been used extensively as stoichiometric electron donors for photocatalysis, the controlled modification of amine substrates through single-electron oxidation is ideal for the synthesis and modification of alkaloids. Here, we report the conversion of the amine (+)-catharanthine into the natural products (−)-pseudotabersonine, (−)-pseudovincadifformine, and (+)-coronaridine utilizing visible light photoredox catalysis. PMID:25003992

Advanced glycation end products induce differential structural modifications and fibrillation of albumin

NASA Astrophysics Data System (ADS)

Awasthi, Saurabh; Sankaranarayanan, Kamatchi; Saraswathi, N. T.

2016-06-01

Glycation induced amyloid fibrillation is fundamental to the development of many neurodegenerative and cardiovascular complications. Excessive non-enzymatic glycation in conditions such as hyperglycaemia results in the increased accumulation of advanced glycation end products (AGEs). AGEs are highly reactive pro-oxidants, which can lead to the activation of inflammatory pathways and development of oxidative stress. Recently, the effect of non-enzymatic glycation on protein structure has been the major research area, but the role of specific AGEs in such structural alteration and induction of fibrillation remains undefined. In this study, we determined the specific AGEs mediated structural modifications in albumin mainly considering carboxymethyllysine (CML), carboxyethyllysine (CEL), and argpyrimidine (Arg-P) which are the major AGEs formed in the body. We studied the secondary structural changes based on circular dichroism (CD) and spectroscopic analysis. The AGEs induced fibrillation was determined by Congo red binding and examination of scanning and transmission electron micrographs. The amyloidogenic regions in the sequence of BSA were determined using FoldAmyloid. It was observed that CEL modification of BSA leads to the development of fibrillar structures, which was evident from both secondary structure changes and TEM analysis.

A Generalizable Platform for Interrogating Target- and Signal-Specific Consequences of Electrophilic Modifications in Redox-Dependent Cell Signaling

PubMed Central

Lin, Hong-Yu; Haegele, Joseph A.; Disare, Michael T.; Lin, Qishan; Aye, Yimon

2015-01-01

Despite the known propensity of small-molecule electrophiles to react with numerous cysteine-active proteins, biological actions of individual signal inducers have emerged to be chemotype-specific. To pinpoint and quantify the impacts of modifying one target out of the whole proteome, we develop a target-protein-personalized “electrophile toolbox” with which specific intracellular targets can be selectively modified at a precise time by specific reactive signals. This general methodology—T-REX (targetable reactive electrophiles & oxidants)—is established by: (1) constructing a platform that can deliver a range of electronic and sterically different bioactive lipid-derived signaling electrophiles to specific proteins in cells; (2) probing the kinetics of targeted delivery concept which revealed that targeting efficiency in cells is largely driven by initial on-rate of alkylation; and (3) evaluating the consequences of protein-target- and small-molecule-signal-specific modifications on the strength of downstream signaling. These data show that T-REX allows quantitative interrogations into the extent to which the Nrf2 transcription factor-dependent antioxidant response element (ARE) signaling is activated by selective electrophilic modifications on Keap1 protein—one of several redox-sensitive regulators of the Nrf2–ARE axis. The results document Keap1 as a promiscuous electrophile-responsive sensor able to respond with similar efficiencies to discrete electrophilic signals, promoting comparable strength of Nrf2–ARE induction. T-REX is also able to elicit cell activation in cases in which whole-cell electrophile flooding fails to stimulate ARE induction prior to causing cytotoxicity. The platform presents a previously unavailable opportunity to elucidate the functional consequences of small-molecule-signal- and protein-target-specific electrophilic modifications in an otherwise unaffected cellular background. PMID:25909755

A generalizable platform for interrogating target- and signal-specific consequences of electrophilic modifications in redox-dependent cell signaling.

PubMed

Lin, Hong-Yu; Haegele, Joseph A; Disare, Michael T; Lin, Qishan; Aye, Yimon

2015-05-20

Despite the known propensity of small-molecule electrophiles to react with numerous cysteine-active proteins, biological actions of individual signal inducers have emerged to be chemotype-specific. To pinpoint and quantify the impacts of modifying one target out of the whole proteome, we develop a target-protein-personalized "electrophile toolbox" with which specific intracellular targets can be selectively modified at a precise time by specific reactive signals. This general methodology, T-REX (targetable reactive electrophiles and oxidants), is established by (1) constructing a platform that can deliver a range of electronic and sterically different bioactive lipid-derived signaling electrophiles to specific proteins in cells; (2) probing the kinetics of targeted delivery concept, which revealed that targeting efficiency in cells is largely driven by initial on-rate of alkylation; and (3) evaluating the consequences of protein-target- and small-molecule-signal-specific modifications on the strength of downstream signaling. These data show that T-REX allows quantitative interrogations into the extent to which the Nrf2 transcription factor-dependent antioxidant response element (ARE) signaling is activated by selective electrophilic modifications on Keap1 protein, one of several redox-sensitive regulators of the Nrf2-ARE axis. The results document Keap1 as a promiscuous electrophile-responsive sensor able to respond with similar efficiencies to discrete electrophilic signals, promoting comparable strength of Nrf2-ARE induction. T-REX is also able to elicit cell activation in cases in which whole-cell electrophile flooding fails to stimulate ARE induction prior to causing cytotoxicity. The platform presents a previously unavailable opportunity to elucidate the functional consequences of small-molecule-signal- and protein-target-specific electrophilic modifications in an otherwise unaffected cellular background.

The combined use of analytical tools for exploring tetanus toxin and tetanus toxoid structures.

PubMed

Bayart, Caroline; Peronin, Sébastien; Jean, Elisa; Paladino, Joseph; Talaga, Philippe; Borgne, Marc Le

2017-06-01

Aldehyde detoxification is a process used to convert toxin into toxoid for vaccine applications. In the case of tetanus toxin (TT), formaldehyde is used to obtain the tetanus toxoid (TTd), which is used either for the tetanus vaccine or as carrier protein in conjugate vaccines. Several studies have already been conducted to better understand the exact mechanism of this detoxification. Those studies led to the identification of a number of formaldehyde-induced modifications on lab scale TTd samples. To obtain greater insights of the changes induced by formaldehyde, we used three industrial TTd batches to identify repeatable modifications in the detoxification process. Our strategy was to combine seven analytical tools to map these changes. Mass spectrometry (MS), colorimetric test and amino acid analysis (AAA) were used to study modifications on amino acids. SDS-PAGE, asymmetric flow field flow fractionation (AF4), fluorescence spectroscopy and circular dichroism (CD) were used to study formaldehyde modifications on the whole protein structure. We identified 41 formaldehyde-induced modifications across the 1315 amino acid primary sequence of TT. Of these, five modifications on lysine residues were repeatable across TTd batches. Changes in protein conformation were also observed using SDS-PAGE, AF4 and CD techniques. Each analytical tool brought a piece of information regarding formaldehyde induced-modifications, and all together, these methods provided a comprehensive overview of the structural changes that occurred with detoxification. These results could be the first step leading to site-directed TT mutagenesis studies that may enable the production of a non-toxic equivalent protein without using formaldehyde. Copyright © 2017 Elsevier B.V. All rights reserved.

Glycan Reader is improved to recognize most sugar types and chemical modifications in the Protein Data Bank.

PubMed

Park, Sang-Jun; Lee, Jumin; Patel, Dhilon S; Ma, Hongjing; Lee, Hui Sun; Jo, Sunhwan; Im, Wonpil

2017-10-01

Glycans play a central role in many essential biological processes. Glycan Reader was originally developed to simplify the reading of Protein Data Bank (PDB) files containing glycans through the automatic detection and annotation of sugars and glycosidic linkages between sugar units and to proteins, all based on atomic coordinates and connectivity information. Carbohydrates can have various chemical modifications at different positions, making their chemical space much diverse. Unfortunately, current PDB files do not provide exact annotations for most carbohydrate derivatives and more than 50% of PDB glycan chains have at least one carbohydrate derivative that could not be correctly recognized by the original Glycan Reader. Glycan Reader has been improved and now identifies most sugar types and chemical modifications (including various glycolipids) in the PDB, and both PDB and PDBx/mmCIF formats are supported. CHARMM-GUI Glycan Reader is updated to generate the simulation system and input of various glycoconjugates with most sugar types and chemical modifications. It also offers a new functionality to edit the glycan structures through addition/deletion/modification of glycosylation types, sugar types, chemical modifications, glycosidic linkages, and anomeric states. The simulation system and input files can be used for CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Glycan Fragment Database in GlycanStructure.Org is also updated to provide an intuitive glycan sequence search tool for complex glycan structures with various chemical modifications in the PDB. http://www.charmm-gui.org/input/glycan and http://www.glycanstructure.org. wonpil@lehigh.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Nanoscale surface modification of Li-rich layered oxides for high-capacity cathodes in Li-ion batteries

NASA Astrophysics Data System (ADS)

Lan, Xiwei; Xin, Yue; Wang, Libin; Hu, Xianluo

2018-03-01

Li-rich layered oxides (LLOs) have been developed as a high-capacity cathode material for Li-ion batteries, but the structural complexity and unique initial charging behavior lead to several problems including large initial capacity loss, capacity and voltage fading, poor cyclability, and inferior rate capability. Since the surface conditions are critical to electrochemical performance and the drawbacks, nanoscale surface modification for improving LLO's properties is a general strategy. This review mainly summarizes the surface modification of LLOs and classifies them into three types of surface pre-treatment, surface gradient doping, and surface coating. Surface pre-treatment usually introduces removal of Li2O for lower irreversible capacity while surface doping is aimed to stabilize the structure during electrochemical cycling. Surface coating layers with different properties, protective layers to suppress the interface side reaction, coating layers related to structural transformation, and electronic/ionic conductive layers for better rate capability, can avoid the shortcomings of LLOs. In addition to surface modification for performance enhancement, other strategies can also be investigated to achieve high-performance LLO-based cathode materials.

Structural characterization of ribosome recruitment and translocation by type IV IRES

PubMed Central

Murray, Jason; Savva, Christos G; Shin, Byung-Sik; Dever, Thomas E; Ramakrishnan, V; Fernández, Israel S

2016-01-01

Viral mRNA sequences with a type IV IRES are able to initiate translation without any host initiation factors. Initial recruitment of the small ribosomal subunit as well as two translocation steps before the first peptidyl transfer are essential for the initiation of translation by these mRNAs. Using electron cryomicroscopy (cryo-EM) we have structurally characterized at high resolution how the Cricket Paralysis Virus Internal Ribosomal Entry Site (CrPV-IRES) binds the small ribosomal subunit (40S) and the translocation intermediate stabilized by elongation factor 2 (eEF2). The CrPV-IRES restricts the otherwise flexible 40S head to a conformation compatible with binding the large ribosomal subunit (60S). Once the 60S is recruited, the binary CrPV-IRES/80S complex oscillates between canonical and rotated states (Fernández et al., 2014; Koh et al., 2014), as seen for pre-translocation complexes with tRNAs. Elongation factor eEF2 with a GTP analog stabilizes the ribosome-IRES complex in a rotated state with an extra ~3 degrees of rotation. Key residues in domain IV of eEF2 interact with pseudoknot I (PKI) of the CrPV-IRES stabilizing it in a conformation reminiscent of a hybrid tRNA state. The structure explains how diphthamide, a eukaryotic and archaeal specific post-translational modification of a histidine residue of eEF2, is involved in translocation. DOI: http://dx.doi.org/10.7554/eLife.13567.001 PMID:27159451

Computationally-Guided Synthetic Control over Pore Size in Isostructural Porous Organic Cages

DOE PAGES

Slater, Anna G.; Reiss, Paul S.; Pulido, Angeles; ...

2017-06-20

The physical properties of 3-D porous solids are defined by their molecular geometry. Hence, precise control of pore size, pore shape, and pore connectivity are needed to tailor them for specific applications. However, for porous molecular crystals, the modification of pore size by adding pore-blocking groups can also affect crystal packing in an unpredictable way. This precludes strategies adopted for isoreticular metal-organic frameworks, where addition of a small group, such as a methyl group, does not affect the basic framework topology. Here, we narrow the pore size of a cage molecule, CC3, in a systematic way by introducing methyl groupsmore » into the cage windows. Computational crystal structure prediction was used to anticipate the packing preferences of two homochiral methylated cages, CC14-R and CC15-R, and to assess the structure-energy landscape of a CC15-R/CC3-S cocrystal, designed such that both component cages could be directed to pack with a 3-D, interconnected pore structure. The experimental gas sorption properties of these three cage systems agree well with physical properties predicted by computational energy-structure-function maps.« less

Anchoring of Heterochromatin to the Nuclear Lamina Reinforces Dosage Compensation-Mediated Gene Repression.

PubMed

Snyder, Martha J; Lau, Alyssa C; Brouhard, Elizabeth A; Davis, Michael B; Jiang, Jianhao; Sifuentes, Margarita H; Csankovszki, Györgyi

2016-09-01

Higher order chromosome structure and nuclear architecture can have profound effects on gene regulation. We analyzed how compartmentalizing the genome by tethering heterochromatic regions to the nuclear lamina affects dosage compensation in the nematode C. elegans. In this organism, the dosage compensation complex (DCC) binds both X chromosomes of hermaphrodites to repress transcription two-fold, thus balancing gene expression between XX hermaphrodites and XO males. X chromosome structure is disrupted by mutations in DCC subunits. Using X chromosome paint fluorescence microscopy, we found that X chromosome structure and subnuclear localization are also disrupted when the mechanisms that anchor heterochromatin to the nuclear lamina are defective. Strikingly, the heterochromatic left end of the X chromosome is less affected than the gene-rich middle region, which lacks heterochromatic anchors. These changes in X chromosome structure and subnuclear localization are accompanied by small, but significant levels of derepression of X-linked genes as measured by RNA-seq, without any observable defects in DCC localization and DCC-mediated changes in histone modifications. We propose a model in which heterochromatic tethers on the left arm of the X cooperate with the DCC to compact and peripherally relocate the X chromosomes, contributing to gene repression.

Anchoring of Heterochromatin to the Nuclear Lamina Reinforces Dosage Compensation-Mediated Gene Repression

PubMed Central

Brouhard, Elizabeth A.; Jiang, Jianhao; Sifuentes, Margarita H.

2016-01-01

Higher order chromosome structure and nuclear architecture can have profound effects on gene regulation. We analyzed how compartmentalizing the genome by tethering heterochromatic regions to the nuclear lamina affects dosage compensation in the nematode C. elegans. In this organism, the dosage compensation complex (DCC) binds both X chromosomes of hermaphrodites to repress transcription two-fold, thus balancing gene expression between XX hermaphrodites and XO males. X chromosome structure is disrupted by mutations in DCC subunits. Using X chromosome paint fluorescence microscopy, we found that X chromosome structure and subnuclear localization are also disrupted when the mechanisms that anchor heterochromatin to the nuclear lamina are defective. Strikingly, the heterochromatic left end of the X chromosome is less affected than the gene-rich middle region, which lacks heterochromatic anchors. These changes in X chromosome structure and subnuclear localization are accompanied by small, but significant levels of derepression of X-linked genes as measured by RNA-seq, without any observable defects in DCC localization and DCC-mediated changes in histone modifications. We propose a model in which heterochromatic tethers on the left arm of the X cooperate with the DCC to compact and peripherally relocate the X chromosomes, contributing to gene repression. PMID:27690361

Challenges in the Development of Functional Assays of Membrane Proteins

PubMed Central

Tiefenauer, Louis; Demarche, Sophie

2012-01-01

Lipid bilayers are natural barriers of biological cells and cellular compartments. Membrane proteins integrated in biological membranes enable vital cell functions such as signal transduction and the transport of ions or small molecules. In order to determine the activity of a protein of interest at defined conditions, the membrane protein has to be integrated into artificial lipid bilayers immobilized on a surface. For the fabrication of such biosensors expertise is required in material science, surface and analytical chemistry, molecular biology and biotechnology. Specifically, techniques are needed for structuring surfaces in the micro- and nanometer scale, chemical modification and analysis, lipid bilayer formation, protein expression, purification and solubilization, and most importantly, protein integration into engineered lipid bilayers. Electrochemical and optical methods are suitable to detect membrane activity-related signals. The importance of structural knowledge to understand membrane protein function is obvious. Presently only a few structures of membrane proteins are solved at atomic resolution. Functional assays together with known structures of individual membrane proteins will contribute to a better understanding of vital biological processes occurring at biological membranes. Such assays will be utilized in the discovery of drugs, since membrane proteins are major drug targets.

Membrane-assisted growth of DNA origami nanostructure arrays.

PubMed

Kocabey, Samet; Kempter, Susanne; List, Jonathan; Xing, Yongzheng; Bae, Wooli; Schiffels, Daniel; Shih, William M; Simmel, Friedrich C; Liedl, Tim

2015-01-01

Biological membranes fulfill many important tasks within living organisms. In addition to separating cellular volumes, membranes confine the space available to membrane-associated proteins to two dimensions (2D), which greatly increases their probability to interact with each other and assemble into multiprotein complexes. We here employed two DNA origami structures functionalized with cholesterol moieties as membrane anchors--a three-layered rectangular block and a Y-shaped DNA structure--to mimic membrane-assisted assembly into hierarchical superstructures on supported lipid bilayers and small unilamellar vesicles. As designed, the DNA constructs adhered to the lipid bilayers mediated by the cholesterol anchors and diffused freely in 2D with diffusion coefficients depending on their size and number of cholesterol modifications. Different sets of multimerization oligonucleotides added to bilayer-bound origami block structures induced the growth of either linear polymers or two-dimensional lattices on the membrane. Y-shaped DNA origami structures associated into triskelion homotrimers and further assembled into weakly ordered arrays of hexagons and pentagons, which resembled the geometry of clathrin-coated pits. Our results demonstrate the potential to realize artificial self-assembling systems that mimic the hierarchical formation of polyhedral lattices on cytoplasmic membranes.

Computationally-Guided Synthetic Control over Pore Size in Isostructural Porous Organic Cages

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

Slater, Anna G.; Reiss, Paul S.; Pulido, Angeles

The physical properties of 3-D porous solids are defined by their molecular geometry. Hence, precise control of pore size, pore shape, and pore connectivity are needed to tailor them for specific applications. However, for porous molecular crystals, the modification of pore size by adding pore-blocking groups can also affect crystal packing in an unpredictable way. This precludes strategies adopted for isoreticular metal-organic frameworks, where addition of a small group, such as a methyl group, does not affect the basic framework topology. Here, we narrow the pore size of a cage molecule, CC3, in a systematic way by introducing methyl groupsmore » into the cage windows. Computational crystal structure prediction was used to anticipate the packing preferences of two homochiral methylated cages, CC14-R and CC15-R, and to assess the structure-energy landscape of a CC15-R/CC3-S cocrystal, designed such that both component cages could be directed to pack with a 3-D, interconnected pore structure. The experimental gas sorption properties of these three cage systems agree well with physical properties predicted by computational energy-structure-function maps.« less

Bayesian structural equation modeling: a more flexible representation of substantive theory.

PubMed

Muthén, Bengt; Asparouhov, Tihomir

2012-09-01

This article proposes a new approach to factor analysis and structural equation modeling using Bayesian analysis. The new approach replaces parameter specifications of exact zeros with approximate zeros based on informative, small-variance priors. It is argued that this produces an analysis that better reflects substantive theories. The proposed Bayesian approach is particularly beneficial in applications where parameters are added to a conventional model such that a nonidentified model is obtained if maximum-likelihood estimation is applied. This approach is useful for measurement aspects of latent variable modeling, such as with confirmatory factor analysis, and the measurement part of structural equation modeling. Two application areas are studied, cross-loadings and residual correlations in confirmatory factor analysis. An example using a full structural equation model is also presented, showing an efficient way to find model misspecification. The approach encompasses 3 elements: model testing using posterior predictive checking, model estimation, and model modification. Monte Carlo simulations and real data are analyzed using Mplus. The real-data analyses use data from Holzinger and Swineford's (1939) classic mental abilities study, Big Five personality factor data from a British survey, and science achievement data from the National Educational Longitudinal Study of 1988.

Surface modification of silk fibroin fabric using layer-by-layer polyelectrolyte deposition and heparin immobilization for small-diameter vascular prostheses.

PubMed

Elahi, M Fazley; Guan, Guoping; Wang, Lu; Zhao, Xinzhe; Wang, Fujun; King, Martin W

2015-03-03

There is an urgent need to develop a biologically active implantable small-diameter vascular prosthesis with long-term patency. Silk-fibroin-based small-diameter vascular prosthesis is a promising candidate having higher patency rate; however, the surface modification is indeed required to improve its further hemocompatibility. In this study, silk fibroin fabric was modified by a two-stage process. First, the surface of silk fibroin fabric was coated using a layer-by-layer polyelectrolyte deposition technique by stepwise dipping the silk fibroin fabric into a solution of cationic poly(allylamine hydrochloride) (PAH) and anionic poly(acrylic acid) (PAA) solution. The dipping procedure was repeated to obtain the PAH/PAA multilayers deposited on the silk fibroin fabrics. Second, the polyelectrolyte-deposited silk fibroin fabrics were treated in EDC/NHS-activated low-molecular-weight heparin (LMWH) solution at 4 °C for 24 h, resulting in immobilization of LMWH on the silk fibroin fabrics surface. Scanning electron microscopy, atomic force microscopy, and energy-dispersive X-ray data revealed the accomplishment of LMWH immobilization on the polyelectrolyte-deposited silk fibroin fabric surface. The higher the number of PAH/PAA coating layers on the silk fibroin fabric, the more surface hydrophilicity could be obtained, resulting in a higher fetal bovine serum protein and platelets adhesion resistance properties when tested in vitro. In addition, compared with untreated sample, the surface-modified silk fibroin fabrics showed negligible loss of bursting strength and thus reveal the acceptability of polyelectrolytes deposition and heparin immobilization approach for silk-fibroin-based small-diameter vascular prostheses modification.

KSC-03pd0262

NASA Image and Video Library

2003-02-04

KENNEDY SPACE CENTER, FLA. -- United Space Alliance (USA) technicians install thermal protection system tiles on Space Shuttle Discovery. Discovery is undergoing its Orbiter Major Modification Period, a regularly scheduled structural inspection and modification downtime, which began in September 2002. .

Evaluation of cab car crashworthiness design modifications

DOT National Transportation Integrated Search

1997-03-01

A study was conducted to evaluate the effectiveness of structural : modifications to rail cab cars for increased crashworthiness protection in train collisions. The crashworthiness benefits were calculated based on a particular design's ability to pr...

A high-throughput and rapid computational method for screening of RNA post-transcriptional modifications that can be recognized by target proteins.

PubMed

Orr, Asuka A; Gonzalez-Rivera, Juan C; Wilson, Mark; Bhikha, P Reena; Wang, Daiqi; Contreras, Lydia M; Tamamis, Phanourios

2018-02-01

There are over 150 currently known, highly diverse chemically modified RNAs, which are dynamic, reversible, and can modulate RNA-protein interactions. Yet, little is known about the wealth of such interactions. This can be attributed to the lack of tools that allow the rapid study of all the potential RNA modifications that might mediate RNA-protein interactions. As a promising step toward this direction, here we present a computational protocol for the characterization of interactions between proteins and RNA containing post-transcriptional modifications. Given an RNA-protein complex structure, potential RNA modified ribonucleoside positions, and molecular mechanics parameters for capturing energetics of RNA modifications, our protocol operates in two stages. In the first stage, a decision-making tool, comprising short simulations and interaction energy calculations, performs a fast and efficient search in a high-throughput fashion, through a list of different types of RNA modifications categorized into trees according to their structural and physicochemical properties, and selects a subset of RNA modifications prone to interact with the target protein. In the second stage, RNA modifications that are selected as recognized by the protein are examined in-detail using all-atom simulations and free energy calculations. We implement and experimentally validate this protocol in a test case involving the study of RNA modifications in complex with Escherichia coli (E. coli) protein Polynucleotide Phosphorylase (PNPase), depicting the favorable interaction between 8-oxo-7,8-dihydroguanosine (8-oxoG) RNA modification and PNPase. Further advancement of the protocol can broaden our understanding of protein interactions with all known RNA modifications in several systems. Copyright © 2018 Elsevier Inc. All rights reserved.

Modification of Silk Fibroin Using Diazonium Coupling Chemistry and the Effects on hMSC Proliferation and Differentiation

PubMed Central

Murphy, Amanda R.; John, Peter St.; Kaplan, David L.

2009-01-01

A simple chemical modification method using diazonium coupling chemistry was developed to tailor the structure and hydrophilicity of silk fibroin protein. The extent of modification using several aniline derivatives was characterized using UV/vis and 1H NMR spectroscopy, and the resulting protein structure was analyzed with ATR-FTIR spectroscopy. Introduction of hydrophobic functional groups facilitated rapid conversion of the protein from a random coil to a β-sheet structure, while addition of hydrophilic groups inhibited this process. hMSCs were grown on these modified silks to assess the biocompatibility of these materials. The hydrophilicity of the silk derivatives was found to affect the growth rate and morphology, but hMSCs were able to attach, proliferate and differentiate into an osteogenic lineage on all of the silk derivatives. PMID:18417206

Modifications of a Composite-Material Combustion Chamber

NASA Technical Reports Server (NTRS)

Williams, Brian E.; McNeal, Shawn R.

2005-01-01

Two short reports discuss modifications of a small, lightweight combustion chamber that comprises a carbon/carbon composite outer shell and an iridium/ rhenium inner liner. The first report discusses chamber design modifications made as results of hot-fire tests and post-test characterization. The Books & Reports 32 NASA Tech Briefs, June 2005 modifications were intended to serve a variety of purposes, including improving fabrication, reducing thermal-expansion mismatch stresses, increasing strength-to-weight ratios of some components, and improving cooling of some components. The second report discusses (1) the origin of stress in the mismatch between the thermal expansions of the Ir/Re liner and a niobium sleeve and flange attached to the carbon/ carbon shell and (2) a modification intended to relieve the stress. The modification involves the redesign of an inlet connection to incorporate a compressible seal between the Ir/Re liner and the Nb flange. A nickel alloy was selected as the seal material on the basis of its thermal-expansion properties and its ability to withstand the anticipated stresses, including the greatest stresses caused by the high temperatures to be used in brazing during fabrication.

Catabolism of native and oxidized low density lipoproteins: in vivo insights from small animal positron emission tomography studies.

PubMed

Pietzsch, J; Bergmann, R; Wuest, F; Pawelke, B; Hultsch, C; van den Hoff, J

2005-12-01

The human organism is exposed to numerous processes that generate reactive oxygen species (ROS). ROS may directly or indirectly cause oxidative modification and damage of proteins. Protein oxidation is regarded as a crucial event in the pathogenesis of various diseases ranging from rheumatoid arthritis to Alzheimer's disease and atherosclerosis. As a representative example, oxidation of low density lipoprotein (LDL) is regarded as a crucial event in atherogenesis. Data concerning the role of circulating oxidized LDL (oxLDL) in the development and outcome of diseases are scarce. One reason for this is the shortage of methods for direct assessment of the metabolic fate of circulating oxLDL in vivo. We present an improved methodology based on the radiolabelling of apoB-100 of native LDL (nLDL) and oxLDL, respectively, with the positron emitter fluorine-18 ((18)F) by conjugation with N-succinimidyl-4-[(18)F]fluorobenzoate ([(18)F]SFB). Radiolabelling of both nLDL and oxLDL using [(18)F]SFB causes neither additional oxidative structural modifications of LDL lipids and proteins nor alteration of their biological activity and functionality, respectively, in vitro. The method was further evaluated with respect to the radiopharmacological properties of both [(18)F]fluorobenzoylated nLDL and oxLDL by biodistribution studies in male Wistar rats. The metabolic fate of [(18)F]fluorobenzoylated nLDL and oxLDL in rats in vivo was further delineated by dynamic positron emission tomography (PET) using a dedicated small animal tomograph (spatial resolution of 2 mm). From this study we conclude that the use of [(18)F]FB-labelled LDL particles is an attractive alternative to, e.g., LDL iodination methods, and is of value to characterize and to discriminate the kinetics and the metabolic fate of nLDL and oxLDL in small animals in vivo.

Effects of Inlet Modification and Rocket-Rack Extension on the Longitudinal Trim and Low-Lift Drag of the Douglas F5D-1 Airplane as Obtained with a 0.125-Scale Rocket-Boosted Model between Mach Numbers of 0.81 and 1.64, TED No. NACA AD 399

NASA Technical Reports Server (NTRS)

Hastings, Earl C., Jr.; Dickens, Waldo L.

1957-01-01

A flight investigation was conducted to determine the effects of an inlet modification and rocket-rack extension on the longitudinal trim and low-lift drag of the Douglas F5D-1 airplane. The investigation was conducted with a 0.125-scale rocket-boosted model which was flight tested at the Langley Pilotless Aircraft Research Station at Wallops Island, Va. Results indicate that the combined effects of the modified inlet and fully extended rocket racks on the trim lift coefficient and trim angle of attack were small between Mach numbers of 0.94 and 1.57. Between Mach numbers of 1.10 and 1.57 there was an average increase in drag coefficient of about o,005 for the model with modified inlet and extended rocket racks. The change in drag coefficient due to the inlet modification alone is small between Mach numbers of 1.59 and 1.64

[Preparation of honeycombed monolithic zeolite and hydrophobic modification with SiCl4].

PubMed

Wang, Xi-Qin; Li, Kai; Wei, Bing; Luan, Zhi-Qiang

2011-12-01

A kind of hydrophobic zeolitic monolith were prepared by mixing HY/ZSM-5, additives and water, followed by processes of extrusion and drying, and then hydrophobic modification with SiCl4. The structures and properties of the adsorbent were examined by nitrogen adsorption and desorption measurement, XRD, and benzene adsorption experiment. The results show that those adsorbents possess hierarchical pore structures and excellent hydrophobicity.

Composition, structure, physicochemical properties, and modifications of cassava starch.

PubMed

Zhu, Fan

2015-05-20

Cassava is highly tolerant to harsh climatic conditions and has great productivity on marginal lands. The supply of cassava starch, the major component of the root, is thus sustainable and cheap. This review summarizes the current knowledge of the composition, physical and chemical structures, physicochemical properties, nutritional quality, and modifications of cassava starch. Research opportunities to better understand this starch are provided. Copyright © 2014 Elsevier Ltd. All rights reserved.

Variation of the chemical reactivity of Thermus thermophilus HB8 ribosomal proteins as a function of pH.

PubMed

Running, William E; Reilly, James P

2010-10-01

Ribosomes occupy a central position in cellular metabolism, converting stored genetic information into active cellular machinery. Ribosomal proteins modulate both the intrinsic function of the ribosome and its interaction with other cellular complexes, such as chaperonins or the signal recognition particle. Chemical modification of proteins combined with mass spectrometric detection of the extent and position of covalent modifications is a rapid, sensitive method for the study of protein structure and flexibility. By altering the pH of the solution, we have induced non-denaturing changes in the structure of bacterial ribosomal proteins and detected these conformational changes by covalent labeling. Changes in ribosomal protein modification across a pH range from 6.6 to 8.3 are unique to each protein, and correlate with their structural environment in the ribosome. Lysine residues whose extent of modification increases as a function of increasing pH are on the surface of proteins, but in close proximity either to glutamate and aspartate residues, or to rRNA backbone phosphates. Increasing pH disrupts tertiary and quaternary interactions mediated by hydrogen bonding or ionic interactions, and regions of protein structure whose conformations are sensitive to these changes are of potential importance in modulating the flexibility of the ribosome or its interaction with other cellular complexes.

Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations.

PubMed

Jiang, Jun; Aduri, Raviprasad; Chow, Christine S; SantaLucia, John

2014-04-01

Helix 69 (H69) is a 19-nt stem-loop region from the large subunit ribosomal RNA. Three pseudouridine (Ψ) modifications clustered in H69 are conserved across phylogeny and known to affect ribosome function. To explore the effects of Ψ on the conformations of Escherichia coli H69 in solution, nuclear magnetic resonance spectroscopy was used to reveal the structural differences between H69 with (ΨΨΨ) and without (UUU) Ψ modifications. Comparison of the two structures shows that H69 ΨΨΨ has the following unique features: (i) the loop region is closed by a Watson-Crick base pair between Ψ1911 and A1919, which is potentially reinforced by interactions involving Ψ1911N1H and (ii) Ψ modifications at loop residues 1915 and 1917 promote base stacking from Ψ1915 to A1918. In contrast, the H69 UUU loop region, which lacks Ψ modifications, is less organized. Structure modulation by Ψ leads to alteration in conformational behavior of the 5' half of the H69 loop region, observed as broadening of C1914 non-exchangeable base proton resonances in the H69 ΨΨΨ nuclear magnetic resonance spectra, and plays an important biological role in establishing the ribosomal intersubunit bridge B2a and mediating translational fidelity.

Ray craters on Ganymede: Implications for cratering apex-antapex asymmetry and surface modification processes

NASA Astrophysics Data System (ADS)

Xu, Luyuan; Hirata, Naoyuki; Miyamoto, Hideaki

2017-10-01

As the youngest features on Ganymede, ray craters are useful in revealing the sources of recent impactors and surface modification processes on the satellite. We examine craters with D > 10 km on Ganymede from images obtained by the Voyager and Galileo spacecraft to identify ray craters and study their spatial distributions. Furthermore, we carefully select images of appropriate solar and emission angles to obtain unbiased ray crater densities. As a result, we find that the density of large ray craters (D > 25 km) on the bright terrain exhibits an apex-antapex asymmetry, and its degree of asymmetry is much lower than the theoretical estimation for ecliptic comets. For large craters (D > 25 km), ecliptic comets ought to be less important than previously assumed, and a possible explanation is that nearly isotropic comets may play a more important role on Ganymede than previously thought. We also find that small ray craters (10 km < D < 25 km) on the bright terrain and ray craters (D > 10 km) on the dark terrain show no apex-antapex asymmetry. We interpret that the distribution difference between the terrain types comes from preferential thermal sublimation on the dark terrain, while the distribution difference between large and small ray craters suggests that rays of small craters are more readily erased by some surface modification processes, such as micrometeorite gardening.

A Novel Proteomics Approach to Identify SUMOylated Proteins and Their Modification Sites in Human Cells*

PubMed Central

Galisson, Frederic; Mahrouche, Louiza; Courcelles, Mathieu; Bonneil, Eric; Meloche, Sylvain; Chelbi-Alix, Mounira K.; Thibault, Pierre

2011-01-01

The small ubiquitin-related modifier (SUMO) is a small group of proteins that are reversibly attached to protein substrates to modify their functions. The large scale identification of protein SUMOylation and their modification sites in mammalian cells represents a significant challenge because of the relatively small number of in vivo substrates and the dynamic nature of this modification. We report here a novel proteomics approach to selectively enrich and identify SUMO conjugates from human cells. We stably expressed different SUMO paralogs in HEK293 cells, each containing a His6 tag and a strategically located tryptic cleavage site at the C terminus to facilitate the recovery and identification of SUMOylated peptides by affinity enrichment and mass spectrometry. Tryptic peptides with short SUMO remnants offer significant advantages in large scale SUMOylome experiments including the generation of paralog-specific fragment ions following CID and ETD activation, and the identification of modified peptides using conventional database search engines such as Mascot. We identified 205 unique protein substrates together with 17 precise SUMOylation sites present in 12 SUMO protein conjugates including three new sites (Lys-380, Lys-400, and Lys-497) on the protein promyelocytic leukemia. Label-free quantitative proteomics analyses on purified nuclear extracts from untreated and arsenic trioxide-treated cells revealed that all identified SUMOylated sites of promyelocytic leukemia were differentially SUMOylated upon stimulation. PMID:21098080

Advances in chemical synthesis of structurally modified bioactive RNAs.

PubMed

Li, Ziyuan; Zhou, Haipin; Wu, Xiaoming; Yao, Hequan

2013-01-01

Methods for the chemical synthesis of RNA have been available for almost half century, and presently, RNA could be chemically synthesized by automated synthesizers, using protected ribonucleosides preactivated as phosphoramidites, which has already been covered by many reviews. In addition to advancement on synthetic methods, a variety of modifications have also been made on the synthesized oligonucleotides, and previous reviews on the general synthesis of RNAs have not covered this area. In this tutorial review, three types of modifications have been summarized standing at the viewpoint of medicinal chemistry: (1) modifications on nucleobase, comprising substituent introduction and replacement with pseudobase; (2) modifications on ribose, consisting of modifications on the 2', 3' or 5'-position, alternation of configuration, and conformational restriction on ribose; (3) modifications on internucleoside linkages, including amide, formacetal, sulfide, sulfone, ether, phosphorothiolate and phosphorothioate linkages. Synthetic methods achieving these modifications along with the functions or values of these modifications have also been discussed and commented on.

Structure-activity relationship of karrikin germination stimulants.

PubMed

Flematti, Gavin R; Scaffidi, Adrian; Goddard-Borger, Ethan D; Heath, Charles H; Nelson, David C; Commander, Lucy E; Stick, Robert V; Dixon, Kingsley W; Smith, Steven M; Ghisalberti, Emilio L

2010-08-11

Karrikins (2H-furo[2,3-c]pyran-2-ones) are potent smoke-derived germination promoters for a diverse range of plant species but, to date, their mode of action remains unknown. This paper reports the structure-activity relationship of numerous karrikin analogues to increase understanding of the key structural features of the molecule that are required for biological activity. The results demonstrate that modification at the C5 position is preferred over modification at the C3, C4, or C7 positions for retaining the highest bioactivity.

NASA reload program

NASA Technical Reports Server (NTRS)

Byington, Marshall

1993-01-01

Atlantic Research Corporation (ARC) contracted with NASA to manufacture and deliver thirteen small scale Solid Rocket Motors (SRM). These motors, containing five distinct propellant formulations, will be used for plume induced radiation studies. The information contained herein summarizes and documents the program accomplishments and results. Several modifications were made to the scope of work during the course of the program. The effort was on hold from late 1991 through August, 1992 while propellant formulation changes were developed. Modifications to the baseline program were completed in late-August and Modification No. 6 was received by ARC on September 14, 1992. The modifications include changes to the propellant formulation and the nozzle design. The required motor deliveries were completed in late-December, 1992. However, ARC agreed to perform an additional mix and cast effort at no cost to NASA and another motor was delivered in March, 1993.

Phosphorylation Interferes with Maturation of Amyloid-β Fibrillar Structure in the N Terminus.

PubMed

Rezaei-Ghaleh, Nasrollah; Kumar, Sathish; Walter, Jochen; Zweckstetter, Markus

2016-07-29

Neurodegeneration is characterized by the ubiquitous presence of modifications in protein deposits. Despite their potential significance in the initiation and progression of neurodegenerative diseases, the effects of posttranslational modifications on the molecular properties of protein aggregates are largely unknown. Here, we study the Alzheimer disease-related amyloid-β (Aβ) peptide and investigate how phosphorylation at serine 8 affects the structure of Aβ aggregates. Serine 8 is shown to be located in a region of high conformational flexibility in monomeric Aβ, which upon phosphorylation undergoes changes in local conformational dynamics. Using hydrogen-deuterium exchange NMR and fluorescence quenching techniques, we demonstrate that Aβ phosphorylation at serine 8 causes structural changes in the N-terminal region of Aβ aggregates in favor of less compact conformations. Structural changes induced by serine 8 phosphorylation can provide a mechanistic link between phosphorylation and other biological events that involve the N-terminal region of Aβ aggregates. Our data therefore support an important role of posttranslational modifications in the structural polymorphism of amyloid aggregates and their modulatory effect on neurodegeneration. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Floor-fractured crater models of the Sudbury structure, Canada

NASA Technical Reports Server (NTRS)

Wichman, R. W.; Schultz, P. H.

1992-01-01

The Sudbury structure in Ontario, Canada, is one of the oldest and largest impact structures recognized in the geological record. It is also one of the most extensively deformed and volcanically modified impact structures on Earth. Although few other terrestrial craters are recognized as volcanically modified, numerous impact craters on the Moon have been volcanically and tectonically modified and provide possible analogs for the observed pattern of modification at Sudbury. We correlate the pattern of early deformation at Sudbury to fracture patterns in two alternative lunar analogs and then use these analogs both to estimate the initial size of the Sudbury structure and to model the nature of early crater modification at Sudbury.

Prediction of possible CaMnO3 modifications using an ab initio minimization data-mining approach.

PubMed

Zagorac, Jelena; Zagorac, Dejan; Zarubica, Aleksandra; Schön, J Christian; Djuris, Katarina; Matovic, Branko

2014-10-01

We have performed a crystal structure prediction study of CaMnO3 focusing on structures generated by octahedral tilting according to group-subgroup relations from the ideal perovskite type (Pm\\overline 3 m), which is the aristotype of the experimentally known CaMnO3 compound in the Pnma space group. Furthermore, additional structure candidates have been obtained using data mining. For each of the structure candidates, a local optimization on the ab initio level using density-functional theory (LDA, hybrid B3LYP) and the Hartree--Fock (HF) method was performed, and we find that several of the modifications may be experimentally accessible. In the high-pressure regime, we identify a post-perovskite phase in the CaIrO3 type, not previously observed in CaMnO3. Similarly, calculations at effective negative pressure predict a phase transition from the orthorhombic perovskite to an ilmenite-type (FeTiO3) modification of CaMnO3.

Chemical Structure and Surface Modification of Dendritic Nanomaterials Tailored for Therapeutic and Diagnostic Applications.

PubMed

Myung, Ja Hye; Hsu, Hao-Jui; Bugno, Jason; Tam, Kevin A; Hong, Seungpyo

2017-01-01

Dendritic nanomaterials have attracted a great deal of scientific interest due to their high capacity for multifunctionalization and potential in various biomedical applications, such as drug/gene delivery and diagnostic systems. Depending on the molecular structure and starting monomers, several different types of dendrimers have been developed, including poly(amidoamine) (PAMAM), poly(propylenimine) (PPI), and poly(L-lysine) (PLL) dendrimers, in addition to modified dendritic nanomaterials, such as Janus dendrimers and dendritic block copolymers. The chemical structure and surface modification of dendritic nanomaterials have been found to play a critical role in governing their biological behaviors. In this review, we present a comprehensive overview focusing on the synthesis and chemical structures of dendrimers and modified dendritic nanomaterials that are currently being investigated for drug delivery, gene delivery, and diagnostic applications. In addition, the impact of chemical surface modification and functionalization to the dendritic nanomaterials on their therapeutic and diagnostic applications are highlighted. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

High temperature extended x-ray absorption fine structure study of multiferroic BiFeO3

NASA Astrophysics Data System (ADS)

Raghavendra Reddy, V.; Meneghini, Carlo; Kothari, Deepti; Gupta, Ajay; Aquilanti, Giuliana

2012-08-01

Local atomic structure modifications around Fe atoms in polycrystalline multiferroic BiFeO3 are studied by Fe K edge x-ray absorption spectroscopy as a function of temperature across the Néel temperature (TN = 643 K) in order to reveal local structure modifications related to the magnetic transition. This work demonstrates that on crossing TN the local structure around Fe shows peculiar changes: the Fe-O bond lengths get shorter, the ligand symmetry increases and the Fe-O bond length disorder (σ2) deviates from Debye behaviour. These results suggest that the structural transition at the ferroelectric Curie temperature (TC = 1103 K) is anticipated by early local rearrangement of the structure starting already at TN.

Hirsutane-type sesquiterpenes with uncommon modifications from three basidiomycetes.

PubMed

Liermann, Johannes C; Schüffler, Anja; Wollinsky, Beate; Birnbacher, Judith; Kolshorn, Heinz; Anke, Timm; Opatz, Till

2010-05-07

From three basidiomycetes, Xeromphalina sp., Stereum sp., and Pleurocybella porrigens, six triquinane sesquiterpenes with unprecendented modifications and a rearranged sesquiterpene related to coriolin C have been isolated. Their isolation, structure elucidation, and biological evaluation are described.

General patterns of niche construction and the management of ‘wild’ plant and animal resources by small-scale pre-industrial societies

PubMed Central

Smith, Bruce D.

2011-01-01

Niche construction efforts by small-scale human societies that involve ‘wild’ species of plants and animals are organized into a set of six general categories based on the shared characteristics of the target species and similar patterns of human management and manipulation: (i) general modification of vegetation communities, (ii) broadcast sowing of wild annuals, (iii) transplantation of perennial fruit-bearing species, (iv) in-place encouragement of economically important perennials, (v) transplantation and in-place encouragement of perennial root crops, and (vi) landscape modification to increase prey abundance in specific locations. Case study examples, mostly drawn from North America, are presented for each of the six general categories of human niche construction. These empirically documented categories of ecosystem engineering form the basis for a predictive model that outlines potential general principles and commonalities in how small-scale human societies worldwide have modified and manipulated their ‘natural’ landscapes throughout the Holocene. PMID:21320898

Structure and Modification of Electrode Materials for Protein Electrochemistry.

PubMed

Jeuken, Lars J C

The interactions between proteins and electrode surfaces are of fundamental importance in bioelectrochemistry, including photobioelectrochemistry. In order to optimise the interaction between electrode and redox protein, either the electrode or the protein can be engineered, with the former being the most adopted approach. This tutorial review provides a basic description of the most commonly used electrode materials in bioelectrochemistry and discusses approaches to modify these surfaces. Carbon, gold and transparent electrodes (e.g. indium tin oxide) are covered, while approaches to form meso- and macroporous structured electrodes are also described. Electrode modifications include the chemical modification with (self-assembled) monolayers and the use of conducting polymers in which the protein is imbedded. The proteins themselves can either be in solution, electrostatically adsorbed on the surface or covalently bound to the electrode. Drawbacks and benefits of each material and its modifications are discussed. Where examples exist of applications in photobioelectrochemistry, these are highlighted.

The role of modifications in codon discrimination by tRNA(Lys)UUU.

PubMed

Murphy, Frank V; Ramakrishnan, Venki; Malkiewicz, Andrzej; Agris, Paul F

2004-12-01

The natural modification of specific nucleosides in many tRNAs is essential during decoding of mRNA by the ribosome. For example, tRNA(Lys)(UUU) requires the modification N6-threonylcarbamoyladenosine at position 37 (t(6)A37), adjacent and 3' to the anticodon, to bind AAA in the A site of the ribosomal 30S subunit. Moreover, it can only bind both AAA and AAG lysine codons when doubly modified with t(6)A37 and either 5-methylaminomethyluridine or 2-thiouridine at the wobble position (mnm(5)U34 or s(2)U34). Here we report crystal structures of modified tRNA anticodon stem-loops bound to the 30S ribosomal subunit with lysine codons in the A site. These structures allow the rationalization of how modifications in the anticodon loop enable decoding of both lysine codons AAA and AAG.

Covalent modification of graphene and graphite using diazonium chemistry: tunable grafting and nanomanipulation.

PubMed

Greenwood, John; Phan, Thanh Hai; Fujita, Yasuhiko; Li, Zhi; Ivasenko, Oleksandr; Vanderlinden, Willem; Van Gorp, Hans; Frederickx, Wout; Lu, Gang; Tahara, Kazukuni; Tobe, Yoshito; Uji-I, Hiroshi; Mertens, Stijn F L; De Feyter, Steven

2015-05-26

We shine light on the covalent modification of graphite and graphene substrates using diazonium chemistry under ambient conditions. We report on the nature of the chemical modification of these graphitic substrates, the relation between molecular structure and film morphology, and the impact of the covalent modification on the properties of the substrates, as revealed by local microscopy and spectroscopy techniques and electrochemistry. By careful selection of the reagents and optimizing reaction conditions, a high density of covalently grafted molecules is obtained, a result that is demonstrated in an unprecedented way by scanning tunneling microscopy (STM) under ambient conditions. With nanomanipulation, i.e., nanoshaving using STM, surface structuring and functionalization at the nanoscale is achieved. This manipulation leads to the removal of the covalently anchored molecules, regenerating pristine sp(2) hybridized graphene or graphite patches, as proven by space-resolved Raman microscopy and molecular self-assembly studies.

Materials modification using ions with energies below 1 MeV/u

NASA Astrophysics Data System (ADS)

Karlušić, M.; Jakšić, M.; Buljan, M.; Sancho-Parramon, J.; Bogdanović-Radović, I.; Radić, N.; Bernstorff, S.

2013-12-01

Materials modifications using swift heavy ion beams provided by large scale accelerators have been used for many years in a wide variety of ways, e.g. to produce ion tracks or to modify the shape of nanoparticles. In all those applications the most relevant parameter for the materials modification is the electronic stopping power and not the ion kinetic energy. For many materials, ions with energies below 1 MeV/u delivered from medium and small size accelerators have already sufficiently high electronic stopping power to modify materials in different ways. Also, in this energy range the nuclear stopping power can be large enough to provide additional opportunities for materials modifications. In the present paper, we review recent experimental activities of the Zagreb group where ion beams with energies below 1 MeV/u, obtained from a 6 MV EN Tandem Van de Graaff accelerator have been used. Additionally, we present several novel examples of materials modifications and their analysis with such ion beams.

K-Ras protein as a drug target.

PubMed

McCormick, Frank

2016-03-01

K-Ras proteins are major drivers of human cancers, playing a direct causal role in about one million cancer cases/year. In cancers driven by mutant K-Ras, the protein is locked in the active, GTP-bound state constitutively, through a defect in the off-switch mechanism. As such, the mutant protein resembles the normal K-Ras protein from a structural perspective, making therapeutic attack extremely challenging. K-Ras is a member of a large family of related proteins, which share very similar GDP/GTP-binding domains, making specific therapies more difficult. Furthermore, Ras proteins lack pockets to which small molecules can bind with high affinity, with a few interesting exceptions. However, new insights into the structure and function of K-Ras proteins reveal opportunities for intervention that were not appreciated many years ago, when efforts were launched to develop K-Ras therapies. Furthermore, K-Ras undergoes post-translational modification and interactions with cellular signaling proteins that present additional therapeutic opportunities, such as specific binding to calmodulin and regulation of non-canonical Wnt signaling.

Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes.

PubMed

Liu, Pi; Zhao, Yan; Liu, Xiaoguo; Sun, Jixue; Xu, Dede; Li, Yang; Li, Qian; Wang, Lihua; Yang, Sichun; Fan, Chunhai; Lin, Jianping

2018-05-04

Reconfiguration of membrane protein channels for gated transport is highly regulated under physiological conditions. However, a mechanistic understanding of such channels remains challenging owing to the difficulty in probing subtle gating-associated structural changes. Herein, we show that charge neutralization can drive the shape reconfiguration of a biomimetic 6-helix bundle DNA nanotube (6HB). Specifically, 6HB adopts a compact state when its charge is neutralized by Mg 2+ ; whereas Na + switches it to the expanded state, as revealed by MD simulations, small-angle X-ray scattering (SAXS), and FRET characterization. Furthermore, partial neutralization of the DNA backbone charges by chemical modification renders 6HB compact and insensitive to ions, suggesting an interplay between electrostatic and hydrophobic forces in the channels. This system provides a platform for understanding the structure-function relationship of biological channels and designing rules for the shape control of DNA nanostructures in biomedical applications. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mechanisms of the epithelial-to-mesenchymal transition in sea urchin embryos

PubMed Central

Katow, Hideki

2015-01-01

Sea urchin mesenchyme is composed of the large micromere-derived spiculogenetic primary mesenchyme cells (PMC), veg2-tier macromere-derived non-spiculogenetic mesenchyme cells, the small micromere-derived germ cells, and the macro- and mesomere-derived neuronal mesenchyme cells. They are formed through the epithelial-to-mesenchymal transition (EMT) and possess multipotency, except PMCs that solely differentiate larval spicules. The process of EMT is associated with modification of epithelial cell surface property that includes loss of affinity to the apical and basal extracellular matrices, inter-epithelial cell adherens junctions and epithelial cell surface-specific proteins. These cell surface structures and molecules are endocytosed during EMT and utilized as initiators of cytoplasmic signaling pathways that often initiate protein phosphorylation to activate the gene regulatory networks. Acquisition of cell motility after EMT in these mesenchyme cells is associated with the expression of proteins such as Lefty, Snail and Seawi. Structural simplicity and genomic database of this model will further promote detailed EMT research. PMID:26716069

Development and Evaluation of Sensor Concepts for Ageless Aerospace Vehicles: Report 6 - Development and Demonstration of a Self-Organizing Diagnostic System for Structural Health Monitoring

NASA Technical Reports Server (NTRS)

Batten, Adam; Edwards, Graeme; Gerasimov, Vadim; Hoschke, Nigel; Isaacs, Peter; Lewis, Chris; Moore, Richard; Oppolzer, Florien; Price, Don; Prokopenko, Mikhail;

Structurally distinct ubiquitin- and sumo-modified PCNA: implications for their distinct roles in the DNA damage response.

PubMed

Tsutakawa, Susan E; Yan, Chunli; Xu, Xiaojun; Weinacht, Christopher P; Freudenthal, Bret D; Yang, Kun; Zhuang, Zhihao; Washington, M Todd; Tainer, John A; Ivanov, Ivaylo

2015-04-07

Proliferating cell nuclear antigen (PCNA) is a pivotal replication protein, which also controls cellular responses to DNA damage. Posttranslational modification of PCNA by SUMO and ubiquitin modulate these responses. How the modifiers alter PCNA-dependent DNA repair and damage tolerance pathways is largely unknown. We used hybrid methods to identify atomic models of PCNAK107-Ub and PCNAK164-SUMO consistent with small-angle X-ray scattering data of these complexes in solution. We show that SUMO and ubiquitin have distinct modes of association to PCNA. Ubiquitin adopts discrete docked binding positions. By contrast, SUMO associates by simple tethering and adopts extended flexible conformations. These structural differences are the result of the opposite electrostatic potentials of SUMO and Ub. The unexpected contrast in conformational behavior of Ub-PCNA and SUMO-PCNA has implications for interactions with partner proteins, interacting surfaces accessibility, and access points for pathway regulation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Quinoa starch: Structure, properties, and applications.

PubMed

Li, Guantian; Zhu, Fan

2018-02-01

Quinoa (Chenopodium quinoa Willd.) has gained popularity worldwide largely due to the attractive nutritional profile. It also has much potential for food security due to the great genetic diversity. Starch is the main component of quinoa grain and makes up to 70% of the dry matter. The starch plays a crucial role in functional properties of quinoa and related food products. The starch granules are rather small (∼1-3μm) with relatively low amylose contents as compared with most of the other starches. Quinoa amylopectin has significant amounts of short chains and super-long chains. These unique features have generated research interest in using the starch for food and other applications such as creating Pickering emulsions. This review summarizes the present knowledge of the isolation, composition, granular and molecular structures, physicochemical properties, modifications, and applications of quinoa starch. It becomes obvious that this starch has great potential for food and nonfood applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structural-modification mechanism for polyimide-doped poly(tetrafluoroethylene)at subthreshold fluences using 248 nm radiation

NASA Astrophysics Data System (ADS)

Davis, C. R.; Snyder, R. W.; Egitto, F. D.; D'Couto, G. C.; Babu, S. V.

1994-09-01

Single-photon excimer laser ablation of neat poly(tetrafluoroethylene) (PTFE) is not observed at emissions in the 'quartz' UV, i.e., from about 190-380 nm. However, it has been successfully demonstrated that, when the fluoropolymer is doped with small quantities of polyimide (PI), ablation in the quartz UV, e.g., at 248 and 308 nm and pulse widths of about 25 ns, is readily achieved. When PI-PTFE blends are exposed to subthreshold fluences, considerable changes in surface topography occur although clearly defined structures, e.g., pits, are not formed. Using photoacoustic infrared spectroscopy to evaluate surface and bulk chemical changes to blends exposed to subthreshold excimer laser fluences, is less than 100 mJ/sq cm, it is shown that PI (1) is distributed throughout the bulk and resides at the surface and (2) is selectively absorbing the high-energy photons and as a result being preferentially removed from the surface.

Structurally Distinct Ubiquitin- and Sumo-Modified PCNA: Implications for Their Distinct Roles in the DNA Damage Response

DOE PAGES

Tsutakawa, Susan E.; Yan, Chunli; Xu, Xiaojun; ...

2015-03-12

Proliferating cell nuclear antigen (PCNA) is a pivotal replication protein, which also controls cellular responses to DNA damage. Posttranslational modification of PCNA by SUMO and ubiquitin modulate these responses. How the modifiers alter PCNA-dependent DNA repair and damage tolerance pathways is largely unknown. Here, we used hybrid methods to identify atomic models of PCNA K107-Ub and PCNA K164-SUMO consistent with small-angle X-ray scattering data of these complexes in solution. We show that SUMO and ubiquitin have distinct modes of association to PCNA. Ubiquitin adopts discrete docked binding positions. By contrast, SUMO associates by simple tethering and adopts extended flexible conformations.more » These structural differences are the result of the opposite electrostatic potentials of SUMO and Ub. In conclusion, the unexpected contrast in conformational behavior of Ub-PCNA and SUMO-PCNA has implications for interactions with partner proteins, interacting surfaces accessibility, and access points for pathway regulation.« less

Enhanced ultrafast relaxation rate in the Weyl semimetal phase of MoTe2 measured by time- and angle-resolved photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Crepaldi, A.; Autès, G.; Gatti, G.; Roth, S.; Sterzi, A.; Manzoni, G.; Zacchigna, M.; Cacho, C.; Chapman, R. T.; Springate, E.; Seddon, E. A.; Bugnon, Ph.; Magrez, A.; Berger, H.; Vobornik, I.; Kalläne, M.; Quer, A.; Rossnagel, K.; Parmigiani, F.; Yazyev, O. V.; Grioni, M.

2017-12-01

MoTe2 has recently been shown to realize in its low-temperature phase the type-II Weyl semimetal (WSM). We investigated by time- and angle- resolved photoelectron spectroscopy (tr-ARPES) the possible influence of the Weyl points on the electron dynamics above the Fermi level EF, by comparing the ultrafast response of MoTe2 in the trivial and topological phases. In the low-temperature WSM phase, we report an enhanced relaxation rate of electrons optically excited to the conduction band, which we interpret as a fingerprint of the local gap closure when Weyl points form. By contrast, we find that the electron dynamics of the related compound WTe2 is slower and temperature independent, consistent with a topologically trivial nature of this material. Our results shows that tr-ARPES is sensitive to the small modifications of the unoccupied band structure accompanying the structural and topological phase transition of MoTe2.

Comparative use of side and main channels by small-bodied fish in a large, unimpounded river

USGS Publications Warehouse

Reinhold, Ann Marie; Bramblett, Robert G.; Zale, Alexander V.; Roberts, David W.; Poole, Geoffrey C.

2016-01-01

Ecological theory and field studies suggest that lateral floodplain connectivity and habitat heterogeneity provided by side channels impart favourable habitat conditions for lotic fishes, especially fluvial fishes dependent on large patches of shallow, slow velocity habitats for some portion of their life cycle. However, anthropogenic modification of large, temperate floodplain rivers has led to extensive channel simplification and side-channel loss. Highly modified rivers consist of simplified channels in contracted, less dynamic floodplains.Most research examining the seasonal importance of side channels for fish assemblages in large rivers has been carried out in heavily modified rivers, where side-channel extents are substantially reduced from pre-settlement times, and has often overlooked small-bodied fishes. Inferences about the ecological importance of side channels for small-bodied fishes in large rivers can be ascertained only from investigations of large rivers with largely intact floodplains. The Yellowstone River, our study area, is a rare example of one such river.We targeted small-bodied fishes and compared their habitat use in side and main channels in two geomorphically distinct types of river bends during early and late snowmelt runoff, and autumn base flow. Species compositions of side and main channels differed throughout hydroperiods concurrent with the seasonal redistribution of the availability of shallow, slow current-velocity habitats. More species of fish used side channels than main channels during runoff. Additionally, catch rates of small fishes were generally greater in side channels than in main channels and quantitative assemblage compositions differed between channel types during runoff, but not during base flow. Presence of and access to diverse habitats facilitated the development and persistence of diverse fish assemblages in our study area.Physical dissimilarities between side and main channels may have differentially structured the side- and main-channel fish assemblages during runoff. Patches of shallow, slow current-velocity (SSCV) habitats in side channels were larger and had slightly slower water velocities than SSCV habitat patches in main channels during runoff, but not during base flow.Our findings establish a baseline importance of side channels to riverine fishes in a large, temperate river without heavy anthropogenic modification. Establishing this baseline contributes to basic fluvial ecology and provides empirical justification for restoration efforts that reconnect large rivers with their floodplains.

Assessing Stream Restoration Potential of Recreational Enhancements on an Urban Stream, Springfield, OH

NASA Astrophysics Data System (ADS)

Ritter, J. B.; Evelsizor, A.; Minter, K.; Rigsby, C.; Shaw, K.; Shearer, K.

2010-12-01

Restoration potential of urban streams is inherently constrained by urban infrastructure. Roads and built structures may necessitate a static stream planform while water, sewage, and electrical utilities buried in the stream channel require a stable grade. A privately-led initiative to improve the recreational potential of a 9-km reach of Buck Creek and its tributary Beaver Creek in Springfield, Ohio, includes the modification of four lowhead dams with hydraulic heights up to 3 m. Modifications to the dams include replacing their hydraulic height with a series of drop structures engineered to create hydraulics conducive to kayak play. Two of the lowhead dams have been modified to date. The purpose of this study is to assess the potential benefits of modifications designed for their recreational value for stream restoration. The drop structure is a constructed channel constriction comprised of a hard step in the long stream profile immediately upstream of a scour pool, forming a morphologic sequence of constriction, step, and pool. Up to 4 drop structures are used along a given stream reach, constructed in the area of the former dam, its scour pool and a portion of the impounded area. Though not designed for stream restoration purposes, these structures potentially act as series a riffle-pool sequences. Changes in the stream habitat, water chemistry, and macroinvertebrates in response to dam modification highlight the potential for incorporating stream restoration into the engineering design. Following modification of two of the dams, the in-stream habitat quality, as measured by physical and biological indices, increased at one site and decreased at the other site, depending on whether the uppermost drop structure at the site reduced or expanded the impounded area. In the best case, channel sands and gravels, free of fine sand, silt, and organics, have deposited in a crescentic-shaped bar paralleling and grading to the constriction and step. Greater abundance and diversity of pollution-intolerant macroinvertebrates, supported by higher dissolved oxygen in the substrate, characterizes riffles at these sites.

Monotopic modifications derived from in vitro glycation of albumin with ribose.

PubMed

Pataridis, Statis; Stastná, Zdeňka; Sedláková, Pavla; Mikšík, Ivan

2013-06-01

Post-translational modifications are significant reactions that occur to proteins. One of these modifications is a non-enzymatic reaction between the oxo-group(s) of sugars and amino-group(s) of protein - glycation. This reaction plays an important role in the chronic complications of diabetes mellitus, or in the aging process of organisms, that is, it has an important role in the pathophysiology and "normal" physiology of animals. In the work presented here, we studied the glycation of albumins (HSA and BSA). Methodologically, we used nano-LC coupled to a QTOF mass spectrometer. In vitro-modified proteins were cleaved by trypsin and the arising peptides were separated on a C(18) nano column with a trap-column. Peptides and their modifications were analysed with a high-resolution QTOF mass spectrometer with a mass determination precision of better than 5 ppm. Non-enzymatic in vitro reaction products between albumin and ribose were identified. Besides well-known carboxymethyl lysine, new modifications were determined - creating mass shifts of 78 and 218. The origin of the first modification is discussed and its possible structure is presented. In addition, a mass shift of 132 belonging to a Schiff base was also identified. The location of all the modifications within the structure of the proteins was determined and their reactivity to various oxo-compounds was also examined. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structual Effects of Cytidine 2^' Ribose Modifications as Determined by Irmpd Action Spectroscopy

NASA Astrophysics Data System (ADS)

Hamlow, Lucas; He, Chenchen; Fan, Lin; Wu, Ranran; Yang, Bo; Rodgers, M. T.; Berden, Giel; Oomens, J.

2015-06-01

Modified nucleosides, both naturally occurring and synthetic play an important role in understanding and manipulating RNA and DNA. Naturally occurring modified nucleosides are commonly found in functionally important regions of RNA and also affect antibiotic resistance or sensitivity. Synthetic modifications of nucleosides such as fluorinated and arabinosyl nucleosides have found uses as anti-virals and chemotherapy agents. Understanding the effect that modifications have on structure and glycosidic bond stability may lend insight into the functions of these modified nucleosides. Modifications such as the naturally occurring 2^'-O-methylation and the synthetic 2^'-fluorination are believed to help stabilize the nucleoside through the glycosidic bond stability and intramolecular hydrogen bonding. Changing the sugar from ribose to arabinose alters the stereochemistry at the 2^' position and thus shifts the 3D orientation of the 2^'-hydroxyl group, which also affects intramolecular hydrogen bonding and glycosidic bond stability. The structures of 2^'-deoxy-2^'-fluorocytidine, 2^'-O-methylcytidine and cytosine arabinoside are examined in the current work by measuring the infrared spectra in the IR fingerprint region using infrared multiple photon dissociation (IRMPD) action spectroscopy. The structures accessed in the experiments were determined via comparison of the measured IRMPD action spectra to the theoretical linear IR spectra determined by density functional theory and molecular modeling for the stable low-energy structures. Although glycosidic bond stability cannot be quantitatively determined from this data, complementary TCID studies will establish the effect of these modifications. Comparison of these modified nucleosides with their RNA and DNA analogues will help elucidate differences in their intrinsic chemistry.

Structural analyses for the modification and verification of the Viking aeroshell

NASA Technical Reports Server (NTRS)

Stephens, W. B.; Anderson, M. S.

1976-01-01

The Viking aeroshell is an extremely lightweight flexible shell structure that has undergone thorough buckling analyses in the course of its development. The analytical tools and modeling technique required to reveal the structural behavior are presented. Significant results are given which illustrate the complex failure modes not usually observed in simple models and analyses. Both shell-of-revolution analysis for the pressure loads and thermal loads during entry and a general shell analysis for concentrated tank loads during launch were used. In many cases fixes or alterations to the structure were required, and the role of the analytical results in determining these modifications is indicated.

Real-time in situ study of femtosecond-laser-induced periodic structures on metals by linear and nonlinear optics.

PubMed

Zhang, Jihua; He, Yizhuo; Lam, Billy; Guo, Chunlei

2017-08-21

Femtosecond-laser surface structuring on metals is investigated in real time by both fundamental and second harmonic generation (SHG) signals. The onset of surface modification and its progress can be monitored by both the fundamental and SHG probes. However, the dynamics of femtosecond-laser-induced periodic surface structures (FLIPSSs) formation can only be revealed by SHG but not fundamental because of the higher sensitivity of SHG to structural geometry on metal. Our technique provides a simple and effective way to monitor the surface modification and FLIPSS formation thresholds and allows us to obtain the optimal FLIPSS for SHG enhancement.

Inhibitors of enzymes catalyzing modifications to histone lysine residues: structure, function and activity.

PubMed

Lillico, Ryan; Stesco, Nicholas; Khorshid Amhad, Tina; Cortes, Claudia; Namaka, Mike P; Lakowski, Ted M

2016-05-01

Gene expression is partly controlled by epigenetic mechanisms including histone-modifying enzymes. Some diseases are caused by changes in gene expression that can be mitigated by inhibiting histone-modifying enzymes. This review covers the enzyme inhibitors targeting histone lysine modifications. We summarize the enzymatic mechanisms of histone lysine acetylation, deacetylation, methylation and demethylation and discuss the biochemical roles of these modifications in gene expression and in disease. We discuss inhibitors of lysine acetylation, deacetylation, methylation and demethylation defining their structure-activity relationships and their potential mechanisms. We show that there are potentially indiscriminant off-target effects on gene expression even with the use of selective epigenetic enzyme inhibitors.

Prodrug Strategies for Paclitaxel.

PubMed

Meng, Ziyuan; Lv, Quanxia; Lu, Jun; Yao, Houzong; Lv, Xiaoqing; Jiang, Feng; Lu, Aiping; Zhang, Ge

2016-05-23

Paclitaxel is an anti-tumor agent with remarkable anti-tumor activity and wide clinical uses. However, it is also faced with various challenges especially for its poor water solubility and low selectivity for the target. To overcome these disadvantages of paclitaxel, approaches using small molecule modifications and macromolecule modifications have been developed by many research groups from all over the world. In this review, we discuss the different strategies especially prodrug strategies that are currently used to make paclitaxel more effective.

CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules.

PubMed

Kim, Seonghoon; Lee, Jumin; Jo, Sunhwan; Brooks, Charles L; Lee, Hui Sun; Im, Wonpil

2017-06-05

Reading ligand structures into any simulation program is often nontrivial and time consuming, especially when the force field parameters and/or structure files of the corresponding molecules are not available. To address this problem, we have developed Ligand Reader & Modeler in CHARMM-GUI. Users can upload ligand structure information in various forms (using PDB ID, ligand ID, SMILES, MOL/MOL2/SDF file, or PDB/mmCIF file), and the uploaded structure is displayed on a sketchpad for verification and further modification. Based on the displayed structure, Ligand Reader & Modeler generates the ligand force field parameters and necessary structure files by searching for the ligand in the CHARMM force field library or using the CHARMM general force field (CGenFF). In addition, users can define chemical substitution sites and draw substituents in each site on the sketchpad to generate a set of combinatorial structure files and corresponding force field parameters for throughput or alchemical free energy simulations. Finally, the output from Ligand Reader & Modeler can be used in other CHARMM-GUI modules to build a protein-ligand simulation system for all supported simulation programs, such as CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Ligand Reader & Modeler is available as a functional module of CHARMM-GUI at http://www.charmm-gui.org/input/ligandrm. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Evaluation of Visual Alerts in the Maritime Domain. Study 2. Program Modifications

DTIC Science & Technology

2009-02-01

feedback that they were wrong, and without consulting the Status screen again enter the alternate answer (“ qwe ”). That is, the need to consult the...Neutral Large Slow No QWE Hostile Small Fast Yes ASD DRDC Atlantic CR 2008-268 5 Table 3. First proposed target types and...classification scheme. Target Size Speed Weapons Flag Response Type Neutral Large Slow No Other QWE Hostile Small Fast Yes Other ASD Friendly Large/Small Slow

Epigenetics of oropharyngeal squamous cell carcinoma: opportunities for novel chemotherapeutic targets.

PubMed

Lindsay, Cameron; Seikaly, Hadi; Biron, Vincent L

2017-01-31

Epigenetic modifications are heritable changes in gene expression that do not directly alter DNA sequence. These modifications include DNA methylation, histone post-translational modifications, small and non-coding RNAs. Alterations in epigenetic profiles cause deregulation of fundamental gene expression pathways associated with carcinogenesis. The role of epigenetics in oropharyngeal squamous cell carcinoma (OPSCC) has recently been recognized, with implications for novel biomarkers, molecular diagnostics and chemotherapeutics. In this review, important epigenetic pathways in human papillomavirus (HPV) positive and negative OPSCC are summarized, as well as the potential clinical utility of this knowledge.This material has never been published and is not currently under evaluation in any other peer-reviewed publication.

Coma of modified Gregorian and Cassegrainian mirror systems

NASA Technical Reports Server (NTRS)

Jones, R. T.

1976-01-01

The equivalence of the classical Newtonian, Cassegrainian, and Gregorian mirror systems with respect to the first two Seidel aberrations is rederived by means of a simple congruence. The effects of arbitrary small modifications of the two mirror systems are then studied and general formulas are derived for the effects of such modifications on the spherical aberration and coma. Spherical aberration is corrected to the third order if the amount of glass removed from one surface is replaced at the corresponding zone of the other surface. Modifications in which one surface is made spherical while the other is adjusted to eliminate spherical aberration result in large increases of coma for systems having the usual amplifying ratios.

Synthesis, structural studies and biological properties of new TBA analogues containing an acyclic nucleotide.

PubMed

Coppola, Teresa; Varra, Michela; Oliviero, Giorgia; Galeone, Aldo; D'Isa, Giuliana; Mayol, Luciano; Morelli, Elena; Bucci, Maria-Rosaria; Vellecco, Valentina; Cirino, Giuseppe; Borbone, Nicola

2008-09-01

A new modified acyclic nucleoside, namely N(1)-(3-hydroxy-2-hydroxymethyl-2-methylpropyl)-thymidine, was synthesized and transformed into a building block useful for oligonucleotide (ON) automated synthesis. A series of modified thrombin binding aptamers (TBAs) in which the new acyclic nucleoside replaces, one at the time, the thymidine residues were then synthesized and characterized by UV, CD, MS, and (1)H NMR. The biological activity of the resulting TBAs was tested by Prothrombin Time assay (PT assay) and by purified fibrinogen clotting assay. From a structural point of view, nearly all the new TBA analogues show a similar behavior as the unmodified counterpart, being able to fold into a bimolecular or monomolecular quadruplex structure depending on the nature of monovalent cations (sodium or potassium) coordinated in the quadruplex core. From the comparison of structural and biological data, some important structure-activity relationships emerged, particularly when the modification involved the TT loops. In agreement with previous studies we found that the folding ability of TBA analogues is more affected by modifications involving positions 4 and 13, rather than positions 3 and 12. On the other hand, the highest anti-thrombin activities were detected for aptamers containing the modification at T13 or T12 positions, thus indicating that the effects produced by the introduction of the acyclic nucleoside on the biological activity are not tightly connected with structure stabilities. It is noteworthy that the modification at T7 produces an ON being more stable and active than the natural TBA.

Immuno-Northern Blotting: Detection of RNA Modifications by Using Antibodies against Modified Nucleosides.

PubMed

Mishima, Eikan; Jinno, Daisuke; Akiyama, Yasutoshi; Itoh, Kunihiko; Nankumo, Shinnosuke; Shima, Hisato; Kikuchi, Koichi; Takeuchi, Yoichi; Elkordy, Alaa; Suzuki, Takehiro; Niizuma, Kuniyasu; Ito, Sadayoshi; Tomioka, Yoshihisa; Abe, Takaaki

2015-01-01

The biological roles of RNA modifications are still largely not understood. Thus, developing a method for detecting RNA modifications is important for further clarification. We developed a method for detecting RNA modifications called immuno-northern blotting (INB) analysis and herein introduce its various capabilities. This method involves the separation of RNAs using either polyacrylamide or agarose gel electrophoresis, followed by transfer onto a nylon membrane and subsequent immunoblotting using antibodies against modified nucleosides for the detection of specific modifications. We confirmed that INB with the antibodies for 1-methyladenosine (m1A), N6-methyladenosine (m6A), pseudouridine, and 5-methylcytidine (m5C) showed different modifications in a variety of RNAs from various species and organelles. INB with the anti-m5C antibody revealed that the antibody cross-reacted with another modification on DNA, suggesting the application of this method for characterization of the antibody for modified nucleosides. Additionally, using INB with the antibody for m1A, which is a highly specific modification in eukaryotic tRNA, we detected tRNA-derived fragments known as tiRNAs under the cellular stress response, suggesting the application for tracking target RNA containing specific modifications. INB with the anti-m6A antibody confirmed the demethylation of m6A by the specific demethylases fat mass and obesity-associated protein (FTO) and ALKBH5, suggesting its application for quantifying target modifications in separated RNAs. Furthermore, INB demonstrated that the knockdown of FTO and ALKBH5 increased the m6A modification in small RNAs as well as in mRNA. The INB method has high specificity, sensitivity, and quantitative capability, and it can be employed with conventional experimental apparatus. Therefore, this method would be useful for research on RNA modifications and metabolism.

Comprehensive Analysis of Protein Modifications by Top-down Mass Spectrometry

PubMed Central

Zhang, Han; Ge, Ying

2012-01-01

Mass spectrometry (MS)-based proteomics is playing an increasingly important role in cardiovascular research. Proteomics includes not only identification and quantification of proteins, but also the characterization of protein modifications such as post-translational modifications and sequence variants. The conventional bottom-up approach, involving proteolytic digestion of proteins into small peptides prior to MS analysis, is routinely used for protein identification and quantification with high throughput and automation. Nevertheless, it has limitations in the analysis of protein modifications mainly due to the partial sequence coverage and loss of connections among modifications on disparate portions of a protein. An alternative approach, top-down MS, has emerged as a powerful tool for the analysis of protein modifications. The top-down approach analyzes whole proteins directly, providing a “bird’s eye” view of all existing modifications. Subsequently, each modified protein form can be isolated and fragmented in the mass spectrometer to locate the modification site. The incorporation of the non-ergodic dissociation methods such as electron capture dissociation (ECD) greatly enhances the top-down capabilities. ECD is especially useful for mapping labile post-translational modifications which are well-preserved during the ECD fragmentation process. Top-down MS with ECD has been successfully applied to cardiovascular research with the unique advantages in unraveling the molecular complexity, quantifying modified protein forms, complete mapping of modifications with full sequence coverage, discovering unexpected modifications, and identifying and quantifying positional isomers and determining the order of multiple modifications. Nevertheless, top-down MS still needs to overcome some technical challenges to realize its full potential. Herein, we reviewed the advantages and challenges of top-down methodology with a focus on its application in cardiovascular research. PMID:22187450

Structural and morphological modifications of polymer thin film in the presence of nonsolvent

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

Talukdar, Hrishikesh, E-mail: hiasst@yahoo.in; Kundu, Sarathi

Thin films of sodium poly(acrylic acid) salt (Na-PAA) have been investigated to obtain the modification of the out-of-plane structure and surface morphology in the presence of toluene which is considered as nonsolvent for Na-PAA. X-ray reflectivity analysis show that the out-of-plane thickness of the Na-PAA film increases if the film is kept for longer time inside the toluene. For the thicker film the effect of toluene is more pronounced than the thinner one. Surface morphology obtained from the atomic force microscopy shows that the top surface becomes relatively rough after the dipping of the Na-PAA film inside toluene. Although toluenemore » is nonsolvent for Na-PAA molecules, however, the effect of restructuring of the nanometer-thick polymer film cannot be ignored. The reason for such structural modification has been proposed.« less

Analysis and modification of defective surface aggregates on PCDTBT:PCBM solar cell blends using combined Kelvin probe, conductive and bimodal atomic force microscopy

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

Noh, Hanaul; Diaz, Alfredo J.; Solares, Santiago D.

Organic photovoltaic systems comprising donor polymers and acceptor fullerene derivatives are attractive for inexpensive energy harvesting. Extensive research on polymer solar cells has provided insight into the factors governing device-level efficiency and stability. However, the detailed investigation of nanoscale structures is still challenging. Here we demonstrate the analysis and modification of unidentified surface aggregates. The aggregates are characterized electrically by Kelvin probe force microscopy and conductive atomic force microscopy (C-AFM), whereby the correlation between local electrical potential and current confirms a defective charge transport. Bimodal AFM modification confirms that the aggregates exist on top of the solar cell structure, andmore » is used to remove them and to reveal the underlying active layer. The systematic analysis of the surface aggregates suggests that the structure consists of PCBM molecules.« less

Analysis and modification of defective surface aggregates on PCDTBT:PCBM solar cell blends using combined Kelvin probe, conductive and bimodal atomic force microscopy

DOE PAGES

Noh, Hanaul; Diaz, Alfredo J.; Solares, Santiago D.

2017-03-08

Organic photovoltaic systems comprising donor polymers and acceptor fullerene derivatives are attractive for inexpensive energy harvesting. Extensive research on polymer solar cells has provided insight into the factors governing device-level efficiency and stability. However, the detailed investigation of nanoscale structures is still challenging. Here we demonstrate the analysis and modification of unidentified surface aggregates. The aggregates are characterized electrically by Kelvin probe force microscopy and conductive atomic force microscopy (C-AFM), whereby the correlation between local electrical potential and current confirms a defective charge transport. Bimodal AFM modification confirms that the aggregates exist on top of the solar cell structure, andmore » is used to remove them and to reveal the underlying active layer. The systematic analysis of the surface aggregates suggests that the structure consists of PCBM molecules.« less

In Vivo Multiparametric Ultrasound Imaging of Structural and Functional Tumor Modifications during Therapy.

PubMed

Dizeux, Alexandre; Payen, Thomas; Le Guillou-Buffello, Delphine; Comperat, Eva; Gennisson, Jean-Luc; Tanter, Mickael; Oelze, Michael; Bridal, S Lori

2017-09-01

Longitudinal imaging techniques are needed that can meaningfully probe the tumor microenvironment and its spatial heterogeneity. Contrast-enhanced ultrasound, shear wave elastography and quantitative ultrasound are ultrasound-based techniques that provide information on the vascular function and micro-/macroscopic tissue structure. Modifications of the tumor microenvironment induced by cytotoxic and anti-angiogenic molecules in ectopic murine Lewis lung carcinoma tumors were monitored. The most heterogenous structures were found in tumors treated with anti-angiogenic drug that simultaneously accumulated the highest levels of necrosis and fibrosis. The anti-angiogenic group presented the highest number of correlations between parameters related to vascular function and those related to the micro-/macrostructure of the tumor microenvironment. Results suggest how patterns of multiparametric ultrasound modifications can be related to provide a more insightful marker of changes occurring within tumors during therapy. Copyright © 2017. Published by Elsevier Inc.

Structuring of material parameters in lithium niobate crystals with low-mass, high-energy ion radiation

NASA Astrophysics Data System (ADS)

Peithmann, K.; Eversheim, P.-D.; Goetze, J.; Haaks, M.; Hattermann, H.; Haubrich, S.; Hinterberger, F.; Jentjens, L.; Mader, W.; Raeth, N. L.; Schmid, H.; Zamani-Meymian, M.-R.; Maier, K.

2011-10-01

Ferroelectric lithium niobate crystals offer a great potential for applications in modern optics. To provide powerful optical components, tailoring of key material parameters, especially of the refractive index n and the ferroelectric domain landscape, is required. Irradiation of lithium niobate crystals with accelerated ions causes strong structured modifications in the material. The effects induced by low-mass, high-energy ions (such as 3He with 41 MeV, which are not implanted, but transmit through the entire crystal volume) are reviewed. Irradiation yields large changes of the refractive index Δn, improved domain engineering capability within the material along the ion track, and waveguiding structures. The periodic modification of Δn as well as the formation of periodically poled lithium niobate (PPLN) (supported by radiation damage) is described. Two-step knock-on displacement processes, 3He→Nb and 3He→O causing thermal spikes, are identified as origin for the material modifications.

Analysis and modification of defective surface aggregates on PCDTBT:PCBM solar cell blends using combined Kelvin probe, conductive and bimodal atomic force microscopy

PubMed Central

Noh, Hanaul; Diaz, Alfredo J

2017-01-01

Organic photovoltaic systems comprising donor polymers and acceptor fullerene derivatives are attractive for inexpensive energy harvesting. Extensive research on polymer solar cells has provided insight into the factors governing device-level efficiency and stability. However, the detailed investigation of nanoscale structures is still challenging. Here we demonstrate the analysis and modification of unidentified surface aggregates. The aggregates are characterized electrically by Kelvin probe force microscopy and conductive atomic force microscopy (C-AFM), whereby the correlation between local electrical potential and current confirms a defective charge transport. Bimodal AFM modification confirms that the aggregates exist on top of the solar cell structure, and is used to remove them and to reveal the underlying active layer. The systematic analysis of the surface aggregates suggests that the structure consists of PCBM molecules. PMID:28382247

An RNA Topoisomerase

NASA Astrophysics Data System (ADS)

Wang, Hui; di Gate, Russell J.; Seeman, Nadrian C.

1996-09-01

A synthetic strand of RNA has been designed so that it can adopt two different topological states (a circle and a trefoil knot) when ligated into a cyclic molecule. The RNA knot and circle have been characterized by their behavior in gel electrophoresis and sedimentation experiments. This system allows one to assay for the existence of an RNA topoisomerase, because the two RNA molecules can be interconverted only by a strand passage event. We find that the interconversion of these two species can be catalyzed by Escherichia coli DNA topoisomerase III, indicating that this enzyme can act as an RNA topoisomerase. The conversion of circles to knots is accompanied by a small amount of RNA catenane generation. These findings suggest that strand passage must be considered a potential component of the folding and modification of RNA structures.

Recombinant organisms for production of industrial products.

PubMed

Adrio, Jose-Luis; Demain, Arnold L

2010-01-01

A revolution in industrial microbiology was sparked by the discoveries of ther double-stranded structure of DNA and the development of recombinant DNA technology. Traditional industrial microbiology was merged with molecular biology to yield improved recombinant processes for the industrial production of primary and secondary metabolites, protein biopharmaceuticals and industrial enzymes. Novel genetic techniques such as metabolic engineering, combinatorial biosynthesis and molecular breeding techniques and their modifications are contributing greatly to the development of improved industrial processes. In addition, functional genomics, proteomics and metabolomics are being exploited for the discovery of novel valuable small molecules for medicine as well as enzymes for catalysis. The sequencing of industrial microbal genomes is being carried out which bodes well for future process improvement and discovery of new industrial products. © 2010 Landes Bioscience

Analytical tools for characterizing biopharmaceuticals and the implications for biosimilars

PubMed Central

Berkowitz, Steven A.; Engen, John R.; Mazzeo, Jeffrey R.; Jones, Graham B.

2013-01-01

Biologics such as monoclonal antibodies are much more complex than small-molecule drugs, which raises challenging questions for the development and regulatory evaluation of follow-on versions of such biopharmaceutical products (also known as biosimilars) and their clinical use once patent protection for the pioneering biologic has expired. With the recent introduction of regulatory pathways for follow-on versions of complex biologics, the role of analytical technologies in comparing biosimilars with the corresponding reference product is attracting substantial interest in establishing the development requirements for biosimilars. Here, we discuss the current state of the art in analytical technologies to assess three characteristics of protein biopharmaceuticals that regulatory authorities have identified as being important in development strategies for biosimilars: post-translational modifications, three-dimensional structures and protein aggregation. PMID:22743980

Aging in the Brain: New Roles of Epigenetics in Cognitive Decline.

PubMed

Barter, Jolie D; Foster, Thomas C

2018-06-01

Gene expression in the aging brain depends on transcription signals generated by senescent physiology, interacting with genetic and epigenetic programs. In turn, environmental factors influence epigenetic mechanisms, such that an epigenetic-environmental link may contribute to the accumulation of cellular damage, susceptibility or resilience to stressors, and variability in the trajectory of age-related cognitive decline. Epigenetic mechanisms, DNA methylation and histone modifications, alter chromatin structure and the accessibility of DNA. Furthermore, small non-coding RNA, termed microRNA (miRNA) bind to messenger RNA (mRNA) to regulate translation. In this review, we examine key questions concerning epigenetic mechanisms in regulating the expression of genes associated with brain aging and age-related cognitive decline. In addition, we highlight the interaction of epigenetics with senescent physiology and environmental factors in regulating transcription.

Epigenetic control of CD8+ T cell differentiation.

PubMed

Henning, Amanda N; Roychoudhuri, Rahul; Restifo, Nicholas P

2018-05-01

Upon stimulation, small numbers of naive CD8 + T cells proliferate and differentiate into a variety of memory and effector cell types. CD8 + T cells can persist for years and kill tumour cells and virally infected cells. The functional and phenotypic changes that occur during CD8 + T cell differentiation are well characterized, but the epigenetic states that underlie these changes are incompletely understood. Here, we review the epigenetic processes that direct CD8 + T cell differentiation and function. We focus on epigenetic modification of DNA and associated histones at genes and their regulatory elements. We also describe structural changes in chromatin organization that affect gene expression. Finally, we examine the translational potential of epigenetic interventions to improve CD8 + T cell function in individuals with chronic infections and cancer.

Kinetic treatment of nonlinear ion-acoustic waves in multi-ion plasma

NASA Astrophysics Data System (ADS)

Ahmad, Zulfiqar; Ahmad, Mushtaq; Qamar, A.

2017-09-01

By applying the kinetic theory of the Valsove-Poisson model and the reductive perturbation technique, a Korteweg-de Vries (KdV) equation is derived for small but finite amplitude ion acoustic waves in multi-ion plasma composed of positive and negative ions along with the fraction of electrons. A correspondent equation is also derived from the basic set of fluid equations of adiabatic ions and isothermal electrons. Both kinetic and fluid KdV equations are stationary solved with different nature of coefficients. Their differences are discussed both analytically and numerically. The criteria of the fluid approach as a limiting case of kinetic theory are also discussed. The presence of negative ion makes some modification in the solitary structure that has also been discussed with its implication at the laboratory level.

Post-translational control of transcription factors: methylation ranks highly.

PubMed

Carr, Simon M; Poppy Roworth, A; Chan, Cheryl; La Thangue, Nicholas B

2015-12-01

Methylation of lysine and arginine residues on histones has long been known to determine both chromatin structure and gene expression. In recent years, the methylation of non-histone proteins has emerged as a prevalent modification which impacts on diverse processes such as cell cycle control, DNA repair, senescence, differentiation, apoptosis and tumourigenesis. Many of these non-histone targets represent transcription factors, cell signalling molecules and tumour suppressor proteins. Evidence now suggests that the dysregulation of methyltransferases, demethylases and reader proteins is involved in the development of many diseases, including cancer, and several of these proteins represent potential therapeutic targets for small molecule compounds, fuelling a recent surge in chemical inhibitor design. Such molecules will greatly help us to understand the role of methylation in both health and disease. © 2015 FEBS.

Overcoming the electroluminescence efficiency limitations of perovskite light-emitting diodes

NASA Astrophysics Data System (ADS)

Cho, Himchan; Jeong, Su-Hun; Park, Min-Ho; Kim, Young-Hoon; Wolf, Christoph; Lee, Chang-Lyoul; Heo, Jin Hyuck; Sadhanala, Aditya; Myoung, NoSoung; Yoo, Seunghyup; Im, Sang Hyuk; Friend, Richard H.; Lee, Tae-Woo

2015-12-01

Organic-inorganic hybrid perovskites are emerging low-cost emitters with very high color purity, but their low luminescent efficiency is a critical drawback. We boosted the current efficiency (CE) of perovskite light-emitting diodes with a simple bilayer structure to 42.9 candela per ampere, similar to the CE of phosphorescent organic light-emitting diodes, with two modifications: We prevented the formation of metallic lead (Pb) atoms that cause strong exciton quenching through a small increase in methylammonium bromide (MABr) molar proportion, and we spatially confined the exciton in uniform MAPbBr3 nanograins (average diameter = 99.7 nanometers) formed by a nanocrystal pinning process and concomitant reduction of exciton diffusion length to 67 nanometers. These changes caused substantial increases in steady-state photoluminescence intensity and efficiency of MAPbBr3 nanograin layers.

High Photoelectric Conversion Efficiency of Metal Phthalocyanine/Fullerene Heterojunction Photovoltaic Device

PubMed Central

Lin, Chi-Feng; Zhang, Mi; Liu, Shun-Wei; Chiu, Tien-Lung; Lee, Jiun-Haw

2011-01-01

This paper introduces the fundamental physical characteristics of organic photovoltaic (OPV) devices. Photoelectric conversion efficiency is crucial to the evaluation of quality in OPV devices, and enhancing efficiency has been spurring on researchers to seek alternatives to this problem. In this paper, we focus on organic photovoltaic (OPV) devices and review several approaches to enhance the energy conversion efficiency of small molecular heterojunction OPV devices based on an optimal metal-phthalocyanine/fullerene (C60) planar heterojunction thin film structure. For the sake of discussion, these mechanisms have been divided into electrical and optical sections: (1) Electrical: Modification on electrodes or active regions to benefit carrier injection, charge transport and exciton dissociation; (2) Optical: Optional architectures or infilling to promote photon confinement and enhance absorption. PMID:21339999

Small Molecule DFPM Derivative-Activated Plant Resistance Protein Signaling in Roots Is Unaffected by EDS1 Subcellular Targeting Signal and Chemical Genetic Isolation of victr R-Protein Mutants

PubMed Central

Mevers, Emily; García, Ana V.; Highhouse, Samantha; Gerwick, William H.; Parker, Jane E.; Schroeder, Julian I.

2016-01-01

The small molecule DFPM ([5-(3,4-dichlorophenyl)furan-2-yl]-piperidine-1-ylmethanethione) was recently shown to trigger signal transduction via early effector-triggered immunity signaling genes including EDS1 and PAD4 in Arabidopsis thaliana accession Col-0. Chemical genetic analyses of A. thaliana natural variants identified the plant Resistance protein-like Toll/Interleukin1 Receptor (TIR)-Nucleotide Binding (NB)-Leucine-Rich Repeat (LRR) protein VICTR as required for DFPM-mediated root growth arrest. Here a chemical genetic screen for mutants which disrupt DFPM-mediated root growth arrest in the Col-0 accession identified new mutant alleles of the TIR-NB-LRR gene VICTR. One allele, victr-6, carries a Gly216-to-Asp mutation in the Walker A domain supporting an important function of the VICTR nucleotide binding domain in DFPM responses consistent with VICTR acting as a canonical Resistance protein. The essential nucleo-cytoplasmic regulator of TIR-NB-LRR-mediated effector-triggered immunity, EDS1, was reported to have both nuclear and cytoplasmic actions in pathogen resistance. DFPM was used to investigate the requirements for subcellular EDS1 localization in DFPM-mediated root growth arrest. EDS1-YFP fusions engineered to localize mainly in the cytoplasm or the nucleus by tagging with a nuclear export signal (NES) or a nuclear localization signal (NLS), respectively, were tested. We found that wild-type EDS1-YFP and both the NES and NLS-tagged EDS1 variants were induced by DFPM treatments and fully complemented eds1 mutant plants in root responses to DFPM, suggesting that enrichment of EDS1 in either compartment could confer DFPM-mediated root growth arrest. We further found that a light and O2-dependent modification of DFPM is necessary to mediate DFPM signaling in roots. Chemical analyses including Liquid Chromatography-Mass Spectrometry and High-Resolution Atmospheric Pressure Chemical Ionization Mass Spectrometry identified a DFPM modification product that is likely responsible for bioactivity mediating root growth arrest. We propose a chemical structure of this product and a possible reaction mechanism for DFPM modification. PMID:27219122

Modifications modulate anticodon loop dynamics and codon recognition of E. coli tRNA(Arg1,2).

PubMed

Cantara, William A; Bilbille, Yann; Kim, Jia; Kaiser, Rob; Leszczyńska, Grażyna; Malkiewicz, Andrzej; Agris, Paul F

2012-03-02

Three of six arginine codons are read by two tRNA(Arg) isoacceptors in Escherichia coli. The anticodon stem and loop of these isoacceptors (ASL(Arg1,2)) differs only in that the position 32 cytidine of tRNA(Arg1) is posttranscriptionally modified to 2-thiocytidine (s(2)C(32)). The tRNA(Arg1,2) are also modified at positions 34 (inosine, I(34)) and 37 (2-methyladenosine, m(2)A(37)). To investigate the roles of modifications in the structure and function, we analyzed six ASL(Arg1,2) constructs differing in their array of modifications by spectroscopy and codon binding assays. Thermal denaturation and circular dichroism spectroscopy indicated that modifications contribute thermodynamic and base stacking properties, resulting in more order but less stability. NMR-derived structures of the ASL(Arg1,2) showed that the solution structures of the ASLs were nearly identical. Surprisingly, none possessed the U-turn conformation required for effective codon binding on the ribosome. Yet, all ASL(Arg1,2) constructs efficiently bound the cognate CGU codon. Three ASLs with I(34) were able to decode CGC, whereas only the singly modified ASL(Arg1,2)(ICG) with I(34) was able to decode CGA. The dissociation constants for all codon bindings were physiologically relevant (0.4-1.4 μM). However, with the introduction of s(2)C(32) or m(2)A(37) to ASL(Arg1,2)(ICG), the maximum amount of ASL bound to CGU and CGC was significantly reduced. These results suggest that, by allowing loop flexibility, the modifications modulate the conformation of the ASL(Arg1,2), which takes one structure free in solution and two others when bound to the cognate arginyl-tRNA synthetase or to codons on the ribosome where modifications reduce or restrict binding to specific codons. Copyright © 2011 Elsevier Ltd. All rights reserved.

Modification of gray iron produced by induction melting with barium strontium

NASA Astrophysics Data System (ADS)

Modzelevskaya, G.; Feoktistov, A. V.; Selyanin, I. F.; Kutsenko, A. I.; Kutsenko, A. A.

2016-09-01

The article provides analysis of results of gray iron experimental melts in induction furnace and the following melt modification with barium-strontium carbonate (BSC-2). It is shown that modification positively affects mechanical and casting properties and as-cast iron structure. It was established that BSC-2 granulated immediately prior to use has greater impact on melt than BSC-2 of the same faction, supplied by the manufacturer.

Sensor Suitcase: Portable System for Increasing Building Energy Efficiency

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

None

PNNL's Sensor Suitcase does an energy assessment of small buildings, enabling building owners to see which low-cost, energy-saving modifications would give them the best payoff. Implementing the recommended changes typically means 10% energy cost savings per small building. No other product provides such easy-to-use, expert-guided capabilities, and at half the cost of a typical energy assessment.

The effects of landscape modifications on the long-term persistence of animal populations.

PubMed

Nabe-Nielsen, Jacob; Sibly, Richard M; Forchhammer, Mads C; Forbes, Valery E; Topping, Christopher J

2010-01-28

The effects of landscape modifications on the long-term persistence of wild animal populations is of crucial importance to wildlife managers and conservation biologists, but obtaining experimental evidence using real landscapes is usually impossible. To circumvent this problem we used individual-based models (IBMs) of interacting animals in experimental modifications of a real Danish landscape. The models incorporate as much as possible of the behaviour and ecology of four species with contrasting life-history characteristics: skylark (Alauda arvensis), vole (Microtus agrestis), a ground beetle (Bembidion lampros) and a linyphiid spider (Erigone atra). This allows us to quantify the population implications of experimental modifications of landscape configuration and composition. Starting with a real agricultural landscape, we progressively reduced landscape complexity by (i) homogenizing habitat patch shapes, (ii) randomizing the locations of the patches, and (iii) randomizing the size of the patches. The first two steps increased landscape fragmentation. We assessed the effects of these manipulations on the long-term persistence of animal populations by measuring equilibrium population sizes and time to recovery after disturbance. Patch rearrangement and the presence of corridors had a large effect on the population dynamics of species whose local success depends on the surrounding terrain. Landscape modifications that reduced population sizes increased recovery times in the short-dispersing species, making small populations vulnerable to increasing disturbance. The species that were most strongly affected by large disturbances fluctuated little in population sizes in years when no perturbations took place. Traditional approaches to the management and conservation of populations use either classical methods of population analysis, which fail to adequately account for the spatial configurations of landscapes, or landscape ecology, which accounts for landscape structure but has difficulty predicting the dynamics of populations living in them. Here we show how realistic and replicable individual-based models can bridge the gap between non-spatial population theory and non-dynamic landscape ecology. A major strength of the approach is its ability to identify population vulnerabilities not detected by standard population viability analyses.

EVALUATION OF A NEW MEAN SCALED AND MOMENT ADJUSTED TEST STATISTIC FOR SEM.

PubMed

Tong, Xiaoxiao; Bentler, Peter M

2013-01-01

Recently a new mean scaled and skewness adjusted test statistic was developed for evaluating structural equation models in small samples and with potentially nonnormal data, but this statistic has received only limited evaluation. The performance of this statistic is compared to normal theory maximum likelihood and two well-known robust test statistics. A modification to the Satorra-Bentler scaled statistic is developed for the condition that sample size is smaller than degrees of freedom. The behavior of the four test statistics is evaluated with a Monte Carlo confirmatory factor analysis study that varies seven sample sizes and three distributional conditions obtained using Headrick's fifth-order transformation to nonnormality. The new statistic performs badly in most conditions except under the normal distribution. The goodness-of-fit χ(2) test based on maximum-likelihood estimation performed well under normal distributions as well as under a condition of asymptotic robustness. The Satorra-Bentler scaled test statistic performed best overall, while the mean scaled and variance adjusted test statistic outperformed the others at small and moderate sample sizes under certain distributional conditions.

Rationalizing Tight Ligand Binding through Cooperative Interaction Networks

PubMed Central

2011-01-01

Small modifications of the molecular structure of a ligand sometimes cause strong gains in binding affinity to a protein target, rendering a weakly active chemical series suddenly attractive for further optimization. Our goal in this study is to better rationalize and predict the occurrence of such interaction hot-spots in receptor binding sites. To this end, we introduce two new concepts into the computational description of molecular recognition. First, we take a broader view of noncovalent interactions and describe protein–ligand binding with a comprehensive set of favorable and unfavorable contact types, including for example halogen bonding and orthogonal multipolar interactions. Second, we go beyond the commonly used pairwise additive treatment of atomic interactions and use a small world network approach to describe how interactions are modulated by their environment. This approach allows us to capture local cooperativity effects and considerably improves the performance of a newly derived empirical scoring function, ScorpionScore. More importantly, however, we demonstrate how an intuitive visualization of key intermolecular interactions, interaction networks, and binding hot-spots supports the identification and rationalization of tight ligand binding. PMID:22087588

Ligand-surface interactions and surface oxidation of colloidal PbSe quantum dots revealed by thin-film positron annihilation methods

NASA Astrophysics Data System (ADS)

Shi, Wenqin; Eijt, Stephan W. H.; Suchand Sandeep, C. S.; Siebbeles, Laurens D. A.; Houtepen, Arjan J.; Kinge, Sachin; Brück, Ekkes; Barbiellini, Bernardo; Bansil, Arun

2016-02-01

Positron Two Dimensional Angular Correlation of Annihilation Radiation (2D-ACAR) measurements reveal modifications of the electronic structure and composition at the surfaces of PbSe quantum dots (QDs), deposited as thin films, produced by various ligands containing either oxygen or nitrogen atoms. In particular, the 2D-ACAR measurements on thin films of colloidal PbSe QDs capped with oleic acid ligands yield an increased intensity in the electron momentum density (EMD) at high momenta compared to PbSe quantum dots capped with oleylamine. Moreover, the EMD of PbSe QDs is strongly affected by the small ethylenediamine ligands, since these molecules lead to small distances between QDs and favor neck formation between near neighbor QDs, inducing electronic coupling between neighboring QDs. The high sensitivity to the presence of oxygen atoms at the surface can be also exploited to monitor the surface oxidation of PbSe QDs upon exposure to air. Our study clearly demonstrates that positron annihilation spectroscopy applied to thin films can probe surface transformations of colloidal semiconductor QDs embedded in functional layers.

Towards Breaking the Histone Code – Bayesian Graphical Models for Histone Modifications

PubMed Central

Mitra, Riten; Müller, Peter; Liang, Shoudan; Xu, Yanxun; Ji, Yuan

2013-01-01

Background Histones are proteins that wrap DNA around in small spherical structures called nucleosomes. Histone modifications (HMs) refer to the post-translational modifications to the histone tails. At a particular genomic locus, each of these HMs can either be present or absent, and the combinatory patterns of the presence or absence of multiple HMs, or the ‘histone codes,’ are believed to co-regulate important biological processes. We aim to use raw data on HM markers at different genomic loci to (1) decode the complex biological network of HMs in a single region and (2) demonstrate how the HM networks differ in different regulatory regions. We suggest that these differences in network attributes form a significant link between histones and genomic functions. Methods and Results We develop a powerful graphical model under Bayesian paradigm. Posterior inference is fully probabilistic, allowing us to compute the probabilities of distinct dependence patterns of the HMs using graphs. Furthermore, our model-based framework allows for easy but important extensions for inference on differential networks under various conditions, such as the different annotations of the genomic locations (e.g., promoters versus insulators). We applied these models to ChIP-Seq data based on CD4+ T lymphocytes. The results confirmed many existing findings and provided a unified tool to generate various promising hypotheses. Differential network analyses revealed new insights on co-regulation of HMs of transcriptional activities in different genomic regions. Conclusions The use of Bayesian graphical models and borrowing strength across different conditions provide high power to infer histone networks and their differences. PMID:23748248

Disturbance facilitates the coexistence of antagonistic ecosystem engineers in California estuaries.

PubMed

Castorani, Max C N; Hovel, Kevin A; Williams, Susan L; Baskett, Marissa L

2014-08-01

Ecological theory predicts that interactions between antagonistic ecosystem engineers can lead to local competitive exclusion, but disturbance can facilitate broader coexistence. However, few empirical studies have tested the potential for disturbance to mediate competition between engineers. We examined the capacity for disturbance and habitat modification to explain the disjunct distributions of two benthic ecosystem engineers, eelgrass Zostera marina and the burrowing ghost shrimp Neotrypaea californiensis, in two California estuaries. Sediment sampling in eelgrass and ghost shrimp patches revealed that ghost shrimp change benthic biogeochemistry over small scales (centimeters) but not patch scales (meters to tens of meters), suggesting a limited capacity for sediment modification to explain species distributions. To determine the relative competitive abilities of engineers, we conducted reciprocal transplantations of ghost shrimp and eelgrass. Local ghost shrimp densities declined rapidly following the addition of eelgrass, and transplanted eelgrass expanded laterally into the surrounding ghost shrimp-dominated areas. When transplanted into eelgrass patches, ghost shrimp failed to persist. Ghost shrimp were also displaced from plots with structural mimics of eelgrass rhizomes and roots, suggesting that autogenic habitat modification by eelgrass is an important mechanism determining ghost shrimp distributions. However, ghost shrimp were able to rapidly colonize experimental disturbances to eelgrass patch edges, which are common in shallow estuaries. We conclude that coexistence in this system is maintained by spatiotemporally asynchronous disturbances and a competition-colonization trade-off: eelgrass is a competitively superior ecosystem engineer, but benthic disturbances permit the coexistence of ghost shrimp at the landscape scale by modulating the availability of space.

Comparison of bare and amino modified mesoporous silica@poly(ethyleneimine)s xerogel as indomethacin carrier: Superiority of amino modification.

PubMed

Li, Jing; Xu, Lu; Wang, Hongyu; Yang, Baixue; Liu, Hongzhuo; Pan, Weisan; Li, Sanming

2016-02-01

The purpose of this study was to facilely develop amino modified mesoporous silica xerogel synthesized using biomimetic method (B-AMSX) and to investigate its potential ability to be a drug carrier for loading poorly water-soluble drug indomethacin (IMC). For comparison, mesoporous silica xerogel without amino modification (B-MSX) was also synthesized using the same method. The changes of characteristics before and after IMC loading were systemically studied using fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), small angle X-ray scattering (SAXS) and nitrogen adsorption/desorption analysis. The results showed that B-MSX and B-AMSX were spherical nanoparticles with mesoporous structure. Compared with B-MSX, IMC loading capacity of B-AMSX was higher because more drug molecules can be loaded through stronger hydrogen bonding force. DSC and SAXS analysis confirmed the amorphous state of IMC after being loaded into B-MSX and B-AMSX. The in vitro drug release study revealed that B-MSX and B-AMSX improved IMC release significantly, and B-AMSX released IMC a little faster than B-MSX because of larger pore diameter of IMC-AMSX. B-MSX and B-AMSX degraded gradually in dissolution medium evidenced by color reaction and absorbance value, and B-AMSX degraded slower than B-MSX due to amino modification. In conclusion, B-AMSX with superiority of higher loading capacity and enhanced dissolution release can be considered to be a good candidate as drug carrier for IMC. Copyright © 2015 Elsevier B.V. All rights reserved.