Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein–Protein Interactions by Chemical Cross-Linking

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

Merkley, Eric D.; Baker, Erin S.; Crowell, Kevin L.

2013-02-20

Chemical cross-linking of proteins followed by proteolysis and mass spectrometric analysis of the resulting cross-linked peptides can provide insights into protein structure and protein-protein interactions. However, cross-linked peptides are by necessity of low stoichometry and have different physicochemical properties than linear peptides, routine unambiguous identification of the cross-linked peptides has remained difficult. To address this challenge, we demonstrated the use of liquid chromatography and ion mobility separations coupled with mass spectrometry in combination with a heavy-isotope labeling method. The combination of mixed-isotope cross-linking and ion mobility provided unique and easily interpretable spectral multiplet features for the intermolecular cross-linked peptides. Applicationmore » of the method to two different homodimeric proteins - SrfN, a virulence factor from Salmonella Typhimurium and SO_2176, a protein of unknown function from Shewanella oneidensis- revealed several cross-linked peptides from both proteins that were identified with a low false discovery rate (estimated using a decoy approach). A greater number of cross-linked peptides were identified using ion mobility drift time information in the analysis than when the data were summed across the drift time dimension before analysis. The identified cross-linked peptides migrated more quickly in the ion mobility drift tube than the unmodified peptides.« less

Cationic Shell-crosslinked Knedel-like (cSCK) Nanoparticles for Highly Efficient PNA Delivery

PubMed Central

Fang, Huafeng; Zhang, Ke; Shen, Gang; Wooley, Karen L.; Taylor, John-Stephen A.

2009-01-01

Peptide nucleic acids have a number of features that make them an ideal platform for the development of in vitro biological probes and tools. Unfortunately, their inability to pass through membranes has limited their in vivo application as diagnostic and therapeutic agents. Herein, we describe the development of cationic shell-crosslinked knedel-like (cSCK) nanoparticles as highly efficient vehicles for the delivery of PNAs into cells, either through electrostatic complexation with a PNA•ODN hybrid, or through a bioreductively cleavable disulfide linkage to a PNA. These delivery systems are better than the standard lipofectamine/ODN-mediated method and much better than the Arg9-mediated method for PNA delivery in HeLa cells, showing lower toxicity and higher bioactivity. The cSCKs were also found to facilitate both endocytosis and endosomal release of the PNAs, while themselves remaining trapped in the endosomes. PMID:19231840

A Crosslinking Analysis of GAP-43 Interactions with Other Proteins in Differentiated N1E-115 Cells

PubMed Central

Ollom, Callise M.; Denny, John B.

2008-01-01

It has been suggested that GAP-43 (growth-associated protein) binds to various proteins in growing neurons as part of its mechanism of action. To test this hypothesis in vivo, differentiated N1E-115 neuroblastoma cells were labeled with [35S]-amino acids and were treated with a cleavable crosslinking reagent. The cells were lysed in detergent and the lysates were centrifuged at 100,000 × g to isolate crosslinked complexes. Following cleavage of the crosslinks and analysis by two-dimensional gel electrophoresis, it was found that the crosslinker increased the level of various proteins, and particularly actin, in this pellet fraction. However, GAP-43 was not present, suggesting that GAP-43 was not extensively crosslinked to proteins of the cytoskeleton and membrane skeleton and did not sediment with them. GAP-43 also did not sediment with the membrane skeleton following nonionic detergent lysis. Calmodulin, but not actin or other proposed interaction partners, co-immunoprecipitated with GAP-43 from the 100,000 × g supernatant following crosslinker addition to cells or cell lysates. Faint spots at 34 kDa and 60 kDa were also present. Additional GAP-43 was recovered from GAP-43 immunoprecipitation supernatants with anti-calmodulin but not with anti-actin. The results suggest that GAP-43 is not present in complexes with actin or other membrane skeletal or cytoskeletal proteins in these cells, but it is nevertheless possible that a small fraction of the total GAP-43 may interact with other proteins. PMID:19325830

Isotope-labeled cross-linkers and Fourier transform ion cyclotron resonance mass spectrometry for structural analysis of a protein/peptide complex.

PubMed

Ihling, Christian; Schmidt, Andreas; Kalkhof, Stefan; Schulz, Daniela M; Stingl, Christoph; Mechtler, Karl; Haack, Michael; Beck-Sickinger, Annette G; Cooper, Dermot M F; Sinz, Andrea

2006-08-01

For structural studies of proteins and their complexes, chemical cross-linking combined with mass spectrometry presents a promising strategy to obtain structural data of protein interfaces from low quantities of proteins within a short time. We explore the use of isotope-labeled cross-linkers in combination with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry for a more efficient identification of cross-linker containing species. For our studies, we chose the calcium-independent complex between calmodulin and a 25-amino acid peptide from the C-terminal region of adenylyl cyclase 8 containing an "IQ-like motif." Cross-linking reactions between calmodulin and the peptide were performed in the absence of calcium using the amine-reactive, isotope-labeled (d0 and d4) cross-linkers BS3 (bis[sulfosuccinimidyl]suberate) and BS2G (bis[sulfosuccinimidyl]glutarate). Tryptic in-gel digestion of excised gel bands from covalently cross-linked complexes resulted in complicated peptide mixtures, which were analyzed by nano-HPLC/nano-ESI-FTICR mass spectrometry. In cases where more than one reactive functional group, e.g., amine groups of lysine residues, is present in a sequence stretch, MS/MS analysis is a prerequisite for unambiguously identifying the modified residues. MS/MS experiments revealed two lysine residues in the central alpha-helix of calmodulin as well as three lysine residues both in the C-terminal and N-terminal lobes of calmodulin to be cross-linked with one single lysine residue of the adenylyl cyclase 8 peptide. Further cross-linking studies will have to be conducted to propose a structural model for the calmodulin/peptide complex, which is formed in the absence of calcium. The combination of using isotope-labeled cross-linkers, determining the accurate mass of intact cross-linked products, and verifying the amino acid sequences of cross-linked species by MS/MS presents a convenient approach that offers the perspective to obtain structural data of protein assemblies within a few days.

Effective Identification of Akt Interacting Proteins by Two-Step Chemical Crosslinking, Co-Immunoprecipitation and Mass Spectrometry

PubMed Central

Huang, Bill X.; Kim, Hee-Yong

2013-01-01

Akt is a critical protein for cell survival and known to interact with various proteins. However, Akt binding partners that modulate or regulate Akt activation have not been fully elucidated. Identification of Akt-interacting proteins has been customarily achieved by co-immunoprecipitation combined with western blot and/or MS analysis. An intrinsic problem of the method is loss of interacting proteins during procedures to remove non-specific proteins. Moreover, antibody contamination often interferes with the detection of less abundant proteins. Here, we developed a novel two-step chemical crosslinking strategy to overcome these problems which resulted in a dramatic improvement in identifying Akt interacting partners. Akt antibody was first immobilized on protein A/G beads using disuccinimidyl suberate and allowed to bind to cellular Akt along with its interacting proteins. Subsequently, dithiobis[succinimidylpropionate], a cleavable crosslinker, was introduced to produce stable complexes between Akt and binding partners prior to the SDS-PAGE and nanoLC-MS/MS analysis. This approach enabled identification of ten Akt partners from cell lysates containing as low as 1.5 mg proteins, including two new potential Akt interacting partners. None of these but one protein was detectable without crosslinking procedures. The present method provides a sensitive and effective tool to probe Akt-interacting proteins. This strategy should also prove useful for other protein interactions, particularly those involving less abundant or weakly associating partners. PMID:23613850

Self-Assembly Assisted Fabrication of Dextran-Based Nanohydrogels with Reduction-Cleavable Junctions for Applications as Efficient Drug Delivery Systems

PubMed Central

Wang, Hao; Dai, Tingting; Zhou, Shuyan; Huang, Xiaoxiao; Li, Songying; Sun, Kang; Zhou, Guangdong; Dou, Hongjing

2017-01-01

In order to overcome the key challenge in improving both fabrication efficiency and their drug delivery capability of anti-cancer drug delivery systems (ACDDS), here polyacrylic acid (PAA) grafted dextran (Dex) nanohydrogels (NGs) with covalent crosslinked structure bearing redox sensitive disulfide crosslinking junctions (Dex-SS-PAA) were synthesized efficiently through a one-step self-assembly assisted methodology (SAA). The Dex-SS-PAA were subsequently conjugated with doxorubicin through an acid-labile hydrazone bond (Dex-SS-PAA-DOX). The in vitro drug release behavior, anti-cancer effects in vivo, and biosafety of the as-prepared acid- and redox-dual responsive biodegradable NGs were systematically investigated. The results revealed that the Dex-SS-PAA-DOX exhibited pH- and redox-controlled drug release, greatly reduced the toxicity of free DOX, while exhibiting a strong ability to inhibit the growth of MDA-MB-231 tumors. Our study demonstrated that the Dex-SS-PAA-DOX NGs are very promising candidates as ACDDS for anti-cancer therapeutics. PMID:28071743

Self-Assembly Assisted Fabrication of Dextran-Based Nanohydrogels with Reduction-Cleavable Junctions for Applications as Efficient Drug Delivery Systems

NASA Astrophysics Data System (ADS)

Wang, Hao; Dai, Tingting; Zhou, Shuyan; Huang, Xiaoxiao; Li, Songying; Sun, Kang; Zhou, Guangdong; Dou, Hongjing

2017-01-01

In order to overcome the key challenge in improving both fabrication efficiency and their drug delivery capability of anti-cancer drug delivery systems (ACDDS), here polyacrylic acid (PAA) grafted dextran (Dex) nanohydrogels (NGs) with covalent crosslinked structure bearing redox sensitive disulfide crosslinking junctions (Dex-SS-PAA) were synthesized efficiently through a one-step self-assembly assisted methodology (SAA). The Dex-SS-PAA were subsequently conjugated with doxorubicin through an acid-labile hydrazone bond (Dex-SS-PAA-DOX). The in vitro drug release behavior, anti-cancer effects in vivo, and biosafety of the as-prepared acid- and redox-dual responsive biodegradable NGs were systematically investigated. The results revealed that the Dex-SS-PAA-DOX exhibited pH- and redox-controlled drug release, greatly reduced the toxicity of free DOX, while exhibiting a strong ability to inhibit the growth of MDA-MB-231 tumors. Our study demonstrated that the Dex-SS-PAA-DOX NGs are very promising candidates as ACDDS for anti-cancer therapeutics.

Quantitative proteomic analysis of human breast epithelial cells with differential telomere length

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

Yu, Li-Rong; Chan, King C.; Tahara, Hidetoshi

Telomeres play important functional roles in cell proliferation, cell cycle regulation, and genetic stability, in which telomere length is critical. In this study, quantitative proteome comparisons for the human breast epithelial cells with short and long telomeres (184-hTERT{sub L} vs. 184-hTERT{sub S} and 90P-hTERT{sub L} vs. 90P-hTERT{sub S}), resulting from transfection of the human telomerase reverse transcriptase (hTERT) gene, were performed using cleavable isotope-coded affinity tags. More than 2000 proteins were quantified in each comparative experiment, with approximately 77% of the proteins identified in both analyses. In the cells with long telomeres, significant and consistent alterations were observed in metabolismmore » (amino acid, nucleotide, and lipid metabolism), genetic information transmission (transcription and translation regulation, spliceosome and ribosome complexes), and cell signaling. Interestingly, the DNA excision repair pathway is enhanced, while integrin and its ligands are downregulated in the cells with long telomeres. These results may provide valuable information related to telomere functions.« less

Protein quantification using a cleavable reporter peptide.

PubMed

Duriez, Elodie; Trevisiol, Stephane; Domon, Bruno

2015-02-06

Peptide and protein quantification based on isotope dilution and mass spectrometry analysis are widely employed for the measurement of biomarkers and in system biology applications. The accuracy and reliability of such quantitative assays depend on the quality of the stable-isotope labeled standards. Although the quantification using stable-isotope labeled peptides is precise, the accuracy of the results can be severely biased by the purity of the internal standards, their stability and formulation, and the determination of their concentration. Here we describe a rapid and cost-efficient method to recalibrate stable isotope labeled peptides in a single LC-MS analysis. The method is based on the equimolar release of a protein reference peptide (used as surrogate for the protein of interest) and a universal reporter peptide during the trypsinization of a concatenated polypeptide standard. The quality and accuracy of data generated with such concatenated polypeptide standards are highlighted by the quantification of two clinically important proteins in urine samples and compared with results obtained with conventional stable isotope labeled reference peptides. Furthermore, the application of the UCRP standards in complex samples is described.

Surface-Cross-Linked Micelles as Multifunctionalized Organic Nanoparticles for Controlled Release, Light Harvesting, and Catalysis

PubMed Central

2016-01-01

Surfactant micelles are dynamic entities with a rapid exchange of monomers. By “clicking” tripropargylammonium-containing surfactants with diazide cross-linkers, we obtained surface-cross-linked micelles (SCMs) that could be multifunctionalized for different applications. They triggered membrane fusion through tunable electrostatic interactions with lipid bilayers. Antenna chromophores could be installed on them to create artificial light-harvesting complexes with efficient energy migration among tens to hundreds of chromophores. When cleavable cross-linkers were used, the SCMs could break apart in response to redox or pH signals, ejecting entrapped contents quickly as a result of built-in electrostatic stress. They served as caged surfactants whose surface activity was turned on by environmental stimuli. They crossed cell membranes readily. Encapsulated fluorophores showed enhanced photophysical properties including improved quantum yields and greatly expanded Stokes shifts. Catalytic groups could be installed on the surface or in the interior, covalently attached or physically entrapped. As enzyme mimics, the SCMs enabled rational engineering of the microenvironment around the catalysts to afford activity and selectivity not possible with conventional catalysts. PMID:27181610

A novel bio-orthogonal cross-linker for improved protein/protein interaction analysis.

PubMed

Nury, Catherine; Redeker, Virginie; Dautrey, Sébastien; Romieu, Anthony; van der Rest, Guillaume; Renard, Pierre-Yves; Melki, Ronald; Chamot-Rooke, Julia

2015-02-03

The variety of protein cross-linkers developed in recent years illustrates the current requirement for efficient reagents optimized for mass spectrometry (MS) analysis. To date, the most widely used strategy relies on commercial cross-linkers that bear an isotopically labeled tag and N-hydroxysuccinimid-ester (NHS-ester) moieties. Moreover, an enrichment step using liquid chromatography is usually performed after enzymatic digestion of the cross-linked proteins. Unfortunately, this approach suffers from several limitations. First, it requires large amounts of proteins. Second, NHS-ester cross-linkers are poorly efficient because of their fast hydrolysis in water. Finally, data analysis is complicated because of uneven fragmentation of complex isotopic cross-linked peptide mixtures. We therefore synthesized a new type of trifunctional cross-linker to overrule these limitations. This reagent, named NNP9, comprises a rigid core and bears two activated carbamate moieties and an azido group. NNP9 was used to establish intra- and intermolecular cross-links within creatine kinase, then to map the interaction surfaces between α-Synuclein (α-Syn), the aggregation of which leads to Parkinson's disease, and the molecular chaperone Hsc70. We show that NNP9 cross-linking efficiency is significantly higher than that of NHS-ester commercial cross-linkers. The number of cross-linked peptides identified was increased, and a high quality of MS/MS spectra leading to high sequence coverage was observed. Our data demonstrate the potential of NNP9 for an efficient and straightforward characterization of protein-protein interfaces and illustrate the power of using different cross-linkers to map thoroughly the surface interfaces within protein complexes.

Enzyme actuated bioresponsive hydrogels

NASA Astrophysics Data System (ADS)

Wilson, Andrew Nolan

Bioresponsive hydrogels are emerging with technological significance in targeted drug delivery, biosensors and regenerative medicine. Conferred with the ability to respond to specific biologically derived stimuli, the design challenge is in effectively linking the conferred biospecificity with an engineered response tailored to the needs of a particular application. Moreover, the fundamental phenomena governing the response must support an appropriate dynamic range and limit of detection. The design of these systems is inherently complicated due to the high interdependency of the governing phenomena that guide the sensing, transduction, and the actuation response of hydrogels. To investigate the dynamics of these materials, model systems may be used which seek to interrogate the system dynamics by uni-variable experimentation and limit confounding phenomena such as: polymer-solute interactions, polymer swelling dynamics and biomolecular reaction-diffusion concerns. To this end, a model system, alpha-chymotrypsin (Cht) (a protease) and a cleavable peptide-chromogen (pro-drug) covalently incorporated into a hydrogel, was investigated to understand the mechanisms of covalent loading and release by enzymatic cleavage in bio-responsive delivery systems. Using EDC and Sulfo-NHS, terminal carboxyl groups of N-succinyl-Ala-Ala-Pro-Phe p-nitroanilide, a cleavable chromogen, were conjugated to primary amines of a hydrated poly(HEMA)-based hydrogel. Hydrogel discs were incubated in buffered Cht causing enzyme-mediated cleavage of the peptide and concomitant release of the chromophore for monitoring. To investigate substrate loading and the effects of hydrogel morphology on the system, the concentration of the amino groups (5, 10, 20, and 30 mol%) and the cross-linked density (1, 5, 7, 9 and 12 mol%) were independently varied. Loading-Release Efficiency of the chromogen was shown to exhibit a positive relation to increasing amino groups (AEMA). The release rates demonstrated a negative relation to increasing cross-linked density attributed to decreasing void fractions and increasing tortuosities. The diffusion coefficient of Cht, D0, Cht, was determined to be 6.9 +/- 0.5 x 10-7 cm2 s -1, and the range of Deff of Cht for 1 to 12 mol% TEGDA was determined to 6.9 x10-8 to 0.1 x 10 -8cm2 s-1. We show how these parameters may be optimized and used to achieve programmed release rates in engineered bio-responsive systems. The field of bioresponsive hydrogels is continuing to expand as the need for such materials persists. Future work will enable more control over the loading and release of therapeutic and diagnostic moieties. Continued research regarding in enzymatically actuated hydrogels will involve pre-polymerization loading methodologies; in silico diffusion-reaction multiphysics modeling; enzyme actuated degradation of the polymer; and substation of various mediating enzyme, cleavable peptides, and release molecules.

Driving Chemical Reactions in Plasmonic Nanogaps with Electrohydrodynamic Flow.

PubMed

Thrift, William J; Nguyen, Cuong Q; Darvishzadeh-Varcheie, Mahsa; Zare, Siavash; Sharac, Nicholas; Sanderson, Robert N; Dupper, Torin J; Hochbaum, Allon I; Capolino, Filippo; Abdolhosseini Qomi, Mohammad Javad; Ragan, Regina

2017-11-28

Nanoparticles from colloidal solution-with controlled composition, size, and shape-serve as excellent building blocks for plasmonic devices and metasurfaces. However, understanding hierarchical driving forces affecting the geometry of oligomers and interparticle gap spacings is still needed to fabricate high-density architectures over large areas. Here, electrohydrodynamic (EHD) flow is used as a long-range driving force to enable carbodiimide cross-linking between nanospheres and produces oligomers exhibiting sub-nanometer gap spacing over mm 2 areas. Anhydride linkers between nanospheres are observed via surface-enhanced Raman scattering (SERS) spectroscopy. The anhydride linkers are cleavable via nucleophilic substitution and enable placement of nucleophilic molecules in electromagnetic hotspots. Atomistic simulations elucidate that the transient attractive force provided by EHD flow is needed to provide a sufficient residence time for anhydride cross-linking to overcome slow reaction kinetics. This synergistic analysis shows assembly involves an interplay between long-range driving forces increasing nanoparticle-nanoparticle interactions and probability that ligands are in proximity to overcome activation energy barriers associated with short-range chemical reactions. Absorption spectroscopy and electromagnetic full-wave simulations show that variations in nanogap spacing have a greater influence on optical response than variations in close-packed oligomer geometry. The EHD flow-anhydride cross-linking assembly method enables close-packed oligomers with uniform gap spacings that produce uniform SERS enhancement factors. These results demonstrate the efficacy of colloidal driving forces to selectively enable chemical reactions leading to future assembly platforms for large-area nanodevices.

Functional Differentiation of Bundle Sheath and Mesophyll Maize Chloroplasts Determined by Comparative ProteomicsW⃞

PubMed Central

Majeran, Wojciech; Cai, Yang; Sun, Qi; van Wijk, Klaas J.

2005-01-01

Chloroplasts of maize (Zea mays) leaves differentiate into specific bundle sheath (BS) and mesophyll (M) types to accommodate C4 photosynthesis. Consequences for other plastid functions are not well understood but are addressed here through a quantitative comparative proteome analysis of purified M and BS chloroplast stroma. Three independent techniques were used, including cleavable stable isotope coded affinity tags. Enzymes involved in lipid biosynthesis, nitrogen import, and tetrapyrrole and isoprenoid biosynthesis are preferentially located in the M chloroplasts. By contrast, enzymes involved in starch synthesis and sulfur import preferentially accumulate in BS chloroplasts. The different soluble antioxidative systems, in particular peroxiredoxins, accumulate at higher levels in M chloroplasts. We also observed differential accumulation of proteins involved in expression of plastid-encoded proteins (e.g., EF-Tu, EF-G, and mRNA binding proteins) and thylakoid formation (VIPP1), whereas others were equally distributed. Enzymes related to the C4 shuttle, the carboxylation and regeneration phase of the Calvin cycle, and several regulators (e.g., CP12) distributed as expected. However, enzymes involved in triose phosphate reduction and triose phosphate isomerase are primarily located in the M chloroplasts, indicating that the M-localized triose phosphate shuttle should be viewed as part of the BS-localized Calvin cycle, rather than a parallel pathway. PMID:16243905

Scalable and cleavable polysaccharide nanocarriers for the delivery of chemotherapy drugs.

PubMed

Wang, Hao; Dai, Tingting; Li, Shengli; Zhou, Shuyan; Yuan, Xiaojing; You, Jiayi; Wang, Chenglong; Mukwaya, Vincent; Zhou, Guangdong; Liu, Guojun; Wei, Xiaohui; Dou, Hongjing

2018-05-01

While polysaccharide-based nanocarriers have been recognized for their crucial roles in tumor theranostics, the industrial-scale production of nanotherapeutics still remains a significant challenge. Most current approaches adopt a postpolymerization self-assembly strategy that follows a separate synthetic step and thus suffers from subgram scale yields and a limited range of application. In this study, we demonstrate the kilogram-scale formation of polysaccharide-polyacrylate nanocarriers at concentrations of up to 5 wt% through a one-pot approach - starting from various acrylate monomers and polysaccharides - that combines aspects of hydrophobicity-induced self-assembly with the free radical graft copolymerization of acrylate monomers from polysaccharide backbones into a single process that is thus denoted as a graft copolymerization induced self-assembly. We also demonstrate that this novel approach is applicable to a broad range of polysaccharides and acrylates. Notably, by choosing a crosslinker that bears a disulfide group and two vinyl capping groups to structurally lock the nanocarriers, the products are rendered cleavable in the reducing environments encountered at tumor sites and thus provide ideal candidates for the construction of anticancer nanotherapeutic systems. In vitro and in vivo studies demonstrated that the use of this nanocarrier for the delivery of doxorubicin hydrochloride (DOX) significantly decreased the side effects of DOX and improved the bio-safety of the chemotherapy accordingly. While polysaccharide-based nanocarriers have been recognized for their crucial roles in tumor theranostics, the industrial-scale production of these nanotherapeutics still remains a significant challenge. Most current approaches adopt a post-polymerization self-assembly strategy which that follows a separate synthetic step, and thus suffers from sub-gram scale yields and a limited range of application. In this study, the hydrophobic effect was combined with free radical polymerization to facilitate the graft copolymerization-induced self-assembly (GISA) of acrylate monomers with various hydrophobicities to construct cleavable polysaccharide-polyacrylate nanocarriers at a high efficiency with excellent potential for industrial-scale production. We envision that these nanocarriers will contribute to the development of tumor nanotheranostics that combine the biological functionalities of polysaccharides with the unmatched application-specific flexibility of nanocarriers. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and tandem mass spectrometry to proteins copurifying with T cell lipid rafts.

PubMed

von Haller, Priska D; Yi, Eugene; Donohoe, Samuel; Vaughn, Kelly; Keller, Andrew; Nesvizhskii, Alexey I; Eng, Jimmy; Li, Xiao-jun; Goodlett, David R; Aebersold, Ruedi; Watts, Julian D

2003-07-01

Lipid rafts were prepared according to standard protocols from Jurkat T cells stimulated via T cell receptor/CD28 cross-linking and from control (unstimulated) cells. Co-isolating proteins from the control and stimulated cell preparations were labeled with isotopically normal (d0) and heavy (d8) versions of the same isotope-coded affinity tag (ICAT) reagent, respectively. Samples were combined, proteolyzed, and resultant peptides fractionated via cation exchange chromatography. Cysteine-containing (ICAT-labeled) peptides were recovered via the biotin tag component of the ICAT reagents by avidin-affinity chromatography. On-line micro-capillary liquid chromatography tandem mass spectrometry was performed on both avidin-affinity (ICAT-labeled) and flow-through (unlabeled) fractions. Initial peptide sequence identification was by searching recorded tandem mass spectrometry spectra against a human sequence data base using SEQUEST software. New statistical data modeling algorithms were then applied to the SEQUEST search results. These allowed for discrimination between likely "correct" and "incorrect" peptide assignments, and from these the inferred proteins that they collectively represented, by calculating estimated probabilities that each peptide assignment and subsequent protein identification was a member of the "correct" population. For convenience, the resultant lists of peptide sequences assigned and the proteins to which they corresponded were filtered at an arbitrarily set cut-off of 0.5 (i.e. 50% likely to be "correct") and above and compiled into two separate datasets. In total, these data sets contained 7667 individual peptide identifications, which represented 2669 unique peptide sequences, corresponding to 685 proteins and related protein groups.

Reverse micelle-based water-soluble nanoparticles for simultaneous bioimaging and drug delivery.

PubMed

Chen, Ying; Liu, Yong; Yao, Yongchao; Zhang, Shiyong; Gu, Zhongwei

2017-04-11

With special confined water pools, reverse micelles (RMs) have shown potential for a wide range of applications. However, the inherent water-insolubility of RMs hinders their further application prospects, especially for applications related to biology. We recently reported the first successful transfer of RMs from organic media to an aqueous phase without changing the smart water pools by the hydrolysis of an arm-cleavable interfacial cross-linked reverse micelles. Herein, we employed another elaborate amphiphile 1 to construct new acrylamide-based cross-linked water-soluble nanoparticles (ACW-NPs) under much gentler conditions. The special property of the water pools of the ACW-NPs was confirmed by both the Förster resonance energy transfer (FRET) between 5-((2-aminoethyl)amino)naphthalene-1-sulfonic acid (1,5-EDANS) and benzoic acid, 4-[2-[4-(dimethylamino)phenyl]diazenyl] (DABCYL) and satisfactory colloidal stability in 10% fetal bovine serum. Importantly, featured by the gentle synthetic strategy, confined water pool, and carboxylic acid-functionalized surface, the new ACW-NPs are well suitable for biological applications. As an example, the fluorescent reagent 8-hydroxy-1,3,6-pyrenetrisulfonic acid trisodium salt (HPTS) was encapsulated in the core and simultaneously, the anticancer drug gemcitabine (Gem) was covalently conjugated onto the surface exterior. As expected, the resulting multifunctional ACW-NPs@HPTS@Gem exhibits a high imaging effect and anticancer activity for non-small lung cancer cells.

Synthesis and evaluations of an acid-cleavable, fluorescently labeled nucleotide as a reversible terminator for DNA sequencing.

PubMed

Tan, Lianjiang; Liu, Yazhi; Li, Xiaowei; Wu, Xin-Yan; Gong, Bing; Shen, Yu-Mei; Shao, Zhifeng

2016-02-11

An acid-cleavable linker based on a dimethylketal moiety was synthesized and used to connect a nucleotide with a fluorophore to produce a 3'-OH unblocked nucleotide analogue as an excellent reversible terminator for DNA sequencing by synthesis.

Functional study of miR-27a in human hepatic stellate cells by proteomic analysis: comprehensive view and a role in myogenic tans-differentiation.

PubMed

Ji, Yuhua; Zhang, Jinsheng; Wang, Wenwen; Ji, Juling

2014-01-01

We previous reported that miR-27a regulates lipid metabolism and cell proliferation during hepatic stellate cells (HSCs) activation. To further explore the biological function and underlying mechanisms of miR-27a in HSCs, global protein expression affected by overexpression of miR-27a in HSCs was analyzed by a cleavable isotope-coded affinity tags (cICAT) based comparative proteomic approach. In the present study, 1267 non-redundant proteins were identified with unique accession numbers (score ≥1.3, i.e. confidence ≥95%), among which 1171 were quantified and 149 proteins (12.72%) were differentially expressed with a differential expression ratio of 1.5. We found that up-regulated proteins by miR-27a mainly participate in cell proliferation and myogenesis, while down-regulated proteins were the key enzymes involved in de novo lipid synthesis. The expression of a group of six miR-27a regulated proteins was validated and the function of one miR-27a regulated protein was further validated. The results not only delineated the underlying mechanism of miR-27a in modulating fat metabolism and cell proliferation, but also revealed a novel role of miR-27a in promoting myogenic tans-differentiation during HSCs activation. This study also exemplified proteomics strategy as a powerful tool for the functional study of miRNA.

New thiol-responsive mono-cleavable block copolymer micelles labeled with single disulfides.

PubMed

Sourkohi, Behnoush Khorsand; Schmidt, Rolf; Oh, Jung Kwon

2011-10-18

Thiol-responsive symmetric triblock copolymers having single disulfide linkages in the middle blocks (called mono-cleavable block copolymers, ss-ABP(2)) were synthesized by atom transfer radical polymerization in the presence of a disulfide-labeled difunctional Br-initiator. These brush-like triblock copolymers consist of a hydrophobic polyacrylate block having pendent oligo(propylene oxide) and a hydrophilic polymethacrylate block having pendent oligo(ethylene oxide). Gel permeation chromatography and (1)H NMR results confirmed the synthesis of well-defined mono-cleavable block copolymers and revealed that polymerizations were well controlled. Because of amphiphilic nature, these copolymers self-assembled to form colloidally stable micelles above critical micellar concentration of 0.032 mg · mL(-1). In response to reductive reactions, disulfides in thiol-responsive micelles were cleaved. Atomic force microscopy and dynamic light scattering analysis suggested that the cleavage of disulfides caused dissociation of micelles to smaller-sized assembled structures in water. Moreover, in a biomedical perspective, the mono-cleavable block copolymer micelles are not cytotoxic and thus biocompatible. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Smart nanogels at the air/water interface: structural studies by neutron reflectivity

NASA Astrophysics Data System (ADS)

Zielińska, Katarzyna; Sun, Huihui; Campbell, Richard A.; Zarbakhsh, Ali; Resmini, Marina

2016-02-01

The development of effective transdermal drug delivery systems based on nanosized polymers requires a better understanding of the behaviour of such nanomaterials at interfaces. N-Isopropylacrylamide-based nanogels synthesized with different percentages of N,N'-methylenebisacrylamide as cross-linker, ranging from 10 to 30%, were characterized at physiological temperature at the air/water interface, using neutron reflectivity (NR), with isotopic contrast variation, and surface tension measurements; this allowed us to resolve the adsorbed amount and the volume fraction of nanogels at the interface. A large conformational change for the nanogels results in strong deformations at the interface. As the percentage of cross-linker incorporated in the nanogels becomes higher, more rigid matrices are obtained, although less deformed, and the amount of adsorbed nanogels is increased. The data provide the first experimental evidence of structural changes of nanogels as a function of the degree of cross-linking at the air/water interface.The development of effective transdermal drug delivery systems based on nanosized polymers requires a better understanding of the behaviour of such nanomaterials at interfaces. N-Isopropylacrylamide-based nanogels synthesized with different percentages of N,N'-methylenebisacrylamide as cross-linker, ranging from 10 to 30%, were characterized at physiological temperature at the air/water interface, using neutron reflectivity (NR), with isotopic contrast variation, and surface tension measurements; this allowed us to resolve the adsorbed amount and the volume fraction of nanogels at the interface. A large conformational change for the nanogels results in strong deformations at the interface. As the percentage of cross-linker incorporated in the nanogels becomes higher, more rigid matrices are obtained, although less deformed, and the amount of adsorbed nanogels is increased. The data provide the first experimental evidence of structural changes of nanogels as a function of the degree of cross-linking at the air/water interface. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr07538f

pH and temperature dual-sensitive liposome gel based on novel cleavable mPEG-Hz-CHEMS polymeric vaginal delivery system

PubMed Central

Chen, Daquan; Sun, Kaoxiang; Mu, Hongjie; Tang, Mingtan; Liang, Rongcai; Wang, Aiping; Zhou, Shasha; Sun, Haijun; Zhao, Feng; Yao, Jianwen; Liu, Wanhui

2012-01-01

Background In this study, a pH and temperature dual-sensitive liposome gel based on a novel cleavable hydrazone-based pH-sensitive methoxy polyethylene glycol 2000-hydrazone-cholesteryl hemisuccinate (mPEG-Hz-CHEMS) polymer was used for vaginal administration. Methods The pH-sensitive, cleavable mPEG-Hz-CHEMS was designed as a modified pH-sensitive liposome that would selectively degrade under locally acidic vaginal conditions. The novel pH-sensitive liposome was engineered to form a thermogel at body temperature and to degrade in an acidic environment. Results A dual-sensitive liposome gel with a high encapsulation efficiency of arctigenin was formed and improved the solubility of arctigenin characterized by Fourier transform infrared spectroscopy and differential scanning calorimetry. The dual-sensitive liposome gel with a sol-gel transition at body temperature was degraded in a pH-dependent manner, and was stable for a long period of time at neutral and basic pH, but cleavable under acidic conditions (pH 5.0). Arctigenin encapsulated in a dual-sensitive liposome gel was more stable and less toxic than arctigenin loaded into pH-sensitive liposomes. In vitro drug release results indicated that dual-sensitive liposome gels showed constant release of arctigenin over 3 days, but showed sustained release of arctigenin in buffers at pH 7.4 and pH 9.0. Conclusion This research has shed some light on a pH and temperature dual-sensitive liposome gel using a cleavable mPEG-Hz-CHEMS polymer for vaginal delivery. PMID:22679372

Elucidation of the Cross-Link Structure of Nadic-End-Capped Polyimides Using NMR of C-13-Labeled Polymers

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B.; Johnston, J. Christopher; Cavano, Paul J.

1997-01-01

Solid NMR of C-13 isotope-labeled samples of PMR-15 was used to follow the cross-linking reaction of the nadic end cap. Some samples were labeled on one of the carbon atoms of the nadic end cap, and others on the methylene carbon atom of the methylenedianiline portion of the polymer. NMR spectra were run on these samples both before and after cross-linking. In this way, direct evidence of the major products of cross-linking under normal cure conditions is provided. The majority (approximately 85%) of the cross-linking derives from olefin polymerization through the double bond of the end cap. Approximately 15% of the products could come from a pathway involving a retro-Diels-Alder reaction. However, all of the products could be explained by a biradical intermediate without a retro-Diels-Alder reaction. Evidence is also presented that the methylene moiety in the methylenedianiline part of the polymer chain also participates in the cross-linking, albeit to a small extent, by a radical transfer reaction. Different cure conditions (higher temperatures, longer times) could change the relative distribution of the products.

Trifunctional cross-linker for mapping protein-protein interaction networks and comparing protein conformational states

PubMed Central

Tan, Dan; Li, Qiang; Zhang, Mei-Jun; Liu, Chao; Ma, Chengying; Zhang, Pan; Ding, Yue-He; Fan, Sheng-Bo; Tao, Li; Yang, Bing; Li, Xiangke; Ma, Shoucai; Liu, Junjie; Feng, Boya; Liu, Xiaohui; Wang, Hong-Wei; He, Si-Min; Gao, Ning; Ye, Keqiong; Dong, Meng-Qiu; Lei, Xiaoguang

2016-01-01

To improve chemical cross-linking of proteins coupled with mass spectrometry (CXMS), we developed a lysine-targeted enrichable cross-linker containing a biotin tag for affinity purification, a chemical cleavage site to separate cross-linked peptides away from biotin after enrichment, and a spacer arm that can be labeled with stable isotopes for quantitation. By locating the flexible proteins on the surface of 70S ribosome, we show that this trifunctional cross-linker is effective at attaining structural information not easily attainable by crystallography and electron microscopy. From a crude Rrp46 immunoprecipitate, it helped identify two direct binding partners of Rrp46 and 15 protein-protein interactions (PPIs) among the co-immunoprecipitated exosome subunits. Applying it to E. coli and C. elegans lysates, we identified 3130 and 893 inter-linked lysine pairs, representing 677 and 121 PPIs. Using a quantitative CXMS workflow we demonstrate that it can reveal changes in the reactivity of lysine residues due to protein-nucleic acid interaction. DOI: http://dx.doi.org/10.7554/eLife.12509.001 PMID:26952210

An atomistic model for cross-linked HNBR elastomers used in seals

NASA Astrophysics Data System (ADS)

Molinari, Nicola; Sutton, Adrian; Stevens, John; Mostofi, Arash

2015-03-01

Hydrogenated nitrile butadiene rubber (HNBR) is one of the most common elastomeric materials used for seals in the oil and gas industry. These seals sometimes suffer ``explosive decompression,'' a costly problem in which gases permeate a seal at the elevated temperatures and pressures pertaining in oil and gas wells, leading to rupture when the seal is brought back to the surface. The experimental evidence that HNBR and its unsaturated parent NBR have markedly different swelling properties suggests that cross-linking may occur during hydrogenation of NBR to produce HNBR. We have developed a code compatible with the LAMMPS molecular dynamics package to generate fully atomistic HNBR configurations by hydrogenating initial NBR structures. This can be done with any desired degree of cross-linking. The code uses a model of atomic interactions based on the OPLS-AA force-field. We present calculations of the dependence of a number of bulk properties on the degree of cross-linking. Using our atomistic representations of HNBR and NBR, we hope to develop a better molecular understanding of the mechanisms that result in explosive decompression.

Jwalk and MNXL Web Server: Model Validation using Restraints from Crosslinking Mass Spectrometry.

PubMed

Bullock, J M A; Thalassinos, K; Topf, M

2018-05-07

Crosslinking Mass Spectrometry generates restraints that can be used to model proteins and protein complexes. Previously, we have developed two methods, to help users achieve better modelling performance from their crosslinking restraints: Jwalk, to estimate solvent accessible distances between crosslinked residues and MNXL, to assess the quality of the models based on these distances. Here we present the Jwalk and MNXL webservers, which streamline the process of validating monomeric protein models using restraints from crosslinks. We demonstrate this by using the MNXL server to filter models made of varying quality, selecting the most native-like. The webserver and source code are freely available from jwalk.ismb.lon.ac.uk and mnxl.ismb.lon.ac.uk. m.topf@cryst.bbk.ac.uk, j.bullock@cryst.bbk.ac.uk.

A Catalytic Asymmetric Synthesis of Polysubstituted Piperidines Using a Rhodium (I) Catalyzed [2+2+2] Cycloaddition Employing a Cleavable Tether

PubMed Central

Martin, Timothy J.; Rovis, Tomislav

2013-01-01

An enantioselective rhodium (I) catalyzed [2+2+2] cycloaddition with a cleavable tether has been developed. The reaction proceeds with a variety of alkyne substrates in good yield and high enantioselectivity. Upon reduction of the vinylogous amide in high diastereoselectivity (>19:1) and cleavage of the tether, N-methylpiperidine products with functional group handles can be accessed. PMID:23606664

Metal Ion Sensor with Catalytic DNA in a Nanofluidic Intelligent Processor

DTIC Science & Technology

2011-12-01

attributed to decreased diffusion and less active DNAzyme complex because of pore constraints. Uncleavable Alexa546 intensity is shown in gray ...is shown in gray , cleavable fluorescein in green, and the ratio of Fl/Alexa in red. Error bars represent one standard deviation of four independent...higher concentrations inhibiting cleaved fragment release. Uncleavable Alexa 546 intensity is shown in gray , cleavable fluorescein in green, and the

Development of a Hypersensitive Periodate-Cleavable Amino Acid that is Methionine- and Disulfide-Compatible and its Application in MHC Exchange Reagents for T Cell Characterisation

PubMed Central

Amore, Alessia; Wals, Kim; Koekoek, Evelyn; Hoppes, Rieuwert; Toebes, Mireille; Schumacher, Ton N M; Rodenko, Boris; Ovaa, Huib

2013-01-01

Incorporation of cleavable linkers into peptides and proteins is of particular value in the study of biological processes. Here we describe the synthesis of a cleavable linker that is hypersensitive to oxidative cleavage as the result of the periodate reactivity of a vicinal amino alcohol moiety. Two strategies directed towards the synthesis of a building block suitable for solid-phase peptide synthesis were developed: a chemoenzymatic route, involving l-threonine aldolase, and an enantioselective chemical route; these led to α,γ-diamino-β-hydroxybutanoic acids in diastereoisomerically mixed and enantiopure forms, respectively. Incorporation of the 1,2-amino alcohol linker into the backbone of a peptide generated a conditional peptide that was rapidly cleaved at very low concentrations of sodium periodate. This cleavable peptide ligand was applied in the generation of MHC exchange reagents for the detection of antigen-specific T cells in peripheral blood cells. The extremely low concentration of periodate required to trigger MHC peptide exchange allowed the co-oxidation of methionine and disulfide residues to be avoided. Conditional MHC reagents hypersensitive to periodate can now be applied without limitations when UV irradiation is undesired or less practical. PMID:23280887

Improvements in the MGA Code Provide Flexibility and Better Error Analysis

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

Ruhter, W D; Kerr, J

2005-05-26

The Multi-Group Analysis (MGA) code is widely used to determine nondestructively the relative isotopic abundances of plutonium by gamma-ray spectrometry. MGA users have expressed concern about the lack of flexibility and transparency in the code. Users often have to ask the code developers for modifications to the code to accommodate new measurement situations, such as additional peaks being present in the plutonium spectrum or expected peaks being absent. We are testing several new improvements to a prototype, general gamma-ray isotopic analysis tool with the intent of either revising or replacing the MGA code. These improvements will give the user themore » ability to modify, add, or delete the gamma- and x-ray energies and branching intensities used by the code in determining a more precise gain and in the determination of the relative detection efficiency. We have also fully integrated the determination of the relative isotopic abundances with the determination of the relative detection efficiency to provide a more accurate determination of the errors in the relative isotopic abundances. We provide details in this paper on these improvements and a comparison of results obtained with current versions of the MGA code.« less

Reactive transport modeling of stable carbon isotope fractionation in a multi-phase multi-component system during carbon sequestration

DOE PAGES

Zhang, Shuo; DePaolo, Donald J.; Zheng, Liange; ...

2014-12-31

Carbon stable isotopes can be used in characterization and monitoring of CO 2 sequestration sites to track the migration of the CO 2 plume and identify leakage sources, and to evaluate the chemical reactions that take place in the CO 2-water-rock system. However, there are few tools available to incorporate stable isotope information into flow and transport codes used for CO 2 sequestration problems. We present a numerical tool for modeling the transport of stable carbon isotopes in multiphase reactive systems relevant to geologic carbon sequestration. The code is an extension of the reactive transport code TOUGHREACT. The transport modulemore » of TOUGHREACT was modified to include separate isotopic species of CO 2 gas and dissolved inorganic carbon (CO 2, CO 3 2-, HCO 3 -,…). Any process of transport or reaction influencing a given carbon species also influences its isotopic ratio. Isotopic fractionation is thus fully integrated within the dynamic system. The chemical module and database have been expanded to include isotopic exchange and fractionation between the carbon species in both gas and aqueous phases. The performance of the code is verified by modeling ideal systems and comparing with theoretical results. Efforts are also made to fit field data from the Pembina CO 2 injection project in Canada. We show that the exchange of carbon isotopes between dissolved and gaseous carbon species combined with fluid flow and transport, produce isotopic effects that are significantly different from simple two-component mixing. These effects are important for understanding the isotopic variations observed in field demonstrations.« less

Evaluation of the accuracy of mono-energetic electron and beta-emitting isotope dose-point kernels using particle and heavy ion transport code system: PHITS.

PubMed

Shiiba, Takuro; Kuga, Naoya; Kuroiwa, Yasuyoshi; Sato, Tatsuhiko

2017-10-01

We assessed the accuracy of mono-energetic electron and beta-emitting isotope dose-point kernels (DPKs) calculated using the particle and heavy ion transport code system (PHITS) for patient-specific dosimetry in targeted radionuclide treatment (TRT) and compared our data with published data. All mono-energetic and beta-emitting isotope DPKs calculated using PHITS, both in water and compact bone, were in good agreement with those in literature using other MC codes. PHITS provided reliable mono-energetic electron and beta-emitting isotope scaled DPKs for patient-specific dosimetry. Copyright © 2017 Elsevier Ltd. All rights reserved.

Poly(ethylene glycol) (PEG)-lactic acid nanocarrier-based degradable hydrogels for restoring the vaginal microenvironment

PubMed Central

Rajan, Sujata Sundara; Turovskiy, Yevgeniy; Singh, Yashveer; Chikindas, Michael L.; Sinko, Patrick J.

2014-01-01

Women with bacterial vaginosis (BV) display reduced vaginal acidity, which make them susceptible to associated infections such as HIV. In the current study, poly(ethylene glycol) (PEG) nanocarrier-based degradable hydrogels were developed for the controlled release of lactic acid in the vagina of BV-infected women. PEG-lactic acid (PEG-LA) nanocarriers were prepared by covalently attaching lactic acid to 8-arm PEG-SH via cleavable thioester bonds. PEG-LA nanocarriers with 4 copies of lactic acid per molecule provided controlled release of lactic acid with a maximum release of 23% and 47% bound lactic acid in phosphate buffered saline (PBS, pH 7.4) and acetate buffer (AB, pH 4.3), respectively. The PEG nanocarrier-based hydrogels were formed by cross-linking the PEG-LA nanocarriers with 4-arm PEG-NHS via degradable thioester bonds. The nanocarrier-based hydrogels formed within 20 min under ambient conditions and exhibited an elastic modulus that was 100-fold higher than the viscous modulus. The nanocarrier-based degradable hydrogels provided controlled release of lactic acid for several hours; however, a maximum release of only 10%–14% bound lactic acid was observed possibly due to steric hindrance of the polymer chains in the cross-linked hydrogel. In contrast, hydrogels with passively entrapped lactic acid showed burst release with complete release within 30 min. Lactic acid showed antimicrobial activity against the primary BV pathogen Gardnerella vaginalis with a minimum inhibitory concentration (MIC) of 3.6 mg/ml. In addition, the hydrogels with passively entrapped lactic acid showed retained antimicrobial activity with complete inhibition G. vaginalis growth within 48 h. The results of the current study collectively demonstrate the potential of PEG nanocarrier-based hydrogels for vaginal administration of lactic acid for preventing and treating BV. PMID:25223229

Fabrication of antibody-loaded microgels using microfluidics and thiol-ene photoclick chemistry.

PubMed

Gregoritza, Manuel; Abstiens, Kathrin; Graf, Moritz; Goepferich, Achim M

2018-06-01

Reducing burst effects, providing controlled release, and safeguarding biologics against degradation are a few of several highly attractive applications for microgels in the field of controlled release. However, the incorporation of proteins into microgels without impairing stability is highly challenging. In this proof of concept study, the combination of microfluidics and thiol-ene photoclick chemistry was evaluated for the fabrication of antibody-loaded microgels with narrow size distribution. Norbornene-modified eight-armed poly(ethylene glycol) with an average molecular mass of 10,000 Da, 20,000 Da, or 40,000 Da were prepared as macromonomers for microgel formation. For functionalization, either hydrolytically cleavable ester or stable amide bonds were used. A microfluidic system was employed to generate precursor solution droplets containing macromonomers, the cross-linker dithiothreitol and the initiator Eosin-Y. Irradiation with visible light was used to trigger thiol-ene reactions which covalently cross-linked the droplets. For all bond-types, molecular masses, and concentrations gelation was very rapid (<20 s) and a plateau for the complex shear modulus was reached after only 5 min. The generated microgels had a rod-like shape and did not show considerable cellular toxicity. Stress conditions during the fabrication process were simulated and it could be shown that fabrication did not impair the activity of the model proteins lysozyme and bevacizumab. It was confirmed that the average hydrogel network mesh size was similar or smaller than the hydrodynamic diameter of bevacizumab which is a crucial factor for restricting diffusion and delaying release. Finally, microgels were loaded with bevacizumab and a sustained release over a period of 30 ± 4 and 47 ± 7 days could be achieved in vitro. Copyright © 2018 Elsevier B.V. All rights reserved.

Shielding from space radiations

NASA Technical Reports Server (NTRS)

Chang, C. Ken; Badavi, Forooz F.; Tripathi, Ram K.

1993-01-01

This Progress Report covering the period of December 1, 1992 to June 1, 1993 presents the development of an analytical solution to the heavy ion transport equation in terms of Green's function formalism. The mathematical development results are recasted into a highly efficient computer code for space applications. The efficiency of this algorithm is accomplished by a nonperturbative technique of extending the Green's function over the solution domain. The code may also be applied to accelerator boundary conditions to allow code validation in laboratory experiments. Results from the isotopic version of the code with 59 isotopes present for a single layer target material, for the case of an iron beam projectile at 600 MeV/nucleon in water is presented. A listing of the single layer isotopic version of the code is included.

Highly ordered gold nanotubes using thiols at a cleavable block copolymer interface.

PubMed

Ryu, Ja-Hyoung; Park, Soojin; Kim, Bokyung; Klaikherd, Akamol; Russell, Thomas P; Thayumanavan, S

2009-07-29

We have prepared functionalized nanoporous thin films from a polystyrene-block-polyethylene oxide block copolymer, which was made cleavable due to the intervening disulfide bond. The cleavage reaction of the disulfide bond leaves behind free thiol groups inside the nanopores of polystyrene thin film. This nanoporous thin film can be used as a template for generating gold nanoring structures. This strategy can provide a facile method to form a highly ordered array of biopolymer or metal-polymer composite structures.

Effect of Isotope Mass in Simulations of JET H-mode Discharges

NASA Astrophysics Data System (ADS)

Snyder, S. E.; Onjun, T.; Kritz, A. H.; Bateman, G.; Parail, V.

2004-11-01

In JET type-I ELMy H-mode discharges, it is found that the height of the pressure pedestal increases and the frequency of the ELMs decreases with increasing isotope mass. These experimentally observed trends are obtained in these simulations only if the pedestal width increases with isotope mass. Simulations are carried out using the JETTO integrated modeling code with a dynamic model for the H-mode pedestal and the ELMs.(T. Onjun et al, Phys. Plasmas 11 (2004) 1469 and 3006.) The HELENA and MISHKA stability codes are applied to calibrate the stability criteria used to trigger ELM crashes in the JETTO code and to explore possible access to second stability in the pedestal. In the simulations, transport in the pedestal is given by the ion thermal neoclassical diffusivity, which increases with isotope mass. Consequently, as the isotope mass is increased, the pressure gradient and the bootstrap current in the pedestal rebuild more slowly after each ELM crash. Several models are explored in which the pedestal width increases with isotope mass.

EarthCollab, building geoscience-centric implementations of the VIVO semantic software suite

NASA Astrophysics Data System (ADS)

Rowan, L. R.; Gross, M. B.; Mayernik, M. S.; Daniels, M. D.; Krafft, D. B.; Kahn, H. J.; Allison, J.; Snyder, C. B.; Johns, E. M.; Stott, D.

2017-12-01

EarthCollab, an EarthCube Building Block project, is extending an existing open-source semantic web application, VIVO, to enable the exchange of information about scientific researchers and resources across institutions. EarthCollab is a collaboration between UNAVCO, a geodetic facility and consortium that supports diverse research projects informed by geodesy, The Bering Sea Project, an interdisciplinary field program whose data archive is hosted by NCAR's Earth Observing Laboratory, and Cornell University. VIVO has been implemented by more than 100 universities and research institutions to highlight research and institutional achievements. This presentation will discuss benefits and drawbacks of working with and extending open source software. Some extensions include plotting georeferenced objects on a map, a mobile-friendly theme, integration of faceting via Elasticsearch, extending the VIVO ontology to capture geoscience-centric objects and relationships, and the ability to cross-link between VIVO instances. Most implementations of VIVO gather information about a single organization. The EarthCollab project created VIVO extensions to enable cross-linking of VIVO instances to reduce the amount of duplicate information about the same people and scientific resources and to enable dynamic linking of related information across VIVO installations. As the list of customizations grows, so does the effort required to maintain compatibility between the EarthCollab forks and the main VIVO code. For example, dozens of libraries and dependencies were updated prior to the VIVO v1.10 release, which introduced conflicts in the EarthCollab cross-linking code. The cross-linking code has been developed to enable sharing of data across different versions of VIVO, however, using a JSON output schema standardized across versions. We will outline lessons learned in working with VIVO and its open source dependencies, which include Jena, Solr, Freemarker, and jQuery and discuss future work by EarthCollab, which includes refining the cross-linking VIVO capabilities by continued integration of persistent and unique identifiers to enable automated lookup and matching across institutional VIVOs.

Development of Bioorthogonally Degradable Linkers and Polymers Using alpha-Azidoethers

NASA Astrophysics Data System (ADS)

Rajagopalan, Chandrasekhar Ramasubramanian

Degradable polymers have gained a lot of attention in recent years for applications in biotechnology and medicine. External control over polymer degradation can be obtained by incorporating functional groups that cleave in the presence of triggers that would normally be absent in biological environments, i.e. are bioorthogonal. This thesis explores the use of chemically cleavable alpha-azidoethers as a new method to obtain external control over the degradation behavior of polymers. My first goal is to illustrate the potential of alpha-azidoethers toward developing cleavable linkers. We have studied the relationship between alpha-azidoether structure and hydrolytic stability, to prepare linkers that withstand background hydrolytic cleavage until they are exposed to the cleaving trigger. The cleavage kinetics of the alpha-azidoether functional group was quantified. In addition to the conventionally used tris(2-carboxyethyl)phosphine (TCEP), dihydrolipoic acid (DHLA), a previously unexplored, biocompatible reducing agent, was also evaluated as a cleaving trigger. Based on these results, we have proposed design rules for utilizing alpha-azidoethers as cleavable linkers in applications that require bioorthogonal control over linker cleavage. Secondly, the alpha-azidoether cleavable linker chemistry was implemented into the development of polymeric materials. Two different types of polymers were developed. Polyamides incorporating alpha-azidoethers along the backbone were synthesized, and their physical properties and chemically triggered degradation behavior were characterized. The degradation timescale of these polymers can be tuned simply by manipulating the concentration of the externally applied chemical trigger. The alpha-azidoether functional group was then utilized to develop a unique triggered-release polymeric adhesive for potential applications in dental adhesive formulations. A methacrylamide-phosphonate adhesive monomer incorporating an alpha-azidoether group was designed and synthesized. The monomer was polymerized to adhere polymer-composite substrates. Adhesion strength was quantified, and on-demand release of bonded substrates was demonstrated using DHLA as a trigger. The results presented here shed some light on the scope, advantages and drawbacks of utilizing alpha-azidoethers to develop new types of cleavable linkers and degradable polymers. In principle, the triggered degradation method described here could be incorporated into polymers with different chemical structures, to develop a variety of materials that offer an external control over degradation.

Stable isotope reactive transport modeling in water-rock interactions during CO2 injection

NASA Astrophysics Data System (ADS)

Hidalgo, Juan J.; Lagneau, Vincent; Agrinier, Pierre

2010-05-01

Stable isotopes can be of great usefulness in the characterization and monitoring of CO2 sequestration sites. Stable isotopes can be used to track the migration of the CO2 plume and identify leakage sources. Moreover, they provide unique information about the chemical reactions that take place on the CO2-water-rock system. However, there is a lack of appropriate tools that help modelers to incorporate stable isotope information into the flow and transport models used in CO2 sequestration problems. In this work, we present a numerical tool for modeling the transport of stable isotopes in groundwater reactive systems. The code is an extension of the groundwater single-phase flow and reactive transport code HYTEC [2]. HYTEC's transport module was modified to include element isotopes as separate species. This way, it is able to track isotope composition of the system by computing the mixing between the background water and the injected solution accounting for the dependency of diffusion on the isotope mass. The chemical module and database have been expanded to included isotopic exchange with minerals and the isotope fractionation associated with chemical reactions and mineral dissolution or precipitation. The performance of the code is illustrated through a series of column synthetic models. The code is also used to model the aqueous phase CO2 injection test carried out at the Lamont-Doherty Earth Observatory site (Palisades, New York, USA) [1]. References [1] N. Assayag, J. Matter, M. Ader, D. Goldberg, and P. Agrinier. Water-rock interactions during a CO2 injection field-test: Implications on host rock dissolution and alteration effects. Chemical Geology, 265(1-2):227-235, July 2009. [2] Jan van der Lee, Laurent De Windt, Vincent Lagneau, and Patrick Goblet. Module-oriented modeling of reactive transport with HYTEC. Computers & Geosciences, 29(3):265-275, April 2003.

Increased brain uptake of targeted nanoparticles by adding an acid-cleavable linkage between transferrin and the nanoparticle core.

PubMed

Clark, Andrew J; Davis, Mark E

2015-10-06

Most therapeutic agents are excluded from entering the central nervous system by the blood-brain barrier (BBB). Receptor mediated transcytosis (RMT) is a common mechanism used by proteins, including transferrin (Tf), to traverse the BBB. Here, we prepared Tf-containing, 80-nm gold nanoparticles with an acid-cleavable linkage between the Tf and the nanoparticle core to facilitate nanoparticle RMT across the BBB. These nanoparticles are designed to bind to Tf receptors (TfRs) with high avidity on the blood side of the BBB, but separate from their multidentate Tf-TfR interactions upon acidification during the transcytosis process to allow release of the nanoparticle into the brain. These targeted nanoparticles show increased ability to cross an in vitro model of the BBB and, most important, enter the brain parenchyma of mice in greater amounts in vivo after systemic administration compared with similar high-avidity nanoparticles containing noncleavable Tf. In addition, we investigated this design with nanoparticles containing high-affinity antibodies (Abs) to TfR. With the Abs, the addition of the acid-cleavable linkage provided no improvement to in vivo brain uptake for Ab-containing nanoparticles, and overall brain uptake was decreased for all Ab-containing nanoparticles compared with Tf-containing ones. These results are consistent with recent reports of high-affinity anti-TfR Abs trafficking to the lysosome within BBB endothelium. In contrast, high-avidity, Tf-containing nanoparticles with the acid-cleavable linkage avoid major endothelium retention by shedding surface Tf during their transcytosis.

Turning gene function ON and OFF using sense and antisense photo-morpholinos in zebrafish

PubMed Central

Tallafuss, Alexandra; Gibson, Dan; Morcos, Paul; Li, Yongfu; Seredick, Steve; Eisen, Judith; Washbourne, Philip

2012-01-01

To understand the molecular mechanisms of development it is essential to be able to turn genes on and off at will and in a spatially restricted fashion. Morpholino oligonucleotides (MOs) are very common tools used in several model organisms with which it is possible to block gene expression. Recently developed photo-activated MOs allow control over the onset of MO activity. However, deactivation of photo-cleavable MO activity has remained elusive. Here, we describe photo-cleavable MOs with which it is possible to activate or de-activate MO function by UV exposure in a temporal and spatial manner. We show, using several different genes as examples, that it is possible to turn gene expression on or off both in the entire zebrafish embryo and in single cells. We use these tools to demonstrate the sufficiency of no tail expression as late as tailbud stage to drive medial precursor cells towards the notochord cell fate. As a broader approach for the use of photo-cleavable MOs, we show temporal control over gal4 function, which has many potential applications in multiple transgenic lines. We demonstrate temporal manipulation of Gal4 transgene expression in only primary motoneurons and not secondary motoneurons, heretofore impossible with conventional transgenic approaches. In another example, we follow and analyze neural crest cells that regained sox10 function after deactivation of a photo-cleavable sox10-MO at different time points. Our results suggest that sox10 function might not be critical during neural crest formation. PMID:22492359

Water Isotopes in the GISS GCM: History, Applications and Potential

NASA Astrophysics Data System (ADS)

Schmidt, G. A.; LeGrande, A. N.; Field, R. D.; Nusbaumer, J. M.

2017-12-01

Water isotopes have been incorporated in the GISS GCMs since the pioneering work of Jean Jouzel in the 1980s. Since 2005, this functionality has been maintained within the master branch of the development code and has been usable (and used) in all subsequent versions. This has allowed a wide variety of applications, across multiple time-scales and interests, to be tackled coherently. Water isotope tracers have been used to debug the atmospheric model code, tune parameterisations of moist processes, assess the isotopic fingerprints of multiple climate drivers, produce forward models for remotely sensed isotope products, and validate paleo-climate interpretations from the last millennium to the Eocene. We will present an overview of recent results involving isotope tracers, including improvements in models for the isotopic fractionation processes themselves, and demonstrate the potential for using these tracers and models more systematically in paleo-climate reconstructions and investigations of the modern hydrological cycle.

Design of Enzymatically Cleavable Prodrugs of a Potent Platinum-Containing Anticancer Agent

PubMed Central

Ding, Song; Pickard, Amanda J.; Kucera, Gregory L.

2014-01-01

Using a versatile synthetic approach, a new class of potential ester prodrugs of highly potent, but systemically too toxic, platinum–acridine anticancer agents was generated. The new hybrids contain a hydroxyl group, which has been masked with a cleavable lipophilic acyl moiety. Both butanoic (butyric) and bulkier 2-propanepentanoic (valproic) esters were introduced. The goals of this design were to improve the drug-like properties (e.g., logD) and to reduce the systemic toxicity of the pharmacophore. Two distinct pathways by which the target compounds undergo effective ester hydrolysis, the proposed activating step, have been confirmed: platinum-assisted, self-immolative ester cleavage in a low-chloride environment (LC-ESMS, NMR spectroscopy) and enzymatic cleavage by human carboxylesterase-2 (hCES-2) (LC-ESMS). The valproic acid ester derivatives are the first example of a metal-containing agent cleavable by the pro-drug-converting enzyme. They show excellent chemical stability and reduced systemic toxicity. Preliminary results from screening in lung adenocarcinoma cell lines (A549, NCI-H1435) suggest that the mechanism of the valproic esters may involve intracellular deesterification. PMID:25303639

Comparison of deterministic and stochastic approaches for isotopic concentration and decay heat uncertainty quantification on elementary fission pulse

NASA Astrophysics Data System (ADS)

Lahaye, S.; Huynh, T. D.; Tsilanizara, A.

2016-03-01

Uncertainty quantification of interest outputs in nuclear fuel cycle is an important issue for nuclear safety, from nuclear facilities to long term deposits. Most of those outputs are functions of the isotopic vector density which is estimated by fuel cycle codes, such as DARWIN/PEPIN2, MENDEL, ORIGEN or FISPACT. CEA code systems DARWIN/PEPIN2 and MENDEL propagate by two different methods the uncertainty from nuclear data inputs to isotopic concentrations and decay heat. This paper shows comparisons between those two codes on a Uranium-235 thermal fission pulse. Effects of nuclear data evaluation's choice (ENDF/B-VII.1, JEFF-3.1.1 and JENDL-2011) is inspected in this paper. All results show good agreement between both codes and methods, ensuring the reliability of both approaches for a given evaluation.

Determination of the NPP Kr\\vsko spent fuel decay heat

NASA Astrophysics Data System (ADS)

Kromar, Marjan; Kurinčič, Bojan

2017-07-01

Nuclear fuel is designed to support fission process in a reactor core. Some of the isotopes, formed during the fission, decay and produce decay heat and radiation. Accurate knowledge of the nuclide inventory producing decay heat is important after reactor shut down, during the fuel storage and subsequent reprocessing or disposal. In this paper possibility to calculate the fuel isotopic composition and determination of the fuel decay heat with the Serpent code is investigated. Serpent is a well-known Monte Carlo code used primarily for the calculation of the neutron transport in a reactor. It has been validated for the burn-up calculations. In the calculation of the fuel decay heat different set of isotopes is important than in the neutron transport case. Comparison with the Origen code is performed to verify that the Serpent is taking into account all isotopes important to assess the fuel decay heat. After the code validation, a sensitivity study is carried out. Influence of several factors such as enrichment, fuel temperature, moderator temperature (density), soluble boron concentration, average power, burnable absorbers, and burnup is analyzed.

Mesoscopic Simulations of Crosslinked Polymer Networks

NASA Astrophysics Data System (ADS)

Megariotis, Grigorios; Vogiatzis, Georgios G.; Schneider, Ludwig; Müller, Marcus; Theodorou, Doros N.

2016-08-01

A new methodology and the corresponding C++ code for mesoscopic simulations of elastomers are presented. The test system, crosslinked ds-1’4-polyisoprene’ is simulated with a Brownian Dynamics/kinetic Monte Carlo algorithm as a dense liquid of soft, coarse-grained beads, each representing 5-10 Kuhn segments. From the thermodynamic point of view, the system is described by a Helmholtz free-energy containing contributions from entropic springs between successive beads along a chain, slip-springs representing entanglements between beads on different chains, and non-bonded interactions. The methodology is employed for the calculation of the stress relaxation function from simulations of several microseconds at equilibrium, as well as for the prediction of stress-strain curves of crosslinked polymer networks under deformation.

Histone-poly(A) hybrid molecules as tools to block nuclear pores.

PubMed

Cremer, G; Wojtech, E; Kalbas, M; Agutter, P S; Prochnow, D

1995-04-01

Histone-poly(A) hybrid molecules were used for transport experiments with resealed nuclear envelopes and after attachment of a cleavable cross-linker (SASD) to identify nuclear proteins. In contrast to histones, the hybrid molecules cannot be accumulated in resealed nuclear envelopes, and in contrast to poly(A), the export of hybrids from preloaded nuclear envelopes is completely impaired. The experiments strongly confirm the existence of poly(A) as an export signal in mRNA which counteracts the nuclear location signals (NLS) in histones. The contradicting transport signals in the hybrid molecules impair translocation through the nuclear pore complex. The failure to accumulate hybrid molecules into resealed nuclear envelopes results from the covalent attachment of polyadenylic acid to histones in a strict 1:1 molar ratio. This was demonstrated in control transport experiments where radiolabeled histones were simply mixed with nonlabeled poly(A) or radiolabeled poly(A) mixed with nonlabeled histones. In comparison, control uptake experiments with histones covalently linked to a single UMP-mononucleotide are strongly enhanced. Such controls exclude the conceivable possibility of a simple masking of the nuclear location signal in the histones by the covalent attached poly(A) moiety. Photoreactive histone-poly(A) hybrid analogs serve to identify nuclear envelope proteins--presumably in the nuclear pore--with molecular weights of 110, 80, and 71.4 kDa.

Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology.

PubMed

DeBlasio, Stacy L; Chavez, Juan D; Alexander, Mariko M; Ramsey, John; Eng, Jimmy K; Mahoney, Jaclyn; Gray, Stewart M; Bruce, James E; Cilia, Michelle

2016-02-15

Demonstrating direct interactions between host and virus proteins during infection is a major goal and challenge for the field of virology. Most protein interactions are not binary or easily amenable to structural determination. Using infectious preparations of a polerovirus (Potato leafroll virus [PLRV]) and protein interaction reporter (PIR), a revolutionary technology that couples a mass spectrometric-cleavable chemical cross-linker with high-resolution mass spectrometry, we provide the first report of a host-pathogen protein interaction network that includes data-derived, topological features for every cross-linked site that was identified. We show that PLRV virions have hot spots of protein interaction and multifunctional surface topologies, revealing how these plant viruses maximize their use of binding interfaces. Modeling data, guided by cross-linking constraints, suggest asymmetric packing of the major capsid protein in the virion, which supports previous epitope mapping studies. Protein interaction topologies are conserved with other species in the Luteoviridae and with unrelated viruses in the Herpesviridae and Adenoviridae. Functional analysis of three PLRV-interacting host proteins in planta using a reverse-genetics approach revealed a complex, molecular tug-of-war between host and virus. Structural mimicry and diversifying selection-hallmarks of host-pathogen interactions-were identified within host and viral binding interfaces predicted by our models. These results illuminate the functional diversity of the PLRV-host protein interaction network and demonstrate the usefulness of PIR technology for precision mapping of functional host-pathogen protein interaction topologies. The exterior shape of a plant virus and its interacting host and insect vector proteins determine whether a virus will be transmitted by an insect or infect a specific host. Gaining this information is difficult and requires years of experimentation. We used protein interaction reporter (PIR) technology to illustrate how viruses exploit host proteins during plant infection. PIR technology enabled our team to precisely describe the sites of functional virus-virus, virus-host, and host-host protein interactions using a mass spectrometry analysis that takes just a few hours. Applications of PIR technology in host-pathogen interactions will enable researchers studying recalcitrant pathogens, such as animal pathogens where host proteins are incorporated directly into the infectious agents, to investigate how proteins interact during infection and transmission as well as develop new tools for interdiction and therapy. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology

PubMed Central

DeBlasio, Stacy L.; Chavez, Juan D.; Alexander, Mariko M.; Ramsey, John; Eng, Jimmy K.; Mahoney, Jaclyn; Gray, Stewart M.; Bruce, James E.

2015-01-01

ABSTRACT Demonstrating direct interactions between host and virus proteins during infection is a major goal and challenge for the field of virology. Most protein interactions are not binary or easily amenable to structural determination. Using infectious preparations of a polerovirus (Potato leafroll virus [PLRV]) and protein interaction reporter (PIR), a revolutionary technology that couples a mass spectrometric-cleavable chemical cross-linker with high-resolution mass spectrometry, we provide the first report of a host-pathogen protein interaction network that includes data-derived, topological features for every cross-linked site that was identified. We show that PLRV virions have hot spots of protein interaction and multifunctional surface topologies, revealing how these plant viruses maximize their use of binding interfaces. Modeling data, guided by cross-linking constraints, suggest asymmetric packing of the major capsid protein in the virion, which supports previous epitope mapping studies. Protein interaction topologies are conserved with other species in the Luteoviridae and with unrelated viruses in the Herpesviridae and Adenoviridae. Functional analysis of three PLRV-interacting host proteins in planta using a reverse-genetics approach revealed a complex, molecular tug-of-war between host and virus. Structural mimicry and diversifying selection—hallmarks of host-pathogen interactions—were identified within host and viral binding interfaces predicted by our models. These results illuminate the functional diversity of the PLRV-host protein interaction network and demonstrate the usefulness of PIR technology for precision mapping of functional host-pathogen protein interaction topologies. IMPORTANCE The exterior shape of a plant virus and its interacting host and insect vector proteins determine whether a virus will be transmitted by an insect or infect a specific host. Gaining this information is difficult and requires years of experimentation. We used protein interaction reporter (PIR) technology to illustrate how viruses exploit host proteins during plant infection. PIR technology enabled our team to precisely describe the sites of functional virus-virus, virus-host, and host-host protein interactions using a mass spectrometry analysis that takes just a few hours. Applications of PIR technology in host-pathogen interactions will enable researchers studying recalcitrant pathogens, such as animal pathogens where host proteins are incorporated directly into the infectious agents, to investigate how proteins interact during infection and transmission as well as develop new tools for interdiction and therapy. PMID:26656710

Synergistic tumor microenvironment targeting and blood-brain barrier penetration via a pH-responsive dual-ligand strategy for enhanced breast cancer and brain metastasis therapy.

PubMed

Li, Man; Shi, Kairong; Tang, Xian; Wei, Jiaojie; Cun, Xingli; Long, Yang; Zhang, Zhirong; He, Qin

2018-05-22

Cancer associated fibroblasts (CAFs) which shape the tumor microenvironment (TME) and the presence of blood brain barrier (BBB) remain great challenges in targeting breast cancer and its brain metastasis. Herein, we reported a strategy using PTX-loaded liposome co-modified with acid-cleavable folic acid (FA) and BBB transmigrating cell penetrating peptide dNP2 peptide (cFd-Lip/PTX) for enhanced delivery to orthotopic breast cancer and its brain metastasis. Compared with single ligand or non-cleavable Fd modified liposomes, cFd-Lip exhibited synergistic TME targeting and BBB transmigration. Moreover, upon arrival at the TME, the acid-cleavable cFd-Lip/PTX showed sensitive cleavage of FA, which reduced the hindrance effect and maximized the function of both FA and dNP2 peptide. Consequently, efficient targeting of folate receptor (FR)-positive tumor cells and FR-negative CAFs was achieved, leading to enhanced anti-tumor activity. This strategy provides a feasible approach to the cascade targeting of TME and BBB transmigration in orthotopic and metastatic cancer treatment. Copyright © 2018. Published by Elsevier Inc.

δ-Conotoxins synthesized using an acid-cleavable solubility tag approach reveal key structural determinants for NaV subtype selectivity.

PubMed

Peigneur, Steve; Paolini-Bertrand, Marianne; Gaertner, Hubert; Biass, Daniel; Violette, Aude; Stöcklin, Reto; Favreau, Philippe; Tytgat, Jan; Hartley, Oliver

2014-12-19

Conotoxins are venom peptides from cone snails with multiple disulfide bridges that provide a rigid structural scaffold. Typically acting on ion channels implicated in neurotransmission, conotoxins are of interest both as tools for pharmacological studies and as potential new medicines. δ-Conotoxins act by inhibiting inactivation of voltage-gated sodium channels (Nav). Their pharmacology has not been extensively studied because their highly hydrophobic character makes them difficult targets for chemical synthesis. Here we adopted an acid-cleavable solubility tag strategy that facilitated synthesis, purification, and directed disulfide bridge formation. Using this approach we readily produced three native δ-conotoxins from Conus consors plus two rationally designed hybrid peptides. We observed striking differences in Nav subtype selectivity across this group of compounds, which differ in primary structure at only three positions: 12, 23, and 25. Our results provide new insights into the structure-activity relationships underlying the Nav subtype selectivity of δ-conotoxins. Use of the acid-cleavable solubility tag strategy should facilitate synthesis of other hydrophobic peptides with complex disulfide bridge patterns. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Intracellular cleavable poly(2-dimethylaminoethyl methacrylate) functionalized mesoporous silica nanoparticles for efficient siRNA delivery in vitro and in vivo.

PubMed

Lin, Daoshu; Cheng, Qiang; Jiang, Qian; Huang, Yuanyu; Yang, Zheng; Han, Shangcong; Zhao, Yuning; Guo, Shutao; Liang, Zicai; Dong, Anjie

2013-05-21

A low cytotoxicity and high efficiency delivery system with the advantages of low cost and facile fabrication is needed for the application of small interfering RNA (siRNA) delivery both in vitro and in vivo. For these prerequisites, cationic polymer-mesoporous silica nanoparticles (ssCP-MSNs) were prepared by surface functionalized mesoporous silica nanoparticles with disulfide bond cross-linked poly(2-dimethylaminoethyl methacrylate) (PDMAEMA). In vitro and in vivo evaluations were performed. The synthesized ssCP-MSNs are 100-150 nm in diameter with a pore size of 10 nm and a positively charged surface with a high zeta potential of 27 mV. Consequently, the ssCP-MSNs showed an excellent binding capacity for siRNA, and an enhancement in the cell uptake and cytosolic availability of siRNA. Furthermore, the intracellular reducing cleavage of the disulfide bonds cross-linking the PDMAEMA segments led to intracellular cleavage of PDMAEMA from ssCP-MSNs, which facilitated the intracellular triggered release of siRNA. Therefore, promoted RNA interference was observed in HeLa-Luc cells, which was equal to that of Lipofectamine 2000. Significantly, compared to Lipofectamine 2000, the ssCP-MSNs were more biocompatible, with low cytotoxicity (even non-cytotoxicity) and promotion of cell proliferation to HeLa-Luc cells. The in vivo systemic distribution studies certified that ssCP-MSNs/siRNA could prolong the duration of siRNA in vivo, and that they accumulated in the adrenal gland, liver, lung, spleen, kidney, heart and thymus after intravenous injection. Encouragingly, with the ability to deliver siRNA to a tumor, ssCP-MSNs/siRNA showed a tumor suppression effect in the HeLa-Luc xenograft murine model after intravenous injection. Therefore, the ssCP-MSNs cationic polymer-mesoporous silica nanoparticles with low cytotoxicity are promising for siRNA delivery.

Synthesis and Characterization of Cleavable Core-Cross-Linked Micelles Based on Amphiphilic Block Copolypeptoids as Smart Drug Carriers.

PubMed

Li, Ang; Zhang, Donghui

2016-03-14

Amphiphilic block copolypeptoids consisting of a hydrophilic poly(N-ethyl glycine) segment and a hydrophobic poly[(N-propargyl glycine)-r-(N-decyl glycine)] random copolymer segment [PNEG-b-P(NPgG-r-NDG), EPgD] have been synthesized by sequential primary amine-initiated ring-opening polymerization (ROP) of the corresponding N-alkyl N-carboxyanhydride monomers. The block copolypeptoids form micelles in water and the micellar core can be cross-linked with a disulfide-containing diazide cross-linker by copper-mediated alkyne-azide cycloaddition (CuAAC) in aqueous solution. Transmission electron microscopy (TEM) and dynamic light scattering (DLS) analysis revealed the formation of spherical micelles with uniform size for both the core-cross-linked micelles (CCLMs) and non-cross-linked micelles (NCLMs) precursors for selective block copolypeptoid polymers. The CCLMs exhibited increased dimensional stability relative to the NCLMs in DMF, a nonselective solvent for the core and corona segments. Micellar dissociation of CCLMs can be induced upon addition of a reducing agent (e.g., dithiothreitol) in dilute aqueous solutions, as verified by a combination of fluorescence spectroscopy, size exclusion chromatography (SEC), and (1)H NMR spectroscopic measurement. Doxorubicin (DOX), an anticancer drug, can be loaded into the hydrophobic core of CCLMs with a maximal 23% drug loading capacity (DLC) and 37% drug loading efficiency (DLE). In vitro DOX release from the CCLMs can be triggered by DTT (10 mM), in contrast to significantly reduced DOX release in the absence of DTT, attesting to the reductively responsive characteristic of the CCLMs. While the CCLMs exhibited minimal cytotoxicity toward HepG2 cancer cells, DOX-loaded CCLMs inhibited the proliferation of the HepG2 cancer cells in a concentration and time dependent manner, suggesting the controlled release of DOX from the DOX-loaded CCLMS in the cellular environment.

Improvement of Modeling HTGR Neutron Physics by Uncertainty Analysis with the Use of Cross-Section Covariance Information

NASA Astrophysics Data System (ADS)

Boyarinov, V. F.; Grol, A. V.; Fomichenko, P. A.; Ternovykh, M. Yu

2017-01-01

This work is aimed at improvement of HTGR neutron physics design calculations by application of uncertainty analysis with the use of cross-section covariance information. Methodology and codes for preparation of multigroup libraries of covariance information for individual isotopes from the basic 44-group library of SCALE-6 code system were developed. A 69-group library of covariance information in a special format for main isotopes and elements typical for high temperature gas cooled reactors (HTGR) was generated. This library can be used for estimation of uncertainties, associated with nuclear data, in analysis of HTGR neutron physics with design codes. As an example, calculations of one-group cross-section uncertainties for fission and capture reactions for main isotopes of the MHTGR-350 benchmark, as well as uncertainties of the multiplication factor (k∞) for the MHTGR-350 fuel compact cell model and fuel block model were performed. These uncertainties were estimated by the developed technology with the use of WIMS-D code and modules of SCALE-6 code system, namely, by TSUNAMI, KENO-VI and SAMS. Eight most important reactions on isotopes for MHTGR-350 benchmark were identified, namely: 10B(capt), 238U(n,γ), ν5, 235U(n,γ), 238U(el), natC(el), 235U(fiss)-235U(n,γ), 235U(fiss).

Amino acid analysis in physiological samples by GC-MS with propyl chloroformate derivatization and iTRAQ-LC-MS/MS.

PubMed

Dettmer, Katja; Stevens, Axel P; Fagerer, Stephan R; Kaspar, Hannelore; Oefner, Peter J

2012-01-01

Two mass spectrometry-based methods for the quantitative analysis of free amino acids are described. The first method uses propyl chloroformate/propanol derivatization and gas chromatography-quadrupole mass spectrometry (GC-qMS) analysis in single-ion monitoring mode. Derivatization is carried out directly in aqueous samples, thereby allowing automation of the entire procedure, including addition of reagents, extraction, and injection into the GC-MS. The method delivers the quantification of 26 amino acids. The isobaric tagging for relative and absolute quantification (iTRAQ) method employs the labeling of amino acids with isobaric iTRAQ tags. The tags contain two different cleavable reporter ions, one for the sample and one for the standard, which are detected by fragmentation in a tandem mass spectrometer. Reversed-phase liquid chromatography of the labeled amino acids is performed prior to mass spectrometric analysis to separate isobaric amino acids. The commercial iTRAQ kit allows for the analysis of 42 physiological amino acids with a respective isotope-labeled standard for each of these 42 amino acids.

Isotope-coded ESI-enhancing derivatization reagents for differential analysis, quantification and profiling of metabolites in biological samples by LC/MS: A review.

PubMed

Higashi, Tatsuya; Ogawa, Shoujiro

2016-10-25

The analysis of the qualitative and quantitative changes of metabolites in body fluids and tissues yields valuable information for the diagnosis, pathological analysis and treatment of many diseases. Recently, liquid chromatography/electrospray ionization-(tandem) mass spectrometry [LC/ESI-MS(/MS)] has been widely used for these purposes due to the high separation capability of LC, broad coverage of ESI for various compounds and high specificity of MS(/MS). However, there are still two major problems to be solved regarding the biological sample analysis; lack of sensitivity and limited availability of stable isotope-labeled analogues (internal standards, ISs) for most metabolites. Stable isotope-coded derivatization (ICD) can be the answer for these problems. By the ICD, different isotope-coded moieties are introduced to the metabolites and one of the resulting derivatives can serve as the IS, which minimize the matrix effects. Furthermore, the derivatization can improve the ESI efficiency, fragmentation property in the MS/MS and chromatographic behavior of the metabolites, which lead to a high sensitivity and specificity in the various detection modes. Based on this background, this article reviews the recently-reported isotope-coded ESI-enhancing derivatization (ICEED) reagents, which are key components for the ICD-based LC/MS(/MS) studies, and their applications to the detection, identification, quantification and profiling of metabolites in human and animal samples. The LC/MS(/MS) using the ICEED reagents is the powerful method especially for the differential analysis (relative quantification) of metabolites in two comparative samples, simultaneous quantification of multiple metabolites whose stable isotope-labeled ISs are not available, and submetabolome profiling. Copyright © 2016 Elsevier B.V. All rights reserved.

Microbially Mediated Kinetic Sulfur Isotope Fractionation: Reactive Transport Modeling Benchmark

NASA Astrophysics Data System (ADS)

Wanner, C.; Druhan, J. L.; Cheng, Y.; Amos, R. T.; Steefel, C. I.; Ajo Franklin, J. B.

2014-12-01

Microbially mediated sulfate reduction is a ubiquitous process in many subsurface systems. Isotopic fractionation is characteristic of this anaerobic process, since sulfate reducing bacteria (SRB) favor the reduction of the lighter sulfate isotopologue (S32O42-) over the heavier isotopologue (S34O42-). Detection of isotopic shifts have been utilized as a proxy for the onset of sulfate reduction in subsurface systems such as oil reservoirs and aquifers undergoing uranium bioremediation. Reactive transport modeling (RTM) of kinetic sulfur isotope fractionation has been applied to field and laboratory studies. These RTM approaches employ different mathematical formulations in the representation of kinetic sulfur isotope fractionation. In order to test the various formulations, we propose a benchmark problem set for the simulation of kinetic sulfur isotope fractionation during microbially mediated sulfate reduction. The benchmark problem set is comprised of four problem levels and is based on a recent laboratory column experimental study of sulfur isotope fractionation. Pertinent processes impacting sulfur isotopic composition such as microbial sulfate reduction and dispersion are included in the problem set. To date, participating RTM codes are: CRUNCHTOPE, TOUGHREACT, MIN3P and THE GEOCHEMIST'S WORKBENCH. Preliminary results from various codes show reasonable agreement for the problem levels simulating sulfur isotope fractionation in 1D.

Impact of Chronic Alcohol Ingestion on Cardiac Muscle Protein Expression

PubMed Central

Fogle, Rachel L.; Lynch, Christopher J.; Palopoli, Mary; Deiter, Gina; Stanley, Bruce A.; Vary, Thomas C.

2014-01-01

Background Chronic alcohol abuse contributes not only to an increased risk of health-related complications, but also to a premature mortality in adults. Myocardial dysfunction, including the development of a syndrome referred to as alcoholic cardiomyopathy, appears to be a major contributing factor. One mechanism to account for the pathogenesis of alcoholic cardiomyopathy involves alterations in protein expression secondary to an inhibition of protein synthesis. However, the full extent to which myocardial proteins are affected by chronic alcohol consumption remains unresolved. Methods The purpose of this study was to examine the effect of chronic alcohol consumption on the expression of cardiac proteins. Male rats were maintained for 16 weeks on a 40% ethanol-containing diet in which alcohol was provided both in drinking water and agar blocks. Control animals were pair-fed to consume the same caloric intake. Heart homogenates from control- and ethanol-fed rats were labeled with the cleavable isotope coded affinity tags (ICAT™). Following the reaction with the ICAT™ reagent, we applied one-dimensional gel electrophoresis with in-gel trypsin digestion of proteins and subsequent MALDI-TOF-TOF mass spectrometric techniques for identification of peptides. Differences in the expression of cardiac proteins from control- and ethanol-fed rats were determined by mass spectrometry approaches. Results Initial proteomic analysis identified and quantified hundreds of cardiac proteins. Major decreases in the expression of specific myocardial proteins were observed. Proteins were grouped depending on their contribution to multiple activities of cardiac function and metabolism, including mitochondrial-, glycolytic-, myofibrillar-, membrane-associated, and plasma proteins. Another group contained identified proteins that could not be properly categorized under the aforementioned classification system. Conclusions Based on the changes in proteins, we speculate modulation of cardiac muscle protein expression represents a fundamental alteration induced by chronic alcohol consumption, consistent with changes in myocardial wall thickness measured under the same conditions. PMID:20477769

Purification of target proteins from intracellular inclusions mediated by intein cleavable polyhydroxyalkanoate synthase fusions.

PubMed

Du, Jinping; Rehm, Bernd H A

2017-11-02

Recombinant protein production and purification from Escherichia coli is often accompanied with expensive and complicated procedures, especially for therapeutic proteins. Here it was demonstrated that, by using an intein cleavable polyhydroxyalkanoate synthase fusion, recombinant proteins can be first produced and sequestered on a natural resin, the polyhydroxyalkanoate (PHA) inclusions, then separated from contaminating host proteins via simple PHA bead isolation steps, and finally purified by specific release into the soluble fraction induced by a pH reduction. By translationally fusing a target protein to PHA synthase using a self-cleaving intein as linker, intracellular production of PHA beads was achieved. Upon isolation of respective PHA beads the soluble pure target protein was released by a simple pH shift to 6. The utility of this approach was exemplified by producing six target proteins, including Aequorea victoria green fluorescent protein (GFP), Mycobacterium tuberculosis vaccine candidate Rv1626, the immunoglobulin G (IgG) binding ZZ domain of protein A derived from Staphylococcus aureus, human tumor necrosis factor alpha (TNFα), human granulocyte colony-stimulating factor (G-CSF), and human interferon alpha 2b (IFNα2b). Here a new method for production and purification of a tag-less protein was developed through intein cleavable polyhydroxyalkanoate synthase fusion. Pure target protein could be easily obtained without laborious downstream processing.

Isotopic Dependence of GCR Fluence behind Shielding

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Wilson, John W.; Saganti, Premkumar; Kim, Myung-Hee Y.; Cleghorn, Timothy; Zeitlin, Cary; Tripathi, Ram K.

2006-01-01

In this paper we consider the effects of the isotopic composition of the primary galactic cosmic rays (GCR), nuclear fragmentation cross-sections, and isotopic-grid on the solution to transport models used for shielding studies. Satellite measurements are used to describe the isotopic composition of the GCR. For the nuclear interaction data-base and transport solution, we use the quantum multiple-scattering theory of nuclear fragmentation (QMSFRG) and high-charge and energy (HZETRN) transport code, respectively. The QMSFRG model is shown to accurately describe existing fragmentation data including proper description of the odd-even effects as function of the iso-spin dependence on the projectile nucleus. The principle finding of this study is that large errors (+/-100%) will occur in the mass-fluence spectra when comparing transport models that use a complete isotopic-grid (approx.170 ions) to ones that use a reduced isotopic-grid, for example the 59 ion-grid used in the HZETRN code in the past, however less significant errors (<+/-20%) occur in the elemental-fluence spectra. Because a complete isotopic-grid is readily handled on small computer workstations and is needed for several applications studying GCR propagation and scattering, it is recommended that they be used for future GCR studies.

Melanoma-targeted delivery system (part 1): design, synthesis and evaluation of releasable disulfide drug by glutathione.

PubMed

El Aissi, Radhia; Chezal, Jean-Michel; Tarrit, Sébastien; Chavignon, Olivier; Moreau, Emmanuel

2015-08-28

Here we describe the design and synthesis of a prodrug developed for pigmented melanoma therapy, consisting of a Melanin-Targeting Probe (MTP) conjugated to 5-iodo-2'-deoxyuridine (IUdR) with a reduction-sensitive pre-determined breaking point. Compared with the non-cleavable conjugate (17b), prodrug (17a) bearing a self-immolative disulfide linker achieved complete release of IUdR within 20 min in the presence of reducing agents such as DTT or glutathione. Analytical results also showed that prodrug (17a) was more sensitive than parent non-cleavable conjugate (17b) for a concentration range of glutathione similar to that found in the intracellular compartment of tumours. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Burnup calculations and chemical analysis of irradiated fuel samples studied in LWR-PROTEUS phase II

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

Grimm, P.; Guenther-Leopold, I.; Berger, H. D.

2006-07-01

The isotopic compositions of 5 UO{sub 2} samples irradiated in a Swiss PWR power plant, which were investigated in the LWR-PROTEUS Phase II programme, were calculated using the CASMO-4 and BOXER assembly codes. The burnups of the samples range from 50 to 90 MWd/kg. The results for a large number of actinide and fission product nuclides were compared to those of chemical analyses performed using a combination of chromatographic separation and mass spectrometry. A good agreement of calculated and measured concentrations is found for many of the nuclides investigated with both codes. The concentrations of the Pu isotopes are mostlymore » predicted within {+-}10%, the two codes giving quite different results, except for {sup 242}Pu. Relatively significant deviations are found for some isotopes of Cs and Sm, and large discrepancies are observed for Eu and Gd. The overall quality of the predictions by the two codes is comparable, and the deviations from the experimental data do not generally increase with burnup. (authors)« less

Experiments on δ34S mixing between organic and inorganic sulfur species during thermal maturation

USGS Publications Warehouse

Amrani, Alon; Said-Ahamed, Ward; Lewan, Michael D.; Aizenshtat, Zeev

2006-01-01

Reduced sulfur species were studied to constrain isotopic exchange-mixing with synthetic polysulfide cross-linked macromolecules (PCLM), model sulfur containing molecules and natural sulfur-rich kerogen, asphalt and oil of the Dead Sea area. PCLM represents protokerogens that are rich in sulfur and thermally unstable. Mixing rates of PCLM with HS-(aq) (added as (NH4)2S(aq)) at low to moderate temperatures (50–200 °C) are rapid. Elemental sulfur and H2S(gas) fully mix isotopes with PCLM during pyrolysis conditions at 200 °C. During these reactions significant structural changes of the PCLM occur to form polysulfide dimers, thiolanes and thiophenes. As pyrolysis temperatures or reaction times increase, the PCLM thermal products are transformed to more aromatic sulfur compounds. Isotopic mixing rates increase with increasing pyrolysis temperature and time. Polysulfide bonds (S–S) in the PCLM are responsible for most of these structural and isotopic changes because of their low stability. Conversely, sulfur isotope mixing does not occur between dibenzothiophene (aromatic S) or hexadecanthiol (C–SH) and HS-(aq) at 200 °C after 48 h. This shows that rates of sulfur isotope mixing are strongly dependent on the functionality of the sulfur in the organic matter. The order of isotopic mixing rates for organic matter is kerogen > asphalt > oil, which is inverse to their sulfur thermal stability. Asphalt and oil with more refractory sulfur show significantly lower isotopes mixing rates than the kerogen with more labile sulfur. Based on the findings of the present study we suggest that sulfur isotopes mixing can occur from early diagenesis into catagenesis and result in isotopic homogenization of the inorganic and organic reduced sulfur pools.

Suppression for lung metastasis by depletion of collagen I and lysyl oxidase via losartan assisted with paclitaxel-loaded pH-sensitive liposomes in breast cancer.

PubMed

Zhang, Li; Wang, Yang; Xia, Tai; Yu, Qianwen; Zhang, Qianyu; Yang, Yuting; Cun, Xingli; Lu, Libao; Gao, Huile; Zhang, Zhirong; He, Qin

2016-10-01

Tumor metastasis would seriously impair the efficacy of chemotherapy. Our previous studies showed losartan combined with paclitaxel-loaded pH-sensitive cleavable liposomes (PTX-Cl-Lip) facilitated paclitaxel accumulation and led to enhanced antitumor efficacy in 4T1 bearing mice. Since losartan could inhibit the level of collagen I which was related to tumor metastasis, this strategy was further applied to suppress tumor metastasis this time. Our in vivo anti-metastatic study manifested losartan could lower the colonies occupied in lungs by 76.4% compared with that of saline group. When losartan and PTX-Cl-Lip were combined, anti-metastatic efficiency reached to 88.2%, which was the best among all the groups. In vitro 3D tumor spheroids studies proved losartan could significantly suppress the invasion of tumor cells. Losartan plus PTX-Cl-Lip could further weaken the metastasis of tumor cells. Mechanism study showed the declination of collagen I level via losartan was caused by inhibition of active transforming growth factor-β1. Western-blot study showed losartan could decrease the level of lysyl oxidase, then inhibit the cross-linking of collagen I, finally weakened the cell signaling transmit via integrin and the metastasis of tumor cells was restrained. All above studies illustrated this combined tactic could achieve favorable effect on suppression of lung tumor metastasis.

Chromatin structure and methylation of rat rRNA genes studied by formaldehyde fixation and psoralen cross-linking.

PubMed Central

Stancheva, I; Lucchini, R; Koller, T; Sogo, J M

1997-01-01

By using formaldehyde cross-linking of histones to DNA and gel retardation assays we show that formaldehyde fixation, similar to previously established psoralen photocross-linking, discriminates between nucleosome- packed (inactive) and nucleosome-free (active) fractions of ribosomal RNA genes. By both cross-linking techniques we were able to purify fragments from agarose gels, corresponding to coding, enhancer and promoter sequences of rRNA genes, which were further investigated with respect to DNA methylation. This approach allows us to analyse independently and in detail methylation patterns of active and inactive rRNA gene copies by the combination of Hpa II and Msp I restriction enzymes. We found CpG methylation mainly present in enhancer and promoter regions of inactive rRNA gene copies. The methylation of one single Hpa II site, located in the promoter region, showed particularly strong correlation with the transcriptional activity. PMID:9108154

Chromatin looping and eRNA transcription precede the transcriptional activation of gene in the β-globin locus

PubMed Central

Kim, Yea Woon; Lee, Sungkung; Yun, Jangmi; Kim, AeRi

2015-01-01

Enhancers are closely positioned with actively transcribed target genes by chromatin looping. Non-coding RNAs are often transcribed on active enhancers, referred to as eRNAs (enhancer RNAs). To explore the kinetics of enhancer–promoter looping and eRNA transcription during transcriptional activation, we induced the β-globin locus by chemical treatment and analysed cross-linking frequency between the β-globin gene and locus control region (LCR) and the amount of eRNAs transcribed on the LCR in a time course manner. The cross-linking frequency was increased after chemical induction but before the transcriptional activation of gene in the β-globin locus. Transcription of eRNAs was increased in concomitant with the increase in cross-linking frequency. These results show that chromatin looping and eRNA transcription precedes the transcriptional activation of gene. Concomitant occurrence of the two events suggests functional relationship between them. PMID:25588787

Photoactive Self-Shaping Hydrogels as Noncontact 3D Macro/Microscopic Photoprinting Platforms.

PubMed

Liao, Yue; An, Ning; Wang, Ning; Zhang, Yinyu; Song, Junfei; Zhou, Jinxiong; Liu, Wenguang

2015-12-01

A photocleavable terpolymer hydrogel cross-linked with o-nitrobenzyl derivative cross-linker is shown to be capable of self-shaping without losing its physical integrity and robustness due to spontaneous asymmetric swelling of network caused by UV-light-induced gradient cleavage of chemical cross-linkages. The continuum model and finite element method are used to elucidate the curling mechanism underlying. Remarkably, based on the self-changing principle, the photosensitive hydrogels can be developed as photoprinting soft and wet platforms onto which specific 3D characters and images are faithfully duplicated in macro/microscale without contact by UV light irradiation under the cover of customized photomasks. Importantly, a quick response (QR) code is accurately printed on the photoactive hydrogel for the first time. Scanning QR code with a smartphone can quickly connect to a web page. This photoactive hydrogel is promising to be a new printing or recording material. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nuclease digestion and mass spectrometric characterization of oligodeoxyribonucleotides containing 1,2-GpG, 1,2-ApG, and 1,3-GpXpG cisplatin intrastrand cross-links.

PubMed

Williams, Renee T; Nalbandian, Jenifer N; Tu, Audrey; Wang, Yinsheng

2013-05-01

The primary mode of action for cis-diamminedichloroplatinum (II), referred to as cisplatin, toward the treatment of solid malignancies is through formation of cross-links with DNA at purine sites, especially guanines. We prepared oligodeoxyribonucleotides (ODNs) containing a 1,2-GpG, 1,2-ApG, or 1,3-GpXpG cisplatin intrastrand cross-link and the corresponding ODNs modified with (15)N2-labeled cisplatin, and characterized these ODNs with electrospray ionization mass spectrometry (ESI-MS) and tandem MS (MS/MS). We also employed LC-MS/MS to characterize the digestion products of these ODNs after treatment with a cocktail of 4 enzymes (nuclease P1, phosphodiesterases I and II, and alkaline phosphatase). 1,2-GpG was released from the ODNs as a dinucleoside monophosphate or a dinucleotide. Analyses of the digestion products of ODNs containing a 1,2-GpG cross-link on the 5' or 3' terminus revealed that the dinucleotide carries a terminal 5' phosphate. On the other hand, digestion of the 1,3-GpXpG intrastrand cross-link yielded 3 dinucleoside products with 0, 1, or 2 phosphate groups. The availability of the ODNs carrying the stable isotope-labeled lesions, MS/MS analyses of the cisplatin-modified ODNs, and the characterization of the enzymatic digestion products of these ODNs set the stage for the future LC-MS/MS quantification of the 1,2-GpG, 1,2-ApG, and 1,3-GpXpG lesions in cellular DNA. Copyright © 2012 Elsevier B.V. All rights reserved.

Nuclease Digestion and Mass Spectrometric Characterization of Oligodeoxyribonucleotides Containing 1,2-GpG, 1,2-ApG, and 1,3-GpXpG Cisplatin Intrastrand Cross-links

PubMed Central

Williams, Renee T.; Nalbandian, Jenifer; Tu, Audrey; Wang, Yinsheng

2013-01-01

Background The primary mode of action for cis-diamminedichloroplatinum (II), referred to as cisplatin, towards the treatment of solid malignancies is through formation of cross-links with DNA at purine sites, especially guanines. Methods We prepared oligodeoxyribonucleotides (ODNs) containing a 1,2-GpG, 1,2-ApG, or 1,3-GpXpG cisplatin intrastrand cross-link and the corresponding ODNs modified with 15N2-labeled cisplatin, and characterized these ODNs with electrospray ionization mass spectrometry (ESI-MS) and tandem MS (MS/MS). We also employed LC-MS/MS to characterize the digestion products of these ODNs after treatment with a cocktail of 4 enzymes (nuclease P1, phosphodiesterases I and II, and alkaline phosphatase). Results 1,2-GpG was released from the ODNs as a dinucleoside monophosphate or a dinucleotide. Analyses of the digestion products of ODNs containing a 1,2-GpG cross-link on the 5′ or 3′ terminus revealed that the dinucleotide carries a terminal 5′ phosphate. On the other hand, digestion of the 1,3-GpXpG intrastrand cross-link yielded 3 dinucleoside products with 0, 1, or 2 phosphate groups. Results The availability of the ODNs carrying the stable isotope-labeled lesions, MS/MS analyses of the cisplatin-modified ODNs, and the characterization of the enzymatic digestion products of these ODNs set the stage for the future LC-MS/MS quantification of the 1,2-GpG, 1,2-ApG, and 1,3-GpXpG lesions in cellular DNA. PMID:23266768

Measurement of endogenous versus exogenous formaldehyde-induced DNA-protein crosslinks in animal tissues by stable isotope labeling and ultrasensitive mass spectrometry

PubMed Central

Lai, Yongquan; Yu, Rui; Hartwell, Hadley J.; Moeller, Benjamin C.; Bodnar, Wanda M.; Swenberg, James A.

2016-01-01

DNA-protein crosslinks (DPCs) arise from a wide range of endogenous and exogenous chemicals, such as chemotherapeutic drugs and formaldehyde. Importantly, recent identification of aldehydes as endogenous genotoxins in Fanconi anemia has provided new insight into disease causation. Due to their bulky nature, DPCs pose severe threats to genome stability, but previous methods to measure formaldehyde-induced DPCs were incapable of discriminating between endogenous and exogenous sources of chemical. In this study, we developed methods that provide accurate and distinct measurements of both exogenous and endogenous DPCs in a structurally-specific manner. We exposed experimental animals to stable isotope-labeled formaldehyde ([13CD2]-formaldehyde) by inhalation and performed ultrasensitive mass spectrometry to measure endogenous (unlabeled) and exogenous (13CD2-labeled) DPCs. We found that exogenous DPCs readily accumulated in nasal respiratory tissues, but were absent in tissues distant to the site of contact. This observation together with the finding that endogenous formaldehyde-induced DPCs were present in all tissues examined suggests that endogenous DPCs may be responsible for increased risks of bone marrow toxicity and leukemia. Furthermore, the slow rate of DPC repair provided evidence for persistence of DPCs. In conclusion, our method for measuring endogenous and exogenous DPCs presents a new perspective for the potential health risks inflicted by endogenous formaldehyde, and may inform improved disease prevention and treatment strategies. PMID:26984759

Mapping sites of aspirin-induced acetylations in live cells by quantitative acid-cleavable activity-based protein profiling (QA-ABPP)

PubMed Central

Wang, Jigang; Zhang, Chong-Jing; Zhang, Jianbin; He, Yingke; Lee, Yew Mun; Chen, Songbi; Lim, Teck Kwang; Ng, Shukie; Shen, Han-Ming; Lin, Qingsong

2015-01-01

Target-identification and understanding of mechanism-of-action (MOA) are challenging for development of small-molecule probes and their application in biology and drug discovery. For example, although aspirin has been widely used for more than 100 years, its molecular targets have not been fully characterized. To cope with this challenge, we developed a novel technique called quantitative acid-cleavable activity-based protein profiling (QA-ABPP) with combination of the following two parts: (i) activity-based protein profiling (ABPP) and iTRAQ™ quantitative proteomics for identification of target proteins and (ii) acid-cleavable linker-based ABPP for identification of peptides with specific binding sites. It is known that reaction of aspirin with its target proteins leads to acetylation. We thus applied the above technique using aspirin-based probes in human cancer HCT116 cells. We identified 1110 target proteins and 2775 peptides with exact acetylation sites. By correlating these two sets of data, 523 proteins were identified as targets of aspirin. We used various biological assays to validate the effects of aspirin on inhibition of protein synthesis and induction of autophagy which were elicited from the pathway analysis of Aspirin target profile. This technique is widely applicable for target identification in the field of drug discovery and biology, especially for the covalent drugs. PMID:25600173

The colibactin warhead crosslinks DNA

NASA Astrophysics Data System (ADS)

Vizcaino, Maria I.; Crawford, Jason M.

2015-05-01

Members of the human microbiota are increasingly being correlated to human health and disease states, but the majority of the underlying microbial metabolites that regulate host-microbe interactions remain largely unexplored. Select strains of Escherichia coli present in the human colon have been linked to the initiation of inflammation-induced colorectal cancer through an unknown small-molecule-mediated process. The responsible non-ribosomal peptide-polyketide hybrid pathway encodes ‘colibactin’, which belongs to a largely uncharacterized family of small molecules. Genotoxic small molecules from this pathway that are capable of initiating cancer formation have remained elusive due to their high instability. Guided by metabolomic analyses, here we employ a combination of NMR spectroscopy and bioinformatics-guided isotopic labelling studies to characterize the colibactin warhead, an unprecedented substituted spirobicyclic structure. The warhead crosslinks duplex DNA in vitro, providing direct experimental evidence for colibactin's DNA-damaging activity. The data support unexpected models for both colibactin biosynthesis and its mode of action.

Cooperation on Improved Isotopic Identification and Analysis Software for Portable, Electrically Cooled High-Resolution Gamma Spectrometry Systems Final Report

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

Dreyer, Jonathan G.; Wang, Tzu-Fang; Vo, Duc T.

Under a 2006 agreement between the Department of Energy (DOE) of the United States of America and the Institut de Radioprotection et de Sûreté Nucléaire (IRSN) of France, the National Nuclear Security Administration (NNSA) within DOE and IRSN initiated a collaboration to improve isotopic identification and analysis of nuclear material [i.e., plutonium (Pu) and uranium (U)]. The specific aim of the collaborative project was to develop new versions of two types of isotopic identification and analysis software: (1) the fixed-energy response-function analysis for multiple energies (FRAM) codes and (2) multi-group analysis (MGA) codes. The project is entitled Action Sheet 4more » – Cooperation on Improved Isotopic Identification and Analysis Software for Portable, Electrically Cooled, High-Resolution Gamma Spectrometry Systems (Action Sheet 4). FRAM and MGA/U235HI are software codes used to analyze isotopic ratios of U and Pu. FRAM is an application that uses parameter sets for the analysis of U or Pu. MGA and U235HI are two separate applications that analyze Pu or U, respectively. They have traditionally been used by safeguards practitioners to analyze gamma spectra acquired with high-resolution gamma spectrometry (HRGS) systems that are cooled by liquid nitrogen. However, it was discovered that these analysis programs were not as accurate when used on spectra acquired with a newer generation of more portable, electrically cooled HRGS (ECHRGS) systems. In response to this need, DOE/NNSA and IRSN collaborated to update the FRAM and U235HI codes to improve their performance with newer ECHRGS systems. Lawrence Livermore National Laboratory (LLNL) and Los Alamos National Laboratory (LANL) performed this work for DOE/NNSA.« less

Joint profiling of greenhouse gases, isotopes, thermodynamic variables, and wind from space by combined microwave and IR laser occultation: the ACCURATE concept

NASA Astrophysics Data System (ADS)

Kirchengast, G.; Schweitzer, S.

2008-12-01

The ACCURATE (Atmospheric Climate and Chemistry in the UTLS Region And climate Trends Explorer) mission was conceived at the Wegener Center in late 2004 and subsequently proposed in 2005 by an international team of more than 20 scientific partners from more than 12 countries to an ESA selection process for next Earth Explorer Missions. While the mission was not selected for formal pre-phase A study, it received very positive evaluation and was recommended for further development and demonstration. ACCURATE employs the occultation measurement principle, known for its unique combination of high vertical resolution, accuracy and long-term stability, in a novel way. It systematically combines use of highly stable signals in the MW 17-23/178-196 GHz bands (LEO-LEO MW crosslink occultation) with laser signals in the SWIR 2-2.5 μm band (LEO-LEO IR laser crosslink occultation) for exploring and monitoring climate and chemistry in the atmosphere with focus on the UTLS region (upper troposphere/lower stratosphere, 5-35 km). The MW occultation is an advanced and at the same time compact version of the LEO-LEO MW occultation concept, studied in 2002-2004 for the ACE+ mission project of ESA for frequencies including the 17-23 GHz band, complemented by U.S. study heritage for frequencies including the 178-196 GHz bands (R. Kursinski et al., Univ. of Arizona, Tucson). The core of ACCURATE is tight synergy of the IR laser crosslinks with the MW crosslinks. The observed parameters, obtained simultaneously and in a self-calibrated manner based on Doppler shift and differential log-transmission profiles, comprise the fundamental thermodynamic variables of the atmosphere (temperature, pressure/geopotential height, humidity) retrieved from the MW bands, complemented by line-of-sight wind, six greenhouse gases (GHGs) and key species of UTLS chemistry (H2O, CO2, CH4, N2O, O3, CO) and four CO2 and H2O isotopes (HDO, H218O, 13CO2, C18OO) from the SWIR band. Furthermore, profiles of aerosol extinction, cloud layering, and turbulence are obtained. All profiles come with accurate height knowledge (< 10 m uncertainty), since measuring height as a function of time is intrinsic to the MW occultation part of ACCURATE. The presentation will introduce ACCURATE along the lines above, with emphasis on the climate science value and the new IR laser occultation capability. The focus will then be on retrieval performance analysis results obtained so far, in particular regarding the profiles of GHGs, isotopes, and wind. The results provide evidence that the GHG and isotope profiles can generally be retrieved within 5-35 km outside clouds with < 1% to 5% rms accuracy at 1-2 km vertical resolution, and wind with < 2 m/s accuracy. Monthly mean climatological profiles, assuming ~40 profiles per climatologic grid box per month, are found unbiased (free of time-varying biases) and at < 0.2% to 0.5% rms accuracy. These encouraging results are discussed in light of the potential of the ACCURATE technique to provide benchmark data for future monitoring of climate, GHGs, and chemistry variability and change. European science and demonstration activities are outlined, including international participation opportunities.

A new algorithm to handle finite nuclear mass effects in electronic calculations: the ISOTOPE program.

PubMed

Gonçalves, Cristina P; Mohallem, José R

2004-11-15

We report the development of a simple algorithm to modify quantum chemistry codes based on the LCAO procedure, to account for the isotope problem in electronic structure calculations. No extra computations are required compared to standard Born-Oppenheimer calculations. An upgrade of the Gamess package called ISOTOPE is presented, and its applicability is demonstrated in some examples.

Dual-radiolabeled nanoparticle probes for depth-independent in vivo imaging of enzyme activation

NASA Astrophysics Data System (ADS)

Black, Kvar C. L.; Zhou, Mingzhou; Sarder, Pinaki; Kuchuk, Maryna; Al-Yasiri, Amal Y.; Gunsten, Sean P.; Liang, Kexian; Hennkens, Heather M.; Akers, Walter J.; Laforest, Richard; Brody, Steven L.; Cutler, Cathy S.; Achilefu, Samuel

2018-02-01

Quantitative and noninvasive measurement of protease activities has remained an imaging challenge in deep tissues such as the lungs. Here, we designed a dual-radiolabeled probe for reporting the activities of proteases such as matrix metalloproteinases (MMPs) with multispectral single photon emission computed tomography (SPECT) imaging. A gold nanoparticle (NP) was radiolabeled with 125I and 111In and functionalized with an MMP9-cleavable peptide to form a multispectral SPECT imaging contrast agent. In another design, incorporation of 199Au radionuclide into the metal crystal structure of gold NPs provided a superior and stable reference signal in lungs, and 111In was linked to the NP surface via a protease-cleavable substrate, which can serve as an enzyme activity reporter. This work reveals strategies to correlate protease activities with diverse pathologies in a tissue-depth independent manner.

Isotopic composition analysis and age dating of uranium samples by high resolution gamma ray spectrometry

NASA Astrophysics Data System (ADS)

Apostol, A. I.; Pantelica, A.; Sima, O.; Fugaru, V.

2016-09-01

Non-destructive methods were applied to determine the isotopic composition and the time elapsed since last chemical purification of nine uranium samples. The applied methods are based on measuring gamma and X radiations of uranium samples by high resolution low energy gamma spectrometric system with planar high purity germanium detector and low background gamma spectrometric system with coaxial high purity germanium detector. The ;Multigroup γ-ray Analysis Method for Uranium; (MGAU) code was used for the precise determination of samples' isotopic composition. The age of the samples was determined from the isotopic ratio 214Bi/234U. This ratio was calculated from the analyzed spectra of each uranium sample, using relative detection efficiency. Special attention is paid to the coincidence summing corrections that have to be taken into account when performing this type of analysis. In addition, an alternative approach for the age determination using full energy peak efficiencies obtained by Monte Carlo simulations with the GESPECOR code is described.

Measurement of Endogenous versus Exogenous Formaldehyde-Induced DNA-Protein Crosslinks in Animal Tissues by Stable Isotope Labeling and Ultrasensitive Mass Spectrometry.

PubMed

Lai, Yongquan; Yu, Rui; Hartwell, Hadley J; Moeller, Benjamin C; Bodnar, Wanda M; Swenberg, James A

2016-05-01

DNA-protein crosslinks (DPC) arise from a wide range of endogenous and exogenous chemicals, such as chemotherapeutic drugs and formaldehyde. Importantly, recent identification of aldehydes as endogenous genotoxins in Fanconi anemia has provided new insight into disease causation. Because of their bulky nature, DPCs pose severe threats to genome stability, but previous methods to measure formaldehyde-induced DPCs were incapable of discriminating between endogenous and exogenous sources of chemical. In this study, we developed methods that provide accurate and distinct measurements of both exogenous and endogenous DPCs in a structurally specific manner. We exposed experimental animals to stable isotope-labeled formaldehyde ([(13)CD2]-formaldehyde) by inhalation and performed ultrasensitive mass spectrometry to measure endogenous (unlabeled) and exogenous ((13)CD2-labeled) DPCs. We found that exogenous DPCs readily accumulated in nasal respiratory tissues but were absent in tissues distant to the site of contact. This observation, together with the finding that endogenous formaldehyde-induced DPCs were present in all tissues examined, suggests that endogenous DPCs may be responsible for increased risks of bone marrow toxicity and leukemia. Furthermore, the slow rate of DPC repair provided evidence for the persistence of DPCs. In conclusion, our method for measuring endogenous and exogenous DPCs presents a new perspective for the potential health risks inflicted by endogenous formaldehyde and may inform improved disease prevention and treatment strategies. Cancer Res; 76(9); 2652-61. ©2016 AACR. ©2016 American Association for Cancer Research.

Simulation of multi-photon emission isotopes using time-resolved SimSET multiple photon history generator

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

Chiang, Chih-Chieh; Lin, Hsin-Hon; Lin, Chang-Shiun

Abstract-Multiple-photon emitters, such as In-111 or Se-75, have enormous potential in the field of nuclear medicine imaging. For example, Se-75 can be used to investigate the bile acid malabsorption and measure the bile acid pool loss. The simulation system for emission tomography (SimSET) is a well-known Monte Carlo simulation (MCS) code in nuclear medicine for its high computational efficiency. However, current SimSET cannot simulate these isotopes due to the lack of modeling of complex decay scheme and the time-dependent decay process. To extend the versatility of SimSET for simulation of those multi-photon emission isotopes, a time-resolved multiple photon history generatormore » based on SimSET codes is developed in present study. For developing the time-resolved SimSET (trSimSET) with radionuclide decay process, the new MCS model introduce new features, including decay time information and photon time-of-flight information, into this new code. The half-life of energy states were tabulated from the Evaluated Nuclear Structure Data File (ENSDF) database. The MCS results indicate that the overall percent difference is less than 8.5% for all simulation trials as compared to GATE. To sum up, we demonstrated that time-resolved SimSET multiple photon history generator can have comparable accuracy with GATE and keeping better computational efficiency. The new MCS code is very useful to study the multi-photon imaging of novel isotopes that needs the simulation of lifetime and the time-of-fight measurements. (authors)« less

Nuclear Forensics and Radiochemistry: Reaction Networks

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

Rundberg, Robert S.

In the intense neutron flux of a nuclear explosion the production of isotopes may occur through successive neutron induced reactions. The pathway to these isotopes illustrates both the complexity of the problem and the need for high quality nuclear data. The growth and decay of radioactive isotopes can follow a similarly complex network. The Bateman equation will be described and modified to apply to the transmutation of isotopes in a high flux reactor. A alternative model of growth and decay, the GD code, that can be applied to fission products will also be described.

Cross sections and differential spectra for reactions of 2-20 MeV neutrons of /sup 27/Al

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

Blann, M.; Komoto, T.T.

1988-01-01

This report summarizes product yields, secondary n,p and ..cap alpha.. spectra, and ..gamma..-ray spectra calculated for incident neutrons of 2-20 MeV on /sup 27/Al targets. Results are all from the code ALICE, using the version ALISO which does weighting of results for targets which are a mix of isotopes. Where natural isotopic targets are involved, yields and n,p,..cap alpha.. spectra will be reported weighted over isotopic yields. Gamma-ray spectra, however, will be reported for the most abundant isotope.

Urinary Amino Acid Analysis: A Comparison of iTRAQ®-LC-MS/MS, GC-MS, and Amino Acid Analyzer

PubMed Central

Kaspar, Hannelore; Dettmer, Katja; Chan, Queenie; Daniels, Scott; Nimkar, Subodh; Daviglus, Martha L.; Stamler, Jeremiah; Elliott, Paul; Oefner, Peter J.

2009-01-01

Urinary amino acid analysis is typically done by cation-exchange chromatography followed by post-column derivatization with ninhydrin and UV detection. This method lacks throughput and specificity. Two recently introduced stable isotope ratio mass spectrometric methods promise to overcome those shortcomings. Using two blinded sets of urine replicates and a certified amino acid standard, we compared the precision and accuracy of gas chromatography/mass spectrometry (GC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) of propyl chloroformate and iTRAQ® derivatized amino acids, respectively, to conventional amino acid analysis. The GC-MS method builds on the direct derivatization of amino acids in diluted urine with propyl chloroformate, GC separation and mass spectrometric quantification of derivatives using stable isotope labeled standards. The LC-MS/MS method requires prior urinary protein precipitation followed by labeling of urinary and standard amino acids with iTRAQ® tags containing different cleavable reporter ions distinguishable by MS/MS fragmentation. Means and standard deviations of percent technical error (%TE) computed for 20 amino acids determined by amino acid analyzer, GC-MS, and iTRAQ®-LC-MS/MS analyses of 33 duplicate and triplicate urine specimens were 7.27±5.22, 21.18±10.94, and 18.34±14.67, respectively. Corresponding values for 13 amino acids determined in a second batch of 144 urine specimens measured in duplicate or triplicate were 8.39±5.35, 6.23±3.84, and 35.37±29.42. Both GC-MS and iTRAQ®-LC-MS/MS are suited for high-throughput amino acid analysis, with the former offering at present higher reproducibility and completely automated sample pretreatment, while the latter covers more amino acids and related amines. PMID:19481989

Urinary amino acid analysis: a comparison of iTRAQ-LC-MS/MS, GC-MS, and amino acid analyzer.

PubMed

Kaspar, Hannelore; Dettmer, Katja; Chan, Queenie; Daniels, Scott; Nimkar, Subodh; Daviglus, Martha L; Stamler, Jeremiah; Elliott, Paul; Oefner, Peter J

2009-07-01

Urinary amino acid analysis is typically done by cation-exchange chromatography followed by post-column derivatization with ninhydrin and UV detection. This method lacks throughput and specificity. Two recently introduced stable isotope ratio mass spectrometric methods promise to overcome those shortcomings. Using two blinded sets of urine replicates and a certified amino acid standard, we compared the precision and accuracy of gas chromatography/mass spectrometry (GC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) of propyl chloroformate and iTRAQ derivatized amino acids, respectively, to conventional amino acid analysis. The GC-MS method builds on the direct derivatization of amino acids in diluted urine with propyl chloroformate, GC separation and mass spectrometric quantification of derivatives using stable isotope labeled standards. The LC-MS/MS method requires prior urinary protein precipitation followed by labeling of urinary and standard amino acids with iTRAQ tags containing different cleavable reporter ions distinguishable by MS/MS fragmentation. Means and standard deviations of percent technical error (%TE) computed for 20 amino acids determined by amino acid analyzer, GC-MS, and iTRAQ-LC-MS/MS analyses of 33 duplicate and triplicate urine specimens were 7.27+/-5.22, 21.18+/-10.94, and 18.34+/-14.67, respectively. Corresponding values for 13 amino acids determined in a second batch of 144 urine specimens measured in duplicate or triplicate were 8.39+/-5.35, 6.23+/-3.84, and 35.37+/-29.42. Both GC-MS and iTRAQ-LC-MS/MS are suited for high-throughput amino acid analysis, with the former offering at present higher reproducibility and completely automated sample pretreatment, while the latter covers more amino acids and related amines.

Superabsorbent biphasic system based on poly(lactic acid) and poly(acrylic acid)

NASA Astrophysics Data System (ADS)

Sartore, Luciana; Pandini, Stefano; Baldi, Francesco; Bignotti, Fabio

2016-05-01

In this research work, biocomposites based on crosslinked particles of poly(acrylic acid), commonly used as superabsorbent polymer (SAP), and poly-L-lactic acid (PLLA) were developed to elucidate the role of the filler (i.e., polymeric crosslinked particles) on the overall physico-mechanical behavior and to obtain superabsorbent thermoplastic products. Samples prepared by melt-blending of components in different ratios showed a biphasic system with a regular distribution of particles, with diameter ranging from 5 to 10 μm, within the PLLA polymeric matrix. The polymeric biphasic system, coded PLASA i.e. superabsorbent poly(lactic acid), showed excellent swelling properties, demonstrating that cross-linked particles retain their superabsorbent ability, as in their free counterparts, even if distributed in a thermoplastic polymeric matrix. The thermal characteristics of the biocomposites evidence enhanced thermal stability in comparison with neat PLLA and also mechanical properties are markedly modified by addition of crosslinked particles which induce regular stiffening effect. Furthermore, in aqueous environments the particles swell and are leached from PLLA matrix generating very high porosity. These new open-pore PLLA foams, produced in absence of organic solvents and chemical foaming agents, with good physico-mechanical properties appear very promising for several applications, for instance in tissue engineering for scaffold production.

Why Were Polysaccharides Necessary?

NASA Astrophysics Data System (ADS)

Tolstoguzov, Vladimir

2004-12-01

The main idea of this paper is that the primordial soup may be modelled by food systems whose structure-property relationship is based on non-specific interactions between denatured biopolymers. According to the proposed hypothesis, polysaccharides were the first biopolymers that decreased concentration of salts in the primordial soup, `compatibilised' and drove the joint evolution of proto-biopolymers. Synthesis of macromolecules within the polysaccharide-rich medium could have resulted in phase separation of the primordial soup and concentration of the polypeptides and nucleic acids in the dispersed phase particles. The concentration of proto-biopolymer mixtures favoured their cross-linking in hybrid supermacromolecules of conjugates. The cross-linking of proto-biopolymers could occur by hydrophobic, electrostatic interactions, H-bonds due to freezing aqueous mixed biopolymer dispersions and/or by covalent bonds due to the Maillard reaction. Cross-linking could have increased the local concentration of chemically different proto-biopolymers, fixed their relative positions and made their interactions reproducible. Attractive-repulsive interactions between cross-linked proto-biopolymer chains could develop pairing of the monomer units, improved chemical stability (against hydrolysis) and led to their mutual catalytic activity and coding. Conjugates could probably evolve to the first self-reproduced entities and then to specialized cellular organelles. Phase separation of the primordial soup with concentration of conjugates in the dispersed particles has probably resulted in proto-cells.

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts.

PubMed

Sanford, Jeremy R; Wang, Xin; Mort, Matthew; Vanduyn, Natalia; Cooper, David N; Mooney, Sean D; Edenberg, Howard J; Liu, Yunlong

2009-03-01

Metazoan genes are encrypted with at least two superimposed codes: the genetic code to specify the primary structure of proteins and the splicing code to expand their proteomic output via alternative splicing. Here, we define the specificity of a central regulator of pre-mRNA splicing, the conserved, essential splicing factor SFRS1. Cross-linking immunoprecipitation and high-throughput sequencing (CLIP-seq) identified 23,632 binding sites for SFRS1 in the transcriptome of cultured human embryonic kidney cells. SFRS1 was found to engage many different classes of functionally distinct transcripts including mRNA, miRNA, snoRNAs, ncRNAs, and conserved intergenic transcripts of unknown function. The majority of these diverse transcripts share a purine-rich consensus motif corresponding to the canonical SFRS1 binding site. The consensus site was not only enriched in exons cross-linked to SFRS1 in vivo, but was also enriched in close proximity to splice sites. mRNAs encoding RNA processing factors were significantly overrepresented, suggesting that SFRS1 may broadly influence the post-transcriptional control of gene expression in vivo. Finally, a search for the SFRS1 consensus motif within the Human Gene Mutation Database identified 181 mutations in 82 different genes that disrupt predicted SFRS1 binding sites. This comprehensive analysis substantially expands the known roles of human SR proteins in the regulation of a diverse array of RNA transcripts.

A guide for the laboratory information management system (LIMS) for light stable isotopes--Versions 7 and 8

USGS Publications Warehouse

Coplen, Tyler B.

2000-01-01

The reliability and accuracy of isotopic data can be improved by utilizing database software to (i) store information about samples, (ii) store the results of mass spectrometric isotope-ratio analyses of samples, (iii) calculate analytical results using standardized algorithms stored in a database, (iv) normalize stable isotopic data to international scales using isotopic reference materials, and (v) generate multi-sheet paper templates for convenient sample loading of automated mass-spectrometer sample preparation manifolds. Such a database program, the Laboratory Information Management System (LIMS) for Light Stable Isotopes, is presented herein. Major benefits of this system include (i) a dramatic improvement in quality assurance, (ii) an increase in laboratory efficiency, (iii) a reduction in workload due to the elimination or reduction of retyping of data by laboratory personnel, and (iv) a decrease in errors in data reported to sample submitters. Such a database provides a complete record of when and how often laboratory reference materials have been analyzed and provides a record of what correction factors have been used through time. It provides an audit trail for laboratories. LIMS for Light Stable Isotopes is available for both Microsoft Office 97 Professional and Microsoft Office 2000 Professional as versions 7 and 8, respectively. Both source code (mdb file) and precompiled executable files (mde) are available. Numerous improvements have been made for continuous flow isotopic analysis in this version (specifically 7.13 for Microsoft Access 97 and 8.13 for Microsoft Access 2000). It is much easier to import isotopic results from Finnigan ISODAT worksheets, even worksheets on which corrections for amount of sample (linearity corrections) have been added. The capability to determine blank corrections using isotope mass balance from analyses of elemental analyzer samples has been added. It is now possible to calculate and apply drift corrections to isotopic data based on the time of day of analysis. Whereas Finnigan ISODAT software is confined to using only a single peak for calculating delta values, LIMS now enables one to use the mean of two or more reference injections during a continuous flow analysis to calculate delta values. This is useful with Finnigan?s GasBench II online sample preparation system. Concentrations of carbon, nitrogen, and sulfur can be calculated based one or more isotopic reference materials analyzed with a group of samples. Both sample data and isotopic analysis data can now be exported to Excel files. A calculator for determining the amount of sample needed for isotopic analysis based on a previous amount of sample and continuous flow area is now an integral part of LIMS for Light Stable Isotopes. LIMS for Light Stable Isotopes can now assign an error code to Finnigan elemental analyzer analyses in which one of the electrometers has saturated due to analysis of too much sample material, giving rise to incorrect isotopic abundances. Information on downloading this report and downloading code and databases is provided at the Internet addresses: http://water.usgs.gov/software/geochemical.html or http://www.geogr.uni-jena.de/software/geochemical.html in the Eastern Hemisphere.

Mapping the local protein interactome of the NuA3 histone acetyltransferase

PubMed Central

Smart, Sherri K; Mackintosh, Samuel G; Edmondson, Ricky D; Taverna, Sean D; Tackett, Alan J

2009-01-01

Protein–protein interactions modulate cellular functions ranging from the activity of enzymes to signal transduction cascades. A technology termed transient isotopic differentiation of interactions as random or targeted (transient I-DIRT) is described for the identification of stable and transient protein–protein interactions in vivo. The procedure combines mild in vivo chemical cross-linking and non-stringent affinity purification to isolate low abundance chromatin-associated protein complexes. Using isotopic labeling and mass spectrometric readout, purified proteins are categorized with respect to the protein ‘bait’ as stable, transient, or contaminant. Here we characterize the local interactome of the chromatin-associated NuA3 histone lysine-acetyltransferase protein complex. We describe transient associations with the yFACT nucleosome assembly complex, RSC chromatin remodeling complex and a nucleosome assembly protein. These novel, physical associations with yFACT, RSC, and Nap1 provide insight into the mechanism of NuA3-associated transcription and chromatin regulation. PMID:19621382

Efficient production of native lunasin with correct N-terminal processing by using the pH-induced self-cleavable Ssp DnaB mini-intein system in Escherichia coli.

PubMed

Setrerrahmane, Sarra; Zhang, Yi; Dai, Guangzhi; Lv, Jing; Tan, Shuhua

2014-09-01

To develop an efficient and cost-effective approach for the production of small preventive peptide lunasin with correct natural N terminus, a synthetic gene was designed by OPTIMIZER & Gene Designer and cloned into pTWIN1 vector at SapI and PstI sites. Thus, lunasin was N-terminally fused to the pH-induced self-cleavable Ssp DnaB mini-intein linked to a chitin binding domain (CBD) with no extra residues. The resultant fusion protein was highly expressed by lactose induction in Escherichia coli BL21 (DE3) in a 7-l bioreactor and bound to a chitin affinity column. After washing the impurities, the Ssp DnaB intein mediated on-column self-cleavage was easily triggered by shifting pH and temperature to allow the native lunasin released. The final purified lunasin yielded up to 75 mg/l medium. Tricine/SDS-PAGE and matrix-assisted laser desorption time-of-flight (MALDI-TOF)/mass spectrometry (MS) verified the structural authenticity of the product, implying the correct cleavage at the junction between Ssp DnaB intein and lunasin. MTT assay confirmed its potent proliferation inhibitory activity to human cancer cells HCT-116 and MDA-MB-231; however, no cytotoxicity to normal human lens epithelial cell SRA01/04 and hepatoma HepG2. Taken together, we provide a novel strategy to produce recombinant native lunasin with correct N-terminal processing by using the pH-induced self-cleavable Ssp DnaB mini-intein.

In situ fabrication of cleavable peptide arrays on polydimethylsiloxane and applications for kinase activity assays.

PubMed

Chen, Huang-Han; Hsiao, Yu-Chieh; Li, Jie-Ren; Chen, Shu-Hui

2015-03-20

Polydimethylsiloxane (PDMS) is widely used for microfabrication and bioanalysis; however, its surface functionalization is limited due to the lack of active functional groups and incompatibility with many solvents. We presented a novel approach for in situ fabrication of cleavable peptide arrays on polydimethylsiloxane (PDMS) viatert-butyloxycarbonyl (t-Boc)/trifluoroacetic acid (TFA) chemistry using gold nanoparticles (AuNPs) as the anchor and a disulfide/amine terminated hetero-polyethylene glycol as the cleavable linker. The method was fine tuned to use reagents compatible with the PDMS. Using 5-mer pentapeptide, Trp5, as a model, step-by-step covalent coupling during the reaction cycles was monitored by Attenuated total reflectance-Fourier transform infrared spectrometer (ATR-FTIR), X-ray photoelectron spectroscopy (XPS), or atomic force microscopy (AFM), and further confirmed by mass spectrometry (MS) detection of the cleaved peptides. Using such a method, heptapeptides of the PKA substrate, LRRASLG (Kemptide), and its point mutated analogs were fabricated in an array format for comparative studies of cAMP-dependent protein kinase (PKA) activity. Based on on-chip detection, Kemptide sequence exhibited the highest phosphorylation activity, which was detected to a 1.5-time lesser extent for the point mutated sequence (LRRGSLG) containing the recognition motif (RRXS), and was nearly undetectable for another point mutated sequence (LRLASLG) that lacked the recognition motif. These results indicate that the reported fabrication method is able to yield highly specific peptide sequences on PDMS, leading to a highly motif-sensitive enzyme activity assay. Copyright © 2015 Elsevier B.V. All rights reserved.

[Poisons of DNA topoisomerases I and II].

PubMed

Charcosset, J Y; Soues, S; Laval, F

1993-11-01

Over the past decade, DNA topoisomerase I and II appeared to be the targets of some antitumor agents: CPT-11 and Topotecan derived from Camptothecin which interact with topoisomerase I; Actinomycin D, Adriamycin and Daunorubicin, Elliptinium Acetate, Mitoxantrone, Etoposide and Teniposide, Amsacrine which interact with topoisomerase II. The multiple functions of these enzymes are important as they play a role during replication, transcription, recombination, repair and chromatine organisation. Particularly, they relax torsional constraints which appear when intertwined DNA strands are separated while replication fork or RNA polymerases are moving. To some extent, topoisomerase I and II are structurally and functionally different. Moreover, topoisomerase I is not indispensable for a living cell whereas topoisomerase II is. Drug-topoisomerase interaction which probably leads to antitumoral effect of the compounds studied in this review is not a trivial inhibition of the enzyme but rather a poisoning due to stabilization of cleavable complexes between the enzyme and DNA. These stabilized complexes are likely to induce apoptosis-like programmed cell death, which is characterised by DNA fragmentation. However, it appears that it is the collision of the replication fork with the drug-stabilized cleavable complex that is responsible for the cytotoxicity of the drug: poisoning of topoisomerases by antitumor agents leads to a new concept of "dynamic toxicity". Although they interact with a common target, topoisomerase II poisons have differential effects on macromolecules syntheses, cell cycle and chromosome fragmentation; a few compounds may produce free radicals. Because of these differential effects in addition to quantitative and qualitative variations of stabilized cleavable complexes, in particular DNA sequences on which topoisomerase II is stabilized, these antitumor agents do not resemble each other. Cellular resistance to topoisomerases poisons results of two principal types of alteration: target and/or drug transport modification. Decreased ability to form the cleavable complex in resistant cells may be the consequence of both decreased amount of topoisomerase or altered enzyme. On the other hand, overexpression of membrane P-glycoprotein, which pumps drugs out of the cell by an energy dependent process provokes a decreased accumulation of these drugs. Cross resistances to other drugs are mainly under control of these two different mechanisms of resistance. A complete knowledge of their individual effects and mechanisms of resistance would allow a better clinical use of topoisomerases poisons, especially when administered in combination chemotherapy.

Relative and accurate measurement of protein abundance using 15N stable isotope labeling in Arabidopsis (SILIA).

PubMed

Guo, Guangyu; Li, Ning

2011-07-01

In the quantitative proteomic studies, numerous in vitro and in vivo peptide labeling strategies have been successfully applied to measure differentially regulated protein and peptide abundance. These approaches have been proven to be versatile and repeatable in biological discoveries. (15)N metabolic labeling is one of these widely adopted and economical methods. However, due to the differential incorporation rates of (15)N or (14)N, the labeling results produce imperfectly matched isotopic envelopes between the heavy and light nitrogen-labeled peptides. In the present study, we have modified the solid Arabidopsis growth medium to standardize the (15)N supply, which led to a uniform incorporation of (15)N into the whole plant protein complement. The incorporation rate (97.43±0.11%) of (15)N into (15)N-coded peptides was determined by correlating the intensities of peptide ions with the labeling efficiencies according to Gaussian distribution. The resulting actual incorporation rate (97.44%) and natural abundance of (15)N/(14)N-coded peptides are used to re-calculate the intensities of isotopic envelopes of differentially labeled peptides, respectively. A modified (15)N/(14)N stable isotope labeling strategy, SILIA, is assessed and the results demonstrate that this approach is able to differentiate the fold change in protein abundance down to 10%. The machine dynamic range limitation and purification step will make the precursor ion ratio deriving from the actual ratio fold change. It is suggested that the differentially mixed (15)N-coded and (14)N-coded plant protein samples that are used to establish the protein abundance standard curve should be prepared following a similar protein isolation protocol used to isolate the proteins to be quantitated. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

Update and evaluation of decay data for spent nuclear fuel analyses

NASA Astrophysics Data System (ADS)

Simeonov, Teodosi; Wemple, Charles

2017-09-01

Studsvik's approach to spent nuclear fuel analyses combines isotopic concentrations and multi-group cross-sections, calculated by the CASMO5 or HELIOS2 lattice transport codes, with core irradiation history data from the SIMULATE5 reactor core simulator and tabulated isotopic decay data. These data sources are used and processed by the code SNF to predict spent nuclear fuel characteristics. Recent advances in the generation procedure for the SNF decay data are presented. The SNF decay data includes basic data, such as decay constants, atomic masses and nuclide transmutation chains; radiation emission spectra for photons from radioactive decay, alpha-n reactions, bremsstrahlung, and spontaneous fission, electrons and alpha particles from radioactive decay, and neutrons from radioactive decay, spontaneous fission, and alpha-n reactions; decay heat production; and electro-atomic interaction data for bremsstrahlung production. These data are compiled from fundamental (ENDF, ENSDF, TENDL) and processed (ESTAR) sources for nearly 3700 nuclides. A rigorous evaluation procedure of internal consistency checks and comparisons to measurements and benchmarks, and code-to-code verifications is performed at the individual isotope level and using integral characteristics on a fuel assembly level (e.g., decay heat, radioactivity, neutron and gamma sources). Significant challenges are presented by the scope and complexity of the data processing, a dearth of relevant detailed measurements, and reliance on theoretical models for some data.

Physics of the Isotopic Dependence of Galactic Cosmic Ray Fluence Behind Shielding

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Saganti, Premkumar B.; Hu, Xiao-Dong; Kim, Myung-Hee Y.; Cleghorn, Timothy F.; Wilson, John W.; Tripathi, Ram K.; Zeitlin, Cary J.

2003-01-01

For over 25 years, NASA has supported the development of space radiation transport models for shielding applications. The NASA space radiation transport model now predicts dose and dose equivalent in Earth and Mars orbit to an accuracy of plus or minus 20%. However, because larger errors may occur in particle fluence predictions, there is interest in further assessments and improvements in NASA's space radiation transport model. In this paper, we consider the effects of the isotopic composition of the primary galactic cosmic rays (GCR) and the isotopic dependence of nuclear fragmentation cross-sections on the solution to transport models used for shielding studies. Satellite measurements are used to describe the isotopic composition of the GCR. Using NASA's quantum multiple-scattering theory of nuclear fragmentation (QMSFRG) and high-charge and energy (HZETRN) transport code, we study the effect of the isotopic dependence of the primary GCR composition and secondary nuclei on shielding calculations. The QMSFRG is shown to accurately describe the iso-spin dependence of nuclear fragmentation. The principal finding of this study is that large errors (plus or minus 100%) will occur in the mass-fluence spectra when comparing transport models that use a complete isotope grid (approximately 170 ions) to ones that use a reduced isotope grid, for example the 59 ion-grid used in the HZETRN code in the past, however less significant errors (less than 20%) occur in the elemental-fluence spectra. Because a complete isotope grid is readily handled on small computer workstations and is needed for several applications studying GCR propagation and scattering, it is recommended that they be used for future GCR studies.

Automated determination of the stable carbon isotopic composition (δ13C) of total dissolved inorganic carbon (DIC) and total nonpurgeable dissolved organic carbon (DOC) in aqueous samples: RSIL lab codes 1851 and 1852

USGS Publications Warehouse

Révész, Kinga M.; Doctor, Daniel H.

2014-01-01

The purposes of the Reston Stable Isotope Laboratory (RSIL) lab codes 1851 and 1852 are to determine the total carbon mass and the ratio of the stable isotopes of carbon (δ13C) for total dissolved inorganic carbon (DIC, lab code 1851) and total nonpurgeable dissolved organic carbon (DOC, lab code 1852) in aqueous samples. The analysis procedure is automated according to a method that utilizes a total carbon analyzer as a peripheral sample preparation device for analysis of carbon dioxide (CO2) gas by a continuous-flow isotope ratio mass spectrometer (CF-IRMS). The carbon analyzer produces CO2 and determines the carbon mass in parts per million (ppm) of DIC and DOC in each sample separately, and the CF-IRMS determines the carbon isotope ratio of the produced CO2. This configuration provides a fully automated analysis of total carbon mass and δ13C with no operator intervention, additional sample preparation, or other manual analysis. To determine the DIC, the carbon analyzer transfers a specified sample volume to a heated (70 °C) reaction vessel with a preprogrammed volume of 10% phosphoric acid (H3PO4), which allows the carbonate and bicarbonate species in the sample to dissociate to CO2. The CO2 from the reacted sample is subsequently purged with a flow of helium gas that sweeps the CO2 through an infrared CO2 detector and quantifies the CO2. The CO2 is then carried through a high-temperature (650 °C) scrubber reactor, a series of water traps, and ultimately to the inlet of the mass spectrometer. For the analysis of total dissolved organic carbon, the carbon analyzer performs a second step on the sample in the heated reaction vessel during which a preprogrammed volume of sodium persulfate (Na2S2O8) is added, and the hydroxyl radicals oxidize the organics to CO2. Samples containing 2 ppm to 30,000 ppm of carbon are analyzed. The precision of the carbon isotope analysis is within 0.3 per mill for DIC, and within 0.5 per mill for DOC.

Accumulation and processing of a recombinant protein designed as a cleavable fusion to the endogenous Rubisco LSU protein in Chlamydomonas chloroplast

PubMed Central

Muto, Machiko; Henry, Ryan E; Mayfield, Stephen P

2009-01-01

Background Expression of recombinant proteins in green algal chloroplast holds substantial promise as a platform for the production of human therapeutic proteins. A number of proteins have been expressed in the chloroplast of Chlamydomonas reinhardtii, including complex mammalian proteins, but many of these proteins accumulate to significantly lower levels than do endogenous chloroplast proteins. We examined if recombinant protein accumulation could be enhanced by genetically fusing the recombinant reporter protein, luciferase, to the carboxy-terminal end of an abundant endogenous protein, the large subunit of ribulose bisphosphate carboxylase (Rubisco LSU). Additionally, as recombinant proteins fused to endogenous proteins are of little clinical or commercial value, we explored the possibility of engineering our recombinant protein to be cleavable from the endogenous protein in vivo. This strategy would obviate the need for further in vitro processing steps in order to produce the desired recombinant protein. To achieve this, a native protein-processing site from preferredoxin (preFd) was placed between the Rubisco LSU and luciferase coding regions in the fusion protein construct. Results The luciferase from the fusion protein accumulated to significantly higher levels than luciferase expressed alone. By eliminating the endogenous Rubisco large subunit gene (rbcL), we achieved a further increase in luciferase accumulation with respect to luciferase expression in the WT background. Importantly, near-wild type levels of functional Rubisco holoenzyme were generated following the proteolytic removal of the fused luciferase, while luciferase activity for the fusion protein was almost ~33 times greater than luciferase expressed alone. These data demonstrate the utility of using fusion proteins to enhance recombinant protein accumulation in algal chloroplasts, and also show that engineered proteolytic processing sites can be used to liberate the exogenous protein from the endogenous fusion partner, allowing for the purification of the intended mature protein. Conclusion These results demonstrate the utility of fusion proteins in algal chloroplast as a method to increase accumulation of recombinant proteins that are difficult to express. Since Rubisco is ubiquitous to land plants and green algae, this strategy may also be applied to higher plant transgenic expression systems. PMID:19323825

A Potential Mechanism for ADC-Induced Neutropenia: Role of Neutrophils in Their Own Demise.

PubMed

Zhao, Hui; Gulesserian, Sara; Malinao, Maria Christina; Ganesan, Sathish Kumar; Song, James; Chang, Mi Sook; Williams, Melissa M; Zeng, Zhilan; Mattie, Michael; Mendelsohn, Brian A; Stover, David R; Doñate, Fernando

2017-09-01

Neutropenia is a common adverse event in cancer patients treated with antibody-drug conjugates (ADC) and we aimed to elucidate the potential mechanism of this toxicity. To investigate whether ADCs affect neutrophil production from bone marrow, an in vitro assay was developed in which hematopoietic stem cells (HSC) were differentiated to neutrophils. Several antibodies against targets absent in HSCs and neutrophils were conjugated to MMAE via a cleavable valine-citrulline linker (vcMMAE-ADC) or MMAF via a noncleavable maleimidocaproyl linker (mcMMAF-ADC), and their cytotoxicity was tested in the neutrophil differentiation assay. Results showed that HSCs had similar sensitivity to vcMMAE-ADCs and mcMMAF-ADCs; however, vcMMAE-ADCs were more cytotoxic to differentiating neutrophils than the same antibody conjugated to mcMMAF. This inhibitory effect was not mediated by internalization of ADC either by macropinocytosis or FcγRs. Our results suggested that extracellular proteolysis of the cleavable valine-citrulline linker is responsible for the cytotoxicity to differentiating neutrophils. Mass spectrometry analyses indicated that free MMAE was released from vcMMAE-ADCs in the extracellular compartment when they were incubated with differentiating neutrophils or neutrophil conditioned medium, but not with HSC-conditioned medium. Using different protease inhibitors, our data suggested that serine, but not cysteine proteases, were responsible for the cleavage. In vitro experiments demonstrated that the purified serine protease, elastase, was capable of releasing free MMAE from a vcMMAE-ADC. Here we propose that ADCs containing protease cleavable linkers can contribute to neutropenia via extracellular cleavage mediated by serine proteases secreted by differentiating neutrophils in bone marrow. Mol Cancer Ther; 16(9); 1866-76. ©2017 AACR See related article by Zhao et al., p. 1877 . ©2017 American Association for Cancer Research.

Aqueous Processing for Printed Organic Electronics: Conjugated Polymers with Multistage Cleavable Side Chains

PubMed Central

2017-01-01

The ability to process conjugated polymers via aqueous solution is highly advantageous for reducing the costs and environmental hazards of large scale roll-to-roll processing of organic electronics. However, maintaining competitive electronic properties while achieving aqueous solubility is difficult for several reasons: (1) Materials with polar functional groups that provide aqueous solubility can be difficult to purify and characterize, (2) many traditional coupling and polymerization reactions cannot be performed in aqueous solution, and (3) ionic groups, though useful for obtaining aqueous solubility, can lead to a loss of solid-state order, as well as a screening of any applied bias. As an alternative, we report a multistage cleavable side chain method that combines desirable aqueous processing attributes without sacrificing semiconducting capabilities. Through the attachment of cleavable side chains, conjugated polymers have for the first time been synthesized, characterized, and purified in organic solvents, converted to a water-soluble form for aqueous processing, and brought through a final treatment to cleave the polymer side chains and leave behind the desired electronic material as a solvent-resistant film. Specifically, we demonstrate an organic soluble polythiophene that is converted to an aqueous soluble polyelectrolyte via hydrolysis. After blade coating from an aqueous solution, UV irradiation is used to cleave the polymer’s side chains, resulting in a solvent-resistant, electroactive polymer thin film. In application, this process results in aqueous printed materials with utility for solid-state charge transport in organic field effect transistors (OFETs), along with red to colorless electrochromism in ionic media for color changing displays, demonstrating its potential as a universal method for aqueous printing in organic electronics. PMID:28979937

Aqueous Processing for Printed Organic Electronics: Conjugated Polymers with Multistage Cleavable Side Chains.

PubMed

Schmatz, Brian; Yuan, Zhibo; Lang, Augustus W; Hernandez, Jeff L; Reichmanis, Elsa; Reynolds, John R

2017-09-27

The ability to process conjugated polymers via aqueous solution is highly advantageous for reducing the costs and environmental hazards of large scale roll-to-roll processing of organic electronics. However, maintaining competitive electronic properties while achieving aqueous solubility is difficult for several reasons: (1) Materials with polar functional groups that provide aqueous solubility can be difficult to purify and characterize, (2) many traditional coupling and polymerization reactions cannot be performed in aqueous solution, and (3) ionic groups, though useful for obtaining aqueous solubility, can lead to a loss of solid-state order, as well as a screening of any applied bias. As an alternative, we report a multistage cleavable side chain method that combines desirable aqueous processing attributes without sacrificing semiconducting capabilities. Through the attachment of cleavable side chains, conjugated polymers have for the first time been synthesized, characterized, and purified in organic solvents, converted to a water-soluble form for aqueous processing, and brought through a final treatment to cleave the polymer side chains and leave behind the desired electronic material as a solvent-resistant film. Specifically, we demonstrate an organic soluble polythiophene that is converted to an aqueous soluble polyelectrolyte via hydrolysis. After blade coating from an aqueous solution, UV irradiation is used to cleave the polymer's side chains, resulting in a solvent-resistant, electroactive polymer thin film. In application, this process results in aqueous printed materials with utility for solid-state charge transport in organic field effect transistors (OFETs), along with red to colorless electrochromism in ionic media for color changing displays, demonstrating its potential as a universal method for aqueous printing in organic electronics.

Re-evaluation of Spent Nuclear Fuel Assay Data for the Three Mile Island Unit 1 Reactor and Application to Code Validation

DOE PAGES

Gauld, Ian C.; Giaquinto, J. M.; Delashmitt, J. S.; ...

2016-01-01

Destructive radiochemical assay measurements of spent nuclear fuel rod segments from an assembly irradiated in the Three Mile Island unit 1 (TMI-1) pressurized water reactor have been performed at Oak Ridge National Laboratory (ORNL). Assay data are reported for five samples from two fuel rods of the same assembly. The TMI-1 assembly was a 15 X 15 design with an initial enrichment of 4.013 wt% 235U, and the measured samples achieved burnups between 45.5 and 54.5 gigawatt days per metric ton of initial uranium (GWd/t). Measurements were performed mainly using inductively coupled plasma mass spectrometry after elemental separation via highmore » performance liquid chromatography. High precision measurements were achieved using isotope dilution techniques for many of the lanthanides, uranium, and plutonium isotopes. Measurements are reported for more than 50 different isotopes and 16 elements. One of the two TMI-1 fuel rods measured in this work had been measured previously by Argonne National Laboratory (ANL), and these data have been widely used to support code and nuclear data validation. Recently, ORNL provided an important opportunity to independently cross check results against previous measurements performed at ANL. The measured nuclide concentrations are used to validate burnup calculations using the SCALE nuclear systems modeling and simulation code suite. These results show that the new measurements provide reliable benchmark data for computer code validation.« less

Determination of the delta(2H/1H)of Water: RSIL Lab Code 1574

USGS Publications Warehouse

Revesz, Kinga; Coplen, Tyler B.

2008-01-01

Reston Stable Isotope Laboratory (RSIL) lab code 1574 describes a method used to determine the relative hydrogen isotope-ratio delta(2H,1H), abbreviated hereafter as d2H of water. The d2H measurement of water also is a component of the National Water Quality Laboratory (NWQL) schedules 1142 and 1172. The water is collected unfiltered in a 60-mL glass bottle and capped with a Polyseal cap. In the laboratory, the water sample is equilibrated with gaseous hydrogen using a platinum catalyst (Horita, 1988; Horita and others, 1989; Coplen and others, 1991). The reaction for the exchange of one hydrogen atom is shown in equation 1.

NeuCode Labeling in Nematodes: Proteomic and Phosphoproteomic Impact of Ascaroside Treatment in Caenorhabditis elegans*

PubMed Central

Rhoads, Timothy W.; Prasad, Aman; Kwiecien, Nicholas W.; Merrill, Anna E.; Zawack, Kelson; Westphall, Michael S.; Schroeder, Frank C.; Kimble, Judith; Coon, Joshua J.

2015-01-01

The nematode Caenorhabditis elegans is an important model organism for biomedical research. We previously described NeuCode stable isotope labeling by amino acids in cell culture (SILAC), a method for accurate proteome quantification with potential for multiplexing beyond the limits of traditional stable isotope labeling by amino acids in cell culture. Here we apply NeuCode SILAC to profile the proteomic and phosphoproteomic response of C. elegans to two potent members of the ascaroside family of nematode pheromones. By consuming labeled E. coli as part of their diet, C. elegans nematodes quickly and easily incorporate the NeuCode heavy lysine isotopologues by the young adult stage. Using this approach, we report, at high confidence, one of the largest proteomic and phosphoproteomic data sets to date in C. elegans: 6596 proteins at a false discovery rate ≤ 1% and 6620 phosphorylation isoforms with localization probability ≥75%. Our data reveal a post-translational signature of pheromone sensing that includes many conserved proteins implicated in longevity and response to stress. PMID:26392051

Production of medical isotopes from a thorium target irradiated by light charged particles up to 70 MeV

NASA Astrophysics Data System (ADS)

Duchemin, C.; Guertin, A.; Haddad, F.; Michel, N.; Métivier, V.

2015-02-01

The irradiation of a thorium target by light charged particles (protons and deuterons) leads to the production of several isotopes of medical interest. Direct nuclear reaction allows the production of Protactinium-230 which decays to Uranium-230 the mother nucleus of Thorium-226, a promising isotope for alpha radionuclide therapy. The fission of Thorium-232 produces fragments of interest like Molybdenum-99, Iodine-131 and Cadmium-115g. We focus our study on the production of these isotopes, performing new cross section measurements and calculating production yields. Our new sets of data are compared with the literature and the last version of the TALYS code.

Production of medical isotopes from a thorium target irradiated by light charged particles up to 70 MeV.

PubMed

Duchemin, C; Guertin, A; Haddad, F; Michel, N; Métivier, V

2015-02-07

The irradiation of a thorium target by light charged particles (protons and deuterons) leads to the production of several isotopes of medical interest. Direct nuclear reaction allows the production of Protactinium-230 which decays to Uranium-230 the mother nucleus of Thorium-226, a promising isotope for alpha radionuclide therapy. The fission of Thorium-232 produces fragments of interest like Molybdenum-99, Iodine-131 and Cadmium-115g. We focus our study on the production of these isotopes, performing new cross section measurements and calculating production yields. Our new sets of data are compared with the literature and the last version of the TALYS code.

Energy-Constrained Recharge, Assimilation, and Fractional Crystallization (EC-RAχFC): A Visual Basic computer code for calculating trace element and isotope variations of open-system magmatic systems

NASA Astrophysics Data System (ADS)

Bohrson, Wendy A.; Spera, Frank J.

2007-11-01

Volcanic and plutonic rocks provide abundant evidence for complex processes that occur in magma storage and transport systems. The fingerprint of these processes, which include fractional crystallization, assimilation, and magma recharge, is captured in petrologic and geochemical characteristics of suites of cogenetic rocks. Quantitatively evaluating the relative contributions of each process requires integration of mass, species, and energy constraints, applied in a self-consistent way. The energy-constrained model Energy-Constrained Recharge, Assimilation, and Fractional Crystallization (EC-RaχFC) tracks the trace element and isotopic evolution of a magmatic system (melt + solids) undergoing simultaneous fractional crystallization, recharge, and assimilation. Mass, thermal, and compositional (trace element and isotope) output is provided for melt in the magma body, cumulates, enclaves, and anatectic (i.e., country rock) melt. Theory of the EC computational method has been presented by Spera and Bohrson (2001, 2002, 2004), and applications to natural systems have been elucidated by Bohrson and Spera (2001, 2003) and Fowler et al. (2004). The purpose of this contribution is to make the final version of the EC-RAχFC computer code available and to provide instructions for code implementation, description of input and output parameters, and estimates of typical values for some input parameters. A brief discussion highlights measures by which the user may evaluate the quality of the output and also provides some guidelines for implementing nonlinear productivity functions. The EC-RAχFC computer code is written in Visual Basic, the programming language of Excel. The code therefore launches in Excel and is compatible with both PC and MAC platforms. The code is available on the authors' Web sites http://magma.geol.ucsb.edu/and http://www.geology.cwu.edu/ecrafc) as well as in the auxiliary material.

Isotopic anomalies from neutron reactions during explosive carbon burning

NASA Technical Reports Server (NTRS)

Lee, T.; Schramm, D. N.; Wefel, J. P.; Blake, J. B.

1978-01-01

The possibility that the newly discovered correlated isotopic anomalies for heavy elements in the Allende meteorite were synthesized in the secondary neutron capture episode during the explosive carbon burning, the possible source of the O-16 and Al-26 anomalies, is examined. Explosive carbon burning calculations under typical conditions were first performed to generate time profiles of temperature, density, and free particle concentrations. These quantities were inputted into a general neutron capture code which calculates the resulting isotopic pattern from exposing the preexisting heavy seed nuclei to these free particles during the explosive carbon burning conditions. The interpretation avoids the problem of the Sr isotopic data and may resolve the conflict between the time scales inferred from 1-129, Pu-244, and Al-26.

ICT: isotope correction toolbox.

PubMed

Jungreuthmayer, Christian; Neubauer, Stefan; Mairinger, Teresa; Zanghellini, Jürgen; Hann, Stephan

2016-01-01

Isotope tracer experiments are an invaluable technique to analyze and study the metabolism of biological systems. However, isotope labeling experiments are often affected by naturally abundant isotopes especially in cases where mass spectrometric methods make use of derivatization. The correction of these additive interferences--in particular for complex isotopic systems--is numerically challenging and still an emerging field of research. When positional information is generated via collision-induced dissociation, even more complex calculations for isotopic interference correction are necessary. So far, no freely available tools can handle tandem mass spectrometry data. We present isotope correction toolbox, a program that corrects tandem mass isotopomer data from tandem mass spectrometry experiments. Isotope correction toolbox is written in the multi-platform programming language Perl and, therefore, can be used on all commonly available computer platforms. Source code and documentation can be freely obtained under the Artistic License or the GNU General Public License from: https://github.com/jungreuc/isotope_correction_toolbox/ {christian.jungreuthmayer@boku.ac.at,juergen.zanghellini@boku.ac.at} Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Glycan reductive isotope labeling for quantitative glycomics.

PubMed

Xia, Baoyun; Feasley, Christa L; Sachdev, Goverdhan P; Smith, David F; Cummings, Richard D

2009-04-15

Many diseases and disorders are characterized by quantitative and/or qualitative changes in complex carbohydrates. Mass spectrometry methods show promise in monitoring and detecting these important biological changes. Here we report a new glycomics method, termed glycan reductive isotope labeling (GRIL), where free glycans are derivatized by reductive amination with the differentially coded stable isotope tags [(12)C(6)]aniline and [(13)C(6)]aniline. These dual-labeled aniline-tagged glycans can be recovered by reverse-phase chromatography and can be quantified based on ultraviolet (UV) absorbance and relative ion abundances. Unlike previously reported isotopically coded reagents for glycans, GRIL does not contain deuterium, which can be chromatographically resolved. Our method shows no chromatographic resolution of differentially labeled glycans. Mixtures of differentially tagged glycans can be directly compared and quantified using mass spectrometric techniques. We demonstrate the use of GRIL to determine relative differences in glycan amount and composition. We analyze free glycans and glycans enzymatically or chemically released from a variety of standard glycoproteins, as well as human and mouse serum glycoproteins, using this method. This technique allows linear relative quantitation of glycans over a 10-fold concentration range and can accurately quantify sub-picomole levels of released glycans, providing a needed advancement in the field of glycomics.

GLYCAN REDUCTIVE ISOTOPE LABELING (GRIL) FOR QUANTITATIVE GLYCOMICS

PubMed Central

Xia, Baoyun; Feasley, Christa L.; Sachdev, Goverdhan P.; Smith, David F.; Cummings, Richard D.

2009-01-01

Many diseases and disorders are characterized by quantitative and/or qualitative changes in complex carbohydrates. Mass spectrometry methods show promise in monitoring and detecting these important biological changes. Here we report a new glycomics method, termed Glycan Reductive Isotope Labeling (GRIL), where free glycans are derivatized by reductive amination with the differentially coded stable isotope tags [12C6]-aniline and [13C6]-aniline. These dual-labeled aniline-tagged glycans can be recovered by reversed-phase chromatography and quantified based on UV-absorbance and relative ion abundances. Unlike previously reported isotopically coded reagents for glycans, GRIL does not contain deuterium, which can be chromatographically resolved. Our method shows no chromatographic resolution of differentially labeled glycans. Mixtures of differentially tagged glycans can be directly compared and quantified using mass spectrometric techniques. We demonstrate the use of GRIL to determine relative differences in glycan amount and composition. We analyze free glycans and glycans enzymatically or chemically released from a variety of standard glycoproteins, as well as human and mouse serum glycoproteins using this method. This technique allows for linear, relative quantitation of glycans over a 10-fold concentration range and can accurately quantify sub-picomole levels of released glycans, providing a needed advancement in the field of Glycomics. PMID:19454239

An extended version of the SERPENT-2 code to investigate fuel burn-up and core material evolution of the Molten Salt Fast Reactor

NASA Astrophysics Data System (ADS)

Aufiero, M.; Cammi, A.; Fiorina, C.; Leppänen, J.; Luzzi, L.; Ricotti, M. E.

2013-10-01

In this work, the Monte Carlo burn-up code SERPENT-2 has been extended and employed to study the material isotopic evolution of the Molten Salt Fast Reactor (MSFR). This promising GEN-IV nuclear reactor concept features peculiar characteristics such as the on-line fuel reprocessing, which prevents the use of commonly available burn-up codes. Besides, the presence of circulating nuclear fuel and radioactive streams from the core to the reprocessing plant requires a precise knowledge of the fuel isotopic composition during the plant operation. The developed extension of SERPENT-2 directly takes into account the effects of on-line fuel reprocessing on burn-up calculations and features a reactivity control algorithm. It is here assessed against a dedicated version of the deterministic ERANOS-based EQL3D procedure (PSI-Switzerland) and adopted to analyze the MSFR fuel salt isotopic evolution. Particular attention is devoted to study the effects of reprocessing time constants and efficiencies on the conversion ratio and the molar concentration of elements relevant for solubility issues (e.g., trivalent actinides and lanthanides). Quantities of interest for fuel handling and safety issues are investigated, including decay heat and activities of hazardous isotopes (neutron and high energy gamma emitters) in the core and in the reprocessing stream. The radiotoxicity generation is also analyzed for the MSFR nominal conditions. The production of helium and the depletion in tungsten content due to nuclear reactions are calculated for the nickel-based alloy selected as reactor structural material of the MSFR. These preliminary evaluations can be helpful in studying the radiation damage of both the primary salt container and the axial reflectors.

Rates for neutron-capture reactions on tungsten isotopes in iron meteorites. [Abstract only

NASA Technical Reports Server (NTRS)

Masarik, J.; Reedy, R. C.

1994-01-01

High-precision W isotopic analyses by Harper and Jacobsen indicate the W-182/W-183 ratio in the Toluca iron meteorite is shifted by -(3.0 +/- 0.9) x 10(exp -4) relative to a terrestrial standard. Possible causes of this shift are neutron-capture reactions on W during Toluca's approximately 600-Ma exposure to cosmic ray particles or radiogenic growth of W-182 from 9-Ma Hf-182 in the silicate portion of the Earth after removal of W to the Earth's core. Calculations for the rates of neutron-capture reactions on W isotopes were done to study the first possibility. The LAHET Code System (LCS) which consists of the Los Alamos High Energy Transport (LAHET) code and the Monte Carlo N-Particle(MCNP) transport code was used to numerically simulate the irradiation of the Toluca iron meteorite by galactic-cosmic-ray (GCR) particles and to calculate the rates of W(n, gamma) reactions. Toluca was modeled as a 3.9-m-radius sphere with the composition of a typical IA iron meteorite. The incident GCR protons and their interactions were modeled with LAHET, which also handled the interactions of neutrons with energies above 20 MeV. The rates for the capture of neutrons by W-182, W-183, and W-186 were calculated using the detailed library of (n, gamma) cross sections in MCNP. For this study of the possible effect of W(n, gamma) reactions on W isotope systematics, we consider the peak rates. The calculated maximum change in the normalized W-182/W-183 ratio due to neutron-capture reactions cannot account for more than 25% of the mass 182 deficit observed in Toluca W.

Quantitative and temporal proteome analysis of butyrate-treated colorectal cancer cells.

PubMed

Tan, Hwee Tong; Tan, Sandra; Lin, Qingsong; Lim, Teck Kwang; Hew, Choy Leong; Chung, Maxey C M

2008-06-01

Colorectal cancer is one of the most common cancers in developed countries, and its incidence is negatively associated with high dietary fiber intake. Butyrate, a short-chain fatty acid fermentation by-product of fiber induces cell maturation with the promotion of growth arrest, differentiation, and/or apoptosis of cancer cells. The stimulation of cell maturation by butyrate in colonic cancer cells follows a temporal progression from the early phase of growth arrest to the activation of apoptotic cascades. Previously we performed two-dimensional DIGE to identify differentially expressed proteins induced by 24-h butyrate treatment of HCT-116 colorectal cancer cells. Herein we used quantitative proteomics approaches using iTRAQ (isobaric tags for relative and absolute quantitation), a stable isotope labeling methodology that enables multiplexing of four samples, for a temporal study of HCT-116 cells treated with butyrate. In addition, cleavable ICAT, which selectively tags cysteine-containing proteins, was also used, and the results complemented those obtained from the iTRAQ strategy. Selected protein targets were validated by real time PCR and Western blotting. A model is proposed to illustrate our findings from this temporal analysis of the butyrate-responsive proteome that uncovered several integrated cellular processes and pathways involved in growth arrest, apoptosis, and metastasis. These signature clusters of butyrate-regulated pathways are potential targets for novel chemopreventive and therapeutic drugs for treatment of colorectal cancer.

Characterization of a Cross-Linked Protein–Nucleic Acid Substrate Radical in the Reaction Catalyzed by RlmN

PubMed Central

2015-01-01

RlmN and Cfr are methyltransferases/methylsynthases that belong to the radical S-adenosylmethionine superfamily of enzymes. RlmN catalyzes C2 methylation of adenosine 2503 (A2503) of 23S rRNA, while Cfr catalyzes C8 methylation of the exact same nucleotide, and will subsequently catalyze C2 methylation if the site is unmethylated. A key feature of the unusual mechanisms of catalysis proposed for these enzymes is the attack of a methylene radical, derived from a methylcysteine residue, onto the carbon center undergoing methylation to generate a paramagnetic protein–nucleic acid cross-linked species. This species has been thoroughly characterized during Cfr-dependent C8 methylation, but does not accumulate to detectible levels in RlmN-dependent C2 methylation. Herein, we show that inactive C118S/A variants of RlmN accumulate a substrate-derived paramagnetic species. Characterization of this species by electron paramagnetic resonance spectroscopy in concert with strategic isotopic labeling shows that the radical is delocalized throughout the adenine ring of A2503, although predominant spin density is on N1 and N3. Moreover, 13C hyperfine interactions between the radical and the methylene carbon of the formerly [methyl-13C]Cys355 residue show that the radical species exists in a covalent cross-link between the protein and the nucleic acid substrate. X-ray structures of RlmN C118A show that, in the presence of SAM, the substitution does not alter the active site structure compared to that of the wild-type enzyme. Together, these findings have new mechanistic implications for the role(s) of C118 and its counterpart in Cfr (C105) in catalysis, and suggest involvement of the residue in resolution of the cross-linked species via a radical mediated process. PMID:24806349

Characterization of a Cross-Linked Protein-Nucleic Acid Substrate Radical in the Reaction Catalyzed by RlmN

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

Silakov, Alexey; Grove, Tyler L.; Radle, Matthew I.

2014-08-14

RlmN and Cfr are methyltransferases/methylsynthases that belong to the radical S-adenosylmethionine superfamily of enzymes. RlmN catalyzes C2 methylation of adenosine 2503 (A2503) of 23S rRNA, while Cfr catalyzes C8 methylation of the exact same nucleotide, and will subsequently catalyze C2 methylation if the site is unmethylated. A key feature of the unusual mechanisms of catalysis proposed for these enzymes is the attack of a methylene radical, derived from a methylcysteine residue, onto the carbon center undergoing methylation to generate a paramagnetic protein–nucleic acid cross-linked species. This species has been thoroughly characterized during Cfr-dependent C8 methylation, but does not accumulate tomore » detectible levels in RlmN-dependent C2 methylation. Herein, we show that inactive C118S/A variants of RlmN accumulate a substrate-derived paramagnetic species. Characterization of this species by electron paramagnetic resonance spectroscopy in concert with strategic isotopic labeling shows that the radical is delocalized throughout the adenine ring of A2503, although predominant spin density is on N1 and N3. Moreover, 13C hyperfine interactions between the radical and the methylene carbon of the formerly [methyl- 13C]Cys355 residue show that the radical species exists in a covalent cross-link between the protein and the nucleic acid substrate. X-ray structures of RlmN C118A show that, in the presence of SAM, the substitution does not alter the active site structure compared to that of the wild-type enzyme. Together, these findings have new mechanistic implications for the role(s) of C118 and its counterpart in Cfr (C105) in catalysis, and suggest involvement of the residue in resolution of the cross-linked species via a radical mediated process« less

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

Gauld, Ian C.; Giaquinto, J. M.; Delashmitt, J. S.

Destructive radiochemical assay measurements of spent nuclear fuel rod segments from an assembly irradiated in the Three Mile Island unit 1 (TMI-1) pressurized water reactor have been performed at Oak Ridge National Laboratory (ORNL). Assay data are reported for five samples from two fuel rods of the same assembly. The TMI-1 assembly was a 15 X 15 design with an initial enrichment of 4.013 wt% 235U, and the measured samples achieved burnups between 45.5 and 54.5 gigawatt days per metric ton of initial uranium (GWd/t). Measurements were performed mainly using inductively coupled plasma mass spectrometry after elemental separation via highmore » performance liquid chromatography. High precision measurements were achieved using isotope dilution techniques for many of the lanthanides, uranium, and plutonium isotopes. Measurements are reported for more than 50 different isotopes and 16 elements. One of the two TMI-1 fuel rods measured in this work had been measured previously by Argonne National Laboratory (ANL), and these data have been widely used to support code and nuclear data validation. Recently, ORNL provided an important opportunity to independently cross check results against previous measurements performed at ANL. The measured nuclide concentrations are used to validate burnup calculations using the SCALE nuclear systems modeling and simulation code suite. These results show that the new measurements provide reliable benchmark data for computer code validation.« less

Dual Targeting of Intracellular Pathogenic Bacteria with a Cleavable Conjugate of Kanamycin and an Antibacterial Cell-Penetrating Peptide.

PubMed

Brezden, Anna; Mohamed, Mohamed F; Nepal, Manish; Harwood, John S; Kuriakose, Jerrin; Seleem, Mohamed N; Chmielewski, Jean

2016-08-31

Bacterial infection caused by intracellular pathogens, such as Mycobacterium, Salmonella, and Brucella, is a burgeoning global health epidemic that necessitates urgent action. However, the therapeutic value of a number of antibiotics, including aminoglycosides, against intracellular pathogenic bacteria is compromised due to their inability to traverse eukaryotic membranes. For this significant problem to be addressed, a cleavable conjugate of the antibiotic kanamycin and a nonmembrane lytic, broad-spectrum antimicrobial peptide with efficient mammalian cell penetration, P14LRR, was prepared. This approach allows kanamycin to enter mammalian cells as a conjugate linked via a tether that breaks down in the reducing environment within cells. Potent antimicrobial activity of the P14KanS conjugate was demonstrated in vitro, and this reducible conjugate effectively cleared intracellular pathogenic bacteria within macrophages more potently than that of a conjugate lacking the disulfide moiety. Notably, successful clearance of Mycobacterium tuberculosis within macrophages was observed with the dual antibiotic conjugate, and Salmonella levels were significantly reduced in an in vivo Caenorhabditis elegans model.

Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme.

PubMed Central

Hermann, T; Auffinger, P; Scott, W G; Westhof, E

1997-01-01

In the presence of magnesium ions, cleavage by the hammerhead ribozyme RNA at a specific residue leads to 2'3'-cyclic phosphate and 5'-OH extremities. In the cleavage reaction an activated ribose 2'-hydroxyl group attacks its attached 3'-phosphate. Molecular dynamics simulations of the crystal structure of the hammerhead ribozyme, obtained after flash-freezing of crystals under conditions where the ribozyme is active, provide evidence that a mu-bridging OH-ion is located between two Mg2+ions close to the cleavable phosphate. Constrained simulations show further that a flip from the C3'- endo to the C2'- endo conformation of the ribose at the cleavable phosphate brings the 2'-hydroxyl in proximity to both the attacked phosphorous atom and the mu-bridging OH-ion. Thus, the simulations lead to a detailed new insight into the mechanism of hammerhead ribozyme cleavage where a mu-hydroxo bridged magnesium cluster, located on the deep groove side, provides an OH-ion that is able to activate the 2'-hydroxyl nucleophile after a minor and localized conformational change in the RNA. PMID:9254698

Polymer-Coated Hollow Mesoporous Silica Nanoparticles for Triple-Responsive Drug Delivery.

PubMed

Zhang, Yuanyuan; Ang, Chung Yen; Li, Menghuan; Tan, Si Yu; Qu, Qiuyu; Luo, Zhong; Zhao, Yanli

2015-08-19

In this study, pH, reduction and light triple-responsive nanocarriers based on hollow mesoporous silica nanoparticles (HMSNs) modified with poly(2-(diethylamino)ethyl methacrylate) (PDEAEMA) were developed via surface-initiated atom transfer radical polymerization. Both reduction-cleavable disulfide bond and light-cleavable o-nitrobenzyl ester were used as the linkages between HMSNs and pH-sensitive PDEAEMA polymer caps. A series of characterization techniques were applied to characterize and confirm the structures of the intermediates and final nanocarriers. Doxorubicin (DOX) was easily encapsulated into the nanocarriers with a high loading capacity, and quickly released in response to the stimuli of reducing agent, acid environment or UV light irradiation. In addition, flow cytometry analysis, confocal laser scanning microscopy observations and cytotoxicity studies indicated that the nanocarriers were efficiently internalized by HeLa cancer cells, exhibiting (i) enhanced release of DOX into the cytoplasm under external UV light irradiation, (ii) better cytotoxicity against HeLa cells, and (iii) superior control over drug delivery and release. Thus, the triple-responsive nanocarriers present highly promising potentials as a drug delivery platform for cancer therapy.

Nanoporous Films with Sub-10 nm in Pore Size from Acid-Cleavable Block Copolymers.

PubMed

Li, Yayuan; Xu, Yawei; Cao, Shubo; Zhao, Yongbin; Qu, Ting; Iyoda, Tomokazu; Chen, Aihua

2017-03-01

Nanoporous thin films with pore size of sub-10 nm are fabricated using an acid-cleavable block copolymer (BCP), a benzoic imine junction between poly(ethylene oxide) (PEO) and poly(methacrylate) (PMAAz) bearing an azobenzene side chain (denoted as PEO-bei-PMAAz) as the precursor. After a thermal annealing, the block copolymers are self-assembled to form highly ordered PEO cylinders within a PMAAz matrix normal to the film, even in the case of low BCP molecular weight due to the existing of the liquid crystalline (LC) azobenzene rigid segment. Thus, PMAAz thin films with pore size of ≈7 nm and density of ≈10 12 cm -2 are obtained after removal of the PEO minor phase by breaking the benzoic imine junction under mild acidic conditions. This work enriches the nanoporous polymer films from BCP precursors and introduces the LC property as a functionality which can further enhance the mechanical properties of the films and broaden their applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Human topoisomerase I poisoning: docking protoberberines into a structure-based binding site model

NASA Astrophysics Data System (ADS)

Kettmann, Viktor; Košt'álová, Daniela; Höltje, Hans-Dieter

2004-12-01

Using the X-ray crystal structure of the human topoisomerase I (top1) - DNA cleavable complex and the Sybyl software package, we have developed a general model for the ternary cleavable complex formed with four protoberberine alkaloids differing in the substitution on the terminal phenyl rings and covering a broad range of the top1-poisoning activities. This model has the drug intercalated with its planar chromophore between the -1 and +1 base pairs flanking the cleavage site, with the nonplanar portion pointing into the minor groove. The ternary complexes were geometry-optimized and relative interaction energies, computed by using the Tripos force field, were found to rank in correct order the biological potency of the compounds; in addition, the model is also consistent with the top1-poisoning inactivity of berberine, a major prototype of the protoberberine alkaloids. The model might serve as a rational basis for elaboration of the most active compound as a lead structure, in order to develop more potent top1 poisons as next generation anti-cancer drugs.

COMPLETE DETERMINATION OF POLARIZATION FOR A HIGH-ENERGY DEUTERON BEAM (thesis)

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

Button, J

1959-05-01

please delete the no. 17076<>13:017077The P/sub 1/ multigroup code was written for the IBM-704 in order to determine the accuracy of the few- group diffusion scheme with various imposed conditions and also to provide an alternate computational method when this scheme fails to be sufficiently accurate. The code solves for the spatially dependent multigroup flux, taking into account such nuclear phenomena is slowing down of neutrons resulting from elastic and inelastic scattering, the removal of neutrons resulting from epithermal capture and fission resonances, and the regeneration of fist neutrons resulting from fissioning which may occur in any of as manymore » as 80 fast multigroups or in the one thermal group. The code will accept as input a physical description of the reactor (that is: slab, cylindrical, or spherical geometry, number of points and regions, composition description group dependent boundary condition, transverse buckling, and mesh sizes) and a prepared library of nuclear properties of all the isotopes in each composition. The code will produce as output multigroup fluxes, currents, and isotopic slowing-down densities, in addition to pointwise and regionwise few-group macroscopic cross sections. (auth)« less

Secondary neutrons as the main source of neutron-rich fission products in the bombardment of a thick U target by 1 GeV protons

NASA Astrophysics Data System (ADS)

Barzakh, A. E.; Lhersonneau, G.; Batist, L. Kh.; Fedorov, D. V.; Ivanov, V. S.; Mezilev, K. A.; Molkanov, P. L.; Moroz, F. V.; Orlov, S. Yu.; Panteleev, V. N.; Volkov, Yu. M.; Alyakrinskiy, O.; Barbui, M.; Stroe, L.; Tecchio, L. B.

2011-05-01

The diffusion-effusion model has been used to analyse the release and yields of Fr and Cs isotopes from uranium carbide targets of very different thicknesses (6.3 and 148 g/cm2) bombarded by a 1 GeV proton beam. Release curves of several isotopes of the same element and production efficiency versus decay half-life are well fitted with the same set of parameters. Comparison of efficiencies for neutron-rich and neutron-deficient Cs isotopes enables separation of the contributions from the primary ( p + 238U) and secondary (n + 238U) reactions to the production of neutron-rich Cs isotopes. A rather simple calculation of the neutron contribution describes these data fairly well. The FLUKA code describes the primary and secondary-reaction contributions to the Cs isotopes production efficiencies for different targets quite well.

Integral nuclear data validation using experimental spent nuclear fuel compositions

DOE PAGES

Gauld, Ian C.; Williams, Mark L.; Michel-Sendis, Franco; ...

2017-07-19

Measurements of the isotopic contents of spent nuclear fuel provide experimental data that are a prerequisite for validating computer codes and nuclear data for many spent fuel applications. Under the auspices of the Organisation for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) and guidance of the Expert Group on Assay Data of Spent Nuclear Fuel of the NEA Working Party on Nuclear Criticality Safety, a new database of expanded spent fuel isotopic compositions has been compiled. The database, Spent Fuel Compositions (SFCOMPO) 2.0, includes measured data for more than 750 fuel samples acquired from 44 different reactors andmore » representing eight different reactor technologies. Measurements for more than 90 isotopes are included. This new database provides data essential for establishing the reliability of code systems for inventory predictions, but it also has broader potential application to nuclear data evaluation. Furthermore, the database, together with adjoint based sensitivity and uncertainty tools for transmutation systems developed to quantify the importance of nuclear data on nuclide concentrations, are described.« less

Integral nuclear data validation using experimental spent nuclear fuel compositions

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

Gauld, Ian C.; Williams, Mark L.; Michel-Sendis, Franco

Measurements of the isotopic contents of spent nuclear fuel provide experimental data that are a prerequisite for validating computer codes and nuclear data for many spent fuel applications. Under the auspices of the Organisation for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) and guidance of the Expert Group on Assay Data of Spent Nuclear Fuel of the NEA Working Party on Nuclear Criticality Safety, a new database of expanded spent fuel isotopic compositions has been compiled. The database, Spent Fuel Compositions (SFCOMPO) 2.0, includes measured data for more than 750 fuel samples acquired from 44 different reactors andmore » representing eight different reactor technologies. Measurements for more than 90 isotopes are included. This new database provides data essential for establishing the reliability of code systems for inventory predictions, but it also has broader potential application to nuclear data evaluation. Furthermore, the database, together with adjoint based sensitivity and uncertainty tools for transmutation systems developed to quantify the importance of nuclear data on nuclide concentrations, are described.« less

A Cleavable N-Terminal Signal Peptide Promotes Widespread Olfactory Receptor Surface Expression in HEK293T Cells

PubMed Central

Shepard, Blythe D.; Natarajan, Niranjana; Protzko, Ryan J.; Acres, Omar W.; Pluznick, Jennifer L.

2013-01-01

Olfactory receptors (ORs) are G protein-coupled receptors that detect odorants in the olfactory epithelium, and comprise the largest gene family in the genome. Identification of OR ligands typically requires OR surface expression in heterologous cells; however, ORs rarely traffic to the cell surface when exogenously expressed. Therefore, most ORs are orphan receptors with no known ligands. To date, studies have utilized non-cleavable rhodopsin (Rho) tags and/or chaperones (i.e. Receptor Transporting Protein, RTP1S, Ric8b and Gαolf) to improve surface expression. However, even with these tools, many ORs still fail to reach the cell surface. We used a test set of fifteen ORs to examine the effect of a cleavable leucine-rich signal peptide sequence (Lucy tag) on OR surface expression in HEK293T cells. We report here that the addition of the Lucy tag to the N-terminus increases the number of ORs reaching the cell surface to 7 of the 15 ORs (as compared to 3/15 without Rho or Lucy tags). Moreover, when ORs tagged with both Lucy and Rho were co-expressed with previously reported chaperones (RTP1S, Ric8b and Gαolf), we observed surface expression for all 15 receptors examined. In fact, two-thirds of Lucy-tagged ORs are able to reach the cell surface synergistically with chaperones even when the Rho tag is removed (10/15 ORs), allowing for the potential assessment of OR function with only an 8-amino acid Flag tag on the mature protein. As expected for a signal peptide, the Lucy tag was cleaved from the mature protein and did not alter OR-ligand binding and signaling. Our studies demonstrate that widespread surface expression of ORs can be achieved in HEK293T cells, providing promise for future large-scale deorphanization studies. PMID:23840901

The microsporidian polar tube: evidence for a third polar tube protein (PTP3) in Encephalitozoon cuniculi.

PubMed

Peuvel, Isabelle; Peyret, Pierre; Méténier, Guy; Vivarès, Christian P; Delbac, Frédéric

2002-06-01

The invasion strategy used by microsporidia is primarily related to spore germination. Small differentiated spores of these fungi-related parasites inject their contents into target cells through the lumen of a rapidly extruded polar tube, as a prerequisite to obligate intracellular development. Previous studies in Encephalitozoon species that infect mammals have identified two major antigenic polar tube proteins (PTP1 and PTP2) which are predicted to contribute to the high tensile strength of the polar tube via an assembly process dependent on disulfide linkages. By immunoscreening of a cDNA library, we found that a novel PTP is encoded by a single transcription unit (3990 bp) located on the chromosome XI of E. cuniculi. PTP3 is predicted to be synthesized as a 1256-amino acid precursor with a cleavable signal peptide. The mature protein lacks cysteine residue and its large acidic core is flanked by highly basic N- and C-terminal regions. Immunolocalization data indicated that PTP3 is involved in the sporoblast-to-spore polar tube biogenesis. A transcriptional up-regulation during sporogony is supported by a strong increase in the relative amount of Ecptp mRNAs within host cells sampled at late post-infection times. To begin to explore polar tube-associated protein interactions, spore proteins were extracted in the presence of SDS and dithiothreitol then incubated with a chemical cross-linker (DSP or sulfo-EGS). A large multimeric complex was formed and shown to contain PTP1, PTP2 and PTP3 with a few other proteins. PTP3 is hypothesized to play a role in the control of the polar tube extrusion as part of a specific response to ionic stimuli.

Studying the protein organization of the postsynaptic density by a novel solid phase- and chemical cross-linking-based technology.

PubMed

Liu, Szu-Heng; Cheng, Huei-Hsuan; Huang, San-Yuan; Yiu, Pei-Chun; Chang, Yen-Chung

2006-06-01

Agarose beads carrying a cleavable, fluorescent, and photoreactive cross-linking reagent on the surface were synthesized and used to selectively pull out the proteins lining the surface of supramolecules. A quantitative comparison of the abundances of various proteins in the sample pulled out by the beads from supramolecules with their original abundances could provide information on the spatial arrangement of these proteins in the supramolecule. The usefulness of these synthetic beads was successfully verified by trials using a synthetic protein complex consisting of three layers of different proteins on glass coverslips. By using these beads, we determined the interior or superficial locations of five major and 19 minor constituent proteins in the postsynaptic density (PSD), a large protein complex and the landmark structure of asymmetric synapses in the mammalian central nervous system. The results indicate that alpha,beta-tubulins, dynein heavy chain, microtubule-associated protein 2, spectrin, neurofilament H and M subunits, an hsp70 protein, alpha-internexin, dynamin, and PSD-95 protein reside in the interior of the PSD. Dynein intermediate chain, alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate receptors, kainate receptors, N-cadherin, beta-catenin, N-ethylmaleimide-sensitive factor, an hsc70 protein, and actin reside on the surface of the PSD. The results further suggest that the N-methyl-d-aspartate receptors and the alpha-subunits of calcium/calmodulin-dependent protein kinase II are likely to reside on the surface of the PSD although with unique local protein organizations. Based on our results and the known interactions between various PSD proteins from data mining, a model for the molecular organization of the PSD is proposed.

Novel approach for a PTX/VEGF dual drug delivery system in cardiovascular applications-an innovative bulk and surface drug immobilization.

PubMed

Wulf, Katharina; Teske, Michael; Matschegewski, Claudia; Arbeiter, Daniela; Bajer, Dalibor; Eickner, Thomas; Schmitz, Klaus-Peter; Grabow, Niels

2018-06-01

The successive incorporation of several drugs into the polymeric bulk of implants mostly results in loss of considerable quantity of one drug, and/or the loss in quality of the coating and also in changes of drug release time points. A dual drug delivery system (DDDS) based on poly-L-lactide (PLLA) copolymers combining the effective inhibition of smooth muscle cell proliferation while simultaneously promoting re-endothelialization was successfully developed. To overcome possible antagonistic drug interactions and the limitation of the polymeric bulk material as release system for dual drugs, a novel concept which combines the bulk and surface drug immobilization for a DDDS was investigated. The advantage of this DDDS is that the bulk incorporation of fluorescein diacetate (FDAc) (model drug for paclitaxel (PTX)) via spray coating enhanced the subsequent cleavable surface coupling of vascular endothelial growth factor (VEGF) via the crosslinker bissulfosuccinimidyl suberate (BS 3 ). In the presence of the embedded FDAc, the VEGF loading and release are about twice times higher than in absence. Furthermore, the DDDS combines the diffusion drug delivery (FDAc or PTX) and the chemical controlled drug release, VEGF via hydrolysable ester bonds, without loss in quantity and quality of the drug release curves. Additionally, the performed in vitro biocompatibility study showed the bimodal influences of PTX and VEGF on human endothelial EA.hy926 cells. In conclusion, it was possible to show the feasibility to develop a novel DDDS which has a high potential for the medical application due to the possible easy and short modification of a polymer-based PTX delivery system.

Biochemical characterization of Yarrowia lipolytica LIP8, a secreted lipase with a cleavable C-terminal region.

PubMed

Kamoun, Jannet; Schué, Mathieu; Messaoud, Wala; Baignol, Justine; Point, Vanessa; Mateos-Diaz, Eduardo; Mansuelle, Pascal; Gargouri, Youssef; Parsiegla, Goetz; Cavalier, Jean-François; Carrière, Frédéric; Aloulou, Ahmed

2015-02-01

Yarrowia lipolytica is a lipolytic yeast possessing 16 paralog genes coding for lipases. Little information on these lipases has been obtained and only the major secreted lipase, namely YLLIP2, had been biochemically and structurally characterized. Another secreted lipase, YLLIP8, was isolated from Y. lipolytica culture medium and compared with the recombinant enzyme produced in Pichia pastoris. N-terminal sequencing showed that YLLIP8 is produced in its active form after the cleavage of a signal peptide. Mass spectrometry analysis revealed that YLLIP8 recovered from culture medium lacks a C-terminal part of 33 amino acids which are present in the coding sequence. A 3D model of YLLIP8 built from the X-ray structure of the homologous YLLIP2 lipase shows that these truncated amino acids in YLLIP8 belong to an additional C-terminal region predicted to be mainly helical. Western blot analysis shows that YLLIP8 C-tail is rapidly cleaved upon enzyme secretion since both cell-bound and culture supernatant lipases lack this extension. Mature recombinant YLLIP8 displays a true lipase activity on short-, medium- and long-chain triacylglycerols (TAG), with an optimum activity at alkaline pH on medium chain TAG. It has no apparent regioselectivity in TAG hydrolysis, thus generating glycerol and FFAs as final lipolysis products. YLLIP8 properties are distinct from those of the 1,3-regioselective YLLIP2, acting optimally at acidic pH. These lipases are tailored for complementary roles in fatty acid uptake by Y. lipolytica. Copyright © 2014 Elsevier B.V. All rights reserved.

Isotopic Effects in Nuclear Fragmentation and GCR Transport Problems

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.

2002-01-01

Improving the accuracy of the galactic cosmic ray (GCR) environment and transport models is an important goal in preparing for studies of the projected risks and the efficiency of potential mitigations methods for space exploration. In this paper we consider the effects of the isotopic composition of the primary cosmic rays and the isotopic dependence of nuclear fragmentation cross sections on GCR transport models. Measurements are used to describe the isotopic composition of the GCR including their modulation throughout the solar cycle. The quantum multiple-scattering approach to nuclear fragmentation (QMSFRG) is used as the data base generator in order to accurately describe the odd-even effect in fragment production. Using the Badhwar and O'Neill GCR model, the QMSFRG model and the HZETRN transport code, the effects of the isotopic dependence of the primary GCR composition and on fragment production for transport problems is described for a complete GCR isotopic-grid. The principle finding of this study is that large errors ( 100%) will occur in the mass-flux spectra when comparing the complete isotopic-grid (141 ions) to a reduced isotopic-grid (59 ions), however less significant errors 30%) occur in the elemental-flux spectra. Because the full isotopic-grid is readily handled on small computer work-stations, it is recommended that they be used for future GCR studies.

Background Perchlorate Source Identification Technical Guidance

DTIC Science & Technology

2013-12-01

Sciences Branch (Code 71752) of the Advanced Systems and Applied Sciences Division (Code 71700), Space and Naval Warfare Systems Center (SSC Pacific), San...Head Advanced Systems & Applied Sciences Division iii EXECUTIVE SUMMARY The objective of this document is to outline the approach, tools, and...Helium HMX Octahydro-1,3,5,7-Tetranitro-1,3,5,7- Tetrazocine IR Installation Restoration IRIS Integrated Risk Information System IR-MS Isotope-Ratio

Effects of Nickel Treatment on H3K4 Trimethylation and Gene Expression

PubMed Central

Tchou-Wong, Kam-Meng; Kluz, Thomas; Arita, Adriana; Smith, Phillip R.; Brown, Stuart; Costa, Max

2011-01-01

Occupational exposure to nickel compounds has been associated with lung and nasal cancers. We have previously shown that exposure of the human lung adenocarcinoma A549 cells to NiCl2 for 24 hr significantly increased global levels of trimethylated H3K4 (H3K4me3), a transcriptional activating mark that maps to the promoters of transcribed genes. To further understand the potential epigenetic mechanism(s) underlying nickel carcinogenesis, we performed genome-wide mapping of H3K4me3 by chromatin immunoprecipitation and direct genome sequencing (ChIP-seq) and correlated with transcriptome genome-wide mapping of RNA transcripts by massive parallel sequencing of cDNA (RNA-seq). The effect of NiCl2 treatment on H3K4me3 peaks within 5,000 bp of transcription start sites (TSSs) on a set of genes highly induced by nickel in both A549 cells and human peripheral blood mononuclear cells were analyzed. Nickel exposure increased the level of H3K4 trimethylation in both the promoters and coding regions of several genes including CA9 and NDRG1 that were increased in expression in A549 cells. We have also compared the extent of the H3K4 trimethylation in the absence and presence of formaldehyde crosslinking and observed that crosslinking of chromatin was required to observe H3K4 trimethylation in the coding regions immediately downstream of TSSs of some nickel-induced genes including ADM and IGFBP3. This is the first genome-wide mapping of trimethylated H3K4 in the promoter and coding regions of genes induced after exposure to NiCl2. This study may provide insights into the epigenetic mechanism(s) underlying the carcinogenicity of nickel compounds. PMID:21455298

Identification of cellular MMP substrates using quantitative proteomics: isotope-coded affinity tags (ICAT) and isobaric tags for relative and absolute quantification (iTRAQ).

PubMed

Butler, Georgina S; Dean, Richard A; Morrison, Charlotte J; Overall, Christopher M

2010-01-01

Identification of protease substrates is essential to understand the functional consequences of normal proteolytic processing and dysregulated proteolysis in disease. Quantitative proteomics and mass spectrometry can be used to identify protease substrates in the cellular context. Here we describe the use of two protein labeling techniques, Isotope-Coded Affinity Tags (ICAT and Isobaric Tags for Relative and Absolute Quantification (iTRAQ), which we have used successfully to identify novel matrix metalloproteinase (MMP) substrates in cell culture systems (1-4). ICAT and iTRAQ can label proteins and protease cleavage products of secreted proteins, protein domains shed from the cell membrane or pericellular matrix of protease-transfected cells that have accumulated in conditioned medium, or cell surface proteins in membrane preparations; isotopically distinct labels are used for control cells. Tryptic digestion and tandem mass spectrometry of the generated fragments enable sequencing of differentially labeled but otherwise identical pooled peptides. The isotopic tag, which is unique for each label, identifies the peptides originating from each sample, for instance, protease-transfected or control cells, and comparison of the peak areas enables relative quantification of the peptide in each sample. Thus proteins present in altered amounts between protease-expressing and null cells are implicated as protease substrates and can be further validated as such.

Computational analysis of ribonomics datasets identifies long non-coding RNA targets of γ-herpesviral miRNAs.

PubMed

Sethuraman, Sunantha; Thomas, Merin; Gay, Lauren A; Renne, Rolf

2018-05-29

Ribonomics experiments involving crosslinking and immuno-precipitation (CLIP) of Ago proteins have expanded the understanding of the miRNA targetome of several organisms. These techniques, collectively referred to as CLIP-seq, have been applied to identifying the mRNA targets of miRNAs expressed by Kaposi's Sarcoma-associated herpes virus (KSHV) and Epstein-Barr virus (EBV). However, these studies focused on identifying only those RNA targets of KSHV and EBV miRNAs that are known to encode proteins. Recent studies have demonstrated that long non-coding RNAs (lncRNAs) are also targeted by miRNAs. In this study, we performed a systematic re-analysis of published datasets from KSHV- and EBV-driven cancers. We used CLIP-seq data from lymphoma cells or EBV-transformed B cells, and a crosslinking, ligation and sequencing of hybrids dataset from KSHV-infected endothelial cells, to identify novel lncRNA targets of viral miRNAs. Here, we catalog the lncRNA targetome of KSHV and EBV miRNAs, and provide a detailed in silico analysis of lncRNA-miRNA binding interactions. Viral miRNAs target several hundred lncRNAs, including a subset previously shown to be aberrantly expressed in human malignancies. In addition, we identified thousands of lncRNAs to be putative targets of human miRNAs, suggesting that miRNA-lncRNA interactions broadly contribute to the regulation of gene expression.

co2amp: A software program for modeling the dynamics of ultrashort pulses in optical systems with CO 2 amplifiers

DOE PAGES

Polyanskiy, Mikhail N.

2015-01-01

We describe a computer code for simulating the amplification of ultrashort mid-infrared laser pulses in CO 2 amplifiers and their propagation through arbitrary optical systems. This code is based on a comprehensive model that includes an accurate consideration of the CO 2 active medium and a physical optics propagation algorithm, and takes into account the interaction of the laser pulse with the material of the optical elements. Finally, the application of the code for optimizing an isotopic regenerative amplifier is described.

HRB-22 preirradiation thermal analysis

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

Acharya, R.; Sawa, K.

1995-05-01

This report describes the preirradiation thermal analysis of the HRB-22 capsule designed for irradiation in the removable beryllium (RB) position of the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL). CACA-2 a heavy isotope and fission product concentration calculational code for experimental irradiation capsules was used to determine time dependent fission power for the fuel compacts. The Heat Engineering and Transfer in Nine Geometries (HEATING) computer code, version 7.2, was used to solve the steady-state heat conduction problem. The diameters of the graphite fuel body that contains the compacts and the primary pressure vessel were selected suchmore » that the requirements of running the compacts at an average temperature of < 1,250 C and not exceeding a maximum fuel temperature of 1,350 C was met throughout the four cycles of irradiation.« less

Earth Processes: Reading the Isotopic Code

NASA Astrophysics Data System (ADS)

Basu, Asish; Hart, Stan

Publication of this monograph will coincide, to a precision of a few per mil, with the centenary of Henri Becquerel's discovery of "radiations actives" (C. R. Acad. Sci., Feb. 24, 1896). In 1896 the Earth was only 40 million years old according to Lord Kelvin. Eleven years later, Boltwood had pushed the Earth's age past 2000 million years, based on the first U/Pb chemical dating results. In exciting progression came discovery of isotopes by J. J. Thomson in 1912, invention of the mass spectrometer by Dempster (1918) and Aston (1919), the first measurement of the isotopic composition of Pb (Aston, 1927) and the final approach, using Pb-Pb isotopic dating, to the correct age of the Earth: close—2.9 Ga (Gerling, 1942), closer—3.0 Ga (Holmes, 1949) and closest—4.50 Ga (Patterson, Tilton and Inghram, 1953).

Planned Monolayer Assemblies by Adsorption

DTIC Science & Technology

1988-09-01

RESEARCH OFFICE OF TBE U.S. ARMY Xcndn, Engan aONRAcM NUMBE DAJA45-84-C-0055 acntractor: The Weizmn InstituteAttn: Ms. N. Guter Office of Research ...ORGANIZATION The Weizmann Inst’,a#. of (if appficable) European Research office ScienceUSARDSG-UK) Sk. ADDRESS (Wiy State, and ZIP Code) 7b. ADDRESS (City...State. and ZIP Code) Department of Isotope Research Box 65 76100 Rehoyot FPO NY 09510-1500 IsraelJ

Vibrationally averaged post Born-Oppenheimer isotopic dipole moment calculations approaching spectroscopic accuracy.

PubMed

Arapiraca, A F C; Jonsson, Dan; Mohallem, J R

2011-12-28

We report an upgrade of the Dalton code to include post Born-Oppenheimer nuclear mass corrections in the calculations of (ro-)vibrational averages of molecular properties. These corrections are necessary to achieve an accuracy of 10(-4) debye in the calculations of isotopic dipole moments. Calculations on the self-consistent field level present this accuracy, while numerical instabilities compromise correlated calculations. Applications to HD, ethane, and ethylene isotopologues are implemented, all of them approaching the experimental values.

Thermal Neutron Capture onto the Stable Tungsten Isotopes

NASA Astrophysics Data System (ADS)

Hurst, A. M.; Firestone, R. B.; Sleaford, B. W.; Summers, N. C.; Revay, Zs.; Szentmiklósi, L.; Belgya, T.; Basunia, M. S.; Capote, R.; Choi, H.; Dashdorj, D.; Escher, J.; Krticka, M.; Nichols, A.

2012-02-01

Thermal neutron-capture measurements of the stable tungsten isotopes have been carried out using the guided thermal-neutron beam at the Budapest Reactor. Prompt singles spectra were collected and analyzed using the HYPERMET γ-ray analysis software package for the compound tungsten systems 183W, 184W, and 187W, prepared from isotopically-enriched samples of 182W, 183W, and 186W, respectively. These new data provide both confirmation and new insights into the decay schemes and structure of the tungsten isotopes reported in the Evaluated Gamma-ray Activation File based upon previous elemental analysis. The experimental data have also been compared to Monte Carlo simulations of γ-ray emission following the thermal neutron-capture process using the statistical-decay code DICEBOX. Together, the experimental cross sections and modeledfeeding contribution from the quasi continuum, have been used to determine the total radiative thermal neutron-capture cross sections for the tungsten isotopes and provide improved decay-scheme information for the structural- and neutron-data libraries.

pH-regulated formation of side products in the reductive amination approach for differential labeling of peptides in relative quantitative experiments.

PubMed

Levi Mortera, Stefano; Dioni, Ilaria; Greco, Viviana; Neri, Cristina; Rovero, Paolo; Urbani, Andrea

2014-05-01

Among the most common stable-isotope labeling strategies, the reaction of formaldehyde with peptides in the presence of NaCNBH₃ features many attractive aspects that are conducive to its employment in quantitation experiments in proteomics. Reductive amination, with formaldehyde and d(2)-formaldehyde, is reported to be a fast, easy, and specific reaction, undoubtedly inexpensive if compared with commercially available kits for differential isotope coding. Acetaldehyde and d(4)-acetaldehyde could be employed as well without a substantial increase in terms of cost, and should provide a wider spacing between the differentially tagged peptides in the mass spectrum. Nevertheless, only a single paper reports about a diethylation approach for quantitation. We undertook a systematic analytical investigation on the reductive amination of some standard peptides pointing out the occasional occurrence of side reactions in dependence of pH or reagents order of addition, particularly observing the formation of cyclic adducts ascribable to rearrangements involving the generated Schiff-base and all the nucleophilic sites of its chemical environment. We also tried to evaluate how much this side-products amount may impair isotope coded relative quantitation.

Cleavable ester linked magnetic nanoparticles for labeling of solvent exposed primary amine groups of peptides/proteins

USDA-ARS?s Scientific Manuscript database

In order to study the solvent exposed lysine residues of peptides/proteins, we previously reported disulfide linked N-hydrosuccinimide ester modified silica coated iron oxide magnetic nanoparticles (NHS-SS-SiO2@Fe3O4 MNPs). The presence of a disulfide bond in the linker limits the use of disulfide r...

Cleavage of cohesin rings coordinates the separation of centrioles and chromatids.

PubMed

Schöckel, Laura; Möckel, Martin; Mayer, Bernd; Boos, Dominik; Stemmann, Olaf

2011-07-10

Cohesin pairs sister chromatids by forming a tripartite Scc1-Smc1-Smc3 ring around them. In mitosis, cohesin is removed from chromosome arms by the phosphorylation-dependent prophase pathway. Centromeric cohesin is protected by shugoshin 1 and protein phosphatase 2A (Sgo1-PP2A) and opened only in anaphase by separase-dependent cleavage of Scc1 (refs 4-6). Following chromosome segregation, centrioles loosen their tight orthogonal arrangement, which licenses later centrosome duplication in S phase. Although a role of separase in centriole disengagement has been reported, the molecular details of this process remain enigmatic. Here, we identify cohesin as a centriole-engagement factor. Both premature sister-chromatid separation and centriole disengagement are induced by ectopic activation of separase or depletion of Sgo1. These unscheduled events are suppressed by expression of non-cleavable Scc1 or inhibition of the prophase pathway. When endogenous Scc1 is replaced by artificially cleavable Scc1, the corresponding site-specific protease triggers centriole disengagement. Separation of centrioles can alternatively be induced by ectopic cleavage of an engineered Smc3. Thus, the chromosome and centrosome cycles exhibit extensive parallels and are coordinated with each other by dual use of the cohesin ring complex.

pH-Responsive Dimeric Zinc(II) Phthalocyanine in Mesoporous Silica Nanoparticles as an Activatable Nanophotosensitizing System for Photodynamic Therapy.

PubMed

Wong, Roy C H; Chow, Sun Y S; Zhao, Shirui; Fong, Wing-Ping; Ng, Dennis K P; Lo, Pui-Chi

2017-07-19

An acid-cleavable acetal-linked zinc(II) phthalocyanine dimer with an azido terminal group (cPc) was prepared and conjugated to alkyne-modified mesoporous silica nanoparticles via copper(I)-catalyzed alkyne-azide cycloaddition reaction. For comparison, an amine-linked analogue (nPc) was also prepared as a non-acid-cleavable counterpart. These dimeric phthalocyanines were significantly self-quenched due to the close proximity of the phthalocyanine units inside the mesopores, resulting in much weaker fluorescence emission and singlet oxygen generation, both in N,N-dimethylformamide and in phosphate-buffered saline (PBS), compared with the free molecular counterparts. Under acidic conditions in PBS, the cPc-encapsulated nanosystem was activated in terms of fluorescence emission and singlet oxygen production. After internalization into human colon adenocarcinoma HT29 cells, it exhibited much higher intracellular fluorescence and photocytotoxicity compared to the nanosystem entrapped with nPc. The activation of this nanosystem was also demonstrated in tumor-bearing nude mice. The intratumoral fluorescence intensity increased gradually over 24 h, while for the nPc counterpart the fluorescence remained very weak. The results suggest that this nanosystem serves as a promising activatable nanophotosensitizing agent for photodynamic therapy.

Matrix Metalloproteinase Responsive Delivery of Myostatin Inhibitors.

PubMed

Braun, Alexandra C; Gutmann, Marcus; Ebert, Regina; Jakob, Franz; Gieseler, Henning; Lühmann, Tessa; Meinel, Lorenz

2017-01-01

The inhibition of myostatin - a member of the transforming growth factor (TGF-β) family - drives regeneration of functional skeletal muscle tissue. We developed a bioresponsive drug delivery system (DDS) linking release of a myostatin inhibitor (MI) to inflammatory flares of myositis to provide self-regulated MI concentration gradients within tissues of need. A protease cleavable linker (PCL) - responding to MMP upregulation - is attached to the MI and site-specifically immobilized on microparticle surfaces. The PCL disintegrated in a matrix metalloproteinase (MMP) 1, 8, and particularly MMP-9 concentration dependent manner, with MMP-9 being an effective surrogate biomarker correlating with the activity of myositis. The bioactivity of particle-surface bound as well as released MI was confirmed by luciferase suppression in stably transfected HEK293 cells responding to myostatin induced SMAD phosphorylation. We developed a MMP-responsive DDS for MI delivery responding to inflammatory flare of a diseased muscle matching the kinetics of MMP-9 upregulation, with MMP-9 kinetics matching (patho-) physiological myostatin levels. ᅟ: Graphical Abstract Schematic illustration of the matrix metalloproteinase responsive delivery system responding to inflammatory flares of muscle disease. The protease cleavable linker readily disintegrates upon entry into the diseased tissue, therby releasing the mystatin inhibitor.

A Micelle Self-Assembled from Doxorubicin-Arabinoxylan Conjugates with pH-Cleavable Bond for Synergistic Antitumor Therapy

NASA Astrophysics Data System (ADS)

Wang, Jie; Li, Yanli; Dong, Xia; Wang, Ying; Chong, Xiaodan; Yu, Tai; Zhang, Fulei; Chen, Di; Zhang, Li; Gao, Jie; Yang, Cheng; Han, Jun; Li, Wei

2017-01-01

Nanomedicine offers new hope to overcome the low solubility and high side toxicity to normal tissue appeared in traditional chemotherapy. The biocompatibility and intracellular drug accumulation is still a big challenge for the nano-based formulations. Herein, a medical-used biocompatible arabinoxylan (AX) is used to develop to delivery chemodrug doxorubicin (DOX). The solubility of DOX is obviously enhanced via the hydrogen bond formed with AX which results in an amphiphilic AX-DOX. A micelle with pH-cleavable bond is thus self-assembled from such AX-DOX with DOX core and AX shell. The inner DOX can be easily released out at low intracellular pH, which obviously enhanced its in vitro cytotoxicity against breast cancer cells (MCF-7). Interestingly, an unexpected apoptosis is evoked except for the proliferation inhibition. Moreover, the therapeutic effects are further synergistically promoted by the enhanced permeability and retention (EPR) and intracellular pH-triggered drug release. Consequently, the in vivo intratumor accumulation of DOX, the tumor inhibition was significantly promoted after intravenous administration to the Balb/c nude mice bearing MCF-7 tumors. These in vitro/vivo results indicated that the AX-DOX micellular formulation holds high potential in cancer therapy.

Molecular Basis of Valine-Citrulline-PABC Linker Instability in Site-Specific ADCs and Its Mitigation by Linker Design.

PubMed

Dorywalska, Magdalena; Dushin, Russell; Moine, Ludivine; Farias, Santiago E; Zhou, Dahui; Navaratnam, Thayalan; Lui, Victor; Hasa-Moreno, Adela; Casas, Meritxell Galindo; Tran, Thomas-Toan; Delaria, Kathy; Liu, Shu-Hui; Foletti, Davide; O'Donnell, Christopher J; Pons, Jaume; Shelton, David L; Rajpal, Arvind; Strop, Pavel

2016-05-01

The degree of stability of antibody-drug linkers in systemic circulation, and the rate of their intracellular processing within target cancer cells are among the key factors determining the efficacy of antibody-drug conjugates (ADC) in vivo Previous studies demonstrated the susceptibility of cleavable linkers, as well as auristatin-based payloads, to enzymatic cleavage in rodent plasma. Here, we identify Carboxylesterase 1C as the enzyme responsible for the extracellular hydrolysis of valine-citrulline-p-aminocarbamate (VC-PABC)-based linkers in mouse plasma. We further show that the activity of Carboxylesterase 1C towards VC-PABC-based linkers, and consequently the stability of ADCs in mouse plasma, can be effectively modulated by small chemical modifications to the linker. While the introduced modifications can protect the VC-PABC-based linkers from extracellular cleavage, they do not significantly alter the intracellular linker processing by the lysosomal protease Cathepsin B. The distinct substrate preference of the serum Carboxylesterase 1C offers the opportunity to modulate the extracellular stability of cleavable ADCs without diminishing the intracellular payload release required for ADC efficacy. Mol Cancer Ther; 15(5); 958-70. ©2016 AACR. ©2016 American Association for Cancer Research.

Disentangling mechanisms involved in collagen pyridinoline cross-linking: The immunophilin FKBP65 is critical for dimerization of lysyl hydroxylase 2

PubMed Central

Gjaltema, Rutger A. F.; van der Stoel, Miesje M.; Boersema, Miriam; Bank, Ruud A.

2016-01-01

Collagens are subjected to extensive posttranslational modifications, such as lysine hydroxylation. Bruck syndrome (BS) is a connective tissue disorder characterized at the molecular level by a loss of telopeptide lysine hydroxylation, resulting in reduced collagen pyridinoline cross-linking. BS results from mutations in the genes coding for lysyl hydroxylase (LH) 2 or peptidyl-prolyl cis-trans isomerase (PPIase) FKBP65. Given that the immunophilin FKBP65 does not exhibit LH activity, it is likely that LH2 activity is somehow dependent on FKPB65. In this report, we provide insights regarding the interplay between LH2 and FKBP65. We found that FKBP65 forms complexes with LH2 splice variants LH2A and LH2B but not with LH1 and LH3. Ablating the catalytic activity of FKBP65 or LH2 did not affect complex formation. Both depletion of FKBP65 and inhibition of FKBP65 PPIase activity reduced the dimeric (active) form of LH2 but did not affect the binding of monomeric (inactive) LH2 to procollagen Iα1. Furthermore, we show that LH2A and LH2B cannot form heterodimers with each other but are able to form heterodimers with LH1 and LH3. Collectively, our results indicate that FKBP65 is linked to pyridinoline cross-linking by specifically mediating the dimerization of LH2. Moreover, FKBP65 does not interact with LH1 and LH3, explaining why in BS triple-helical hydroxylysines are not affected. Our results provide a mechanistic link between FKBP65 and the loss of pyridinolines and may hold the key to future treatments for diseases related to collagen cross-linking anomalies, such as fibrosis and cancer. PMID:27298363

Genetic code expansion for multiprotein complex engineering.

PubMed

Koehler, Christine; Sauter, Paul F; Wawryszyn, Mirella; Girona, Gemma Estrada; Gupta, Kapil; Landry, Jonathan J M; Fritz, Markus Hsi-Yang; Radic, Ksenija; Hoffmann, Jan-Erik; Chen, Zhuo A; Zou, Juan; Tan, Piau Siong; Galik, Bence; Junttila, Sini; Stolt-Bergner, Peggy; Pruneri, Giancarlo; Gyenesei, Attila; Schultz, Carsten; Biskup, Moritz Bosse; Besir, Hueseyin; Benes, Vladimir; Rappsilber, Juri; Jechlinger, Martin; Korbel, Jan O; Berger, Imre; Braese, Stefan; Lemke, Edward A

2016-12-01

We present a baculovirus-based protein engineering method that enables site-specific introduction of unique functionalities in a eukaryotic protein complex recombinantly produced in insect cells. We demonstrate the versatility of this efficient and robust protein production platform, 'MultiBacTAG', (i) for the fluorescent labeling of target proteins and biologics using click chemistries, (ii) for glycoengineering of antibodies, and (iii) for structure-function studies of novel eukaryotic complexes using single-molecule Förster resonance energy transfer as well as site-specific crosslinking strategies.

Calculation of electron and isotopes dose point kernels with fluka Monte Carlo code for dosimetry in nuclear medicine therapy

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

Botta, F; Di Dia, A; Pedroli, G

The calculation of patient-specific dose distribution can be achieved by Monte Carlo simulations or by analytical methods. In this study, fluka Monte Carlo code has been considered for use in nuclear medicine dosimetry. Up to now, fluka has mainly been dedicated to other fields, namely high energy physics, radiation protection, and hadrontherapy. When first employing a Monte Carlo code for nuclear medicine dosimetry, its results concerning electron transport at energies typical of nuclear medicine applications need to be verified. This is commonly achieved by means of calculation of a representative parameter and comparison with reference data. Dose point kernel (DPK),more » quantifying the energy deposition all around a point isotropic source, is often the one.Methods: fluka DPKs have been calculated in both water and compact bone for monoenergetic electrons (10–3 MeV) and for beta emitting isotopes commonly used for therapy (89Sr, 90Y, 131I, 153Sm, 177Lu, 186Re, and 188Re). Point isotropic sources have been simulated at the center of a water (bone) sphere, and deposed energy has been tallied in concentric shells. fluka outcomes have been compared to penelope v.2008 results, calculated in this study as well. Moreover, in case of monoenergetic electrons in water, comparison with the data from the literature (etran, geant4, mcnpx) has been done. Maximum percentage differences within 0.8·RCSDA and 0.9·RCSDA for monoenergetic electrons (RCSDA being the continuous slowing down approximation range) and within 0.8·X90 and 0.9·X90 for isotopes (X90 being the radius of the sphere in which 90% of the emitted energy is absorbed) have been computed, together with the average percentage difference within 0.9·RCSDA and 0.9·X90 for electrons and isotopes, respectively.Results: Concerning monoenergetic electrons, within 0.8·RCSDA (where 90%–97% of the particle energy is deposed), fluka and penelope agree mostly within 7%, except for 10 and 20 keV electrons (12% in water, 8.3% in bone). The discrepancies between fluka and the other codes are of the same order of magnitude than those observed when comparing the other codes among them, which can be referred to the different simulation algorithms. When considering the beta spectra, discrepancies notably reduce: within 0.9·X90, fluka and penelope differ for less than 1% in water and less than 2% in bone with any of the isotopes here considered. Complete data of fluka DPKs are given as Supplementary Material as a tool to perform dosimetry by analytical point kernel convolution.Conclusions: fluka provides reliable results when transporting electrons in the low energy range, proving to be an adequate tool for nuclear medicine dosimetry.« less

Determination of the δ15N of total nitrogen in solids; RSIL lab code 2893

USGS Publications Warehouse

Revesz, Kinga; Qi, Haiping; Coplen, Tyler B.

2006-01-01

The purpose of the Reston Stable Isotope Laboratory (RSIL) lab code 2893 is to determine the δ(15N/14N), abbreviated as δ15N , of total nitrogen in solid samples. A Carlo Erba NC 2500 elemental analyzer (EA) is used to convert total nitrogen in a solid sample into N2 gas. The EA is connected to a continuous flow isotope-ratio mass spectrometer (CF-IRMS), which determines relative difference in the isotope-amount ratios of stable nitrogen isotopes (15N/14N)of the product N2 gas. The combustion is quantitative; no isotopic fractionation is involved. Samples are placed in a tin capsule and loaded into the Costech Zero Blank Autosampler of the EA. Under computer control, samples are dropped into a heated reaction tube that contains an oxidant, where the combustion takes place in a helium atmosphere containing an excess of oxygen gas. Combustion products are transported by a helium carrier through a reduction tube to remove excess oxygen and convert all nitrous oxides into N2 and through a drying tube to remove water. The gas-phase products, mainly CO2 and N2, are separated by a gas chromatograph. The gas is then introduced into the isotope-ratio mass spectrometer (IRMS) through a Finnigan MAT (now Thermo Scientific) ConFlo II interface, which also is used to inject N2 reference gas and helium for sample dilution. The IRMS is a Thermo Scientific Delta V Plus CF-IRMS. It has a universal triple collector, two wide cups with a narrow cup in the middle, capable of measuring mass/charge (m/z) 28, 29, 30, simultaneously. The ion beams from N2 are as follows: m/z 28 = N2 = 14N14N; m/z 29 = N2 = 14N15N primarily; m/z 30 = NO = 14N16O primarily, which is a sign of contamination or incomplete reduction.

Benchmarking of Neutron Production of Heavy-Ion Transport Codes

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

Remec, Igor; Ronningen, Reginald M.; Heilbronn, Lawrence

Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondary neutron production. Results are encouraging; however, further improvements in models andmore » codes and additional benchmarking are required.« less

Benchmarking of Heavy Ion Transport Codes

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

Remec, Igor; Ronningen, Reginald M.; Heilbronn, Lawrence

Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in designing and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondary neutron production. Results are encouraging; however, further improvements in models andmore » codes and additional benchmarking are required.« less

Extending VIVO, a semantic web app, to share semantic data across institutions

NASA Astrophysics Data System (ADS)

Rowan, Linda R.; Gross, M. Benjamin; Mayernik, Matthew; Khan, Huda; Boler, Frances; Maull, Keith; Stott, Don; Johns, Erica; Daniels, Michael; Krafft, Dean; Meertens, Charles

2017-04-01

The EarthCollab project, a U.S. National Science Foundation EarthCube Building Block, is extending an existing open-source semantic web application, VIVO, to enable the exchange of information about scientific researchers and resources across institutions. VIVO has been implemented by more than 100 universities and research institutions to highlight research and institutional achievements. Most implementations of VIVO, however, gather information about a single organization. The EarthCollab project VIVO extensions enable cross-linking of VIVO instances to reduce duplication of information about the same people and scientific resources, and enable dynamic linking of related information across VIVO installations. EarthCollab is a collaboration between UNAVCO, a geodetic facility and consortium that supports diverse research projects informed by geodesy, The Bering Sea Project, an interdisciplinary field program whose data archive is hosted by NCAR's Earth Observing Laboratory, and Cornell University. Test cross-linking implementations have been deployed by UNAVCO and Cornell to demonstrate the following core features: 1. Look up people and things at an external VIVO instance, 2. Assert equivalence between URIs at the two institutions (i.e., a person) using the 'owl:sameAs' property, 3. Provide a subset of data as RDF and JSON as a service from one institution, 4. Display the data requested from the service at the other institution's site, and 5. Allow a user to distinguish between data sources when displayed on one page. Currently, a curator makes the 'sameAs' assertions manually, but persistent and unique identifiers such as ORCIDs for people and DOIs for datasets could be used to automate the process. As development of the cross-linking extension continues, we must address a number of open questions. For example, if cross-linking institutions have duplicate or conflicting information, should one institution be considered the canonical source, or should the information be displayed in parallel? Should cross-linked data be cached locally in case of a service disruption on the external system? For what types of information can we leverage public persistent identifier lookup services to automate 'sameAs' assertions? Solutions to these challenges will be the focus of EarthCollab's continued development and eventual inclusion of cross-linking features in the core VIVO code.

Spent fuel pool storage calculations using the ISOCRIT burnup credit tool

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

Kucukboyaci, Vefa; Marshall, William BJ J

2012-01-01

In order to conservatively apply burnup credit in spent fuel pool criticality safety analyses, Westinghouse has developed a software tool, ISOCRIT, for generating depletion isotopics. This tool is used to create isotopics data based on specific reactor input parameters, such as design basis assembly type; bounding power/burnup profiles; reactor specific moderator temperature profiles; pellet percent theoretical density; burnable absorbers, axial blanket regions, and bounding ppm boron concentration. ISOCRIT generates burnup dependent isotopics using PARAGON; Westinghouse's state-of-the-art and licensed lattice physics code. Generation of isotopics and passing the data to the subsequent 3D KENO calculations are performed in an automated fashion,more » thus reducing the chance for human error. Furthermore, ISOCRIT provides the means for responding to any customer request regarding re-analysis due to changed parameters (e.g., power uprate, exit temperature changes, etc.) with a quick turnaround.« less

An Approach for Validating Actinide and Fission Product Burnup Credit Criticality Safety Analyses-Isotopic Composition Predictions

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

Radulescu, Georgeta; Gauld, Ian C; Ilas, Germina

2011-01-01

The expanded use of burnup credit in the United States (U.S.) for storage and transport casks, particularly in the acceptance of credit for fission products, has been constrained by the availability of experimental fission product data to support code validation. The U.S. Nuclear Regulatory Commission (NRC) staff has noted that the rationale for restricting the Interim Staff Guidance on burnup credit for storage and transportation casks (ISG-8) to actinide-only is based largely on the lack of clear, definitive experiments that can be used to estimate the bias and uncertainty for computational analyses associated with using burnup credit. To address themore » issues of burnup credit criticality validation, the NRC initiated a project with the Oak Ridge National Laboratory to (1) develop and establish a technically sound validation approach for commercial spent nuclear fuel (SNF) criticality safety evaluations based on best-available data and methods and (2) apply the approach for representative SNF storage and transport configurations/conditions to demonstrate its usage and applicability, as well as to provide reference bias results. The purpose of this paper is to describe the isotopic composition (depletion) validation approach and resulting observations and recommendations. Validation of the criticality calculations is addressed in a companion paper at this conference. For isotopic composition validation, the approach is to determine burnup-dependent bias and uncertainty in the effective neutron multiplication factor (keff) due to bias and uncertainty in isotopic predictions, via comparisons of isotopic composition predictions (calculated) and measured isotopic compositions from destructive radiochemical assay utilizing as much assay data as is available, and a best-estimate Monte Carlo based method. This paper (1) provides a detailed description of the burnup credit isotopic validation approach and its technical bases, (2) describes the application of the approach for representative pressurized water reactor and boiling water reactor safety analysis models to demonstrate its usage and applicability, (3) provides reference bias and uncertainty results based on a quality-assurance-controlled prerelease version of the Scale 6.1 code package and the ENDF/B-VII nuclear cross section data.« less

Treatment of isomers in nucleosynthesis codes

NASA Astrophysics Data System (ADS)

Reifarth, René; Fiebiger, Stefan; Göbel, Kathrin; Heftrich, Tanja; Kausch, Tanja; Köppchen, Christoph; Kurtulgil, Deniz; Langer, Christoph; Thomas, Benedikt; Weigand, Mario

2018-03-01

The decay properties of long-lived excited states (isomers) can have a significant impact on the destruction channels of isotopes under stellar conditions. In sufficiently hot environments, the population of isomers can be altered via thermal excitation or de-excitation. If the corresponding lifetimes are of the same order of magnitude as the typical time scales of the environment, the isomers have to be treated explicitly. We present a general approach to the treatment of isomers in stellar nucleosynthesis codes and discuss a few illustrative examples. The corresponding code is available online at http://exp-astro.de/isomers/.

Molecular mechanisms of ribosomal protein gene coregulation

PubMed Central

Reja, Rohit; Vinayachandran, Vinesh; Ghosh, Sujana; Pugh, B. Franklin

2015-01-01

The 137 ribosomal protein genes (RPGs) of Saccharomyces provide a model for gene coregulation. We examined the positional and functional organization of their regulators (Rap1 [repressor activator protein 1], Fhl1, Ifh1, Sfp1, and Hmo1), the transcription machinery (TFIIB, TFIID, and RNA polymerase II), and chromatin at near-base-pair resolution using ChIP-exo, as RPGs are coordinately reprogrammed. Where Hmo1 is enriched, Fhl1, Ifh1, Sfp1, and Hmo1 cross-linked broadly to promoter DNA in an RPG-specific manner and demarcated by general minor groove widening. Importantly, Hmo1 extended 20–50 base pairs (bp) downstream from Fhl1. Upon RPG repression, Fhl1 remained in place. Hmo1 dissociated, which was coupled to an upstream shift of the +1 nucleosome, as reflected by the Hmo1 extension and core promoter region. Fhl1 and Hmo1 may create two regulatable and positionally distinct barriers, against which chromatin remodelers position the +1 nucleosome into either an activating or a repressive state. Consistent with in vitro studies, we found that specific TFIID subunits, in addition to cross-linking at the core promoter, made precise cross-links at Rap1 sites, which we interpret to reflect native Rap1–TFIID interactions. Our findings suggest how sequence-specific DNA binding regulates nucleosome positioning and transcription complex assembly >300 bp away and how coregulation coevolved with coding sequences. PMID:26385964

An upgraded bacterial surface display system to express cleavable capsid protein of human noroviruses: A novel system to discover candidate receptors for HuNoV

USDA-ARS?s Scientific Manuscript database

Human noroviruses (HuNoVs) are the dominant cause of food-borne outbreaks of gastroenteritis. However, the fundamental of the research on the viruses were restricted by the current immature system to culture HuNoVs and lacking of efficient small animal models. Previously, we demonstrated that the re...

Lysosomal pH-inducible supramolecular dissociation of polyrotaxanes possessing acid-labile N-triphenylmethyl end groups and their therapeutic potential for Niemann-Pick type C disease

NASA Astrophysics Data System (ADS)

Tamura, Atsushi; Nishida, Kei; Yui, Nobuhiko

2016-01-01

Niemann-Pick type C (NPC) disease is characterized by the accumulation of cholesterol in lysosomes. We have previously reported that biocleavable polyrotaxanes (PRXs) composed of β-cyclodextrins (β-CDs) threaded onto a linear polymer capped with bulky stopper molecules via intracellularly cleavable linkers show remarkable cholesterol reducing effects in NPC disease patient-derived fibroblasts owing to the stimuli-responsive intracellular dissociation of PRXs and subsequent β-CD release from the PRXs. Herein, we describe a series of novel acid-labile 2-(2-hydroxyethoxy)ethyl group-modified PRXs (HEE-PRXs) bearing terminal N-triphenylmethyl (N-Trt) groups as a cleavable component for the treatment of NPC disease. The N-Trt end groups of the HEE-PRXs underwent acidic pH-induced cleavage and led to the dissociation of their supramolecular structure. A kinetic study revealed that the number of HEE groups on the PRX did not affect the cleavage kinetics of the N-Trt end groups of the HEE-PRXs. The effect of the number of HEE groups of the HEE-PRXs, which was modified to impart water solubility to the PRXs, on cellular internalization efficiency, lysosomal localization efficiency, and cholesterol reduction ability in NPC disease-derived fibroblasts (NPC1 fibroblasts) was also investigated. The cellular uptake and lysosomal localization efficiency were almost equivalent for HEE-PRXs with different numbers of HEE groups. However, the cholesterol reducing ability of the HEE-PRXs in NPC1 fibroblasts was affected by the number of HEE groups, and HEE-PRXs with a high number of HEE groups were unable to reduce lysosomal cholesterol accumulation. This deficiency is most likely due to the cholesterol-solubilizing ability of HEE-modified β-CDs released from the HEE-PRXs. We conclude that the N-Trt group acts as a cleavable component to induce the lysosomal dissociation of HEE-PRXs, and acid-labile HEE-PRXs with an optimal number of HEE groups (4.1 to 5.4 HEE groups per single β-CD threaded onto the PRX) have great therapeutic potential for treating NPC disease.

Quantitative profiling of O-glycans by electrospray ionization- and matrix-assisted laser desorption ionization-time-of-flight-mass spectrometry after in-gel derivatization with isotope-coded 1-phenyl-3-methyl-5-pyrazolone.

PubMed

Sić, Siniša; Maier, Norbert M; Rizzi, Andreas M

2016-09-07

The potential and benefits of isotope-coded labeling in the context of MS-based glycan profiling are evaluated focusing on the analysis of O-glycans. For this purpose, a derivatization strategy using d0/d5-1-phenyl-3-methyl-5-pyrazolone (PMP) is employed, allowing O-glycan release and derivatization to be achieved in one single step. The paper demonstrates that this release and derivatization reaction can be carried out also in-gel with only marginal loss in sensitivity compared to in-solution derivatization. Such an effective in-gel reaction allows one to extend this release/labeling method also to glycoprotein/glycoform samples pre-separated by gel-electrophoresis without the need of extracting the proteins/digested peptides from the gel. With highly O-glycosylated proteins (e.g. mucins) LODs in the range of 0.4 μg glycoprotein (100 fmol) loaded onto the electrophoresis gel can be attained, with minor glycosylated proteins (like IgAs, FVII, FIX) the LODs were in the range of 80-100 μg (250 pmol-1.5 nmol) glycoprotein loaded onto the gel. As second aspect, the potential of isotope coded labeling as internal standardization strategy for the reliable determination of quantitative glycan profiles via MALDI-MS is investigated. Towards this goal, a number of established and emerging MALDI matrices were tested for PMP-glycan quantitation, and their performance is compared with that of ESI-based measurements. The crystalline matrix 2,6-dihydroxyacetophenone (DHAP) and the ionic liquid matrix N,N-diisopropyl-ethyl-ammonium 2,4,6-trihydroxyacetophenone (DIEA-THAP) showed potential for MALDI-based quantitation of PMP-labeled O-glycans. We also provide a comprehensive overview on the performance of MS-based glycan quantitation approaches by comparing sensitivity, LOD, accuracy and repeatability data obtained with RP-HPLC-ESI-MS, stand-alone nano-ESI-MS with a spray-nozzle chip, and MALDI-MS. Finally, the suitability of the isotope-coded PMP labeling strategy for O-glycan profiling of biological important proteins is demonstrated by comparative analysis of IgA immunoglobulins and two coagulation factors. Copyright © 2016 Elsevier B.V. All rights reserved.

Target mimicry provides a new mechanism for regulation of microRNA activity.

PubMed

Franco-Zorrilla, José Manuel; Valli, Adrián; Todesco, Marco; Mateos, Isabel; Puga, María Isabel; Rubio-Somoza, Ignacio; Leyva, Antonio; Weigel, Detlef; García, Juan Antonio; Paz-Ares, Javier

2007-08-01

MicroRNAs (miRNA) regulate key aspects of development and physiology in animals and plants. These regulatory RNAs act as guides of effector complexes to recognize specific mRNA sequences based on sequence complementarity, resulting in translational repression or site-specific cleavage. In plants, most miRNA targets are cleaved and show almost perfect complementarity with the miRNAs around the cleavage site. Here, we examined the non-protein coding gene IPS1 (INDUCED BY PHOSPHATE STARVATION 1) from Arabidopsis thaliana. IPS1 contains a motif with sequence complementarity to the phosphate (Pi) starvation-induced miRNA miR-399, but the pairing is interrupted by a mismatched loop at the expected miRNA cleavage site. We show that IPS1 RNA is not cleaved but instead sequesters miR-399. Thus, IPS1 overexpression results in increased accumulation of the miR-399 target PHO2 mRNA and, concomitantly, in reduced shoot Pi content. Engineering of IPS1 to be cleavable abolishes its inhibitory activity on miR-399. We coin the term 'target mimicry' to define this mechanism of inhibition of miRNA activity. Target mimicry can be generalized beyond the control of Pi homeostasis, as demonstrated using artificial target mimics.

Carbon-13 Isotopic Abundance and Concentration of Atmospheric Methane for Background Air in the Southern and Northern Hemispheres from 1978 to 1989 (NDP-049)

DOE Data Explorer

Stevens, C. M. [Chemical Technology Division, Argonne National Laboratory, Argonne, Illinois (USA)

2012-01-01

This data package presents atmospheric CH4 concentration and 13C isotopic abundance data derived from air samples collected over the period 1978-1989 at globally distributed clean-air sites. The data set comprises 201 records, 166 from the Northern Hemisphere and 35 from the Southern Hemisphere. The air samples were collected mostly in rural or marine locations remote from large sources of CH4 and are considered representative of tropospheric background conditions. The air samples were processed by isolation of CH4 from air and conversion to CO2 for isotopic analysis by isotope ratio mass spectrometry. These data represent one of the earliest records of 13C isotopic yy!measurements for atmospheric methane and have been used to refine estimates of CH4 emissions, calculate annual growth rates of emissions from changing sources, and provide evidence for changes in the rate of atmospheric removal of CH4. The data records consist of sample collection date; number of samples combined for analysis; sampling location; analysis date; CH4 concentration; 13C isotopic abundance; and flag codes to indicate outliers, repeated analyses, and other information.

Nuclear Fuel Depletion Analysis Using Matlab Software

NASA Astrophysics Data System (ADS)

Faghihi, F.; Nematollahi, M. R.

Coupled first order IVPs are frequently used in many parts of engineering and sciences. In this article, we presented a code including three computer programs which are joint with the Matlab software to solve and plot the solutions of the first order coupled stiff or non-stiff IVPs. Some engineering and scientific problems related to IVPs are given and fuel depletion (production of the 239Pu isotope) in a Pressurized Water Nuclear Reactor (PWR) are computed by the present code.

Large-scale shell-model calculations for 32-39P isotopes

NASA Astrophysics Data System (ADS)

Srivastava, P. C.; Hirsch, J. G.; Ermamatov, M. J.; Kota, V. K. B.

2012-10-01

In this work, the structure of 32-39P isotopes is described in the framework of stateof-the-art large-scale shell-model calculations, employing the code ANTOINE with three modern effective interactions: SDPF-U, SDPF-NR and the extended pairing plus quadrupole-quadrupoletype forces with inclusion of monopole interaction (EPQQM). Protons are restricted to fill the sd shell, while neutrons are active in the sd - pf valence space. Results for positive and negative level energies and electromagnetic observables are compared with the available experimental data.

ORNL Resolved Resonance Covariance Generation for ENDF/B-VII.1

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

Leal, Luiz C.; Guber, Klaus H.; Wiarda, Dorothea

2012-12-01

Resonance-parameter covariance matrix (RPCM) evaluations in the resolved resonance regionwere done at the Oak Ridge National Laboratory (ORNL) for the chromium isotopes, titanium isotopes, 19F, 58Ni, 60Ni, 35Cl, 37Cl, 39K, 41K, 55Mn, 233U, 235U, 238U, and 239Pu using the computer code SAMMY. The retroactive approach of the code SAMMY was used to generate the RPCMs for 233U. For 235U, the approach used for covariance generation was similar to the retroactive approach with the distinction that real experimental data were used as opposed to data generated from the resonance parameters. RPCMs for 238U and 239Pu were generated together with the resonancemore » parameter evaluations. The RPCMs were then converted in the ENDF format using the FILE32 representation. Alternatively, for computer storage reasons, the FILE32 was converted in the FILE33 cross section covariance matrix (CSCM). Both representations were processed using the computer code PUFF-IV. This paper describes the procedures used to generate the RPCM and CSCM in the resonance region for ENDF/B-VII.1. The impact of data uncertainty in nuclear reactor benchmark calculations is also presented.« less

77 FR 37446 - Advisory Committee on the Medical Uses of Isotopes: Meeting Notice

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-21

...; and (6) update on domestic production of molybdenum-99. The regular meeting agenda is subject to..., Advisory Committee Management Officer. [FR Doc. 2012-15173 Filed 6-20-12; 8:45 am] BILLING CODE 7590-01-P ...

Benchmarking of neutron production of heavy-ion transport codes

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

Remec, I.; Ronningen, R. M.; Heilbronn, L.

Document available in abstract form only, full text of document follows: Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondarymore » neutron production. Results are encouraging; however, further improvements in models and codes and additional benchmarking are required. (authors)« less

Quantitative isomer-specific N-glycan fingerprinting using isotope coded labeling and high performance liquid chromatography-electrospray ionization-mass spectrometry with graphitic carbon stationary phase.

PubMed

Michael, Claudia; Rizzi, Andreas M

2015-02-27

Glycan reductive isotope labeling (GRIL) using (12)C6-/(13)C6-aniline as labeling reagent is reported with the aim of quantitative N-glycan fingerprinting. Porous graphitized carbon (PGC) as stationary phase in capillary scale HPLC coupled to electrospray mass spectrometry with time of flight analyzer was applied for the determination of labeled N-glycans released from glycoproteins. The main benefit of using stable isotope-coding in the context of comparative glycomics lies in the improved accuracy and precision of the quantitative analysis in combined samples and in the potential of correcting for structure-dependent incomplete enzymatic release of oligosaccharides when comparing identical target proteins. The method was validated with respect to mobile phase parameters, reproducibility, accuracy, linearity and limit of detection/quantification (LOD/LOQ) using test glycoproteins. It is shown that the developed method is capable of determining relative amounts of N-glycans (including isomers) comparing two samples in one single HPLC-MS run. The analytical potential and usefulness of GRIL in combination with PGC-ESI-TOF-MS is demonstrated comparing glycosylation in human monoclonal antibodies produced in Chinese hamster ovary cells (CHO) and hybridoma cell lines. Copyright © 2015 Elsevier B.V. All rights reserved.

Statistical uncertainty analysis applied to the DRAGONv4 code lattice calculations and based on JENDL-4 covariance data

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

Hernandez-Solis, A.; Demaziere, C.; Ekberg, C.

2012-07-01

In this paper, multi-group microscopic cross-section uncertainty is propagated through the DRAGON (Version 4) lattice code, in order to perform uncertainty analysis on k{infinity} and 2-group homogenized macroscopic cross-sections predictions. A statistical methodology is employed for such purposes, where cross-sections of certain isotopes of various elements belonging to the 172 groups DRAGLIB library format, are considered as normal random variables. This library is based on JENDL-4 data, because JENDL-4 contains the largest amount of isotopic covariance matrixes among the different major nuclear data libraries. The aim is to propagate multi-group nuclide uncertainty by running the DRAGONv4 code 500 times, andmore » to assess the output uncertainty of a test case corresponding to a 17 x 17 PWR fuel assembly segment without poison. The chosen sampling strategy for the current study is Latin Hypercube Sampling (LHS). The quasi-random LHS allows a much better coverage of the input uncertainties than simple random sampling (SRS) because it densely stratifies across the range of each input probability distribution. Output uncertainty assessment is based on the tolerance limits concept, where the sample formed by the code calculations infers to cover 95% of the output population with at least a 95% of confidence. This analysis is the first attempt to propagate parameter uncertainties of modern multi-group libraries, which are used to feed advanced lattice codes that perform state of the art resonant self-shielding calculations such as DRAGONv4. (authors)« less

EASY-II Renaissance: n, p, d, α, γ-induced Inventory Code System

NASA Astrophysics Data System (ADS)

Sublet, J.-Ch.; Eastwood, J. W.; Morgan, J. G.

2014-04-01

The European Activation SYstem has been re-engineered and re-written in modern programming languages so as to answer today's and tomorrow's needs in terms of activation, transmutation, depletion, decay and processing of radioactive materials. The new FISPACT-II inventory code development project has allowed us to embed many more features in terms of energy range: up to GeV; incident particles: alpha, gamma, proton, deuteron and neutron; and neutron physics: self-shielding effects, temperature dependence and covariance, so as to cover all anticipated application needs: nuclear fission and fusion, accelerator physics, isotope production, stockpile and fuel cycle stewardship, materials characterization and life, and storage cycle management. In parallel, the maturity of modern, truly general purpose libraries encompassing thousands of target isotopes such as TENDL-2012, the evolution of the ENDF-6 format and the capabilities of the latest generation of processing codes PREPRO, NJOY and CALENDF have allowed the activation code to be fed with more robust, complete and appropriate data: cross sections with covariance, probability tables in the resonance ranges, kerma, dpa, gas and radionuclide production and 24 decay types. All such data for the five most important incident particles (n, p, d, α, γ), are placed in evaluated data files up to an incident energy of 200 MeV. The resulting code system, EASY-II is designed as a functional replacement for the previous European Activation System, EASY-2010. It includes many new features and enhancements, but also benefits already from the feedback from extensive validation and verification activities performed with its predecessor.

Calculation of electron and isotopes dose point kernels with fluka Monte Carlo code for dosimetry in nuclear medicine therapy

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

Botta, F.; Mairani, A.; Battistoni, G.

Purpose: The calculation of patient-specific dose distribution can be achieved by Monte Carlo simulations or by analytical methods. In this study, fluka Monte Carlo code has been considered for use in nuclear medicine dosimetry. Up to now, fluka has mainly been dedicated to other fields, namely high energy physics, radiation protection, and hadrontherapy. When first employing a Monte Carlo code for nuclear medicine dosimetry, its results concerning electron transport at energies typical of nuclear medicine applications need to be verified. This is commonly achieved by means of calculation of a representative parameter and comparison with reference data. Dose point kernelmore » (DPK), quantifying the energy deposition all around a point isotropic source, is often the one. Methods: fluka DPKs have been calculated in both water and compact bone for monoenergetic electrons (10{sup -3} MeV) and for beta emitting isotopes commonly used for therapy ({sup 89}Sr, {sup 90}Y, {sup 131}I, {sup 153}Sm, {sup 177}Lu, {sup 186}Re, and {sup 188}Re). Point isotropic sources have been simulated at the center of a water (bone) sphere, and deposed energy has been tallied in concentric shells. fluka outcomes have been compared to penelope v.2008 results, calculated in this study as well. Moreover, in case of monoenergetic electrons in water, comparison with the data from the literature (etran, geant4, mcnpx) has been done. Maximum percentage differences within 0.8{center_dot}R{sub CSDA} and 0.9{center_dot}R{sub CSDA} for monoenergetic electrons (R{sub CSDA} being the continuous slowing down approximation range) and within 0.8{center_dot}X{sub 90} and 0.9{center_dot}X{sub 90} for isotopes (X{sub 90} being the radius of the sphere in which 90% of the emitted energy is absorbed) have been computed, together with the average percentage difference within 0.9{center_dot}R{sub CSDA} and 0.9{center_dot}X{sub 90} for electrons and isotopes, respectively. Results: Concerning monoenergetic electrons, within 0.8{center_dot}R{sub CSDA} (where 90%-97% of the particle energy is deposed), fluka and penelope agree mostly within 7%, except for 10 and 20 keV electrons (12% in water, 8.3% in bone). The discrepancies between fluka and the other codes are of the same order of magnitude than those observed when comparing the other codes among them, which can be referred to the different simulation algorithms. When considering the beta spectra, discrepancies notably reduce: within 0.9{center_dot}X{sub 90}, fluka and penelope differ for less than 1% in water and less than 2% in bone with any of the isotopes here considered. Complete data of fluka DPKs are given as Supplementary Material as a tool to perform dosimetry by analytical point kernel convolution. Conclusions: fluka provides reliable results when transporting electrons in the low energy range, proving to be an adequate tool for nuclear medicine dosimetry.« less

Near-IR Light-Cleavable Antibody Conjugates and Conjugate Precursors | NCI Technology Transfer Center | TTC

Cancer.gov

Researchers at the National Cancer Institute (NCI) developed novel groups of cyanine (Cy) based antibody-drug conjugate (ADC) chemical linkers that undergo photolytic cleavage upon irradiation with near-IR light. By using the fluorescent properties of the Cy linker to monitor localization of the ADC, and subsequent near-IR irradiation of cancerous tissue, drug release could be confined to the tumor microenvironment.

Reactive Fluid Flow and Applications to Diagenesis, Mineral Deposits, and Crustal Rocks

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

Rye, Danny M.; Bolton, Edward W.

2002-11-04

The objective is to initiate new: modeling of coupled fluid flow and chemical reactions of geologic environments; experimental and theoretical studies of water-rock reactions; collection and interpretation of stable isotopic and geochemical field data at many spatial scales of systems involving fluid flow and reaction in environments ranging from soils to metamorphic rocks. Theoretical modeling of coupled fluid flow and chemical reactions, involving kinetics, has been employed to understand the differences between equilibrium, steady-state, and non-steady-state behavior of the chemical evolution of open fluid-rock systems. The numerical codes developed in this project treat multi-component, finite-rate reactions combined with advective andmore » dispersive transport in multi-dimensions. The codes incorporate heat, mass, and isotopic transfer in both porous and fractured media. Experimental work has obtained the kinetic rate laws of pertinent silicate-water reactions and the rates of Sr release during chemical weathering. Ab-initio quantum mechanical techniques have been applied to obtain the kinetics and mechanisms of silicate surface reactions and isotopic exchange between water and dissolved species. Geochemical field-based studies were carried out on the Wepawaug metamorphic schist, on the Irish base-metal sediment-hosted ore system, in the Dalradian metamorphic complex in Scotland, and on weathering in the Columbia River flood basalts. The geochemical and isotopic field data, and the experimental and theoretical rate data, were used as constraints on the numerical models and to determine the length and time scales relevant to each of the field areas.« less

Site-directed decapsulation of bolaamphiphilic vesicles with enzymatic cleavable surface groups.

PubMed

Popov, Mary; Grinberg, Sarina; Linder, Charles; Waner, Tal; Levi-Hevroni, Bosmat; Deckelbaum, Richard J; Heldman, Eliahu

2012-06-10

Stable nano-sized vesicles with a monolayer encapsulating membrane were prepared from novel bolaamphiphiles with choline ester head groups. The head groups were covalently bound to the alkyl chain of the bolaamphiphiles either via the nitrogen atom of the choline moiety, or via the choline ester's methyl group. Both types of bolaamphiphiles competed with acetylthiocholine for binding to acetylcholine esterase (AChE), yet, only the choline ester head groups bound to the alkyl chain via the nitrogen atom of the choline moiety were hydrolyzed by the enzyme. Likewise, only vesicles composed of bolaamphiphiles with head groups that were hydrolyzed by AChE released their encapsulated material upon exposure to the enzyme. Injection of carboxyfluorescein (CF)-loaded vesicles with cleavable choline ester head groups into mice resulted in the accumulation of CF in tissues that express high AChE activity, including the brain. By comparison, when vesicles with choline ester head groups that are not hydrolyzed by AChE were injected into mice, there was no accumulation of CF in tissues that highly express the enzyme. These results imply that bolaamphiphilic vesicles with surface groups that are substrates to enzymes which are highly expressed in target organs may potentially be used as a drug delivery system with controlled site-directed drug release. Copyright © 2011 Elsevier B.V. All rights reserved.

Specific capture, recovery and culture of cancer cells using oriented antibody-modified polystyrene chips coated with agarose film.

PubMed

Jeong, Jiyun; Lee, Yeolin; Yoo, Yeongeun; Lee, Myung Kyu

2018-02-01

Agarose gel can be used for three dimensional (3D) cell culture because it prevents cell attachment. The dried agarose film coated on a culture plate also protected cell attachment and allowed 3D growth of cancer cells. We developed an efficient method for agarose film coating on an oxygen-plasma treated micropost polystyrene chip prepared by an injection molding process. The agarose film was modified to maleimide or Ni-NTA groups for covalent or cleavable attachment of photoactivatable Fc-specific antibody binding proteins (PFcBPs) via their N-terminal cysteine residues or 6xHis tag, respectively. The antibodies photocrosslinked onto the PFcBP-modified chips specifically captured the target cells without nonspecific binding, and the captured cells grew 3D modes on the chips. The captured cells on the cleavable antibody-modified chips were easily recovered by treatment of commercial trypsin-EDTA solution. Under fluidic conditions using an antibody-modified micropost chip, the cells were mainly captured on the micropost walls of the chip rather than on the bottom of it. The presented method will also be applicable for immobilization of oriented antibodies on various microfluidic chips with different structures. Copyright © 2017 Elsevier B.V. All rights reserved.

A novel high drug loading mussel-inspired polydopamine hybrid nanoparticle as a pH-sensitive vehicle for drug delivery.

PubMed

Hou, Jie; Guo, Chunlei; Shi, Yuzhi; Liu, Ergang; Dong, Weibing; Yu, Bo; Liu, Shiyuan; Gong, Junbo

2017-11-25

A novel high drug loading pH-cleavable polymer hybrid nanoparticle was prepared via doxorubicin (DOX) grafted onto PEGylated, mussel-inspired polydopamine (PDA) and then coated onto hollow silica nanoparticles for drug delivery. A series of characterization shed light on the formation mechanisms of PDA coatings on hollow silica. We hypothesized that dopamine was first absorbed onto the surface of hollow silica and then began self-polymerization. A Dox-containing thiol moiety was fabricated with conjugation between doxorubicin hydrochloride and Mercaptopropionyalkali with a pH-cleavable hydrozone bond. Using a Michael addition reaction, several Dox-containing thiol moieties were grafted onto the surface of the PDA. The drug loading capacity can reach 35.43%. It can minimize the metabolic problem of silica. The released behavior of Dox can be significantly enhanced at endosomal pH compared to physiological pH. After folate modification, nanoparticles can lead to more cellular endocytosis. Meanwhile animal assays showed that more Dox accumulated in tumor tissue, which can enhanced the cytotoxicity to 4T1 cancer cells with a targeting group compared to free DOX and untargeted groups. Meanwhile, the tumor growth was significantly inhibited. This promising material shows a promising future as a drug delivery system. Copyright © 2017 Elsevier B.V. All rights reserved.

Targeted Drug Delivery with Polymers and Magnetic Nanoparticles: Covalent and Noncovalent Approaches, Release Control, and Clinical Studies.

PubMed

Ulbrich, Karel; Holá, Kateřina; Šubr, Vladimir; Bakandritsos, Aristides; Tuček, Jiří; Zbořil, Radek

2016-05-11

Targeted delivery combined with controlled drug release has a pivotal role in the future of personalized medicine. This review covers the principles, advantages, and drawbacks of passive and active targeting based on various polymer and magnetic iron oxide nanoparticle carriers with drug attached by both covalent and noncovalent pathways. Attention is devoted to the tailored conjugation of targeting ligands (e.g., enzymes, antibodies, peptides) to drug carrier systems. Similarly, the approaches toward controlled drug release are discussed. Various polymer-drug conjugates based, for example, on polyethylene glycol (PEG), N-(2-hydroxypropyl)methacrylamide (HPMA), polymeric micelles, and nanoparticle carriers are explored with respect to absorption, distribution, metabolism, and excretion (ADME scheme) of administrated drug. Design and structure of superparamagnetic iron oxide nanoparticles (SPION) and condensed magnetic clusters are classified according to the mechanism of noncovalent drug loading involving hydrophobic and electrostatic interactions, coordination chemistry, and encapsulation in porous materials. Principles of covalent conjugation of drugs with SPIONs including thermo- and pH-degradable bonds, amide linkage, redox-cleavable bonds, and enzymatically-cleavable bonds are also thoroughly described. Finally, results of clinical trials obtained with polymeric and magnetic carriers are analyzed highlighting the potential advantages and future directions in targeted anticancer therapy.

Acid-Labile Amphiphilic PEO-b-PPO-b-PEO Copolymers: Degradable Poloxamer Analogs.

PubMed

Worm, Matthias; Kang, Biao; Dingels, Carsten; Wurm, Frederik R; Frey, Holger

2016-05-01

Poly ((ethylene oxide)-b-(propylene oxide)-b-(ethylene oxide)) triblock copolymers commonly known as poloxamers or Pluronics constitute an important class of nonionic, biocompatible surfactants. Here, a method is reported to incorporate two acid-labile acetal moieties in the backbone of poloxamers to generate acid-cleavable nonionic surfactants. Poly(propylene oxide) is functionalized by means of an acetate-protected vinyl ether to introduce acetal units. Three cleavable PEO-PPO-PEO triblock copolymers (Mn,total = 6600, 8000, 9150 g·mol(-1) ; Mn,PEO = 2200, 3600, 4750 g·mol(-1) ) have been synthesized using anionic ring-opening polymerization. The amphiphilic copolymers exhibit narrow molecular weight distributions (Ð = 1.06-1.08). Surface tension measurements reveal surface-active behavior in aqueous solution comparable to established noncleavable poloxamers. Complete hydrolysis of the labile junctions after acidic treatment is verified by size exclusion chromatography. The block copolymers have been employed as surfactants in a miniemulsion polymerization to generate polystyrene (PS) nanoparticles with mean diameters of ≈200 nm and narrow size distribution, as determined by dynamic light scattering and scanning electron microscopy. Acid-triggered precipitation facilitates removal of surfactant fragments from the nanoparticles, which simplifies purification and enables nanoparticle precipitation "on demand." © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Deciphering Systemic Wound Responses of the Pumpkin Extrafascicular Phloem by Metabolomics and Stable Isotope-Coded Protein Labeling1[C][W

PubMed Central

Gaupels, Frank; Sarioglu, Hakan; Beckmann, Manfred; Hause, Bettina; Spannagl, Manuel; Draper, John; Lindermayr, Christian; Durner, Jörg

2012-01-01

In cucurbits, phloem latex exudes from cut sieve tubes of the extrafascicular phloem (EFP), serving in defense against herbivores. We analyzed inducible defense mechanisms in the EFP of pumpkin (Cucurbita maxima) after leaf damage. As an early systemic response, wounding elicited transient accumulation of jasmonates and a decrease in exudation probably due to partial sieve tube occlusion by callose. The energy status of the EFP was enhanced as indicated by increased levels of ATP, phosphate, and intermediates of the citric acid cycle. Gas chromatography coupled to mass spectrometry also revealed that sucrose transport, gluconeogenesis/glycolysis, and amino acid metabolism were up-regulated after wounding. Combining ProteoMiner technology for the enrichment of low-abundance proteins with stable isotope-coded protein labeling, we identified 51 wound-regulated phloem proteins. Two Sucrose-Nonfermenting1-related protein kinases and a 32-kD 14-3-3 protein are candidate central regulators of stress metabolism in the EFP. Other proteins, such as the Silverleaf Whitefly-Induced Protein1, Mitogen Activated Protein Kinase6, and Heat Shock Protein81, have known defensive functions. Isotope-coded protein labeling and western-blot analyses indicated that Cyclophilin18 is a reliable marker for stress responses of the EFP. As a hint toward the induction of redox signaling, we have observed delayed oxidation-triggered polymerization of the major Phloem Protein1 (PP1) and PP2, which correlated with a decline in carbonylation of PP2. In sum, wounding triggered transient sieve tube occlusion, enhanced energy metabolism, and accumulation of defense-related proteins in the pumpkin EFP. The systemic wound response was mediated by jasmonate and redox signaling. PMID:23085839

Molecular mechanisms of ribosomal protein gene coregulation.

PubMed

Reja, Rohit; Vinayachandran, Vinesh; Ghosh, Sujana; Pugh, B Franklin

2015-09-15

The 137 ribosomal protein genes (RPGs) of Saccharomyces provide a model for gene coregulation. We examined the positional and functional organization of their regulators (Rap1 [repressor activator protein 1], Fhl1, Ifh1, Sfp1, and Hmo1), the transcription machinery (TFIIB, TFIID, and RNA polymerase II), and chromatin at near-base-pair resolution using ChIP-exo, as RPGs are coordinately reprogrammed. Where Hmo1 is enriched, Fhl1, Ifh1, Sfp1, and Hmo1 cross-linked broadly to promoter DNA in an RPG-specific manner and demarcated by general minor groove widening. Importantly, Hmo1 extended 20-50 base pairs (bp) downstream from Fhl1. Upon RPG repression, Fhl1 remained in place. Hmo1 dissociated, which was coupled to an upstream shift of the +1 nucleosome, as reflected by the Hmo1 extension and core promoter region. Fhl1 and Hmo1 may create two regulatable and positionally distinct barriers, against which chromatin remodelers position the +1 nucleosome into either an activating or a repressive state. Consistent with in vitro studies, we found that specific TFIID subunits, in addition to cross-linking at the core promoter, made precise cross-links at Rap1 sites, which we interpret to reflect native Rap1-TFIID interactions. Our findings suggest how sequence-specific DNA binding regulates nucleosome positioning and transcription complex assembly >300 bp away and how coregulation coevolved with coding sequences. © 2015 Reja et al.; Published by Cold Spring Harbor Laboratory Press.

Steroid isotopic standards for gas chromatography-combustion isotope ratio mass spectrometry (GCC-IRMS).

PubMed

Zhang, Ying; Tobias, Herbert J; Brenna, J Thomas

2009-03-01

Carbon isotope ratio (CIR) analysis of urinary steroids using gas chromatography-combustion isotope ratio mass spectrometry (GCC-IRMS) is a recognized test to detect illicit doping with synthetic testosterone. There are currently no universally used steroid isotopic standards (SIS). We adapted a protocol to prepare isotopically uniform steroids for use as a calibrant in GCC-IRMS that can be analyzed under the same conditions as used for steroids extracted from urine. Two separate SIS containing a mixture of steroids were created and coded CU/USADA 33-1 and CU/USADA 34-1, containing acetates and native steroids, respectively. CU/USADA 33-1 contains 5alpha-androstan-3beta-ol acetate (5alpha-A-AC), 5alpha-androstan-3alpha-ol-17-one acetate (androsterone acetate, A-AC), 5beta-androstan-3alpha-ol-11, 17-dione acetate (11-ketoetiocholanolone acetate, 11k-AC) and 5alpha-cholestane (Cne). CU/USADA 34-1 contains 5beta-androstan-3alpha-ol-17-one (etiocholanolone, E), 5alpha-androstan-3alpha-ol-17-one (androsterone, A), and 5beta-pregnane-3alpha, 20alpha-diol (5betaP). Each mixture was prepared and dispensed into a set of about 100 ampoules using a protocol carefully designed to minimize isotopic fractionation and contamination. A natural gas reference material, NIST RM 8559, traceable to the international standard Vienna PeeDee Belemnite (VPDB) was used to calibrate the SIS. Absolute delta(13)C(VPDB) and Deltadelta(13)C(VPDB) values from randomly selected ampoules from both SIS indicate uniformity of steroid isotopic composition within measurement reproducibility, SD(delta(13)C)<0.2 per thousand. This procedure for creation of isotopic steroid mixtures results in consistent standards with isotope ratios traceable to the relevant international reference material.

Total and Compound Formation Cross Sections for Americium Nuclei: Recommendations for Coupled-Channels Calculations

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

Escher, J. E.

Calculations for total cross sections and compound-nucleus (CN) formation cross sections for americium isotopes are described, for use in the 2017 NA-22 evaluation effort. The code ECIS 2006 was used in conjunction with Frank Dietrich's wrapper `runtemplate'.

Adjoint-Based Sensitivity and Uncertainty Analysis for Density and Composition: A User’s Guide

DOE PAGES

Favorite, Jeffrey A.; Perko, Zoltan; Kiedrowski, Brian C.; ...

2017-03-01

The ability to perform sensitivity analyses using adjoint-based first-order sensitivity theory has existed for decades. This paper provides guidance on how adjoint sensitivity methods can be used to predict the effect of material density and composition uncertainties in critical experiments, including when these uncertain parameters are correlated or constrained. Two widely used Monte Carlo codes, MCNP6 (Ref. 2) and SCALE 6.2 (Ref. 3), are both capable of computing isotopic density sensitivities in continuous energy and angle. Additionally, Perkó et al. have shown how individual isotope density sensitivities, easily computed using adjoint methods, can be combined to compute constrained first-order sensitivitiesmore » that may be used in the uncertainty analysis. This paper provides details on how the codes are used to compute first-order sensitivities and how the sensitivities are used in an uncertainty analysis. Constrained first-order sensitivities are computed in a simple example problem.« less

Determination of the δ34S of Total Sulfur in Solids: RSIL Lab Code 1800

USGS Publications Warehouse

Revesz, Kinga; Coplen, Tyler B.

2006-01-01

The purpose of Reston Stable Isotope Laboratory Lab (RSIL) Code 1800 is to determine the δ(34S/32S), abbreviated as δ34S, of total sulfur in a solid sample. A Carlo Erba NC 2500 elemental analyzer (EA) is used to convert total sulfur in a solid sample into SO2 gas. The EA is connected to a continuous flow isotope-ratio mass spectrometer (CF-IRMS), which determines the relative difference in stable sulfur isotope-amount ratio (34S/32S) of the product SO2 gas. The combustion is quantitative; no isotopic fractionation is involved. Samples are placed in tin capsules and loaded into a Costech Zero-Blank Autosampler on the EA. Under computer control, samples are dropped into a heated tube reaction tube that combines both the oxidation and the reduction reactions. The combustion takes place in a He atmosphere that contains an excess of oxygen gas at the oxidation zone at the top of the reaction tube. Combustion products are transported by a He carrier through the reduction zone at the bottom of the reaction tube to remove excess oxygen and through a separate drying tube to remove any water. The gas-phase products, mainly CO2, N2, and SO2, are separated by a gas chromatograph (GC). The gas is then introduced into the isotope-ratio mass spectrometer (IRMS) through a Thermo-Finnigan ConFlo II interface, which also is used to inject SO2 reference gas and He for sample dilution. The IRMS is a Thermo-Finnigan DeltaPlus CF-IRMS. It has a universal triple collector with two wide cups and a narrow cup in the middle. It is capable of measuring mass/charge (m/z) 64 and 66 simultaneously. The ion beams from SO2 are as follows: m/z 64 = SO2 = 32S16O16O; and m/z 66 = SO2 = 34S16O16O primarily.

Controlled grafting of vinylic monomers on polyolefins: a robust mathematical modeling approach

PubMed Central

Saeb, Mohammad Reza; Rezaee, Babak; Shadman, Alireza; Formela, Krzysztof; Ahmadi, Zahed; Hemmati, Farkhondeh; Kermaniyan, Tayebeh Sadat; Mohammadi, Yousef

2017-01-01

Abstract Experimental and mathematical modeling analyses were used for controlling melt free-radical grafting of vinylic monomers on polyolefins and, thereby, reducing the disturbance of undesired cross-linking of polyolefins. Response surface, desirability function, and artificial intelligence methodologies were blended to modeling/optimization of grafting reaction in terms of vinylic monomer content, peroxide initiator concentration, and melt-processing time. An in-house code was developed based on artificial neural network that learns and mimics processing torque and grafting of glycidyl methacrylate (GMA) typical vinylic monomer on high-density polyethylene (HDPE). Application of response surface and desirability function enabled concurrent optimization of processing torque and GMA grafting on HDPE, through which we quantified for the first time competition between parallel reactions taking place during melt processing: (i) desirable grafting of GMA on HDPE; (ii) undesirable cross-linking of HDPE. The proposed robust mathematical modeling approach can precisely learn the behavior of grafting reaction of vinylic monomers on polyolefins and be placed into practice in finding exact operating condition needed for efficient grafting of reactive monomers on polyolefins. PMID:29491797

Controlled grafting of vinylic monomers on polyolefins: a robust mathematical modeling approach.

PubMed

Saeb, Mohammad Reza; Rezaee, Babak; Shadman, Alireza; Formela, Krzysztof; Ahmadi, Zahed; Hemmati, Farkhondeh; Kermaniyan, Tayebeh Sadat; Mohammadi, Yousef

2017-01-01

Experimental and mathematical modeling analyses were used for controlling melt free-radical grafting of vinylic monomers on polyolefins and, thereby, reducing the disturbance of undesired cross-linking of polyolefins. Response surface, desirability function, and artificial intelligence methodologies were blended to modeling/optimization of grafting reaction in terms of vinylic monomer content, peroxide initiator concentration, and melt-processing time. An in-house code was developed based on artificial neural network that learns and mimics processing torque and grafting of glycidyl methacrylate (GMA) typical vinylic monomer on high-density polyethylene (HDPE). Application of response surface and desirability function enabled concurrent optimization of processing torque and GMA grafting on HDPE, through which we quantified for the first time competition between parallel reactions taking place during melt processing: (i) desirable grafting of GMA on HDPE; (ii) undesirable cross-linking of HDPE. The proposed robust mathematical modeling approach can precisely learn the behavior of grafting reaction of vinylic monomers on polyolefins and be placed into practice in finding exact operating condition needed for efficient grafting of reactive monomers on polyolefins.

Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

PubMed Central

Hafner, Markus; Landthaler, Markus; Burger, Lukas; Khorshid, Mohsen; Hausser, Jean; Berninger, Philipp; Rothballer, Andrea; Ascano, Manuel; Jungkamp, Anna-Carina; Munschauer, Mathias; Ulrich, Alexander; Wardle, Greg S.; Dewell, Scott; Zavolan, Mihaela; Tuschl, Thomas

2010-01-01

Summary RNA transcripts are subject to post-transcriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases. PMID:20371350

Synthesis of an immunoconjugate of camptothecin.

PubMed

Walker, Michael A; Dubowchik, Gene M; Hofstead, Sandra J; Trail, Pamela A; Firestone, Raymond A

2002-01-21

The first immunoconjugate of camptothecin has been synthesized wherein the drug is attached to the tumor-recognizing antibody BR96 via a Cathepsin B cleavable linker. Endocytosis of the immunoconjugate upon binding to the tumor cell followed by enzymatic cleavage of the linker inside the endosome ensures tumor-specific release of the drug. In this way, it is hoped that the dose-limiting side effects associated with camptothecin can be eliminated while the antitumor activity is preserved.

Metabolically Generated Stable Isotope-Labeled Deoxynucleoside Code for Tracing DNA N6-Methyladenine in Human Cells.

PubMed

Liu, Baodong; Liu, Xiaoling; Lai, Weiyi; Wang, Hailin

2017-06-06

DNA N 6 -methyl-2'-deoxyadenosine (6mdA) is an epigenetic modification in both eukaryotes and bacteria. Here we exploited stable isotope-labeled deoxynucleoside [ 15 N 5 ]-2'-deoxyadenosine ([ 15 N 5 ]-dA) as an initiation tracer and for the first time developed a metabolically differential tracing code for monitoring DNA 6mdA in human cells. We demonstrate that the initiation tracer [ 15 N 5 ]-dA undergoes a specific and efficient adenine deamination reaction leading to the loss the exocyclic amine 15 N, and further utilizes the purine salvage pathway to generate mainly both [ 15 N 4 ]-dA and [ 15 N 4 ]-2'-deoxyguanosine ([ 15 N 4 ]-dG) in mammalian genomes. However, [ 15 N 5 ]-dA is largely retained in the genomes of mycoplasmas, which are often found in cultured cells and experimental animals. Consequently, the methylation of dA generates 6mdA with a consistent coding pattern, with a predominance of [ 15 N 4 ]-6mdA. Therefore, mammalian DNA 6mdA can be potentially discriminated from that generated by infecting mycoplasmas. Collectively, we show a promising approach for identification of authentic DNA 6mdA in human cells and determine if the human cells are contaminated with mycoplasmas.

Development of PEGylated peptide probes conjugated with (18)F-labeled BODIPY for PET/optical imaging of MT1-MMP activity.

PubMed

Kondo, Naoya; Temma, Takashi; Deguchi, Jun; Sano, Kohei; Ono, Masahiro; Saji, Hideo

2015-12-28

Since the processing activity of the matrix metalloproteinase MT1-MMP regulates various cellular functions such as motility, invasion, growth, differentiation and apoptosis, precise in vivo evaluation of MT1-MMP activity in cancers can provide beneficial information for both basic and clinical studies. For this purpose, we designed a cleavable Positron Emission Tomography (PET)/optical imaging probe consisting of BODIPY650/665 and polyethylene glycol (PEG) conjugated to opposite ends of MT1-MMP substrate peptides. We used in vitro and in vivo fluorescence experiments to select suitable substrate peptide sequences and PEG sizes for the MT1-MMP probes and obtained an optimized structure referred to here as MBP-2k. Radiofluorinated MBP-2k ([(18)F]MBP-2k) was then successfully synthesized via an (18)F-(19)F isotopic exchange reaction in BODIPY650/665. After intravenous injection into mice with xenografted tumors, [(18)F]MBP-2k showed significantly higher accumulation in HT1080 tumors with high MT1-MMP activity than in A549 tumors that have low MT1-MMP activity. Moreover, PET images showed better contrast in HT1080 tumors. These results show that [(18)F]MBP-2k can be used as a hybrid PET/optical imaging agent and is a promising probe for non-invasive monitoring of MT1-MMP activity in cancers. This probe may also efficiently combine targeted tumor imaging with image-guided surgery that could be beneficial for patients in the future. Copyright © 2015 Elsevier B.V. All rights reserved.

Shell-model-based deformation analysis of light cadmium isotopes

NASA Astrophysics Data System (ADS)

Schmidt, T.; Heyde, K. L. G.; Blazhev, A.; Jolie, J.

2017-07-01

Large-scale shell-model calculations for the even-even cadmium isotopes 98Cd-108Cd have been performed with the antoine code in the π (2 p1 /2;1 g9 /2) ν (2 d5 /2;3 s1 /2;2 d3 /2;1 g7 /2;1 h11 /2) model space without further truncation. Known experimental energy levels and B (E 2 ) values could be well reproduced. Taking these calculations as a starting ground we analyze the deformation parameters predicted for the Cd isotopes as a function of neutron number N and spin J using the methods of model independent invariants introduced by Kumar [Phys. Rev. Lett. 28, 249 (1972), 10.1103/PhysRevLett.28.249] and Cline [Annu. Rev. Nucl. Part. Sci. 36, 683 (1986), 10.1146/annurev.ns.36.120186.003343].

Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain

PubMed Central

Scheckel, Claudia; Drapeau, Elodie; Frias, Maria A; Park, Christopher Y; Fak, John; Zucker-Scharff, Ilana; Kou, Yan; Haroutunian, Vahram; Ma'ayan, Avi

2016-01-01

Neuronal ELAV-like (nELAVL) RNA binding proteins have been linked to numerous neurological disorders. We performed crosslinking-immunoprecipitation and RNAseq on human brain, and identified nELAVL binding sites on 8681 transcripts. Using knockout mice and RNAi in human neuroblastoma cells, we showed that nELAVL intronic and 3' UTR binding regulates human RNA splicing and abundance. We validated hundreds of nELAVL targets among which were important neuronal and disease-associated transcripts, including Alzheimer's disease (AD) transcripts. We therefore investigated RNA regulation in AD brain, and observed differential splicing of 150 transcripts, which in some cases correlated with differential nELAVL binding. Unexpectedly, the most significant change of nELAVL binding was evident on non-coding Y RNAs. nELAVL/Y RNA complexes were specifically remodeled in AD and after acute UV stress in neuroblastoma cells. We propose that the increased nELAVL/Y RNA association during stress may lead to nELAVL sequestration, redistribution of nELAVL target binding, and altered neuronal RNA splicing. DOI: http://dx.doi.org/10.7554/eLife.10421.001 PMID:26894958

SFCOMPO-2.0: An OECD NEA database of spent nuclear fuel isotopic assays, reactor design specifications, and operating data

DOE PAGES

Michel-Sendis, F.; Gauld, I.; Martinez, J. S.; ...

2017-08-02

SFCOMPO-2.0 is the new release of the Organisation for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) database of experimental assay measurements. These measurements are isotopic concentrations from destructive radiochemical analyses of spent nuclear fuel (SNF) samples. We supplement the measurements with design information for the fuel assembly and fuel rod from which each sample was taken, as well as with relevant information on operating conditions and characteristics of the host reactors. These data are necessary for modeling and simulation of the isotopic evolution of the fuel during irradiation. SFCOMPO-2.0 has been developed and is maintained by the OECDmore » NEA under the guidance of the Expert Group on Assay Data of Spent Nuclear Fuel (EGADSNF), which is part of the NEA Working Party on Nuclear Criticality Safety (WPNCS). Significant efforts aimed at establishing a thorough, reliable, publicly available resource for code validation and safety applications have led to the capture and standardization of experimental data from 750 SNF samples from more than 40 reactors. These efforts have resulted in the creation of the SFCOMPO-2.0 database, which is publicly available from the NEA Data Bank. Our paper describes the new database, and applications of SFCOMPO-2.0 for computer code validation, integral nuclear data benchmarking, and uncertainty analysis in nuclear waste package analysis are briefly illustrated.« less

SFCOMPO-2.0: An OECD NEA database of spent nuclear fuel isotopic assays, reactor design specifications, and operating data

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

Michel-Sendis, F.; Gauld, I.; Martinez, J. S.

SFCOMPO-2.0 is the new release of the Organisation for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) database of experimental assay measurements. These measurements are isotopic concentrations from destructive radiochemical analyses of spent nuclear fuel (SNF) samples. We supplement the measurements with design information for the fuel assembly and fuel rod from which each sample was taken, as well as with relevant information on operating conditions and characteristics of the host reactors. These data are necessary for modeling and simulation of the isotopic evolution of the fuel during irradiation. SFCOMPO-2.0 has been developed and is maintained by the OECDmore » NEA under the guidance of the Expert Group on Assay Data of Spent Nuclear Fuel (EGADSNF), which is part of the NEA Working Party on Nuclear Criticality Safety (WPNCS). Significant efforts aimed at establishing a thorough, reliable, publicly available resource for code validation and safety applications have led to the capture and standardization of experimental data from 750 SNF samples from more than 40 reactors. These efforts have resulted in the creation of the SFCOMPO-2.0 database, which is publicly available from the NEA Data Bank. Our paper describes the new database, and applications of SFCOMPO-2.0 for computer code validation, integral nuclear data benchmarking, and uncertainty analysis in nuclear waste package analysis are briefly illustrated.« less

Stable chromosome condensation revealed by chromosome conformation capture

PubMed Central

Eagen, Kyle P.; Hartl, Tom A.; Kornberg, Roger D.

2015-01-01

SUMMARY Chemical cross-linking and DNA sequencing have revealed regions of intra-chromosomal interaction, referred to as topologically associating domains (TADs), interspersed with regions of little or no interaction, in interphase nuclei. We find that TADs and the regions between them correspond with the bands and interbands of polytene chromosomes of Drosophila. We further establish the conservation of TADs between polytene and diploid cells of Drosophila. From direct measurements on light micrographs of polytene chromosomes, we then deduce the states of chromatin folding in the diploid cell nucleus. Two states of folding, fully extended fibers containing regulatory regions and promoters, and fibers condensed up to ten-fold containing coding regions of active genes, constitute the euchromatin of the nuclear interior. Chromatin fibers condensed up to 30-fold, containing coding regions of inactive genes, represent the heterochromatin of the nuclear periphery. A convergence of molecular analysis with direct observation thus reveals the architecture of interphase chromosomes. PMID:26544940

Gamma-ray spectroscopy: The diffuse galactic glow

NASA Technical Reports Server (NTRS)

Hartmann, Dieter H.

1991-01-01

The goal of this project is the development of a numerical code that provides statistical models of the sky distribution of gamma-ray lines due to the production of radioactive isotopes by ongoing Galactic nucleosynthesis. We are particularly interested in quasi-steady emission from novae, supernovae, and stellar winds, but continuum radiation and transient sources must also be considered. We have made significant progress during the first half period of this project and expect the timely completion of a code that can be applied to Oriented Scintillation Spectrometer Experiment (OSSE) Galactic plane survey data.

Attenuation of drug-stimulated topoisomerase II-DNA cleavable complex formation in wild-type HL-60 cells treated with an intracellular calcium buffer is correlated with decreased cytotoxicity and site-specific hypophosphorylation of topoisomerase IIalpha.

PubMed Central

Aoyama, M; Grabowski, D R; Dubyak, G R; Constantinou, A I; Rybicki, L A; Bukowski, R M; Ganapathi, M K; Hickson, I D; Ganapathi, R

1998-01-01

Topoisomerase II (topo II), an essential enzyme for cell viability, is also the target for clinically important anti-neoplastic agents that stimulate topo II-mediated DNA scission. The role of alterations in topo IIalpha phosphorylation and its effect on drug-induced DNA damage and cytotoxicity were investigated. Following loading of HL-60 cells with the calcium buffer 1, 2-bis-(o-aminophenoxy)ethane-N,N,N',N'-tetra-acetic acid tetra(acetoxymethyl) ester (BAPTA-AM), which abrogates intracellular Ca2+ transients, a significant decrease in etoposide (VP-16)- or amsacrine (m-AMSA)-stabilized topo II-DNA cleavable complex formation and a corresponding decrease in cytotoxicity was observed. In a cell-free system, nuclear extracts from BAPTA-AM-treated cells exhibited markedly less activity when assayed for VP-16-stabilized topo II-DNA complex formation, but not decatenation of kinetoplast DNA. In contrast, the loading of HL-60 cells with N,N,N', N'-tetrakis-(2-pyridyl)ethylenediamine (TPEN), which binds heavy metals without disturbing calcium or magnesium concentrations, did not significantly affect VP-16-stimulated topo II-DNA cleavable complex formation or cytotoxicity. In HL-60 cells the accumulation of BAPTA, but not TPEN, also led to the hypophosphorylation of topo IIalpha. Tryptic phosphopeptide mapping of topo IIalpha protein from HL-60 cells revealed: (a) eight major phosphorylation sites in untreated cells; (b) hypophosphorylation of two out of eight sites in BAPTA-AM-treated cells; and (c) hypophosphorylation of between two and four out of eight sites in topo II-poison-resistant HL-60 cells. The two hypophosphorylated sites present following BAPTA-AM treatment of wild-type cells were identical with the hypophosphorylated sites in the resistant cells, but were not the same as the sites that are substrates for casein kinase II [Wells, Addison, Fry, Ganapathi and Hickson (1994) J. Biol. Chem. 269, 29746-29751]. In summary, changes in intracellular Ca2+ transients that lead to the site-specific hypophosphorylation of topo IIalpha are possibly involved in regulating the DNA damage caused by and the cytotoxic potential of topo II poisons. PMID:9841887

Light water detritiation

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

Fedorchenko, O.A.; Aleksee, I.A.; Bondarenko, S.D.

2015-03-15

Hundreds of thousands of tons of tritiated light water have been accumulating from the enterprises of nuclear fuel cycles around the world. The Dual-Temperature Water-Hydrogen (DTWH) process looks like the only practical alternative to Combined Electrolysis and Catalytic Exchange (CECE). In DTWH power-consuming lower reflux device (electrolytic cell) is replaced by a so-called 'hot tower' (LPCE column operating at conditions which ensure relatively small value of elementary separation factor α(hot)). In the upper, cold tower, the tritium transfers from hydrogen to water while in the lower, hot tower - in the opposite direction - from water to hydrogen. The DTWHmore » process is much more complicated compared to CECE; it must be thoroughly computed and strictly controlled by an automatic control system. The use of a simulation code for DTWH is absolutely important. The simulation code EVIO-5 deals with 3 flows inside a column (hydrogen gas, water vapour and liquid water) and 2 simultaneous isotope exchange sub-processes (counter-current phase exchange and co-current catalytic exchange). EVIO-5 takes into account the strong dependence of process performance on given conditions (temperature and pressure). It calculates steady-state isotope concentration profiles considering a full set of reversible exchange reactions between different isotope modifications of water and hydrogen (12 molecular species). So the code can be used for simulation of LPCE column operation for detritiation of hydrogen and water feed, which contains H and D not only at low concentrations but above 10 at.% also. EVIO-5 code is used to model a Tritium Removal Facility with a throughput capacity of about 400 m{sup 3}/day. Simulation results show that a huge amount of wet-proofed catalyst is required (about 6000 m{sup 3}), mainly (90%) in the first stage. One reason for these large expenses (apart from a big scale of the problem itself) is the relatively high tritium separation factor in the hot tower. The introduction of some quantity of deuterium into the gaseous flow before the hot tower lowers the tritium separation factor in that column. One possible variant of deuterium introduction to the hot tower of the first stage was modelled. The decontamination capacity increases by a 2.5 factor.« less

Computer codes for checking, plotting and processing of neutron cross-section covariance data and their application

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

Sartori, E.; Roussin, R.W.

This paper presents a brief review of computer codes concerned with checking, plotting, processing and using of covariances of neutron cross-section data. It concentrates on those available from the computer code information centers of the United States and the OECD/Nuclear Energy Agency. Emphasis will be placed also on codes using covariances for specific applications such as uncertainty analysis, data adjustment and data consistency analysis. Recent evaluations contain neutron cross section covariance information for all isotopes of major importance for technological applications of nuclear energy. It is therefore important that the available software tools needed for taking advantage of this informationmore » are widely known as hey permit the determination of better safety margins and allow the optimization of more economic, I designs of nuclear energy systems.« less

Biocompatible, Biodegradable, and Enzymatic-Cleavable MRI Contrast Agents for Early Detection of Bone Metastatic Breast Cancer

DTIC Science & Technology

2012-04-01

detection of bone metastasis from breast cancer. The proposed imaging agent is consist of bone targeting moiety of Asp8 and MRI imaging moiety of DOTA ...peptide onto DOTA followed by Gd complexation was performed to achieve the proposed imaging agent. Non-targeting and CTSK-insensitive controls were...synthesis (SPPS) strategy, and purified by preparative HPLC. The chemical structures of peptides were shown below. Peptides reacted with DOTA -NHS

Preventing mutant huntingtin proteolysis and intermittent fasting promote autophagy in models of Huntington disease.

PubMed

Ehrnhoefer, Dagmar E; Martin, Dale D O; Schmidt, Mandi E; Qiu, Xiaofan; Ladha, Safia; Caron, Nicholas S; Skotte, Niels H; Nguyen, Yen T N; Vaid, Kuljeet; Southwell, Amber L; Engemann, Sabine; Franciosi, Sonia; Hayden, Michael R

2018-03-06

Huntington disease (HD) is caused by the expression of mutant huntingtin (mHTT) bearing a polyglutamine expansion. In HD, mHTT accumulation is accompanied by a dysfunction in basal autophagy, which manifests as specific defects in cargo loading during selective autophagy. Here we show that the expression of mHTT resistant to proteolysis at the caspase cleavage site D586 (C6R mHTT) increases autophagy, which may be due to its increased binding to the autophagy adapter p62. This is accompanied by faster degradation of C6R mHTT in vitro and a lack of mHTT accumulation the C6R mouse model with age. These findings may explain the previously observed neuroprotective properties of C6R mHTT. As the C6R mutation cannot be easily translated into a therapeutic approach, we show that a scheduled feeding paradigm is sufficient to lower mHTT levels in YAC128 mice expressing cleavable mHTT. This is consistent with a previous model, where the presence of cleavable mHTT impairs basal autophagy, while fasting-induced autophagy remains functional. In HD, mHTT clearance and autophagy may become increasingly impaired as a function of age and disease stage, because of gradually increased activity of mHTT-processing enzymes. Our findings imply that mHTT clearance could be enhanced by a regulated dietary schedule that promotes autophagy.

Engineered hybrid spider silk particles as delivery system for peptide vaccines.

PubMed

Lucke, Matthias; Mottas, Inès; Herbst, Tina; Hotz, Christian; Römer, Lin; Schierling, Martina; Herold, Heike M; Slotta, Ute; Spinetti, Thibaud; Scheibel, Thomas; Winter, Gerhard; Bourquin, Carole; Engert, Julia

2018-07-01

The generation of strong T-cell immunity is one of the main challenges for the development of successful vaccines against cancer and major infectious diseases. Here we have engineered spider silk particles as delivery system for a peptide-based vaccination that leads to effective priming of cytotoxic T-cells. The recombinant spider silk protein eADF4(C16) was fused to the antigenic peptide from ovalbumin, either without linker or with a cathepsin cleavable peptide linker. Particles prepared from the hybrid proteins were taken up by dendritic cells, which are essential for T-cell priming, and successfully activated cytotoxic T-cells, without signs of immunotoxicity or unspecific immunostimulatory activity. Upon subcutaneous injection in mice, the particles were taken up by dendritic cells and accumulated in the lymph nodes, where immune responses are generated. Particles from hybrid proteins containing a cathepsin-cleavable linker induced a strong antigen-specific proliferation of cytotoxic T-cells in vivo, even in the absence of a vaccine adjuvant. We thus demonstrate the efficacy of a new vaccine strategy using a protein-based all-in-one vaccination system, where spider silk particles serve as carriers with an incorporated peptide antigen. Our study further suggests that engineered spider silk-based vaccines are extremely stable, easy to manufacture, and readily customizable. Copyright © 2018 Elsevier Ltd. All rights reserved.

pH-Cleavable Nucleoside Lipids: A New Paradigm for Controlling the Stability of Lipid-Based Delivery Systems.

PubMed

Oumzil, Khalid; Benizri, Sébastien; Tonelli, Giovanni; Staedel, Cathy; Appavoo, Ananda; Chaffanet, Max; Navailles, Laurence; Barthélémy, Philippe

2015-11-01

Lipid-based delivery systems are an established technology with considerable clinical acceptance and several applications in human. Herein, we report the design, synthesis and evaluation of novel orthoester nucleoside lipids (ONLs) for the modulation of liposome stability. The ONLs contain head groups with 3'-orthoester nucleoside derivatives featuring positive or negative charges. The insertion of the orthoester function in the NL structures allows the formation of pH-sensitive liposomes. ONL-based liposomes can be hydrolyzed to provide nontoxic products, including nucleoside derivatives and hexadecanol. To allow the release to be tunable at different hydrolysis rates, the charge of the polar head structure is modulated, and the head group can be released at a biologically relevant pH. Crucially, when ONLs are mixed with natural phosphocholine lipids (PC), the resultant liposome evolves toward the formation of a hexadecanol/PC lamellar system. Biological evaluation shows that stable nucleic acid lipid particles (SNALPs) formulated with ONLs and siRNAs can effectively enter into tumor cells and release their nucleic acid payload in response to an intracellular acidic environment. This results in a much higher antitumor activity than conventional SNALPs. The ability to use pH-cleavable nucleolipids to control the stability of lipid-based delivery systems represents a promising approach for the intracellular delivery of drug cargos. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mmp-9 responsive PEG cleavable nanovesicles for efficient delivery of chemotherapeutics to pancreatic cancer.

PubMed

Kulkarni, Prajakta S; Haldar, Manas K; Nahire, Rahul R; Katti, Preeya; Ambre, Avinash H; Muhonen, Wallace W; Shabb, John B; Padi, Sathish K R; Singh, Raushan K; Borowicz, Pawel P; Shrivastava, D K; Katti, Kalpana S; Reindl, Katie; Guo, Bin; Mallik, Sanku

2014-07-07

Significant differences in biochemical parameters between normal and tumor tissues offer an opportunity to chemically design drug carriers which respond to these changes and deliver the drugs at the desired site. For example, overexpression of the matrix metalloproteinase-9 (MMP-9) enzyme in the extracellular matrix of tumor tissues can act as a trigger to chemically modulate the drug delivery from the carriers. In this study, we have synthesized an MMP-9-cleavable, collagen mimetic lipopeptide which forms nanosized vesicles with the POPC, POPE-SS-PEG, and cholesteryl-hemisuccinate lipids. The lipopeptide retains the triple-helical conformation when incorporated into these nanovesicles. The PEG groups shield the substrate lipopeptides from hydrolysis by MMP-9. However, in the presence of elevated glutathione levels, the PEG groups are reductively removed, exposing the lipopeptides to MMP-9. The resultant peptide-bond cleavage disturbs the vesicles' lipid bilayer, leading to the release of encapsulated contents. These PEGylated nanovesicles are capable of encapsulating the anticancer drug gemcitabine with 50% efficiency. They were stable in physiological conditions and in human serum. Effective drug release was demonstrated using the pancreatic ductal carcinoma cells (PANC-1 and MIAPaCa-2) in two-dimensional and three-dimensional "tumor-like" spheroid cultures. A reduction in tumor growth was observed after intravenous administration of the gemcitabine-encapsulated nanovesicles in the xenograft model of athymic, female nude mice.

MMP-9 Responsive PEG Cleavable Nanovesicles for Efficient Delivery of Chemotherapeutics to Pancreatic Cancer

PubMed Central

2015-01-01

Significant differences in biochemical parameters between normal and tumor tissues offer an opportunity to chemically design drug carriers which respond to these changes and deliver the drugs at the desired site. For example, overexpression of the matrix metalloproteinase-9 (MMP-9) enzyme in the extracellular matrix of tumor tissues can act as a trigger to chemically modulate the drug delivery from the carriers. In this study, we have synthesized an MMP-9-cleavable, collagen mimetic lipopeptide which forms nanosized vesicles with the POPC, POPE-SS-PEG, and cholesteryl-hemisuccinate lipids. The lipopeptide retains the triple-helical conformation when incorporated into these nanovesicles. The PEG groups shield the substrate lipopeptides from hydrolysis by MMP-9. However, in the presence of elevated glutathione levels, the PEG groups are reductively removed, exposing the lipopeptides to MMP-9. The resultant peptide-bond cleavage disturbs the vesicles’ lipid bilayer, leading to the release of encapsulated contents. These PEGylated nanovesicles are capable of encapsulating the anticancer drug gemcitabine with 50% efficiency. They were stable in physiological conditions and in human serum. Effective drug release was demonstrated using the pancreatic ductal carcinoma cells (PANC-1 and MIAPaCa-2) in two-dimensional and three-dimensional “tumor-like” spheroid cultures. A reduction in tumor growth was observed after intravenous administration of the gemcitabine-encapsulated nanovesicles in the xenograft model of athymic, female nude mice. PMID:24827725

Cleavable DNA-protein hybrid molecular beacon: A novel efficient signal translator for sensitive fluorescence anisotropy bioassay.

PubMed

Hu, Pan; Yang, Bin

2016-01-15

Due to its unique features such as high sensitivity, homogeneous format, and independence on fluorescent intensity, fluorescence anisotropy (FA) assay has become a hotspot of study in oligonucleotide-based bioassays. However, until now most FA probes require carefully customized structure designs, and thus are neither generalizable for different sensing systems nor effective to obtain sufficient signal response. To address this issue, a cleavable DNA-protein hybrid molecular beacon was successfully engineered for signal amplified FA bioassay, via combining the unique stable structure of molecular beacon and the large molecular mass of streptavidin. Compared with single DNA strand probe or conventional molecular beacon, the DNA-protein hybrid molecular beacon exhibited a much higher FA value, which was potential to obtain high signal-background ratio in sensing process. As proof-of-principle, this novel DNA-protein hybrid molecular beacon was further applied for FA bioassay using DNAzyme-Pb(2+) as a model sensing system. This FA assay approach could selectively detect as low as 0.5nM Pb(2+) in buffer solution, and also be successful for real samples analysis with good recovery values. Compatible with most of oligonucleotide probes' designs and enzyme-based signal amplification strategies, the molecular beacon can serve as a novel signal translator to expand the application prospect of FA technology in various bioassays. Copyright © 2015 Elsevier B.V. All rights reserved.

Isotope and mixture effects on neoclassical transport in the pedestal

NASA Astrophysics Data System (ADS)

Pusztai, Istvan; Buller, Stefan; Omotani, John T.; Newton, Sarah L.

2017-10-01

The isotope mass scaling of the energy confinement time in tokamak plasmas differs from gyro-Bohm estimates, with implications for the extrapolation from current experiments to D-T reactors. Differences in mass scaling in L-mode and various H-mode regimes suggest that the isotope effect may originate from the pedestal. In the pedestal, sharp gradients render local diffusive estimates invalid, and global effects due to orbit-width scale profile variations have to be taken into account. We calculate neoclassical cross-field fluxes from a radially global drift-kinetic equation using the PERFECT code, to study isotope composition effects in density pedestals. The relative reduction to the peak heat flux due to global effects as a function of the density scale length is found to saturate at an isotope-dependent value that is larger for heavier ions. We also consider D-T and H-D mixtures with a focus on isotope separation. The ability to reproduce the mixture results via single-species simulations with artificial ``DT'' and ``HD'' species has been considered. These computationally convenient single ion simulations give a good estimate of the total ion heat flux in corresponding mixtures. Funding received from the International Career Grant of Vetenskapsradet (VR) (330-2014-6313) with Marie Sklodowska Curie Actions, Cofund, Project INCA 600398, and Framework Grant for Strategic Energy Research of VR (2014-5392).

SFCOMPO 2.0 - A relational database of spent fuel isotopic measurements, reactor operational histories, and design data

NASA Astrophysics Data System (ADS)

Michel-Sendis, Franco; Martinez-González, Jesus; Gauld, Ian

2017-09-01

SFCOMPO-2.0 is a database of experimental isotopic concentrations measured in destructive radiochemical analysis of spent nuclear fuel (SNF) samples. The database includes corresponding design description of the fuel rods and assemblies, relevant operating conditions and characteristics of the host reactors necessary for modelling and simulation. Aimed at establishing a thorough, reliable, and publicly available resource for code and data validation of safety-related applications, SFCOMPO-2.0 is developed and maintained by the OECD Nuclear Energy Agency (NEA). The SFCOMPO-2.0 database is a Java application which is downloadable from the NEA website.

Sea surface salinity of the Eocene Arctic Azolla event using innovative isotope modeling

NASA Astrophysics Data System (ADS)

Speelman, E. N.; Sewall, J. O.; Noone, D.; Huber, M.; Sinninghe Damste, J. S.; Reichart, G. J.

2009-04-01

With the realization that the Eocene Arctic Ocean was covered with enormous quantities of the free floating freshwater fern Azolla, new questions regarding Eocene conditions facilitating these blooms arose. Our present research focuses on constraining the actual salinity of, and water sources for, the Eocene Arctic basin through the application of stable water isotope tracers. Precipitation pathways potentially strongly affect the final isotopic composition of water entering the Arctic Basin. Therefore we use the Community Atmosphere Model (CAM3), developed by NCAR, combined with a recently developed integrated isotope tracer code to reconstruct the isotopic composition of global Eocene precipitation and run-off patterns. We further addressed the sensitivity of the modeled hydrological cycle to changes in boundary conditions, such as pCO2, sea surface temperatures (SSTs) and sea ice formation. In this way it is possible to assess the effect of uncertainties in proxy estimates of these parameters. Overall, results of all runs with Eocene boundary conditions, including Eocene topography, bathymetry, vegetation patterns, TEX86 derived SSTs and pCO2 estimates, show the presence of an intensified hydrological cycle with precipitation exceeding evaporation in the Arctic region. Enriched, precipitation weighted, isotopic values of around -120‰ are reported for the Arctic region. Combining new results obtained from compound specific isotope analyses (δD) on terrestrially derived n-alkanes extracted from Eocene sediments, and model outcomes make it possible to verify climate reconstructions for the middle Eocene Arctic. Furthermore, recently, characteristic long-chain mid-chain ω20 hydroxy wax constituents of Azolla were found in ACEX sediments. δD values of these C32 - C36 diols provide insight into the isotopic composition of the Eocene Arctic surface water. As the isotopic signature of the runoff entering the Arctic is modelled, and the final isotopic composition of the surface waters can be deduced from the isotopic composition of the diols, we can calculate the degree of mixing between freshwater (isotopically light) and seawater (isotopically heavy) in the surface waters. This way we quantify Eocene Arctic surface water salinity, which in turn will shed light on the degree of (seasonal) mixing and stratification.

Microtubule actin cross-linking factor (MACF): a hybrid of dystonin and dystrophin that can interact with the actin and microtubule cytoskeletons.

PubMed

Leung, C L; Sun, D; Zheng, M; Knowles, D R; Liem, R K

1999-12-13

We cloned and characterized a full-length cDNA of mouse actin cross-linking family 7 (mACF7) by sequential rapid amplification of cDNA ends-PCR. The completed mACF7 cDNA is 17 kb and codes for a 608-kD protein. The closest relative of mACF7 is the Drosophila protein Kakapo, which shares similar architecture with mACF7. mACF7 contains a putative actin-binding domain and a plakin-like domain that are highly homologous to dystonin (BPAG1-n) at its NH(2) terminus. However, unlike dystonin, mACF7 does not contain a coiled-coil rod domain; instead, the rod domain of mACF7 is made up of 23 dystrophin-like spectrin repeats. At its COOH terminus, mACF7 contains two putative EF-hand calcium-binding motifs and a segment homologous to the growth arrest-specific protein, Gas2. In this paper, we demonstrate that the NH(2)-terminal actin-binding domain of mACF7 is functional both in vivo and in vitro. More importantly, we found that the COOH-terminal domain of mACF7 interacts with and stabilizes microtubules. In transfected cells full-length mACF7 can associate not only with actin but also with microtubules. Hence, we suggest a modified name: MACF (microtubule actin cross-linking factor). The properties of MACF are consistent with the observation that mutations in kakapo cause disorganization of microtubules in epidermal muscle attachment cells and some sensory neurons.

Friedel-Crafts Crosslinked Highly Sulfonated Polyether Ether Ketone (SPEEK) Membranes for a Vanadium/Air Redox Flow Battery.

PubMed

Merle, Géraldine; Ioana, Filipoi Carmen; Demco, Dan Eugen; Saakes, Michel; Hosseiny, Seyed Schwan

2013-12-30

Highly conductive and low vanadium permeable crosslinked sulfonated poly(ether ether ketone) (cSPEEK) membranes were prepared by electrophilic aromatic substitution for a Vanadium/Air Redox Flow Battery (Vanadium/Air-RFB) application. Membranes were synthesized from ethanol solution and crosslinked under different temperatures with 1,4-benzenedimethanol and ZnCl2 via the Friedel-Crafts crosslinking route. The crosslinking mechanism under different temperatures indicated two crosslinking pathways: (a) crosslinking on the sulfonic acid groups; and (b) crosslinking on the backbone. It was observed that membranes crosslinked at a temperature of 150 °C lead to low proton conductive membranes, whereas an increase in crosslinking temperature and time would lead to high proton conductive membranes. High temperature crosslinking also resulted in an increase in anisotropy and water diffusion. Furthermore, the membranes were investigated for a Vanadium/Air Redox Flow Battery application. Membranes crosslinked at 200 °C for 30 min with a molar ratio between 2:1 (mol repeat unit:mol benzenedimethanol) showed a proton conductivity of 27.9 mS/cm and a 100 times lower VO2+ crossover compared to Nafion.

Enrichment of Cross-Linked Peptides Using Charge-Based Fractional Diagonal Chromatography (ChaFRADIC).

PubMed

Tinnefeld, Verena; Venne, A Saskia; Sickmann, Albert; Zahedi, René P

2017-02-03

Chemical cross-linking of proteins is an emerging field with huge potential for the structural investigation of proteins and protein complexes. Owing to the often relatively low yield of cross-linking products, their identification in complex samples benefits from enrichment procedures prior to mass spectrometry analysis. So far, this is mainly accomplished by using biotin moieties in specific cross-linkers or by applying strong cation exchange chromatography (SCX) for a relatively crude enrichment. We present a novel workflow to enrich cross-linked peptides by utilizing charge-based fractional diagonal chromatography (ChaFRADIC). On the basis of two-dimensional diagonal SCX separation, we could increase the number of identified cross-linked peptides for samples of different complexity: pure cross-linked BSA, cross-linked BSA spiked into a simple protein mixture, and cross-linked BSA spiked into a HeLa lysate. We also compared XL-ChaFRADIC with size exclusion chromatography-based enrichment of cross-linked peptides. The XL-ChaFRADIC approach is straightforward, reproducible, and independent of the cross-linking chemistry and cross-linker properties.

Projectile fragmentation of 40,48Ca and isotopic scaling in a transport approach

NASA Astrophysics Data System (ADS)

Mikhailova, T. I.; Erdemchimeg, B.; Artukh, A. G.; Di Toro, M.; Wolter, H. H.

2016-07-01

We investigate theoretically projectile fragmentation in reactions of 40,48Ca on 9Be and 181Ta targets using a Boltzmann-type transport approach, which is supplemented by a statistical decay code to describe the de-excitation of the hot primary fragments. We determine the thermodynamical properties of the primary fragments and calculate the isotope distributions of the cold final fragments. These describe the data reasonably well. For the pairs of projectiles with different isotopic content we analyze the isotopic scaling (or isoscaling) of the final fragment distributions, which has been used to extract the symmetry energy of the primary source. The calculation exhibits isoscaling behavior for the total yields as do the experiments. We also perform an impact-parameter-dependent isoscaling analysis in view of the fact that the primary systems at different impact parameters have very different properties. Then the isoscaling behavior is less stringent, which we can attribute to specific structure effects of the 40,48Ca pair. The symmetry energy determined in this way depends on these structure effects.

Projectile fragmentation of {sup 40,48}Ca and isotopic scaling in a transport approach

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

Mikhailova, T. I., E-mail: tmikh@jinr.ru; Erdemchimeg, B.; Artukh, A. G.

2016-07-15

We investigate theoretically projectile fragmentation in reactions of {sup 40,48}Ca on {sup 9}Be and {sup 181}Ta targets using a Boltzmann-type transport approach, which is supplemented by a statistical decay code to describe the de-excitation of the hot primary fragments. We determine the thermodynamical properties of the primary fragments and calculate the isotope distributions of the cold final fragments. These describe the data reasonably well. For the pairs of projectiles with different isotopic content we analyze the isotopic scaling (or isoscaling) of the final fragment distributions, which has been used to extract the symmetry energy of the primary source. The calculationmore » exhibits isoscaling behavior for the total yields as do the experiments. We also perform an impact-parameter-dependent isoscaling analysis in view of the fact that the primary systems at different impact parameters have very different properties. Then the isoscaling behavior is less stringent, which we can attribute to specific structure effects of the {sup 40,48}Ca pair. The symmetry energy determined in this way depends on these structure effects.« less

Interlinked Test Results for Fusion Fuel Processing and Blanket Tritium Recovery Systems Using Cryogenic Molecular Sieve Bed

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

Yamanishi, Toshihiko; Hayashi, Takumi; Kawamura, Yoshinori

2005-07-15

A simulated fuel processing (cryogenic distillation columns and a palladium diffuser) and CMSB (cryogenic molecular sieve bed) systems were linked together, and were operated. The validity of the CMSB was discussed through this experiment as an integrated system for the recovery of blanket tritium. A gas stream of hydrogen isotopes and He was supplied to the CMSB as the He sweep gas in blanket of a fusion reactor. After the breakthrough of tritium was observed, regeneration of the CMSB was carried out by evacuating and heating. The hydrogen isotopes were finally recovered by the diffuser. At first, only He gasmore » was sent by the evacuating. The hydrogen isotopes gas was then rapidly released by the heating. The system worked well against the above drastic change of conditions. The amount of hydrogen isotopes gas finally recovered by the diffuser was in good agreement with that adsorbed by the CMSB. The dynamic behaviors (breakthrough and regeneration) of the system were explained well by a set of basic codes.« less

Crosslinking of agarose bioplastic using citric acid.

PubMed

Awadhiya, Ankur; Kumar, David; Verma, Vivek

2016-10-20

We report chemical crosslinking of agarose bioplastic using citric acid. Crosslinking was confirmed using Fourier transform infrared (FTIR) spectroscopy. The effects of crosslinking on the tensile strength, swelling, thermal stability, and degradability of the bioplastic were studied in detail. The tensile strength of the bioplastic films increased from 25.1MPa for control films up to a maximum of 52.7MPa for citric acid crosslinked films. At 37°C, the amount of water absorbed by crosslinked agarose bioplastic was only 11.5% of the amount absorbed by non-crosslinked controls. Thermogravimetric results showed that the crosslinked samples retain greater mass at high temperature (>450°C) than control samples. Moreover, while the crosslinked films were completely degradable, the rate of degradation was lower compared to non-crosslinked controls. Copyright © 2016 Elsevier Ltd. All rights reserved.

Methotrexate loaded alginate microparticles and effect of Ca2+ post-crosslinking: An in vitro physicochemical and biological evaluation.

PubMed

Dhanka, Mukesh; Shetty, Chaitra; Srivastava, Rohit

2018-04-15

Methotrexate (MTX) loaded alginate microparticles were produced by simple water-in-oil (W/O) emulsion solvent diffusion method with homogenization and then subsequently cross-linked by Ca 2+ . The mean sizes of developed microparticles (bare non-crosslinked, crosslinked, drug-loaded non-crosslinked, and drug-loaded cross-linked) were found to be <11μm. The morphology of bare non-crosslinked and crosslinked microparticles were observed to be spherical with smooth surface morphology. However, MTX loaded non-crosslinked and crosslinked microparticles were found to have an irregular shape with rough surface morphology. The encapsulation efficiency (% EE) and loading capacity (% LC) of MTX loaded non-crosslinked microparticles were estimated to be 92.19±1.85 and 9.35±0.22, respectively. However, in case of cross-linked microparticles, the % EE and % LC values slightly decreased, i.e., 83.26±1.69% and 8.44±0.21%, respectively. Crosslinked microparticles were found to release MTX at a slower rate as compared to non-crosslinked microparticles. The physicochemical characterizations of microparticles by Fourier Transform Infrared Spectroscopy and High-Resolution X-Ray Diffraction have shown that drug encapsulated in the microparticles without chemical interactions has lost its crystalline nature. The biocompatibility and hemocompatibility studies of the microparticles have demonstrated that microparticles are biocompatible and were non-hemolytic at low concentrations. Copyright © 2017 Elsevier B.V. All rights reserved.

Structure-based non-canonical amino acid design to covalently crosslink an antibody–antigen complex

PubMed Central

Xu, Jianqing; Tack, Drew; Hughes, Randall A.; Ellington, Andrew D.; Gray, Jeffrey J.

2014-01-01

Engineering antibodies to utilize non-canonical amino acids (NCAA) should greatly expand the utility of an already important biological reagent. In particular, introducing crosslinking reagents into antibody complementarity determining regions (CDRs) should provide a means to covalently crosslink residues at the antibody–antigen interface. Unfortunately, finding the optimum position for crosslinking two proteins is often a matter of iterative guessing, even when the interface is known in atomic detail. Computer-aided antibody design can potentially greatly restrict the number of variants that must be explored in order to identify successful crosslinking sites. We have therefore used Rosetta to guide the introduction of an oxidizable crosslinking NCAA, l-3,4-dihydroxyphenylalanine (l-DOPA), into the CDRs of the anti-protective antigen scFv antibody M18, and have measured crosslinking to its cognate antigen, domain 4 of the anthrax protective antigen. Computed crosslinking distance, solvent accessibility, and interface energetics were three factors considered that could impact the efficiency of l-DOPA-mediated crosslinking. In the end, 10 variants were synthesized, and crosslinking efficiencies were generally 10% or higher, with the best variant crosslinking to 52% of the available antigen. The results suggest that computational analysis can be used in a pipeline for engineering crosslinking antibodies. The rules learned from l-DOPA crosslinking of antibodies may also be generalizable to the formation of other crosslinked interfaces and complexes. PMID:23680795

Digital Isotope Coding to Trace the Growth Process of Individual Single-Walled Carbon Nanotubes.

PubMed

Otsuka, Keigo; Yamamoto, Shun; Inoue, Taiki; Koyano, Bunsho; Ukai, Hiroyuki; Yoshikawa, Ryo; Xiang, Rong; Chiashi, Shohei; Maruyama, Shigeo

2018-04-24

Single-walled carbon nanotubes (SWCNTs) are attracting increasing attention as an ideal material for high-performance electronics through the preparation of arrays of purely semiconducting SWCNTs. Despite significant progress in the controlled synthesis of SWCNTs, their growth mechanism remains unclear due to difficulties in analyzing the time-resolved growth of individual SWCNTs under practical growth conditions. Here we present a method for tracing the diverse growth profiles of individual SWCNTs by embedding digitally coded isotope labels. Raman mapping showed that, after various incubation times, SWCNTs elongated monotonically until their abrupt termination. Ex situ analysis offered an opportunity to capture rare chirality changes along the SWCNTs, which resulted in sudden acceleration/deceleration of the growth rate. Dependence on growth parameters, such as temperature and carbon concentration, was also traced along individual SWCNTs, which could provide clues to chirality control. Systematic growth studies with a variety of catalysts and conditions, which combine the presented method with other characterization techniques, will lead to further understanding and control of chirality, length, and density of SWCNTs.

Thermo-hydrological and chemical (THC) modeling to support Field Test Design

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

Stauffer, Philip H.; Jordan, Amy B.; Harp, Dylan Robert

This report summarizes ongoing efforts to simulate coupled thermal-hydrological-chemical (THC) processes occurring within a hypothetical high-level waste (HLW) repository in bedded salt. The report includes work completed since the last project deliverable, “Coupled model for heat and water transport in a high level waste repository in salt”, a Level 2 milestone submitted to DOE in September 2013 (Stauffer et al., 2013). Since the last deliverable, there have been code updates to improve the integration of the salt module with the pre-existing code and development of quality assurance (QA) tests of constitutive functions and precipitation/dissolution reactions. Simulations of bench-scale experiments, bothmore » historical and currently in the planning stages have been performed. Additional simulations have also been performed on the drift-scale model that incorporate new processes, such as an evaporation function to estimate water vapor removal from the crushed salt backfill and isotopic fractionation of water isotopes. Finally, a draft of a journal paper on the importance of clay dehydration on water availability is included as Appendix I.« less

Friedel–Crafts Crosslinked Highly Sulfonated Polyether Ether Ketone (SPEEK) Membranes for a Vanadium/Air Redox Flow Battery

PubMed Central

Merle, Géraldine; Ioana, Filipoi Carmen; Demco, Dan Eugen; Saakes, Michel; Hosseiny, Seyed Schwan

2014-01-01

Highly conductive and low vanadium permeable crosslinked sulfonated poly(ether ether ketone) (cSPEEK) membranes were prepared by electrophilic aromatic substitution for a Vanadium/Air Redox Flow Battery (Vanadium/Air-RFB) application. Membranes were synthesized from ethanol solution and crosslinked under different temperatures with 1,4-benzenedimethanol and ZnCl2 via the Friedel–Crafts crosslinking route. The crosslinking mechanism under different temperatures indicated two crosslinking pathways: (a) crosslinking on the sulfonic acid groups; and (b) crosslinking on the backbone. It was observed that membranes crosslinked at a temperature of 150 °C lead to low proton conductive membranes, whereas an increase in crosslinking temperature and time would lead to high proton conductive membranes. High temperature crosslinking also resulted in an increase in anisotropy and water diffusion. Furthermore, the membranes were investigated for a Vanadium/Air Redox Flow Battery application. Membranes crosslinked at 200 °C for 30 min with a molar ratio between 2:1 (mol repeat unit:mol benzenedimethanol) showed a proton conductivity of 27.9 mS/cm and a 100 times lower VO2+ crossover compared to Nafion. PMID:24957118

The Formation Mechanism of Hydrogels.

PubMed

Lu, Liyan; Yuan, Shiliang; Wang, Jing; Shen, Yun; Deng, Shuwen; Xie, Luyang; Yang, Qixiang

2017-06-12

Hydrogels are degradable polymeric networks, in which cross-links play a vital role in structure formation and degradation. Cross-linking is a stabilization process in polymer chemistry that leads to the multi-dimensional extension of polymeric chains, resulting in network structures. By cross-linking, hydrogels are formed into stable structures that differ from their raw materials. Generally, hydrogels can be prepared from either synthetic or natural polymers. Based on the types of cross-link junctions, hydrogels can be categorized into two groups: the chemically cross-linked and the physically cross-linked. Chemically cross-linked gels have permanent junctions, in which covalent bonds are present between different polymer chains, thus leading to excellent mechanical strength. Although chemical cross-linking is a highly resourceful method for the formation of hydrogels, the cross-linkers used in hydrogel preparation should be extracted from the hydrogels before use, due to their reported toxicity, while, in physically cross-linked gels, dissolution is prevented by physical interactions, such as ionic interactions, hydrogen bonds or hydrophobic interactions. Physically cross-linked methods for the preparation of hydrogels are the alternate solution for cross-linker toxicity. Both methods will be discussed in this essay. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Determination of the δ34S of low-concentration sulfate in water; RSIL lab code 1949

USGS Publications Warehouse

Revesz, Kinga; Qi, Haiping; Coplen, Tyler B.

2006-01-01

The purpose of the Reston Stable Isotope Laboratory (RSIL) lab code 1949 is to determine the δ(34S/32S), abbreviated as δ34S, of dissolved sulfate having a concentration less than 20 milligrams per liter. Dissolved sulfate is collected on an anion-exchange resin in the field, eluted in the laboratory with 3 M KCl, and precipitated with BaCl2 at pH 3 to 4 as BaSO4. The precipitated BaSO4 is filtered and dried before introduction into an elemental analyzer (EA) Carlo Erba NC 2500. The EA is used to convert sulfur in a BaSO4 solid sample into SO2 gas, and the EA is connected to a continuous flow isotope-ratio mass spectrometer (CF-IRMS), which determines differences in the isotope-amount ratios of stable sulfur isotopes (34S/32S) of the product SO2 gas. The combustion is quantitative; no isotopic fractionation is involved. Samples are placed in a tin capsule and loaded into the Costech Zero Blank Autosampler of the EA. Under computer control, samples are dropped into a heated reaction tube that combines the oxidation and reduction reactions. The combustion takes place in a helium atmosphere containing an excess of oxygen gas at the oxidation zone at the top of the reaction tube. Combustion products are transported by a helium carrier through the reduction zone at the bottom of the reaction tube to remove excess oxygen and through a separate drying tube to remove any water. The gas-phase products, mainly CO2, N2, and SO2, are separated by a gas chromatograph. The gas is then introduced into the isotope-ratio mass spectrometer (IRMS) through a Finnigan MAT (now Thermo Scientific) ConFlo II interface, which is also used to inject SO2 reference gas and helium for sample dilution. The IRMS is a Thermo Scientific Delta V Plus CF-IRMS. It has a universal triple collector with two wide cups and a narrow cup in the middle. It is capable of measuring mass/charge (m/z) 64 and 66 simultaneously. The ion beams from SO2 are as follows: m/z 64 = SO2 = 32S16O16O; m/z 66 = SO2 = 34S16O16O primarily.

Nuclear data uncertainty propagation by the XSUSA method in the HELIOS2 lattice code

NASA Astrophysics Data System (ADS)

Wemple, Charles; Zwermann, Winfried

2017-09-01

Uncertainty quantification has been extensively applied to nuclear criticality analyses for many years and has recently begun to be applied to depletion calculations. However, regulatory bodies worldwide are trending toward requiring such analyses for reactor fuel cycle calculations, which also requires uncertainty propagation for isotopics and nuclear reaction rates. XSUSA is a proven methodology for cross section uncertainty propagation based on random sampling of the nuclear data according to covariance data in multi-group representation; HELIOS2 is a lattice code widely used for commercial and research reactor fuel cycle calculations. This work describes a technique to automatically propagate the nuclear data uncertainties via the XSUSA approach through fuel lattice calculations in HELIOS2. Application of the XSUSA methodology in HELIOS2 presented some unusual challenges because of the highly-processed multi-group cross section data used in commercial lattice codes. Currently, uncertainties based on the SCALE 6.1 covariance data file are being used, but the implementation can be adapted to other covariance data in multi-group structure. Pin-cell and assembly depletion calculations, based on models described in the UAM-LWR Phase I and II benchmarks, are performed and uncertainties in multiplication factor, reaction rates, isotope concentrations, and delayed-neutron data are calculated. With this extension, it will be possible for HELIOS2 users to propagate nuclear data uncertainties directly from the microscopic cross sections to subsequent core simulations.

Novel magnetic cross-linked lipase aggregates for improving the resolution of (R, S)-2-octanol.

PubMed

Liu, Ying; Guo, Chen; Liu, Chun-Zhao

2015-03-01

Novel magnetic cross-linked lipase aggregates were fabricated by immobilizing the cross-linked lipase aggregates onto magnetic particles with a high number of -NH2 terminal groups using p-benzoquinone as the cross-linking agent. At the optimal fabrication conditions, 100% of immobilization efficiency and 139% of activity recovery of the magnetic cross-linked lipase aggregates were achieved. The magnetic cross-linked lipase aggregates were able to efficiently resolve (R, S)-2-octanol, and retained 100% activity and 100% enantioselectivity after 10 cycles of reuse, whereas the cross-linked lipase aggregates only retained about 50% activity and 70% enantioselectivity due to insufficient cross-linking. These results provide a great potential for industrial applications of the magnetic cross-linked lipase aggregates. © 2014 Wiley Periodicals, Inc.

Mechanical Properties and Morphologies of Carboxyl-Terminated Butadiene Acrylonitrile Liquid Rubber/Epoxy Blends Compatibilized by Pre-Crosslinking.

PubMed

Xu, Shiai; Song, Xiaoxue; Cai, Yangben

2016-07-29

In order to enhance the compatibilization and interfacial adhesion between epoxy and liquid carboxyl-terminated butadiene acrylonitrile (CTBN) rubber, an initiator was introduced into the mixture and heated to initiate the cross-linking reaction of CTBN. After the addition of curing agents, the CTBN/epoxy blends with a localized interpenetrating network structure were prepared. The mechanical properties and morphologies of pre-crosslinked and non-crosslinked CTBN/epoxy blends were investigated. The results show that the tensile strength, elongation at break and impact strength of pre-crosslinked CTBN/epoxy blends are significantly higher than those of non-crosslinked CTBN/epoxy blends, which is primarily due to the enhanced interfacial strength caused by the chemical bond between the two phases and the localized interpenetrating network structure. Both pre-crosslinked and non-crosslinked CTBN/epoxy blends show a bimodal distribution of micron- and nano-sized rubber particles. However, pre-crosslinked CTBN/epoxy blends have smaller micron-sized rubber particles and larger nano-sized rubber particles than non-crosslinked CTBN/epoxy blends. The dynamic mechanical analysis shows that the storage modulus of pre-crosslinked CTBN/epoxy blends is higher than that of non-crosslinked CTBN/epoxy blends. The glass transition temperature of the CTBN phase in pre-crosslinked CTBN/epoxy blends increases slightly compared with the CTBN/epoxy system. The pre-crosslinking of rubber is a promising method for compatibilization and controlling the morphology of rubber-modified epoxy materials.

Mechanical Properties and Morphologies of Carboxyl-Terminated Butadiene Acrylonitrile Liquid Rubber/Epoxy Blends Compatibilized by Pre-Crosslinking

PubMed Central

Xu, Shiai; Song, Xiaoxue; Cai, Yangben

2016-01-01

In order to enhance the compatibilization and interfacial adhesion between epoxy and liquid carboxyl-terminated butadiene acrylonitrile (CTBN) rubber, an initiator was introduced into the mixture and heated to initiate the cross-linking reaction of CTBN. After the addition of curing agents, the CTBN/epoxy blends with a localized interpenetrating network structure were prepared. The mechanical properties and morphologies of pre-crosslinked and non-crosslinked CTBN/epoxy blends were investigated. The results show that the tensile strength, elongation at break and impact strength of pre-crosslinked CTBN/epoxy blends are significantly higher than those of non-crosslinked CTBN/epoxy blends, which is primarily due to the enhanced interfacial strength caused by the chemical bond between the two phases and the localized interpenetrating network structure. Both pre-crosslinked and non-crosslinked CTBN/epoxy blends show a bimodal distribution of micron- and nano-sized rubber particles. However, pre-crosslinked CTBN/epoxy blends have smaller micron-sized rubber particles and larger nano-sized rubber particles than non-crosslinked CTBN/epoxy blends. The dynamic mechanical analysis shows that the storage modulus of pre-crosslinked CTBN/epoxy blends is higher than that of non-crosslinked CTBN/epoxy blends. The glass transition temperature of the CTBN phase in pre-crosslinked CTBN/epoxy blends increases slightly compared with the CTBN/epoxy system. The pre-crosslinking of rubber is a promising method for compatibilization and controlling the morphology of rubber-modified epoxy materials. PMID:28773762

Mapping Local Cytosolic Enzymatic Activity in Human Esophageal Mucosa with Porous Silicon Nanoneedles.

PubMed

Chiappini, Ciro; Campagnolo, Paola; Almeida, Carina S; Abbassi-Ghadi, Nima; Chow, Lesley W; Hanna, George B; Stevens, Molly M

2015-09-16

Porous silicon nanoneedles can map Cathepsin B activity across normal and tumor human esophageal mucosa. Assembling a peptide-based Cathepsin B cleavable sensor over a large array of nano-needles allows the discrimination of cancer cells from healthy ones in mixed culture. The same sensor applied to tissue can map Cathepsin B activity with high resolution across the tumor margin area of esophageal adenocarcinoma. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Status Report on NEAMS PROTEUS/ORIGEN Integration

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

Wieselquist, William A

2016-02-18

The US Department of Energy’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) Program has contributed significantly to the development of the PROTEUS neutron transport code at Argonne National Laboratory and to the Oak Ridge Isotope Generation and Depletion Code (ORIGEN) depletion/decay code at Oak Ridge National Laboratory. PROTEUS’s key capability is the efficient and scalable (up to hundreds of thousands of cores) neutron transport solver on general, unstructured, three-dimensional finite-element-type meshes. The scalability and mesh generality enable the transfer of neutron and power distributions to other codes in the NEAMS toolkit for advanced multiphysics analysis. Recently, ORIGEN has received considerablemore » modernization to provide the high-performance depletion/decay capability within the NEAMS toolkit. This work presents a description of the initial integration of ORIGEN in PROTEUS, mainly performed during FY 2015, with minor updates in FY 2016.« less

Modeling Protein Excited-state Structures from "Over-length" Chemical Cross-links.

PubMed

Ding, Yue-He; Gong, Zhou; Dong, Xu; Liu, Kan; Liu, Zhu; Liu, Chao; He, Si-Min; Dong, Meng-Qiu; Tang, Chun

2017-01-27

Chemical cross-linking coupled with mass spectroscopy (CXMS) provides proximity information for the cross-linked residues and is used increasingly for modeling protein structures. However, experimentally identified cross-links are sometimes incompatible with the known structure of a protein, as the distance calculated between the cross-linked residues far exceeds the maximum length of the cross-linker. The discrepancies may persist even after eliminating potentially false cross-links and excluding intermolecular ones. Thus the "over-length" cross-links may arise from alternative excited-state conformation of the protein. Here we present a method and associated software DynaXL for visualizing the ensemble structures of multidomain proteins based on intramolecular cross-links identified by mass spectrometry with high confidence. Representing the cross-linkers and cross-linking reactions explicitly, we show that the protein excited-state structure can be modeled with as few as two over-length cross-links. We demonstrate the generality of our method with three systems: calmodulin, enzyme I, and glutamine-binding protein, and we show that these proteins alternate between different conformations for interacting with other proteins and ligands. Taken together, the over-length chemical cross-links contain valuable information about protein dynamics, and our findings here illustrate the relationship between dynamic domain movement and protein function. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Levels of mature cross-links and advanced glycation end product cross-links in human vitreous.

PubMed

Matsumoto, Yukihiro; Takahashi, Masaaki; Chikuda, Makoto; Arai, Kiyomi

2002-01-01

To determine the levels of pyridinoline and deoxypyridinoline, two mature enzymatic cross-links, and pentosidine, an advanced glycation end product (AGE) cross-link, in the human vitreous, and to investigate the correlations among the cross-links and the effects of aging and diabetes mellitus (DM) on the levels of cross-links. Forty-five vitreous samples were collected from 32 patients (32 eyes) undergoing vitrectomy for diabetic retinopathy (DM group) and from 13 patients (13 eyes) (control group) who were age- and sex-matched patients with idiopathic macular hole or epiretinal membrane with no systemic conditions. The levels of the cross-links were determined using high-performance liquid chromatography after acid hydrolysis and pretreatment with SP-Sephadex. The levels of pentosidine, pyridinoline, and deoxypyridinoline were 27.3 +/- 23.1 (mean +/- SD) pmol/mL (detectable in 45 of 45 specimens), 79.0 +/- 40.2 ng/mL (43 of 45 specimens), and 54.0 +/- 9.5 (32 of 45 specimens) ng/mL, respectively. When the vitreous samples from the DM and the control groups were compared, a significant difference (P <.05) was found in the pentosidine level but not in the levels of pyridinoline or deoxypyridinoline. No significant correlations were found between age and the cross-links. Significant correlations (P <.01) were found among the cross-links. The results indicate that mature cross-link substances exist in the human vitreous. The results also suggest that glycation may occur in the vitreous after mature cross-links form and result in the formation of AGE cross-links. In human vitreous from patients with DM, increased levels of AGE cross-links may stabilize the formation of mature cross-links, but they did not increase the mature cross-links.

The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs

PubMed Central

Garzia, Aitor; Jafarnejad, Seyed Mehdi; Meyer, Cindy; Chapat, Clément; Gogakos, Tasos; Morozov, Pavel; Amiri, Mehdi; Shapiro, Maayan; Molina, Henrik; Tuschl, Thomas; Sonenberg, Nahum

2017-01-01

Cryptic polyadenylation within coding sequences (CDS) triggers ribosome-associated quality control (RQC), followed by degradation of the aberrant mRNA and polypeptide, ribosome disassembly and recycling. Although ribosomal subunit dissociation and nascent peptide degradation are well-understood, the molecular sensors of aberrant mRNAs and their mechanism of action remain unknown. We studied the Zinc Finger Protein 598 (ZNF598) using PAR-CLIP and revealed that it cross-links to tRNAs, mRNAs and rRNAs, thereby placing the protein on translating ribosomes. Cross-linked reads originating from AAA-decoding tRNALys(UUU) were 10-fold enriched over its cellular abundance, and poly-lysine encoded by poly(AAA) induced RQC in a ZNF598-dependent manner. Encounter with translated polyA segments by ZNF598 triggered ubiquitination of several ribosomal proteins, requiring the E2 ubiquitin ligase UBE2D3 to initiate RQC. Considering that human CDS are devoid of >4 consecutive AAA codons, sensing of prematurely placed polyA tails by a specialized RNA-binding protein is a novel nucleic-acid-based surveillance mechanism of RQC. PMID:28685749

The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs.

PubMed

Garzia, Aitor; Jafarnejad, Seyed Mehdi; Meyer, Cindy; Chapat, Clément; Gogakos, Tasos; Morozov, Pavel; Amiri, Mehdi; Shapiro, Maayan; Molina, Henrik; Tuschl, Thomas; Sonenberg, Nahum

2017-07-07

Cryptic polyadenylation within coding sequences (CDS) triggers ribosome-associated quality control (RQC), followed by degradation of the aberrant mRNA and polypeptide, ribosome disassembly and recycling. Although ribosomal subunit dissociation and nascent peptide degradation are well-understood, the molecular sensors of aberrant mRNAs and their mechanism of action remain unknown. We studied the Zinc Finger Protein 598 (ZNF598) using PAR-CLIP and revealed that it cross-links to tRNAs, mRNAs and rRNAs, thereby placing the protein on translating ribosomes. Cross-linked reads originating from AAA-decoding tRNA Lys (UUU) were 10-fold enriched over its cellular abundance, and poly-lysine encoded by poly(AAA) induced RQC in a ZNF598-dependent manner. Encounter with translated polyA segments by ZNF598 triggered ubiquitination of several ribosomal proteins, requiring the E2 ubiquitin ligase UBE2D3 to initiate RQC. Considering that human CDS are devoid of >4 consecutive AAA codons, sensing of prematurely placed polyA tails by a specialized RNA-binding protein is a novel nucleic-acid-based surveillance mechanism of RQC.

To Cross-Link or Not to Cross-Link? Cross-Linking Associated Foreign Body Response of Collagen-Based Devices

PubMed Central

Delgado, Luis M.; Bayon, Yves; Pandit, Abhay

2015-01-01

Collagen-based devices, in various physical conformations, are extensively used for tissue engineering and regenerative medicine applications. Given that the natural cross-linking pathway of collagen does not occur in vitro, chemical, physical, and biological cross-linking methods have been assessed over the years to control mechanical stability, degradation rate, and immunogenicity of the device upon implantation. Although in vitro data demonstrate that mechanical properties and degradation rate can be accurately controlled as a function of the cross-linking method utilized, preclinical and clinical data indicate that cross-linking methods employed may have adverse effects on host response, especially when potent cross-linking methods are employed. Experimental data suggest that more suitable cross-linking methods should be developed to achieve a balance between stability and functional remodeling. PMID:25517923

Enzyme-catalyzed crosslinkable hydrogels: emerging strategies for tissue engineering.

PubMed

Teixeira, Liliana S Moreira; Feijen, Jan; van Blitterswijk, Clemens A; Dijkstra, Pieter J; Karperien, Marcel

2012-02-01

State-of-the-art bioactive hydrogels can easily and efficiently be formed by enzyme-catalyzed mild-crosslinking reactions in situ. Yet this cell-friendly and substrate-specific method remains under explored. Hydrogels prepared by using enzyme systems like tyrosinases, transferases and lysyl oxidases show interesting characteristics as dynamic scaffolds and as systems for controlled release. Increased attention is currently paid to hydrogels obtained via crosslinking of precursors by transferases or peroxidases as catalysts. Enzyme-mediated crosslinking has proven its efficiency and attention has now shifted to the development of enzymatically crosslinked hydrogels with higher degrees of complexity, mimicking extracellular matrices. Moreover, bottom-up approaches combining biocatalysts and self-assembly are being explored for the development of complex nano-scale architectures. In this review, the use of enzymatic crosslinking for the preparation of hydrogels as an innovative alternative to other crosslinking methods, such as the commonly used UV-mediated photo-crosslinking or physical crosslinking, will be discussed. Photo-initiator-based crosslinking may induce cytotoxicity in the formed gels, whereas physical crosslinking may lead to gels which do not have sufficient mechanical strength and stability. These limitations can be overcome using enzymes to form covalently crosslinked hydrogels. Herewith, we report the mechanisms involved and current applications, focusing on emerging strategies for tissue engineering and regenerative medicine. Copyright © 2011 Elsevier Ltd. All rights reserved.

Link establishment criterion and topology optimization for hybrid GPS satellite communications with laser crosslinks

NASA Astrophysics Data System (ADS)

Li, Lun; Wei, Sixiao; Tian, Xin; Hsieh, Li-Tse; Chen, Zhijiang; Pham, Khanh; Lyke, James; Chen, Genshe

2018-05-01

In the current global positioning system (GPS), the reliability of information transmissions can be enhanced with the aid of inter-satellite links (ISLs) or crosslinks between satellites. Instead of only using conventional radio frequency (RF) crosslinks, the laser crosslinks provide an option to significantly increase the data throughput. The connectivity and robustness of ISL are needed for analysis, especially for GPS constellations with laser crosslinks. In this paper, we first propose a hybrid GPS communication architecture in which uplinks and downlinks are established via RF signals and crosslinks are established via laser links. Then, we design an optical crosslink assignment criteria considering the practical optical communication factors such as optical line- of-sight (LOS) range, link distance, and angular velocity, etc. After that, to further improve the rationality of establishing crosslinks, a topology control algorithm is formulated to optimize GPS crosslink networks at both physical and network layers. The RF transmission features for uplink and downlink and optical transmission features for crosslinks are taken into account as constraints for the optimization problem. Finally, the proposed link establishment criteria are implemented for GPS communication with optical crosslinks. The designs of this paper provide a potential crosslink establishment and topology control algorithm for the next generation GPS.

Synthesis and properties of reprocessable sulfonated polyimides cross-linked via acid stimulation for use as proton exchange membranes

NASA Astrophysics Data System (ADS)

Zhang, Boping; Ni, Jiangpeng; Xiang, Xiongzhi; Wang, Lei; Chen, Yongming

2017-01-01

Cross-linked sulfonated polyimides are one of the most promising materials for proton exchange membrane (PEM) applications. However, these cross-linked membranes are difficult to reprocess because they are insoluble. In this study, a series of cross-linkable sulfonated polyimides with flexible pendant alkyl side chains containing trimethoxysilyl groups is successfully synthesized. The cross-linkable polymers are highly soluble in common solvents and can be used to prepare tough and smooth films. Before the cross-linking reaction is complete, the membranes can be reprocessed, and the recovery rate of the prepared films falls within an acceptable range. The cross-linked membranes are obtained rapidly when the cross-linkable membranes are immersed in an acid solution, yielding a cross-linking density of the gel fraction of greater than 90%. The cross-linked membranes exhibit high proton conductivities and tensile strengths under hydrous conditions. Compared with those of pristine membranes, the oxidative and hydrolytic stabilities of the cross-linked membranes are significantly higher. The CSPI-70 membrane shows considerable power density in a direct methanol fuel cell (DMFC) test. All of these results suggest that the prepared cross-linked membranes have great potential for applications in proton exchange membrane fuel cells.

N(4)C-ethyl-N(4)C cross-linked DNA: synthesis and characterization of duplexes with interstrand cross-links of different orientations.

PubMed

Noronha, Anne M; Noll, David M; Wilds, Christopher J; Miller, Paul S

2002-01-22

The preparation and physical properties of short DNA duplexes that contain a N(4)C-ethyl-N(4)C interstrand cross-link are described. Duplexes that contain an interstrand cross-link between mismatched C-C residues and duplexes in which the C residues of a -CG- or -GC- step are linked to give "staggered" interstrand cross-links were prepared using a novel N(4)C-ethyl-N(4)C phosphoramidite reagent. Duplexes with the C-C mismatch cross-link have UV thermal transition temperatures that are 25 degrees C higher than the melting temperatures of control duplexes in which the cross-link is replaced with a G-C base pair. It appears that this cross-link stabilizes adjacent base pairs and does not perturb the structure of the helix, a conclusion that is supported by the CD spectrum of this duplex and by molecular models. An even higher level of stabilization, 49 degrees C, is seen with the duplex that contains a -CG- staggered cross-link. Molecular models suggest that this cross-link may induce propeller twisting in the cross-linked base pairs, and the CD spectrum of this duplex exhibits an unusual negative band at 298 nm, although the remainder of the spectrum is similar to that of B-form DNA. Mismatched C-C or -CG- staggered cross-linked duplexes that have complementary overhanging ends can undergo self-ligation catalyzed by T4 DNA ligase. Analysis of the ligated oligomers by nondenaturing polyacrylamide gel electrophoresis shows that the resulting oligomers migrate in a manner similar to that of a mixture of non-cross-linked control oligomers and suggests that these cross-links do not result in significant bending of the helix. However, the orientation of the staggered cross-link can have a significant effect on the structure and stability of the cross-linked duplex. Thus, the thermal stability of the duplex that contains a -GC- staggered cross-link is 10 degrees C lower than the melting temperature of the control, non-cross-linked duplex. Unlike the -CG- staggered cross-link, in which the cross-linked base pairs can still maintain hydrogen bond contacts, molecular models suggest that formation of the -GC- staggered cross-link disrupts hydrogen bonding and may also perturb adjacent base pairs leading to an overall reduction in helix stability. Duplexes with specifically positioned and oriented cross-links can be used as substrates to study DNA repair mechanisms.

Application of a fast sorting algorithm to the assignment of mass spectrometric cross-linking data.

PubMed

Petrotchenko, Evgeniy V; Borchers, Christoph H

2014-09-01

Cross-linking combined with MS involves enzymatic digestion of cross-linked proteins and identifying cross-linked peptides. Assignment of cross-linked peptide masses requires a search of all possible binary combinations of peptides from the cross-linked proteins' sequences, which becomes impractical with increasing complexity of the protein system and/or if digestion enzyme specificity is relaxed. Here, we describe the application of a fast sorting algorithm to search large sequence databases for cross-linked peptide assignments based on mass. This same algorithm has been used previously for assigning disulfide-bridged peptides (Choi et al., ), but has not previously been applied to cross-linking studies. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biodegradable organic acid-crosslinked alkali-treated gelatins with anti-thrombogenic and endothelialization properties

PubMed Central

Inoue, Motoki; Sasaki, Makoto; Taguchi, Tetsushi

2012-01-01

Gelatins were crosslinked with organic acids and treated with alkali to impart to them endothelialization and anti-thrombogenic properties. These matrices were characterized by biochemical and physicochemical techniques. The amounts of residual amino groups in the matrices decreased with increasing crosslinker concentration. The matrices with the highest crosslinking densities showed excellent endothelial cell adhesion and proliferation. In addition, the adhesion of platelets and formation of fibrin networks on the matrices were suppressed with increasing crosslinker concentration. The matrices also exhibited excellent biodegradability, and the degradation rate decreased with increasing crosslinking density. All the organic acid-crosslinked alkali-treated gelatins showed excellent anti-thrombogenic and endothelialization properties, superior to those of glutaraldehyde-crosslinked alkali-treated gelatins. PMID:27877542

Alkali-catalyzed low temperature wet crosslinking of plant proteins using carboxylic acids.

PubMed

Reddy, Narendra; Li, Ying; Yang, Yiqi

2009-01-01

We report the development of a new method of alkali-catalyzed low temperature wet crosslinking of plant proteins to improve their breaking tenacity without using high temperatures or phosphorus-containing catalysts used in conventional poly(carboxylic acid) crosslinking of cellulose and proteins. Carboxylic acids are preferred over aldehyde-containing crosslinkers for crosslinking proteins and cellulose because of their low toxicity and cost and ability to improve the desired properties of the materials. However, current knowledge in carboxylic acid crosslinking of proteins and cellulose requires the use of carboxylic acids with at least three carboxylic groups, toxic phosphorous-containing catalysts and curing at high temperatures (150-185 degrees C). The use of high temperatures and low pH in conventional carboxylic acid crosslinking has been reported to cause substantial strength loss and/or undesired changes in the properties of the crosslinked materials. In this research, gliadin, soy protein, and zein fibers have been crosslinked with malic acid, citric acid, and butanetetracarboxylic acid to improve the tenacity of the fibers without using high temperatures and phosphorus-containing catalysts. The new method of wet crosslinking using carboxylic acids containing two or more carboxylic groups will be useful to crosslink proteins for various industrial applications.

The changes in crosslink contents in tissues after formalin fixation.

PubMed

Abe, Masashi; Takahashi, Masaaki; Horiuchi, Kentaro; Nagano, Akira

2003-07-01

The aim of this study was to detect crosslinks of collagen and elastin in formalin-fixed tissue, to perform quantification of these crosslinks, and to investigate the effects of formalin fixation on crosslink contents in human yellow ligament and cartilage. Pyridinoline (Pyr) is a stable and nonreducible crosslink of collagen. Pentosidine (Pen) is a senescent crosslink formed between arginine and lysine in matrix proteins, including collagen. Desmosine (Des) and its isomer isodesmosine (Isodes) are crosslinks specifically found in elastin. It is useful to measure crosslink contents of collagen and elastin as a way of investigating the properties of various tissues or their pathological changes. If it is possible to evaluate crosslinks of collagen and elastin in formalin-fixed tissues, we can investigate crosslinks in a wide variety of tissues. We used HPLC to compare the concentrations of Pyr, Pen, Des, and Isodes in the formalin-fixed tissues with their concentrations in the frozen tissues. Pyr and Pen were detected in both the formalin-fixed yellow ligament and the cartilage, and their concentrations were not significantly affected by or related to the duration of formalin fixation. Des and Isodes were detected in the formalin-fixed yellow ligament but in significantly lower amounts compared to the frozen samples. We concluded that crosslinks of collagen were preserved in formalin, but crosslinks of elastin were not preserved in it. The reason for this might be that formalin did not fix elastin tissues sufficiently or it destroyed, masked, or altered elastin crosslinks.

Intra-molecular cross-linking of acidic residues for protein structure studies.

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

Kruppa, Gary Hermann; Young, Malin M.; Novak, Petr

2005-03-01

Intra-molecular cross-linking has been suggested as a method of obtaining distance constraints that would be useful in developing structural models of proteins. Recent work published on intra-molecular cross-linking for protein structural studies has employed commercially available primary amine selective reagents that can cross-link lysine residues to other lysine residues or the amino terminus. Previous work using these cross-linkers has shown that for several proteins of known structure, the number of cross-links that can be obtained experimentally may be small compared to what would be expected from the known structure, due to the relative reactivity, distribution, and solvent accessibility of themore » lysines in the protein sequence. To overcome these limitations we have investigated the use of cross-linking reagents that can react with other reactive sidechains in proteins. We used 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) to activate the carboxylic acid containing residues, aspartic acid (D), glutamic acid (E), and the carboxy terminus (O), for cross-linking reactions. Once activated, the DEO sidechains can react to form 'zero-length' cross-links with nearby primary amine containing resides, lysines (K) and the amino terminus (X), via the formation of a new amide bond. We also show that the EDC-activated DEO sidechains can be cross-linked to each other using dihydrazides, two hydrazide moieties connected by an alkyl cross-linker ann of variable length. Using these reagents, we have found three new 'zero-length' cross-links in ubiquitin consistent with its known structure (M1-E16, M1-E18, and K63-E64). Using the dihydrazide cross-linkers, we have identified 2 new cross-links (D21-D32 and E24-D32) unambiguously. Using a library of dihydrazide cross-linkers with varying arm length, we have shown that there is a minimum arm length required for the DEO-DEO cross-links of 5.8 angstroms. These results show that additional structural information can be obtained by exploiting new cross-linker chemistry, increasing the probability that the protein target of choice will yield sufficient distance constraints to develop a structural model.« less

Evidence for collective expansion in light-particle emission following Au+Au collisions at 100, 150 and 250 A·MeV

NASA Astrophysics Data System (ADS)

Poggi, G.; Pasquali, G.; Bini, M.; Maurenzig, P.; Olmi, A.; Taccetti, N.; Alard, J. P.; Amouroux, V.; Basrak, Z.; Bastid, N.; Belayev, I. M.; Berger, L.; Blaich, Th.; Boussange, S.; Buta, A.; Čaplar, R.; Cerruti, C.; Cindro, N.; Coffin, J. P.; Donà, R.; Dupieux, P.; Dželalija, M.; Erö, J.; Fan, Z. G.; Fintz, P.; Fodor, Z.; Fraysse, L.; Freifelder, R.; Frolov, S.; Gobbi, A.; Grigorian, Y.; Guillaume, G.; Herrmann, N.; Hildenbrand, K. D.; Hölbling, S.; Houari, A.; Jeong, S. C.; Jundt, F.; Kecskemeti, J.; Koncz, P.; Korchagin, Y.; Kotte, R.; Krämer, M.; Kuhn, C.; Ibnouzahir, M.; Legrand, I.; Lebedev, A.; Maguire, C.; Manko, V.; Mgebrishvili, G.; Mösner, J.; Moisa, D.; Montarou, G.; Montbel, I.; Morel, P.; Neubert, W.; Pelte, D.; Petrovici, M.; Rami, F.; Ramillien, V.; Reisdorf, W.; Sadchikov, A.; Schüll, D.; Seres, Z.; Sikora, B.; Simion, V.; Smolyankin, S.; Sodan, U.; The, K.; Tezkratt, R.; Trzaska, M.; Vasiliev, M. A.; Wagner, P.; Wessels, J. P.; Wienold, T.; Wilhelmi, Z.; Wohlfarth, D.; Zhilin, A. V.; Danielewicz, P.; FOPI Collaboration

1995-02-01

Light-particle emission from Au+Au collisions has been studied in the bombarding-energy range 100-250 A·MeV, using ΔE- ER telescopes in coincidence with the FOPI detector in its phase I configuration. Center-of-mass energy spectra have been measured for Z = 1,2 isotopes emitted in central collisions at CM polar angles between 60° and 90°. Evidence for a collective expansion is reported, on the basis of the mean kinetic energies of hydrogen isotopes. Comparison is presented with statistical calculations (WIX code). For CM kinetic energy spectra, fair agreement is found between data and a recently developed transport model.

Evaluation of excitation functions of proton and deuteron induced reactions on enriched tellurium isotopes with special relevance to the production of iodine-124.

PubMed

Aslam, M N; Sudár, S; Hussain, M; Malik, A A; Shah, H A; Qaim, S M

2010-09-01

Cross-section data for the production of medically important radionuclide (124)I via five proton and deuteron induced reactions on enriched tellurium isotopes were evaluated. The nuclear model codes, STAPRE, EMPIRE and TALYS, were used for consistency checks of the experimental data. Recommended excitation functions were derived using a well-defined statistical procedure. Therefrom integral yields were calculated. The various production routes of (124)I were compared. Presently the (124)Te(p,n)(124)I reaction is the method of choice; however, the (125)Te(p,2n)(124)I reaction also appears to have great potential.

Integrated modelling of enhanced in situ biodenitrification in a fractured aquifer: biogeochemistry and isotope geochemistry

NASA Astrophysics Data System (ADS)

Rodríguez-Escales, Paula; Folch, Albert; van Breukelen, Boris M.; Vidal-Gavilan, Georgina; Soler, Albert

2014-05-01

Enhanced in-situ biodenitrification is a feasible technology to recovery groundwater polluted by nitrates and achieves drinking water standards. Under optimum conditions, nitrate is reduced by autochthonous bacteria trough different reactions until arrive to harmless dinitrogen gas. Isotopic fractionation monitoring in field applications allows knowing the exact degree and the real scope of this technology. Using the Rayleigh equation the change in the isotope ratio of the nitrate molecule (δ15N-NO3-, δ18O-NO3-) is related to the fraction of molecules remaining as a result of biodenitrification. However, Rayleigh application at field scale is sometimes limited due to other processes involved during groundwater flow such as dispersion or adsorption and geological media heterogeneities that interferes in concentration values. Then, include isotope fractionation processes in reactive transport models is a useful tool to interpret and predict data from in-situ biodenitrification. We developed a reactive transport model of enhanced in situ application at field scale in a fractured aquifer that considers biogeochemical processes as well as isotope fractionation to enable better monitoring and management of this technology. Processes considered were: microbiological- exogenous and endogenous nitrate and sulfate respiration coupled with microbial growth and decay, geochemical reactions (precipitation of calcite) and isotopic fractionation (δ15N-NO3-; δ18O- NO3- and carbon isotope network). The 2-D simulations at field scale were developed using PHAST code. Modeling of nitrate isotope geochemistry has allowed determining the extent of biodenitrification in model domain. We have quantified which is the importance in decreasing of nitrate concentrations due to biodegradation (percentage of biodegradation, 'B%') and due to dilution process (percentage of dilution, 'D%'). On the other hand, the stable carbon isotope geochemistry has been modeled. We have considered the isotopic carbon fractionation of different carbon species involved in enhanced biodenitrification: external organic carbon, biomass, inorganic carbon (in different forms) and calcite. The inclusion of carbon isotopes in the model, which are involved in both direct (oxidation of organic carbon) and indirect (carbonate mineral interaction) processes of enhanced biodenitrification, improves the evaluation of the overall model consistency due to the central role of carbon in the reaction network.

Photo-inducible Crosslinked Nanoassemblies for pH-Controlled Drug Release

PubMed Central

Dickerson, Matthew; Winquist, Nickolas; Bae, Younsoo

2014-01-01

Purpose To control drug release from block copolymer nanoassemblies by variation in the degree of photo-crosslinking and inclusion of acid sensitive linkers. Methods Poly(ethylene glycol)-poly(aspartate-hydrazide-cinnamate) (PEG-CNM) block copolymers were prepared and conjugated with a model drug, doxorubicin (DOX), through acid sensitive hydrazone linkers. The block copolymers formed photo-inducible, self-assembled nanoassemblies (piSNAs), which were used to produce photo-inducible crosslinked nanoassemblies (piCNAs) through UV crosslinking. The nanoassemblies were characterized to determine particle size, surface charge, pH- and crosslinking-dependent DOX release, in vitro cytotoxicity, and intracellular uptake as a function of photo-crosslinking degree. Results Nanoassemblies with varying photo-crosslinking degrees were successfully prepared while retaining particle size and surface charge. Photo-crosslinking caused no noticeable change in DOX release from the nanoassemblies at pH 7.4, but the DOX-loaded nanoassemblies modulated drug release as a function of crosslinking at pH 6.0. The nanoassemblies showed similar cytotoxicity regardless of crosslinking degrees, presumably due to the low cellular uptake and cell nucleus drug accumulation. Conclusion Photo-crosslinking is useful to control drug release from pH-sensitive block copolymer nanoassemblies as a function of crosslinking without altering the particle properties, and thus providing unique tools to investigate the pharmaceutical effects of drug release on cellular response. PMID:24254196

Identification of Crosslinked Peptides after Click-based Enrichment Using Sequential CID and ETD Tandem Mass Spectrometry

PubMed Central

Chowdhury, Saiful M.; Du, Xiuxia; Tolić, Nikola; Wu, Si; Moore, Ronald J.; Mayer, M. Uljana; Smith, Richard D.; Adkins, Joshua N.

2010-01-01

Chemical crosslinking combined with mass spectrometry can be a powerful approach for the identification of protein-protein interactions and for providing constraints on protein structures. However, enrichment of crosslinked peptides is crucial to reduce sample complexity before mass spectrometric analysis. In addition compact crosslinkers are often preferred to provide short spacer lengths, surface accessibility to the protein complexes, and must have reasonable solubility under condition where the native complex structure is stable. In this study, we present a novel compact crosslinker that contains two distinct features: 1) an alkyne tag and 2) a small molecule detection tag (NO2-) to maintain reasonable solubility in water. The alkyne tag enables enrichment of the crosslinked peptide after proteolytic cleavage after coupling of an affinity tag using alkyne-azido click chemistry. Neutral loss of the small NO2- moiety provides a secondary means of detecting crosslinked peptides in MS/MS analyses, providing additional confidence in peptide identifications. We show the labeling efficiency of this crosslinker, which we termed CLIP (Click-enabled Linker for Interacting Proteins) using ubiquitin. The enrichment capability of CLIP is demonstrated for crosslinked ubiquitin in highly complex E. coli cell lysates. Sequential CID-MS/MS and ETD-MS/MS of inter-crosslinked peptides (two peptides connected with a crosslinker) are also demonstrated for improved automated identification of crosslinked peptides. PMID:19496583

Comparison of glutaraldehyde and carbodiimides to crosslink tissue engineering scaffolds fabricated by decellularized porcine menisci.

PubMed

Gao, Shuang; Yuan, Zhiguo; Guo, Weimin; Chen, Mingxue; Liu, Shuyun; Xi, Tingfei; Guo, Quanyi

2017-02-01

The objectives of this study were to fabricate porous scaffolds using decellularized meniscus, and to explore a preferable crosslinking condition to enhance mechanical properties of scaffolds. Moreover, the microstructure, porosity, biodegradation and cytotoxicity were also evaluated. EDAC or GTA in different concentration was used to crosslink scaffolds. FTIR demonstrated functional groups change in crosslinking process. SEM photography showed that crosslinked scaffolds had blurry edges, which resulted scaffolds crosslinked by 1.2mol/l EDAC had smaller porosity than other groups. The structure change enhanced antidegradation property. After immersing in enzyme solution for 96h, scaffolds crosslinked by GTA and EDAC could maintain their mass >70% and 80%. Most importantly, mechanical properties of crosslinked scaffolds were also improved. Uncrosslinked Scaffolds had only 0.49kPa in compression modulus and 12.81kPa in tensile modulus. The compression and tensile modulus of scaffolds crosslinked by 1.0% GTA were 1.42 and 567.44kPa respectively. The same value of scaffolds crosslinked by 1.2mol/l EDAC were 1.49 and 532.50kPa. Scaffolds crosslinked by 1.0% and 2.5% GTA were toxic to cells, while EDAC groups showed no cytotoxicity. Chondrocytes could proliferate and infiltrate within scaffolds after seeding. Overall, 1.2mol/l EDAC was a preferable crosslinking condition. Copyright © 2016 Elsevier B.V. All rights reserved.

Xilmass: A New Approach toward the Identification of Cross-Linked Peptides.

PubMed

Yılmaz, Şule; Drepper, Friedel; Hulstaert, Niels; Černič, Maša; Gevaert, Kris; Economou, Anastassios; Warscheid, Bettina; Martens, Lennart; Vandermarliere, Elien

2016-10-18

Chemical cross-linking coupled with mass spectrometry plays an important role in unravelling protein interactions, especially weak and transient ones. Moreover, cross-linking complements several structural determination approaches such as cryo-EM. Although several computational approaches are available for the annotation of spectra obtained from cross-linked peptides, there remains room for improvement. Here, we present Xilmass, a novel algorithm to identify cross-linked peptides that introduces two new concepts: (i) the cross-linked peptides are represented in the search database such that the cross-linking sites are explicitly encoded, and (ii) the scoring function derived from the Andromeda algorithm was adapted to score against a theoretical tandem mass spectrometry (MS/MS) spectrum that contains the peaks from all possible fragment ions of a cross-linked peptide pair. The performance of Xilmass was evaluated against the recently published Kojak and the popular pLink algorithms on a calmodulin-plectin complex data set, as well as three additional, published data sets. The results show that Xilmass typically had the highest number of identified distinct cross-linked sites and also the highest number of predicted cross-linked sites.

Reduction-responsive interlayer-crosslinked micelles prepared from star-shaped copolymer via click chemistry for drug controlled release

NASA Astrophysics Data System (ADS)

Dai, Yu; Wang, Hongquan; Zhang, Xiaojin

2017-12-01

To improve the stability of polymeric micelles, here we describe interlayer-crosslinked micelles prepared from star-shaped copolymer via click chemistry. The formation of interlayer-crosslinked micelles was investigated and confirmed by proton nuclear magnetic resonance, Fourier-transform infrared spectroscopy, and fluorescence spectroscopy. The morphology of un-crosslinked micelles and crosslinked micelles observed by transmission electron microscope is both uniform nano-sized spheres (approximately 20 nm). The crosslinking enhances the stability of polymeric micelles and improves the drug loading capacity of polymeric micelles. The interlayer-crosslinked micelles prepared from star-shaped copolymer and a crosslinker containing a disulfide bond are reduction-responsive and can release the drug quickly in the presence of the reducing agents such as glutathione (GSH).

Constitutive Modeling of Crosslinked Nanotube Materials

NASA Technical Reports Server (NTRS)

Odegard, G. M.; Frankland, S. J. V.; Herzog, M. N.; Gates, T. S.; Fay, C. C.

2004-01-01

A non-linear, continuum-based constitutive model is developed for carbon nanotube materials in which bundles of aligned carbon nanotubes have varying amounts of crosslinks between the nanotubes. The model accounts for the non-linear elastic constitutive behavior of the material in terms of strain, and is developed using a thermodynamic energy approach. The model is used to examine the effect of the crosslinking on the overall mechanical properties of variations of the crosslinked carbon nanotube material with varying degrees of crosslinking. It is shown that the presence of the crosslinks has significant effects on the mechanical properties of the carbon nanotube materials. An increase in the transverse shear properties is observed when the nanotubes are crosslinked. However, this increase is accompanied by a decrease in axial mechanical properties of the nanotube material upon crosslinking.

Anthocyanin Interactions with DNA: Intercalation, Topoisomerase I Inhibition and Oxidative Reactions

PubMed Central

Webb, Michael R.; Min, Kyungmi; Ebeler, Susan E.

2009-01-01

Anthocyanins and their aglycone anthocyanidins are pigmented flavonoids found in significant amounts in many commonly consumed foods. They exhibit a complex chemistry in aqueous solution, which makes it difficult to study their chemistry under physiological conditions. Here we used a gel electrophoresis assay employing supercoiled DNA plasmid to examine the ability of these compounds (1) to intercalate DNA, (2) to inhibit human topoisomerase I through both inhibition of plasmid relaxation activity (catalytic inhibition) and stabilization of the cleavable DNA-topoisomerase complex (poisoning), and (3) to inhibit or enhance oxidative single-strand DNA nicking. We found no evidence of DNA intercalation by anthocyan(id)ins in the physiological pH range for any of the compounds used in this study—cyanidin chloride, cyanidin 3-O-glucoside, cyanidin 3,5-O-diglucoside, malvidin 3-O-glucoside and luteolinidin chloride. The anthocyanins inhibited topoisomerase relaxation activity only at high concentrations (> 50 μM) and we could find no evidence of topoisomerase I cleavable complex stabilization by these compounds. However, we observed that all of the anthocyan(id)ins used in this study were capable of inducing significant oxidative DNA strand cleavage (nicking) in the presence of 1 mM DTT (dithiothreitol), while the free radical scavenger, DMSO, at concentrations typically used in similar studies, completely inhibited DNA nicking. Finally, we propose a mechanism to explain the anthocyan(id)in induced oxidative DNA cleavage observed under our experimental conditions. PMID:19924259

Nitric oxide inhibits topoisomerase II activity and induces resistance to topoisomerase II-poisons in human tumor cells.

PubMed

Kumar, Ashutosh; Ehrenshaft, Marilyn; Tokar, Erik J; Mason, Ronald P; Sinha, Birandra K

2016-07-01

Etoposide and doxorubicin, topoisomerase II poisons, are important drugs for the treatment of tumors in the clinic. Topoisomerases contain several free sulfhydryl groups which are important for their activity and are also potential targets for nitric oxide (NO)-induced nitrosation. NO, a physiological signaling molecule nitrosates many cellular proteins, causing altered protein and cellular functions. Here, we have evaluated the roles of NO/NO-derived species in the activity/stability of topo II both in vitro and in human tumor cells, and in the cytotoxicity of topo II-poisons, etoposide and doxorubicin. Treatment of purified topo IIα with propylamine propylamine nonoate (PPNO), an NO donor, resulted in inhibition of both the catalytic and relaxation activity in vitro, and decreased etoposide-dependent cleavable complex formation in both human HT-29 colon and MCF-7 breast cancer cells. PPNO treatment also induced significant nitrosation of topo IIα protein in these human tumor cells. These events, taken together, caused a significant resistance to etoposide in both cell lines. However, PPNO had no effect on doxorubicin-induced cleavable complex formation, or doxorubicin cytotoxicity in these cell lines. Inhibition of topo II function by NO/NO-derived species induces significant resistance to etoposide, without affecting doxorubicin cytotoxicity in human tumor cells. As tumors express inducible nitric oxide synthase and generate significant amounts of NO, modulation of topo II functions by NO/NO-derived species could render tumors resistant to certain topo II-poisons in the clinic. Published by Elsevier B.V.

Analysis of reaction cross-section production in neutron induced fission reactions on uranium isotope using computer code COMPLET.

PubMed

Asres, Yihunie Hibstie; Mathuthu, Manny; Birhane, Marelgn Derso

2018-04-22

This study provides current evidence about cross-section production processes in the theoretical and experimental results of neutron induced reaction of uranium isotope on projectile energy range of 1-100 MeV in order to improve the reliability of nuclear stimulation. In such fission reactions of 235 U within nuclear reactors, much amount of energy would be released as a product that able to satisfy the needs of energy to the world wide without polluting processes as compared to other sources. The main objective of this work is to transform a related knowledge in the neutron-induced fission reactions on 235 U through describing, analyzing and interpreting the theoretical results of the cross sections obtained from computer code COMPLET by comparing with the experimental data obtained from EXFOR. The cross section value of 235 U(n,2n) 234 U, 235 U(n,3n) 233 U, 235 U(n,γ) 236 U, 235 U(n,f) are obtained using computer code COMPLET and the corresponding experimental values were browsed by EXFOR, IAEA. The theoretical results are compared with the experimental data taken from EXFOR Data Bank. Computer code COMPLET has been used for the analysis with the same set of input parameters and the graphs were plotted by the help of spreadsheet & Origin-8 software. The quantification of uncertainties stemming from both experimental data and computer code calculation plays a significant role in the final evaluated results. The calculated results for total cross sections were compared with the experimental data taken from EXFOR in the literature, and good agreement was found between the experimental and theoretical data. This comparison of the calculated data was analyzed and interpreted with tabulation and graphical descriptions, and the results were briefly discussed within the text of this research work. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Bone Collagen: New Clues to its Mineralization Mechanism From Recessive Osteogenesis Imperfecta

PubMed Central

Eyre, David R.; Ann Weis, Mary

2013-01-01

Until 2006 the only mutations known to cause osteogenesis imperfecta (OI) were in the two genes coding for type I collagen chains. These dominant mutations affecting the expression or primary sequence of collagen α1(I) and α2(I) chains account for over 90% of OI cases. Since then a growing list of mutant genes causing the 5–10% of recessive cases has rapidly emerged. They include CRTAP, LEPRE1 and PPIB, which encode three proteins forming the prolyl 3-hydroxylase complex; PLOD2 and FKBP10, which encode respectively lysyl hydroxylase 2 and a foldase required for its activity in forming mature cross-links in bone collagen; SERPIN H1, which encodes the collagen chaperone HSP47; SERPIN F1, which encodes pigment epithelium-derived factor required for osteoid mineralization; and BMP1, which encodes the type I procollagen C-propeptidase. All cause fragile bone in infancy, which can include over-mineralization or under-mineralization defects as well as abnormal collagen post-translational modifications. Consistently both dominant and recessive variants lead to abnormal cross-linking chemistry in bone collagen. These recent discoveries strengthen the potential for a common pathogenic mechanism of misassembled collagen fibrils. Of the new genes identified, eight encode proteins required for collagen post-translational modification, chaperoning of newly synthesized collagen chains into native molecules or transport through the endoplasmic reticulum and Golgi for polymerization, cross-linking and mineralization. In reviewing these findings, we conclude that a common theme is emerging in the pathogenesis of brittle bone disease of mishandled collagen assembly with important insights on post-translational features of bone collagen that have evolved to optimize it as a biomineral template. PMID:23508630

Oxidation resistant peroxide cross-linked UHMWPE produced by blending and surface diffusion

NASA Astrophysics Data System (ADS)

Gul, Rizwan M.; Oral, Ebru; Muratoglu, Orhun K.

2014-06-01

Ultra-high molecular weight polyethylene (UHMWPE) has been widely used as acetabular cup in total hip replacement (THR) and tibial component in total knee replacement (TKR). Crosslinking of UHMWPE has been successful used to improve its wear performance leading to longer life of orthopedic implants. Crosslinking can be performed by radiation or organic peroxides. Peroxide crosslinking is a convenient process as it does not require specialized equipment and the level of crosslinking can be manipulated by changing the amount of peroxide added. However, there is concern about the long-term stability of these materials due to possible presence of by-products. Vitamin E has been successfully used to promote long-term oxidative stability of UHMWPE. In this study, UHMWPE has been crosslinked using organic peroxide in the presence of Vitamin E to produce an oxidation resistant peroxide crosslinked material. Crosslinking was performed both in bulk by mixing peroxide and resin, and only on the surface using diffusion of peroxides.The results show that UHMWPE can be crosslinked using organic peroxides in the presence of vitamin E by both methods. However, the level of crosslinking decreases with the increase in vitamin E content. The wear resistance increases with the increase in crosslink density, and oxidation resistance significantly increases due to the presence of vitamin E.

Preparation of decellularized vascular matrix by co-crosslinking of procyanidins and glutaraldehyde.

PubMed

Wang, Xiaotong; Ma, Bing; Chang, Jiang

2015-01-01

Vascular extracellular matrices (vECMs) have shown potential for small-diameter blood vessel tissue engineering applications. However, problems such as chemical instability and easy calcification are still remained. Chemical crosslinking using crosslinkers such as glutaraldehyde (GA) can improve mechanical properties and proteolysis resistance of vECMs, but leads to calcification and cytotoxicity. Procyanidins (PC) can crosslink ECMs with anti-calcification property and cytocompatibility, but the mechanical properties and chemical stability are unsatisfactory. A novel co-crosslinking technique using PC and GA was developed, which combines the advantages of both PC and GA for enhancing mechanical properties and stability of vECMs with reduced calcification and cytotoxicity. Fresh carotid were decellularized and then crosslinked by PC and subsequent GA for 6 h respectively. The mechanical properties, dynamic release of PC, enzymatic degradation, calcification and cytotoxicity of crosslinked samples were evaluated. The co-crosslinked vECMs showed enhanced tensile strength, chemical and biological stability, comparable anti-calcification property as compared to pure PC-crosslinked samples. Cytotoxicity assay showed that the co-crosslinked vECMs were cytocompatible for supporting the adhesion and proliferation of HUVECs. Co-crosslinking with PC and GA might be a useful method for preparation of vECM scaffolds with potential applications in small-diameter blood vessel tissue engineering.

ChelomEx: Isotope-assisted discovery of metal chelates in complex media using high-resolution LC-MS.

PubMed

Baars, Oliver; Morel, François M M; Perlman, David H

2014-11-18

Chelating agents can control the speciation and reactivity of trace metals in biological, environmental, and laboratory-derived media. A large number of trace metals (including Fe, Cu, Zn, Hg, and others) show characteristic isotopic fingerprints that can be exploited for the discovery of known and unknown organic metal complexes and related chelating ligands in very complex sample matrices using high-resolution liquid chromatography mass spectrometry (LC-MS). However, there is currently no free open-source software available for this purpose. We present a novel software tool, ChelomEx, which identifies isotope pattern-matched chromatographic features associated with metal complexes along with free ligands and other related adducts in high-resolution LC-MS data. High sensitivity and exclusion of false positives are achieved by evaluation of the chromatographic coherence of the isotope pattern within chromatographic features, which we demonstrate through the analysis of bacterial culture media. A built-in graphical user interface and compound library aid in identification and efficient evaluation of results. ChelomEx is implemented in MatLab. The source code, binaries for MS Windows and MAC OS X as well as test LC-MS data are available for download at SourceForge ( http://sourceforge.net/projects/chelomex ).

The impact of nuclear mass models on r-process nucleosynthesis network calculations

NASA Astrophysics Data System (ADS)

Vaughan, Kelly

2002-10-01

An insight into understanding various nucleosynthesis processes is via modelling of the process with network calculations. My project focus is r-process network calculations where the r-process is nucleosynthesis via rapid neutron capture thought to take place in high entropy supernova bubbles. One of the main uncertainties of the simulations is the Nuclear Physics input. My project investigates the role that nuclear masses play in the resulting abundances. The code tecode, involves rapid (n,γ) capture reactions in competition with photodisintegration and β decay onto seed nuclei. In order to fully analyze the effects of nuclear mass models on the relative isotopic abundances, calculations were done from the network code, keeping the initial environmental parameters constant throughout. The supernova model investigated by Qian et al (1996) in which two r-processes, of high and low frequency with seed nucleus ^90Se and of fixed luminosity (fracL_ν_e(0)r_7(0)^2 ˜= 8.77), contribute to the nucleosynthesis of the heavier elements. These two r-processes, however, do not contribute equally to the total abundance observed. The total isotopic abundance produced from both events was therefore calculated using equation refabund. Y(H+L) = fracY(H)+fY(L)f+1 <~belabund where Y(H) denotes the relative isotopic abundance produced in the high frequency event, Y(L) corresponds to the low freqeuncy event and f is the ratio of high event matter to low event matter produced. Having established reliable, fixed parameters, the network code was run using data files containing parameters such as the mass excess, neutron separation energy, β decay rates and neutron capture rates based around three different nuclear mass models. The mass models tested are the HFBCS model (Hartree-Fock BCS) derived from first principles, the ETFSI-Q model (Extended Thomas-Fermi with Strutinsky Integral including shell Quenching) known for its particular successes in the replication of Solar System abundances, and the P-Scheme Model tePscheme. The aims of this research is to test the applicability of the P-Scheme in relation to the other mass models to the r-process network calculations. 02 Pscheme Aprahamian,A., Gadala-Maria,A. & Cuka,N. 1996, Revista Mexicana de Fisica,42,1 code Surman,R. & Engel,J. 1998, Phys.Rev. C,54,4 thebibliography

Physical interactions between bacteriophage and Escherichia coli proteins required for initiation of lambda DNA replication.

PubMed

Liberek, K; Osipiuk, J; Zylicz, M; Ang, D; Skorko, J; Georgopoulos, C

1990-02-25

The process of initiation of lambda DNA replication requires the assembly of the proper nucleoprotein complex at the origin of replication, ori lambda. The complex is composed of both phage and host-coded proteins. The lambda O initiator protein binds specifically to ori lambda. The lambda P initiator protein binds to both lambda O and the host-coded dnaB helicase, giving rise to an ori lambda DNA.lambda O.lambda P.dnaB structure. The dnaK and dnaJ heat shock proteins have been shown capable of dissociating this complex. The thus freed dnaB helicase unwinds the duplex DNA template at the replication fork. In this report, through cross-linking, size chromatography, and protein affinity chromatography, we document some of the protein-protein interactions occurring at ori lambda. Our results show that the dnaK protein specifically interacts with both lambda O and lambda P, and that the dnaJ protein specifically interacts with the dnaB helicase.

Photouncaged Sequence-specific Interstrand DNA Cross-Linking with Photolabile 4-oxo-enal-modified Oligonucleotides

PubMed Central

Sun, Jingjing; Tang, Xinjing

2015-01-01

DNA cross-linking technology is an attractive tool for the detection, regulation, and manipulation of genes. In this study, a series of photolabile 4-oxo-enal-modified oligonucleotides functionalized with photosensitive ο-nitrobenzyl derivatives were rationally designed as a new kind of photocaged cross-linking agents. A comprehensive evaluation of cross-linking reactions for different nucleobases in complementary strands under different conditions suggested that the modified DNA oligonucleotides tended to form interstrand cross-linking to nucleobases with the potential of thymidine > guanosine » cytidine ~ adenosine. Different from previous literature reports that cytidine and adenosine were preferential cross-linked nucleobases with 4-oxo-enal moieties, our study represents the first example of DNA cross-linking for T and G selectivity using 4-oxo-enal moiety. The cross-linked adducts were identified and their cross-linking mechanism was also illustrated. This greatly expands the applications of 4-oxo-enal derivatives in the studies of DNA damage and RNA structure PMID:26020694

Photouncaged Sequence-specific Interstrand DNA Cross-Linking with Photolabile 4-oxo-enal-modified Oligonucleotides.

PubMed

Sun, Jingjing; Tang, Xinjing

2015-05-28

DNA cross-linking technology is an attractive tool for the detection, regulation, and manipulation of genes. In this study, a series of photolabile 4-oxo-enal-modified oligonucleotides functionalized with photosensitive ο-nitrobenzyl derivatives were rationally designed as a new kind of photocaged cross-linking agents. A comprehensive evaluation of cross-linking reactions for different nucleobases in complementary strands under different conditions suggested that the modified DNA oligonucleotides tended to form interstrand cross-linking to nucleobases with the potential of thymidine > guanosine » cytidine ~ adenosine. Different from previous literature reports that cytidine and adenosine were preferential cross-linked nucleobases with 4-oxo-enal moieties, our study represents the first example of DNA cross-linking for T and G selectivity using 4-oxo-enal moiety. The cross-linked adducts were identified and their cross-linking mechanism was also illustrated. This greatly expands the applications of 4-oxo-enal derivatives in the studies of DNA damage and RNA structure.

Determination of the delta(18O/16O)of Water: RSIL Lab Code 489

USGS Publications Warehouse

Revesz, Kinga; Coplen, Tyler

2008-01-01

The purpose of the technique described by the Reston Stable Isotope Laboratory (RSIL) lab code 489 is to present a method to determine the delta(180/160), abbreviated as delta-180, of water. This delta-18O measurement of water also is a component of National Water Quality Laboratory (NWQL in USGS) schedules 1142 and 1172. Water samples are loaded into glass sample containers on a vacuum manifold to equilibrate gaseous CO2 at constant temperature (25 deg C) with water samples. After loading water samples on the vacuum manifold, air is evacuated through capillary to avoid evaporation, and CO2 is added. The samples are shaken to increase the equilibration rate of water and CO2. When isotopic equilibrium has been attained, an aliquot of CO2 is extracted sequentially from each sample container, separated from water vapor by means of a dry ice trap, and introduced into a dual-inlet isotope-ratio mass spectrometer (DI-IRMS) for determination of the delta-18O value. There is oxygen isotopic fractionation between water and CO2, but it is constant at constant temperature. The DI-IRMS is a DuPont double-focusing mass spectrometer. It has a double collector. One ion beam passes through a slit in a forward collector and is collected in the rear collector. The other ion beams are collected in the front collector. The instrument is capable of measuring mass/charge (m/z) 44 and 45 or 44 and 46 by changing the ion-accelerating voltage under computer control. The ion beams from these m/z values are as follows: m/z 44=CO2=12C16O16O, m/z 45=CO2=13C16O16O primarily, and m/z 46 = CO2=12C16O18O primarily. The data acquisition and control software calculates delta-18O values.

Effect of Rubber Polarity on Cluster Formation in Rubbers Cross-Linked with Diels–Alder Chemistry

PubMed Central

2017-01-01

Diels–Alder chemistry has been used for the thermoreversible cross-linking of furan-functionalized ethylene/propylene (EPM) and ethylene/vinyl acetate (EVM) rubbers. Both furan-functionalized elastomers were successfully cross-linked with bismaleimide to yield products with a similar cross-link density. NMR relaxometry and SAXS measurements both show that the apolar EPM-g-furan precursor contains phase-separated polar clusters and that cross-linking with polar bismaleimide occurs in these clusters. The heterogeneously cross-linked network of EPM-g-furan contrasts with the homogeneous network in the polar EVM-g-furan. The heterogeneous character of the cross-links in EPM-g-furan results in a relatively high Young’s modulus, whereas the more uniform cross-linking in EVM-g-furan results in a higher tensile strength and elongation at break. PMID:29213149

Cross-linked polyelectrolyte for direct methanol fuel cells applications based on a novel sulfonated cross-linker

NASA Astrophysics Data System (ADS)

Li, Mingyu; Zhang, Gang; Xu, Shuai; Zhao, Chengji; Han, Miaomiao; Zhang, Liyuan; Jiang, Hao; Liu, Zhongguo; Na, Hui

2014-06-01

A novel type of cross-linked proton exchange membrane of lower methanol permeation and high proton conductivity is prepared, based on a newly synthesized sulfonated cross-linker: carboxyl terminated benzimidazole trimer bearing sulfonic acid groups (s-BI). Compared to membranes cross-linked with non-sulfonated cross-linker (BI), SPEEK/s-BI-n membranes show higher IEC values and proton conductivities. Meanwhile, oxidative stability and mechanical property of SPEEK/s-BI-n membranes are obviously improved. Among SPEEK/s-BI-n membranes, SPEEK/s-BI-2 exhibits high proton conductivity, low swelling ratio (0.122 S cm-1 and 15.2% at 60 °C, respectively) and low methanol permeability coefficient. These results imply that the cross-linked membranes prepared with the newly sulfonated cross-linker are promising for the direct methanol fuel cells (DMFCs) application.

Desmosine-Inspired Cross-Linkers for Hyaluronan Hydrogels

NASA Astrophysics Data System (ADS)

Hagel, Valentin; Mateescu, Markus; Southan, Alexander; Wegner, Seraphine V.; Nuss, Isabell; Haraszti, Tamás; Kleinhans, Claudia; Schuh, Christian; Spatz, Joachim P.; Kluger, Petra J.; Bach, Monika; Tussetschläger, Stefan; Tovar, Günter E. M.; Laschat, Sabine; Boehm, Heike

2013-06-01

We designed bioinspired cross-linkers based on desmosine, the cross-linker in natural elastin, to prepare hydrogels with thiolated hyaluronic acid. These short, rigid cross-linkers are based on pyridinium salts (as in desmosine) and can connect two polymer backbones. Generally, the obtained semi-synthetic hydrogels are form-stable, can withstand repeated stress, have a large linear-elastic range, and show strain stiffening behavior typical for biopolymer networks. In addition, it is possible to introduce a positive charge to the core of the cross-linker without affecting the gelation efficiency, or consequently the network connectivity. However, the mechanical properties strongly depend on the charge of the cross-linker. The properties of the presented hydrogels can thus be tuned in a range important for engineering of soft tissues by controlling the cross-linking density and the charge of the cross-linker.

Discovery of Undefined Protein Crosslinking Chemistry: A Comprehensive Methodology Utilizing 18O-labeling and Mass Spectrometry

PubMed Central

Liu, Min; Zhang, Zhongqi; Zang, Tianzhu; Spahr, Chris; Cheetham, Janet; Ren, Da; Sunny Zhou, Zhaohui

2013-01-01

Characterization of protein crosslinking, particularly without prior knowledge of the chemical nature and site of crosslinking, poses a significant challenge due to their intrinsic structural complexity and the lack of a comprehensive analytical approach. Towards this end, we have developed a generally applicable workflow—XChem-Finder that involves four stages. (1) Detection of crosslinked peptides via 18O-labeling at C-termini. (2) Determination of the putative partial sequences of each crosslinked peptide pair using a fragment ion mass database search against known protein sequences coupled with a de novo sequence tag search. (3) Extension to full sequences based on protease specificity, the unique combination of mass, and other constraints. (4) Deduction of crosslinking chemistry and site. The mass difference between the sum of two putative full-length peptides and the crosslinked peptide provides the formulas (elemental composition analysis) for the functional groups involved in each cross- linking. Combined with sequence restraint from MS/MS data, plausible crosslinking chemistry and site were inferred, and ultimately, confirmed by matching with all data. Applying our approach to a stressed IgG2 antibody, ten cross-linked peptides were discovered and found to be connected via thioether originating from disulfides at locations that had not been previously recognized. Furthermore, once the crosslink chemistry was revealed, a targeted crosslink search yielded four additional crosslinked peptides that all contain the C-terminus of the light chain. PMID:23634697

The effects of crosslinkers on physical, mechanical, and cytotoxic properties of gelatin sponge prepared via in-situ gas foaming method as a tissue engineering scaffold.

PubMed

Poursamar, S Ali; Lehner, Alexander N; Azami, Mahmoud; Ebrahimi-Barough, Somayeh; Samadikuchaksaraei, Ali; Antunes, A P M

2016-06-01

In this study porous gelatin scaffolds were prepared using in-situ gas foaming, and four crosslinking agents were used to determine a biocompatible and effective crosslinker that is suitable for such a method. Crosslinkers used in this study included: hexamethylene diisocyanate (HMDI), poly(ethylene glycol) diglycidyl ether (epoxy), glutaraldehyde (GTA), and genipin. The prepared porous structures were analyzed using Fourier Transform Infrared Spectroscopy (FT-IR), thermal and mechanical analysis as well as water absorption analysis. The microstructures of the prepared samples were analyzed using Scanning Electron Microscopy (SEM). The effects of the crosslinking agents were studied on the cytotoxicity of the porous structure indirectly using MTT analysis. The affinity of L929 mouse fibroblast cells for attachment on the scaffold surfaces was investigated by direct cell seeding and DAPI-staining technique. It was shown that while all of the studied crosslinking agents were capable of stabilizing prepared gelatin scaffolds, there are noticeable differences among physical and mechanical properties of samples based on the crosslinker type. Epoxy-crosslinked scaffolds showed a higher capacity for water absorption and more uniform microstructures than the rest of crosslinked samples, whereas genipin and GTA-crosslinked scaffolds demonstrated higher mechanical strength. Cytotoxicity analysis showed the superior biocompatibility of the naturally occurring genipin in comparison with other synthetic crosslinking agents, in particular relative to GTA-crosslinked samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Early biocompatibility of crosslinked and non-crosslinked biologic meshes in a porcine model of ventral hernia repair.

PubMed

Melman, L; Jenkins, E D; Hamilton, N A; Bender, L C; Brodt, M D; Deeken, C R; Greco, S C; Frisella, M M; Matthews, B D

2011-04-01

Biologic meshes have unique physical properties as a result of manufacturing techniques such as decellularization, crosslinking, and sterilization. The purpose of this study is to directly compare the biocompatibility profiles of five different biologic meshes, AlloDerm(®) (non-crosslinked human dermal matrix), PeriGuard(®) (crosslinked bovine pericardium), Permacol(®) (crosslinked porcine dermal matrix), Strattice(®) (non-crosslinked porcine dermal matrix), and Veritas(®) (non-crosslinked bovine pericardium), using a porcine model of ventral hernia repair. Full-thickness fascial defects were created in 20 Yucatan minipigs and repaired with the retromuscular placement of biologic mesh 3 weeks later. Animals were euthanized at 1 month and the repair sites were subjected to tensile testing and histologic analysis. Samples of unimplanted (de novo) meshes and native porcine abdominal wall were also analyzed for their mechanical properties. There were no significant differences in the biomechanical characteristics between any of the mesh-repaired sites at 1 month postimplantation or between the native porcine abdominal wall without implanted mesh and the mesh-repaired sites (P > 0.05 for all comparisons). Histologically, non-crosslinked materials exhibited greater cellular infiltration, extracellular matrix (ECM) deposition, and neovascularization compared to crosslinked meshes. While crosslinking differentiates biologic meshes with regard to cellular infiltration, ECM deposition, scaffold degradation, and neovascularization, the integrity and strength of the repair site at 1 month is not significantly impacted by crosslinking or by the de novo strength/stiffness of the mesh.

Probe Into the Influence of Crosslinking on CO2 Permeation of Membranes

PubMed Central

Li, Jinghui; Chen, Zhuo; Umar, Ahmad; Liu, Yang; Shang, Ying; Zhang, Xiaokai; Wang, Yao

2017-01-01

Crosslinking is an effective way to fabricate high-selective CO2 separation membranes because of its unique crosslinking framework. Thus, it is essentially significant to study the influence of crosslinking degree on the permeation selectivities of CO2. Herein, we report a successful and facile synthesis of a series of polyethylene oxide (PEO)-based diblock copolymers (BCP) incorporated with an unique UV-crosslinkable chalcone unit using Reversible Addition-Fragmentation Chain Transfer Polymerization (RAFT) process. The membranes of as-prepared BCPs show superior carbon dioxide (CO2) separation properties as compared to nitrogen (N2) after UV-crosslinking. Importantly, the influence of different proportions of crosslinked chalcone on CO2 selectivities was systematically investigated, which revealed that CO2 selectivities increased obviously with the enhancement of chalcone fractions within a certain limit. Further, the CO2 selectivities of block copolymer with the best block proportion was studied by varying the crosslinking time which confirmed that the high crosslinking degree exhibited a better CO2/N2 (αCO2/N2) selectivities. A possible mechanism model revealing that the crosslinking degree played a key role in the gas separation process was also proposed. PMID:28051190

Chemical and radiation crosslinked polymer electrolyte membranes prepared from radiation-grafted ETFE films for DMFC applications

NASA Astrophysics Data System (ADS)

Chen, Jinhua; Asano, Masaharu; Yamaki, Tetsuya; Yoshida, Masaru

To develop a highly chemically stable polymer electrolyte membrane for application in a direct methanol fuel cell (DMFC), doubly crosslinked membranes were prepared by chemical crosslinking using bifunctional monomers, such as divinylbenzene (DVB) and bis(p, p-vinyl phenyl) ethane (BVPE), and by radiation crosslinking. The membranes were prepared by grafting of m, p-methylstyrene (MeSt) and p-tert-butylstyrene (tBuSt) into poly(ethylene- co-tetrafluoroethylene) (ETFE) films and subsequent sulfonation. The effects of the DVB and BVPE crosslinkers on the grafting kinetics and the properties of the prepared membranes, such as water uptake, proton conductivity and chemical stability were investigated. Radiation crosslinking was introduced by irradiation of the ETFE base film, the grafted film or the sulfonated membrane. The membrane crosslinked by DVB and BVPE crosslinkers and post-crosslinked by γ-ray irradiation of the corresponding grafted film possessed the highest chemical stability among the prepared membranes, a significantly lower methanol permeability compared to Nafion ® membranes, and a better DMFC performance for high methanol feed concentration. Therefore, this doubly crosslinked membrane was promising for application in a DMFC where relatively high methanol concentration could be fed.

Mechanically tunable actin networks using programmable DNA based cross-linkers

NASA Astrophysics Data System (ADS)

Schnauss, Joerg; Lorenz, Jessica; Schuldt, Carsten; Kaes, Josef; Smith, David

Cells employ multiple cross-linkers with very different properties. Studies of the entire phase space, however, were infeasible since they were restricted to naturally occurring cross-linkers. These components cannot be controllably varied and differ in many parameters. We resolve this limitation by forming artificial actin cross-linkers, which can be controllably varied. The basic building block is DNA enabling a well-defined length variation. DNA can be attached to actin binding peptides with known binding affinities. We used bulk rheology to investigate mechanical properties of these networks. We were able to reproduce mechanical features of actin networks cross-linked by fascin by using a short version of our artificial complex with a high binding affinity. Additionally, we were able to resemble findings for the cross-linker alpha-actinin by employing a long cross-linker with a low binding affinity. Between these natural limits we investigated three different cross-linker lengths each with two different binding affinities. With these controlled variations we are able to precisely screen the phase space of cross-linked actin networks by changing only one specific parameter and not the entire set of properties as in the case of naturally occurring cross-linking complexes.

Probe Into the Influence of Crosslinking on CO2 Permeation of Membranes

NASA Astrophysics Data System (ADS)

Li, Jinghui; Chen, Zhuo; Umar, Ahmad; Liu, Yang; Shang, Ying; Zhang, Xiaokai; Wang, Yao

2017-01-01

Crosslinking is an effective way to fabricate high-selective CO2 separation membranes because of its unique crosslinking framework. Thus, it is essentially significant to study the influence of crosslinking degree on the permeation selectivities of CO2. Herein, we report a successful and facile synthesis of a series of polyethylene oxide (PEO)-based diblock copolymers (BCP) incorporated with an unique UV-crosslinkable chalcone unit using Reversible Addition-Fragmentation Chain Transfer Polymerization (RAFT) process. The membranes of as-prepared BCPs show superior carbon dioxide (CO2) separation properties as compared to nitrogen (N2) after UV-crosslinking. Importantly, the influence of different proportions of crosslinked chalcone on CO2 selectivities was systematically investigated, which revealed that CO2 selectivities increased obviously with the enhancement of chalcone fractions within a certain limit. Further, the CO2 selectivities of block copolymer with the best block proportion was studied by varying the crosslinking time which confirmed that the high crosslinking degree exhibited a better CO2/N2 (αCO2/N2) selectivities. A possible mechanism model revealing that the crosslinking degree played a key role in the gas separation process was also proposed.

Mechanistic insights into a hydrate contribution to the Paleocene-Eocene carbon cycle perturbation from coupled thermohydraulic simulations

NASA Astrophysics Data System (ADS)

Minshull, T. A.; Marín-Moreno, H.; Armstrong McKay, D. I.; Wilson, P. A.

2016-08-01

During the Paleocene-Eocene Thermal Maximum (PETM), the carbon isotopic signature (δ13C) of surface carbon-bearing phases decreased abruptly by at least 2.5 to 3.0‰. This carbon isotope excursion (CIE) has been attributed to widespread methane hydrate dissociation in response to rapid ocean warming. We ran a thermohydraulic modeling code to simulate hydrate dissociation due to ocean warming for various PETM scenarios. Our results show that hydrate dissociation in response to such warming can be rapid but suggest that methane release to the ocean is modest and delayed by hundreds to thousands of years after the onset of dissociation, limiting the potential for positive feedback from emission-induced warming. In all of our simulations at least half of the dissociated hydrate methane remains beneath the seabed, suggesting that the pre-PETM hydrate inventory needed to account for all of the CIE is at least double that required for isotopic mass balance.

High-coverage quantitative proteomics using amine-specific isotopic labeling.

PubMed

Melanson, Jeremy E; Avery, Steven L; Pinto, Devanand M

2006-08-01

Peptide dimethylation with isotopically coded formaldehydes was evaluated as a potential alternative to techniques such as the iTRAQ method for comparative proteomics. The isotopic labeling strategy and custom-designed protein quantitation software were tested using protein standards and then applied to measure proteins levels associated with Alzheimer's disease (AD). The method provided high accuracy (10% error), precision (14% RSD) and coverage (70%) when applied to the analysis of a standard solution of BSA by LC-MS/MS. The technique was then applied to measure protein abundance levels in brain tissue afflicted with AD relative to normal brain tissue. 2-D LC-MS analysis identified 548 unique proteins (p<0.05). Of these, 349 were quantified with two or more peptides that met the statistical criteria used in this study. Several classes of proteins exhibited significant changes in abundance. For example, elevated levels of antioxidant proteins and decreased levels of mitochondrial electron transport proteins were observed. The results demonstrate the utility of the labeling method for high-throughput quantitative analysis.

Electron Scattering from MERCURY-198 and Mercury -204.

NASA Astrophysics Data System (ADS)

Laksanaboonsong, Jarungsaeng

This experiment is the first electron scattering study on mercury isotopes. Electron scattering from ^{198}Hg and ^{204 }Hg has been performed at the NIKHEF-K Medium Energy Accelerator. Measured cross sections cover an effective momentum transfer range from 0.4 to 2.9 fm^ {-1}. Elastic cross sections were determined for scattering from both isotopes. Cross section for inelastic excitations in ^{198}Hg below 3 MeV were also determined. Measured cross sections were fit using DWBA phase shift codes to determine coefficients for Fourier-Bessel expansions of ground state and transition charge densities. Differences between the ground state charge densities of the two isotopes reveal the effect of the polarization of the proton core in response to the addition of neutrons. Spin and parity of several excited states of ^{198}Hg were determined. Extracted transition densities of these states show their predominantly collective nature. Charge densities for members of the ground state rotational band were compared with axially symmetric Hartree-Fock and geometrical model predictions.

Rovibrational bound states of SO2 isotopologues. II: Total angular momentum J = 11-20

NASA Astrophysics Data System (ADS)

Kumar, Praveen; Poirier, Bill

2015-11-01

In a two-part series, the rovibrational bound states of SO2 are investigated in comprehensive detail, for all four stable sulfur isotopes 32-34,36S. All low-lying rovibrational energy levels-both permutation-symmetry-allowed and not allowed-are computed, for all values of total angular momentum in the range J = 0-20. The calculations have carried out using the ScalIT suite of parallel codes. The present study (Paper II) examines the J = 11-20 rovibrational levels, providing symmetry and rovibrational labels for every computed state, relying on a new lambda-doublet splitting technique to make completely unambiguous assignments. Isotope shifts are analyzed, as is the validity of ;J-shifting; as a predictor of rotational fine structure. Among other ramifications, this work will facilitate understanding of mass-independent fractionation of sulfur isotopes (S-MIF) observed in the Archean rock record-particularly as this may have arisen from self shielding. S-MIF, in turn is highly relevant in the broader context of understanding the ;oxygen revolution;.

Rovibrational bound states of SO2 isotopologues. I: Total angular momentum J = 0-10

NASA Astrophysics Data System (ADS)

Kumar, Praveen; Ellis, Joseph; Poirier, Bill

2015-04-01

Isotopic variation of the rovibrational bound states of SO2 for the four stable sulfur isotopes 32-34,36S is investigated in comprehensive detail. In a two-part series, we compute the low-lying energy levels for all values of total angular momentum in the range J = 0-20. All rovibrational levels are computed, to an extremely high level of numerical convergence. The calculations have been carried out using the ScalIT suite of parallel codes. The present study (Paper I) examines the J = 0-10 rovibrational levels, providing unambiguous symmetry and rovibrational label assignments for each computed state. The calculated vibrational energy levels exhibit very good agreement with previously reported experimental and theoretical data. Rovibrational energy levels, calculated without any Coriolis approximations, are reported here for the first time. Among other potential ramifications, this data will facilitate understanding of the origin of mass-independent fractionation of sulfur isotopes in the Archean rock record-of great relevance for understanding the "oxygen revolution".

Effect of crosslink torsional stiffness on elastic behavior of semiflexible polymer networks

NASA Astrophysics Data System (ADS)

Hatami-Marbini, H.

2018-02-01

Networks of semiflexible filaments are building blocks of different biological and structural materials such as cytoskeleton and extracellular matrix. The mechanical response of these systems when subjected to an applied strain at zero temperature is often investigated numerically using networks composed of filaments, which are either rigidly welded or pinned together at their crosslinks. In the latter, filaments during deformation are free to rotate about their crosslinks while the relative angles between filaments remain constant in the former. The behavior of crosslinks in actual semiflexible networks is different than these idealized models and there exists only partial constraint on torques at crosslinks. The present work develops a numerical model in which two intersecting filaments are connected to each other by torsional springs with arbitrary stiffness. We show that fiber networks composed of rigid and freely rotating crosslinks are the limiting case of the present model. Furthermore, we characterize the effects of stiffness of crosslinks on effective Young's modulus of semiflexible networks as a function of filament flexibility and crosslink density. The effective Young's modulus is determined as a function of the mechanical properties of crosslinks and is found to vanish for networks composed of very weak torsional springs. Independent of the stiffness of crosslinks, it is found that the effective Young's modulus is a function of fiber flexibility and crosslink density. In low density networks, filaments primarily bend and the effective Young's modulus is much lower than the affine estimate. With increasing filament bending stiffness and/or crosslink density, the mechanical behavior of the networks becomes more affine and the stretching of filaments depicts itself as the dominant mode of deformation. The torsional stiffness of the crosslinks significantly affects the effective Young's modulus of the semiflexible random fiber networks.

In vitro cross-linking of elastin peptides and molecular characterization of the resultant biomaterials.

PubMed

Heinz, Andrea; Ruttkies, Christoph K H; Jahreis, Günther; Schräder, Christoph U; Wichapong, Kanin; Sippl, Wolfgang; Keeley, Fred W; Neubert, Reinhard H H; Schmelzer, Christian E H

2013-04-01

Elastin is a vital protein and the major component of elastic fibers which provides resilience to many vertebrate tissues. Elastin's structure and function are influenced by extensive cross-linking, however, the cross-linking pattern is still unknown. Small peptides containing reactive allysine residues based on sequences of cross-linking domains of human elastin were incubated in vitro to form cross-links characteristic of mature elastin. The resultant insoluble polymeric biomaterials were studied by scanning electron microscopy. Both, the supernatants of the samples and the insoluble polymers, after digestion with pancreatic elastase or trypsin, were furthermore comprehensively characterized on the molecular level using MALDI-TOF/TOF mass spectrometry. MS(2) data was used to develop the software PolyLinX, which is able to sequence not only linear and bifunctionally cross-linked peptides, but for the first time also tri- and tetrafunctionally cross-linked species. Thus, it was possible to identify intra- and intermolecular cross-links including allysine aldols, dehydrolysinonorleucines and dehydromerodesmosines. The formation of the tetrafunctional cross-link desmosine or isodesmosine was unexpected, however, could be confirmed by tandem mass spectrometry and molecular dynamics simulations. The study demonstrated that it is possible to produce biopolymers containing polyfunctional cross-links characteristic of mature elastin from small elastin peptides. MALDI-TOF/TOF mass spectrometry and the newly developed software PolyLinX proved suitable for sequencing of native cross-links in proteolytic digests of elastin-like biomaterials. The study provides important insight into the formation of native elastin cross-links and represents a considerable step towards the characterization of the complex cross-linking pattern of mature elastin. Copyright © 2013 Elsevier B.V. All rights reserved.

Influence of different crosslinking treatments on the physical properties of collagen membranes.

PubMed

Charulatha, V; Rajaram, A

2003-02-01

The physical properties of collagen-based biomaterials are profoundly influenced by the method and extent of crosslinking. In this study, the influence of various crosslinking treatments on the physical properties of reconstituted collagen membranes was assessed. Five crosslinking agents viz., GTA, DMS, DTBP, a combination of DMS and GTA and acyl azide method were used to stabilize collagen matrices. Crosslinking density, swelling ratio, thermo-mechanical properties, stress-strain characteristics and resistance to collagenase digestion were determined to evaluate the physical properties of crosslinked matrices. GTA treatment induced the maximum number of crosslinks (13) while DMS treatment induced the minimum (7). Of the two diimidoesters (DMS and DTBP), DTBP was a more effective crosslinking agent due to the presence of disulphide bonds in the DTBP crosslinks. T(s) for DTBP and DMS crosslinked collagen were 80 degrees C and 70 degrees C, and their HIT values were 5.4 and 2.85MN/m(2), respectively. Low concentration of GTA (0.01%) increased the crosslinking density of an already crosslinked matrix (DMS treated matrix) from 7 to 12. Lowest fracture energy was observed for the acyl azide treated matrix (0.61MJ/m(3)) while the highest was observed for the GTA treated matrix (1.97MJ/m(3)). The tensile strength of GTA treated matrix was maximum (12.4MPa) and that of acyl azide treated matrix was minimum (7.2MPa). GTA, DTBP and acyl azide treated matrices were equally resistant to collagenase degradation with approximately 6% solubilization after 5h while the DMS treated was least stable with 52.4% solubilization after the same time period. The spatial orientation of amino acid side chain residues on collagen plays an important role in determining the crosslinking density and consequent physical properties of the collagen matrix.

Metal isotope coded profiling of organic ligands by mass spectrometry in aquatic environments

NASA Astrophysics Data System (ADS)

Wichard, Thomas; Deicke, Michael; Frieder Mohr, Jan; Klein, Martin

2017-04-01

Metal isotope coded profiling (MICP) introduces a universal discovery platform for metal chelating natural products that act as metallophores, ion buffers or sequestering agents. The detection of cation and oxoanion complexing ligands is facilitated by the identification of unique isotopic signatures created by the application of isotopically pure metals. We present a targeted analysis of low-molecular-weight organic ligands based on fast UHPLC-ESI-MS measurements. Replacement of, for example, natural iron or molybdenum with isotopically pure 54Fe/58Fe (ratio 1:1) or 95Mo/98Mo (ratio 1:1) causes easily detectable unique isotopic signatures in the mass spectra of potential metal-complexing ligands. This can be achieved under laboratory conditions not only in growth media, but also by spiking directly aqueous samples or solid-phase extracts. Importantly, as the relative affinity of the metallophores for e.g., Mo or Fe is dependent on the pH, all experiments needs to be conducted under pH-controlled conditions. The improved ionization efficiency of some metal complexes helps to enhance the signal-to-noise ratio compared to the free ligand at the same chromatographic conditions. The methodology does not necessarily depend on HR-ESI-MS measurements (e.g., Q-Exactive Orbitrap) and can be applied to any mass spectrometer. With MICP, two birds can be killed with one stone: (i) the identification of metallophores (e.g., siderophores, molybdophores) for metal uptake by any organism and (ii) organic ligands which solely work as metal buffer in dissolved organic matter (DOM). We currently address following two main research lines: First, DOM has often been used as a proxy for bio-productivity in terms of a carbon source; however, the specific impact of DOM as a "metal buffer" for biological processes is still under-investigated. Upon the administration of individual isotopes or isotopic pairs, for example, 54Fe/58Fe, 63Cu/65Cu, 66Zn/68Zn, or 95Mo/98Mo and subsequent measurements by mass spectrometry, organic ligands can be identified that contribute potentially to the regulation of bioavailability and toxicity of metals in the water column. Secondly, metal acquisition by ligand exchange processes is vital for macroalgae-bacteria interactions. Both alga and bacteria contribute to the "soup of organic ligands" which potentially increases the bioavailability of metals due to various ligand exchanges with DOM. In particular, we will outline the analytical process resulting in the identification of ligands in the chemosphere of the marine macroalga Ulva (Chlorophyta) and its associated bacteria. In summary, the identification of metal organic ligands in natural samples will pave the way for understanding the organic ligand-mediated metal acquisition shuttled from DOM to alga. (References: Wichard T. (2016) Front. Mar. Sci. 3:131; Deicke M., Mohr J.M., Wichard T. (2014) Analyst, 139, 6096-6099)

PCP METHODOLOGY FOR DETERMINING DOSE RATES FOR SMALL GRAM QUANTITIES IN SHIPPING PACKAGINGS

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

Nathan, S.

The Small Gram Quantity (SGQ) concept is based on the understanding that small amounts of hazardous materials, in this case radioactive materials, are significantly less hazardous than large amounts of the same materials. This study describes a methodology designed to estimate an SGQ for several neutron and gamma emitting isotopes that can be shipped in a package compliant with 10 CFR Part 71 external radiation level limits regulations. These regulations require packaging for the shipment of radioactive materials perform, under both normal and accident conditions, the essential functions of material containment, subcriticality, and maintain external radiation levels within regulatory limits.more » 10 CFR 71.33(b)(1)(2)&(3) state radioactive and fissile materials must be identified and their maximum quantity, chemical and physical forms be included in an application. Furthermore, the U.S. Federal Regulations require application contain an evaluation demonstrating the package (i.e., the packaging and its contents) satisfies the external radiation standards for all packages (10 CFR 71.31(2), 71.35(a), & 71.47). By placing the contents in a He leak-tight containment vessel, and limiting the mass to ensure subcriticality, the first two essential functions are readily met. Some isotopes emit sufficiently strong photon radiation that small amounts of material can yield a large external dose rate. Quantifying of the dose rate for a proposed content is a challenging issue for the SGQ approach. It is essential to quantify external radiation levels from several common gamma and neutron sources that can be safely placed in a specific packaging, to ensure compliance with federal regulations. The Packaging Certification Program (PCP) Methodology for Determining Dose Rate for Small Gram Quantities in Shipping Packagings described in this report provides bounding mass limits for a set of proposed SGQ isotopes. Methodology calculations were performed to estimate external radiation levels for the 9977 shipping package using the MCNP radiation transport code to develop a set of response multipliers (Green's functions) for 'dose per particle' for each neutron and photon spectral group. The source spectrum for each isotope generated using the ORIGEN-S and RASTA computer codes was folded with the response multipliers to generate the dose rate per gram of each isotope in the 9977 shipping package and its associated shielded containers. The maximum amount of a single isotope that could be shipped within the regulatory limits contained in 10 CFR 71.47 for dose rate at the surface of the package is determined. If a package contains a mixture of isotopes, the acceptability for shipment can be determined by a sum of fractions approach. Furthermore, the results of this analysis can be easily extended to additional radioisotopes by simply evaluating the neutron and/or photon spectra of those isotopes and folding the spectral data with the Green's functions provided.« less

DNA cross-linking by dehydromonocrotaline lacks apparent base sequence preference.

PubMed

Rieben, W Kurt; Coulombe, Roger A

2004-12-01

Pyrrolizidine alkaloids (PAs) are ubiquitous plant toxins, many of which, upon oxidation by hepatic mixed-function oxidases, become reactive bifunctional pyrrolic electrophiles that form DNA-DNA and DNA-protein cross-links. The anti-mitotic, toxic, and carcinogenic action of PAs is thought to be caused, at least in part, by these cross-links. We wished to determine whether the activated PA pyrrole dehydromonocrotaline (DHMO) exhibits base sequence preferences when cross-linked to a set of model duplex poly A-T 14-mer oligonucleotides with varying internal and/or end 5'-d(CG), 5'-d(GC), 5'-d(TA), 5'-d(CGCG), or 5'-d(GCGC) sequences. DHMO-DNA cross-links were assessed by electrophoretic mobility shift assay (EMSA) of 32P endlabeled oligonucleotides and by HPLC analysis of cross-linked DNAs enzymatically digested to their constituent deoxynucleosides. The degree of DNA cross-links depended upon the concentration of the pyrrole, but not on the base sequence of the oligonucleotide target. Likewise, HPLC chromatograms of cross-linked and digested DNAs showed no discernible sequence preference for any nucleotide. Added glutathione, tyrosine, cysteine, and aspartic acid, but not phenylalanine, threonine, serine, lysine, or methionine competed with DNA as alternate nucleophiles for cross-linking by DHMO. From these data it appears that DHMO exhibits no strong base preference when forming cross-links with DNA, and that some cellular nucleophiles can inhibit DNA cross-link formation.

Cross-Link Guided Molecular Modeling with ROSETTA

PubMed Central

Leitner, Alexander; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars

2013-01-01

Chemical cross-links identified by mass spectrometry generate distance restraints that reveal low-resolution structural information on proteins and protein complexes. The technology to reliably generate such data has become mature and robust enough to shift the focus to the question of how these distance restraints can be best integrated into molecular modeling calculations. Here, we introduce three workflows for incorporating distance restraints generated by chemical cross-linking and mass spectrometry into ROSETTA protocols for comparative and de novo modeling and protein-protein docking. We demonstrate that the cross-link validation and visualization software Xwalk facilitates successful cross-link data integration. Besides the protocols we introduce XLdb, a database of chemical cross-links from 14 different publications with 506 intra-protein and 62 inter-protein cross-links, where each cross-link can be mapped on an experimental structure from the Protein Data Bank. Finally, we demonstrate on a protein-protein docking reference data set the impact of virtual cross-links on protein docking calculations and show that an inter-protein cross-link can reduce on average the RMSD of a docking prediction by 5.0 Å. The methods and results presented here provide guidelines for the effective integration of chemical cross-link data in molecular modeling calculations and should advance the structural analysis of particularly large and transient protein complexes via hybrid structural biology methods. PMID:24069194

Study of components and statistical reaction mechanism in simulation of nuclear process for optimized production of {sup 64}Cu and {sup 67}Ga medical radioisotopes using TALYS, EMPIRE and LISE++ nuclear reaction and evaporation codes

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

Nasrabadi, M. N., E-mail: mnnasrabadi@ast.ui.ac.ir; Sepiani, M.

2015-03-30

Production of medical radioisotopes is one of the most important tasks in the field of nuclear technology. These radioactive isotopes are mainly produced through variety nuclear process. In this research, excitation functions and nuclear reaction mechanisms are studied for simulation of production of these radioisotopes in the TALYS, EMPIRE and LISE++ reaction codes, then parameters and different models of nuclear level density as one of the most important components in statistical reaction models are adjusted for optimum production of desired radioactive yields.

Study of components and statistical reaction mechanism in simulation of nuclear process for optimized production of 64Cu and 67Ga medical radioisotopes using TALYS, EMPIRE and LISE++ nuclear reaction and evaporation codes

NASA Astrophysics Data System (ADS)

Nasrabadi, M. N.; Sepiani, M.

2015-03-01

Production of medical radioisotopes is one of the most important tasks in the field of nuclear technology. These radioactive isotopes are mainly produced through variety nuclear process. In this research, excitation functions and nuclear reaction mechanisms are studied for simulation of production of these radioisotopes in the TALYS, EMPIRE & LISE++ reaction codes, then parameters and different models of nuclear level density as one of the most important components in statistical reaction models are adjusted for optimum production of desired radioactive yields.

Study of Reactive Melt Processing Behavior of Externally Plasticized Cellulose Acetate in Presence of Isocyanate

PubMed Central

Erdmann, Rafael; Kabasci, Stephan; Kurek, Joanna; Zepnik, Stefan

2014-01-01

Two types of externally plasticized cellulose acetate (CA) were chemically modified using 4,4'-methylene diphenyl diisocyanate (MDI) as crosslinking agent. Crosslinking was performed in the molten state by means of melt mixing in an internal mixer. The viscoelastic properties of the non-crosslinked, externally plasticized CA show typical temperature dependence, similar to conventional thermoplastics. A strong increase in storage modulus is observed with increasing crosslink density indicating that the crosslinked compounds exhibit predominately elastic response. The complex viscosity also increases considerably with increasing crosslink density and does not reach the typical Newtonian plateau at low radial frequencies any more. The viscoelastic properties correlate well with the data recorded online during reactive melt processing in the internal mixer. In comparison to the non-crosslinked CA, the crosslinked compounds show higher glass transition temperature, higher VICAT softening temperatures, improved thermal stability and lower plasticizer evaporation at evaluated temperatures. PMID:28788273

'Genipin' - the natural water soluble cross-linking agent and its importance in the modified drug delivery systems: an overview.

PubMed

Manickam, Balamurugan; Sreedharan, Rajesh; Elumalai, Manogaran

2014-01-01

One of the popular approaches in controlling drug delivery from the polymeric carriers is suitably achieved by the inclusion of crosslinking agents into the formulations at different concentrations. Nevertheless, addition of the chemical crosslinkers such as glutaraldehyde, formaldehyde etc, used in the drug delivery systems causes very serious cytotoxic reactions. These chemical crosslinking agents did not offer any significant advantageous effects when compared to the natural crosslinking agents for instance genipin, which is quite less toxic, biocompatible and offers very stable crosslinked products. Based on the earlier reports the safety of this particular natural crosslinker is very well established, since it has been widely used as a Chinese traditional medicine for long-time, isolated from fruits of the plant Gardenia jasminoides Ellis. This concise article largely portrayed the value of this unique natural crosslinker, utilized in controlling the drug delivery from the various formulations.

Study of Reactive Melt Processing Behavior of Externally Plasticized Cellulose Acetate in Presence of Isocyanate.

PubMed

Erdmann, Rafael; Kabasci, Stephan; Kurek, Joanna; Zepnik, Stefan

2014-12-04

Two types of externally plasticized cellulose acetate (CA) were chemically modified using 4,4'-methylene diphenyl diisocyanate (MDI) as crosslinking agent. Crosslinking was performed in the molten state by means of melt mixing in an internal mixer. The viscoelastic properties of the non-crosslinked, externally plasticized CA show typical temperature dependence, similar to conventional thermoplastics. A strong increase in storage modulus is observed with increasing crosslink density indicating that the crosslinked compounds exhibit predominately elastic response. The complex viscosity also increases considerably with increasing crosslink density and does not reach the typical Newtonian plateau at low radial frequencies any more. The viscoelastic properties correlate well with the data recorded online during reactive melt processing in the internal mixer. In comparison to the non-crosslinked CA, the crosslinked compounds show higher glass transition temperature, higher VICAT softening temperatures, improved thermal stability and lower plasticizer evaporation at evaluated temperatures.

Yield and Failure Behavior Investigated for Cross-Linked Phenolic Resins Using Molecular Dynamics

NASA Technical Reports Server (NTRS)

Monk, Joshua D.; Lawson, John W.

2016-01-01

Molecular dynamics simulations were conducted to fundamentally evaluate the yield and failure behavior of cross-linked phenolic resins at temperatures below the glass transition. Yield stress was investigated at various temperatures, strain rates, and degrees of cross-linking. The onset of non-linear behavior in the cross-linked phenolic structures was caused by localized irreversible molecular rearrangements through the rotation of methylene linkers followed by the formation or annihilation of neighboring hydrogen bonds. The yield stress results, with respect to temperature and strain rate, could be fit by existing models used to describe yield behavior of amorphous glasses. The degree of cross-linking only indirectly influences the maximum yield stress through its influence on glass transition temperature (Tg), however there is a strong relationship between the degree of cross-linking and the failure mechanism. Low cross-linked samples were able to separate through void formation, whereas the highly cross-linked structures exhibited bond scission.

Reactive transport modeling of Li isotope fractionation

NASA Astrophysics Data System (ADS)

Wanner, C.; Sonnenthal, E. L.

2013-12-01

The fractionation of Li isotopes has been used as a proxy for interaction processes between silicate rocks and any kind of fluids. In particular, Li isotope measurements are powerful because Li is almost exclusively found in silicate minerals. Moreover, the two stable Li isotopes, 6Li and 7Li, differ by 17% in mass introducing a large mass dependent isotope fractionation even at high temperature. Typical applications include Li isotope measurements along soil profiles and of river waters to track silicate weathering patterns and Li isotope measurements of geothermal wells and springs to assess water-rock interaction processes in geothermal systems. For this contribution we present a novel reactive transport modeling approach for the simulation of Li isotope fractionation using the code TOUGHREACT [1]. It is based on a 6Li-7Li solid solution approach similar to the one recently described for simulating Cr isotope fractionation [2]. Model applications include the simulation of granite weathering along a 1D flow path as well as the simulation of a column experiment related to an enhanced geothermal system. Results show that measured δ7Li values are mainly controlled by (i) the degree of interaction between Li bearing primary silicate mineral phases (e.g., micas, feldspars) and the corresponding fluid, (ii) the Li isotope fractionation factor during precipitation of secondary mineral phases (e.g., clays), (iii) the Li concentration in primary and secondary Li bearing mineral phases and (iv) the proportion of dissolved Li that adsorbs to negatively charged surfaces (e.g., clays, Fe/Al-hydroxides). To date, most of these parameters are not very well constrained. Reactive transport modeling thus currently has to rely on many assumptions. Nevertheless, such models are powerful because they are the only viable option if individual contributions of all potential processes on the resulting (i.e., measured) Li isotopic ratio have to be quantitatively assessed. Accordingly, we suggest performing more experimental work in conjunction with reactive transport modeling to better understand Li isotope fractionation processes and to obtain a better understanding of water rock interaction processes, eventually. [1] Xu, T., Spycher, N., Sonnenthal, E. L., Zhang, G., Zheng, L., Pruess, K. (2011), Comput. Geosci. 37, 763-774. [2] Wanner, C., Sonnenthal, E. L. (2013), Chem. Geol. 337, 88-98.

Inverted bulk-heterojunction solar cell with cross-linked hole-blocking layer

PubMed Central

Udum, Yasemin; Denk, Patrick; Adam, Getachew; Apaydin, Dogukan H.; Nevosad, Andreas; Teichert, Christian; S. White, Matthew.; S. Sariciftci, Niyazi.; Scharber, Markus C.

2014-01-01

We have developed a hole-blocking layer for bulk-heterojunction solar cells based on cross-linked polyethylenimine (PEI). We tested five different ether-based cross-linkers and found that all of them give comparable solar cell efficiencies. The initial idea that a cross-linked layer is more solvent resistant compared to a pristine PEI layer could not be confirmed. With and without cross-linking, the PEI layer sticks very well to the surface of the indium–tin–oxide electrode and cannot be removed by solvents used to process PEI or common organic semiconductors. The cross-linked PEI hole-blocking layer functions for multiple donor–acceptor blends. We found that using cross-linkers improves the reproducibility of the device fabrication process. PMID:24817837

Evaluation of different multidimensional LC-MS/MS pipelines for iTRAQ-based proteomic analysis of potato tubers in response to cold storage

USDA-ARS?s Scientific Manuscript database

Cold-induced sweetening in potato tubers is a costly problem for food industry. To systematically identify the proteins associated with this process, we employed a comparative proteomics approach using isobaric, stable isotope coded labels to compare the proteomes of potato tubers after 0 and 5 mont...

Simulation of HEAO 3 Background

DTIC Science & Technology

2007-01-01

i i o iipp i i o iinn VdE A NaEEf VdE A NaEEfprod ji ji j R where i is a stable isotope in volume V, ai is its fractional abundance, i the...National Nuclear Data Center (NNDC), Brookhaven National Laboratory, Brookhaven, NY. [10] W. Nelson et al., ”The EGS4 code system ”, SLAC-Report-265

Multiple tag labeling method for DNA sequencing

DOEpatents

Mathies, Richard A.; Huang, Xiaohua C.; Quesada, Mark A.

1995-01-01

A DNA sequencing method described which uses single lane or channel electrophoresis. Sequencing fragments are separated in said lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radio-isotope labels.

RADSOURCE. Volume 1, Part 1, A scaling factor prediction computer program technical manual and code validation: Final report

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

Vance, J.N.; Holderness, J.H.; James, D.W.

1992-12-01

Waste stream scaling factors based on sampling programs are vulnerable to one or more of the following factors: sample representativeness, analytic accuracy, and measurement sensitivity. As an alternative to sample analyses or as a verification of the sampling results, this project proposes the use of the RADSOURCE code, which accounts for the release of fuel-source radionuclides. Once the release rates of these nuclides from fuel are known, the code develops scaling factors for waste streams based on easily measured Cobalt-60 (Co-60) and Cesium-137 (Cs-137). The project team developed mathematical models to account for the appearance rate of 10CFR61 radionuclides inmore » reactor coolant. They based these models on the chemistry and nuclear physics of the radionuclides involved. Next, they incorporated the models into a computer code that calculates plant waste stream scaling factors based on reactor coolant gamma- isotopic data. Finally, the team performed special sampling at 17 reactors to validate the models in the RADSOURCE code.« less

Proteomic validation of protease drug targets: pharmacoproteomics of matrix metalloproteinase inhibitor drugs using isotope-coded affinity tag labelling and tandem mass spectrometry.

PubMed

Butler, G S; Overall, C M

2007-01-01

We illustrate the use of quantitative proteomics, namely isotope-coded affinity tag labelling and tandem mass spectrometry, to assess the targets and effects of the blockade of matrix metalloproteinases by an inhibitor drug in a breast cancer cell culture system. Treatment of MT1-MMP-transfected MDA-MB-231 cells with AG3340 (Prinomastat) directly affected the processing a multitude of matrix metalloproteinase substrates, and indirectly altered the expression of an array of other proteins with diverse functions. Therefore, broad spectrum blockade of MMPs has wide-ranging biological consequences. In this human breast cancer cell line, secreted substrates accumulated uncleaved in the conditioned medium and plasma membrane protein substrates were retained on the cell surface, due to reduced processing and shedding of these proteins (cell surface receptors, growth factors and bioactive molecules) to the medium in the presence of the matrix metalloproteinase inhibitor. Hence, proteomic investigation of drug-perturbed cellular proteomes can identify new protease substrates and at the same time provides valuable information for target validation, drug efficacy and potential side effects prior to commitment to clinical trials.

Bypass of a psoralen DNA interstrand cross-link by DNA polymerases beta, iota, and kappa in vitro

PubMed Central

Smith, Leigh A.; Makarova, Alena V.; Samson, Laura; Thiesen, Katherine E.; Dhar, Alok; Bessho, Tadayoshi

2012-01-01

Repair of DNA inter-strand cross-links in mammalian cells involves several biochemically distinctive processes, including the release of one of the cross-linked strands and translesion DNA synthesis (TLS). In this report, we investigated in vitro TLS activity of psoralen DNA inter-strand cross-link by three DNA repair polymerases, DNA polymerase beta, kappa and iota. DNA polymerase beta is capable of bypassing a psoralen cross-link with a low efficiency. Cell extracts prepared from DNA polymerase beta knockout mouse embryonic fibroblast showed a reduced bypass activity of the psoralen cross-link and purified DNA polymerase beta restored the bypass activity. In addition, DNA polymerase iota mis-incorporated thymine across the psoralen cross-link and DNA polymerase kappa extended these mis-paired primer ends, suggesting that DNA polymerase iota may serve as an inserter and DNA polymerase kappa may play a role as an extender in the repair of psoralen DNA inter-strand cross-links. The results demonstrated here indicate that multiple DNA polymerases could participate in TLS steps in mammalian DNA inter-strand cross-link repair. PMID:23106263

Anion exchange membranes based on terminally crosslinked methyl morpholinium-functionalized poly(arylene ether sulfone)s

NASA Astrophysics Data System (ADS)

Kwon, Sohyun; Rao, Anil H. N.; Kim, Tae-Hyun

2018-01-01

Azide-assisted terminal crosslinking of methyl morpholinium-functionalized poly(arylene ether sulfone) block copolymers yields products (xMM-PESs) suitable for use as anion exchange membranes. By combining the advantages of bulky morpholinium conductors and our unique polymer network crosslinked only at the termini of the polymer chains, we can produce AEMs that after the crosslinking show minimal loss in conductivity, yet with dramatically reduced water uptake. Terminal crosslinking also significantly increases the thermal, mechanical and chemical stability levels of the membranes. A high ion conductivity of 73.4 mS cm-1 and low water uptake of 26.1% at 80 °C are obtained for the crosslinked membrane with higher amount of hydrophilic composition, denoted as xMM-PES-1.5-1. In addition, the conductivity of the crosslinked xMM-PES-1.5-1 membrane exceeds that of its non-crosslinked counterpart (denoted as MM-PES-1.5-1) above 60 °C at 95% relative humidity because of its enhanced water retention capacity caused by the terminally-crosslinked structure.

Conventional Matrices Loaded Onto a Graphene Layer Enhances MALDI-TOF/TOF Signal: Its Application to Improve Detection of Phosphorylated Peptides

NASA Astrophysics Data System (ADS)

Rodríguez, Carlos E.; Palacios, Javier; Fajardo, Ignacio; Urdiales, José Luis; Le Guével, Xavier; Lozano, José; Sánchez-Jiménez, Francisca

2016-02-01

This is the first study where graphene is used as a MALDI adjuvant in combination with the traditional matrix α-cyano-4-hydroxycinnamic acid (CHCA) to improve the signal intensity of peptide samples. Use of this amended matrix not only leads to increased signals but also to a higher number of peaks detected in complex samples. Additionally, the use of graphene has a stabilizing effect that can also be exploited to improve the detection of easily cleavable molecules.

Biocompatible, Biodegradable, and Enzymatic-Cleavable MRI Contrast Agents for Early Detection of Bone Metastatic Breast cancer

DTIC Science & Technology

2013-04-01

metastasis from breast cancer. The proposed imaging agent is consist of bone targeting moiety of Asp8 and MRI imaging moiety of DOTA (Gd) with a cathepsin K...the Gd chelator of DOTA . Asp8 has a high affinity for bone mineral and has been used as bone-targeting moiety in molecular therapeutics.(1-6) The use...findings in literature.(4, 7, 17) To obtain imaging agents for MRI studies, the above mentioned peptides were allowed to react with DOTA -NHS

Thermally cleavable surfactants

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

McElhanon, James R; Simmons, Blake A; Zifer, Thomas

2009-11-24

Two new surfactant molecules are reported which contain thermally labile Diels-Alder adducts connecting the polar and non-polar sections of each molecule. The two surfactants possess identical non-polar dodecyl tail segments but exhibit different polar headgroups. The surfactants become soluble in water when anionic salts are formed through the deprotonation of the surfactant headgroups by the addition of potassium hydroxide. When either surfactant is exposed to temperature above about 60.degree. C., the retro Diels-Alder reaction occurs, yielding hydrophilic and hydrophobic fragments or the aqueous solutions of the surfactants subsequently exhibit loss of all surface-active behavior.

Thermally cleavable surfactants

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

McElhanon, James R; Simmons, Blake A; Zifer, Thomas

2009-09-29

Two new surfactant molecules are reported which contain thermally labile Diels-Alder adducts connecting the polar and non-polar sections of each molecule. The two surfactants possess identical non-polar dodecyl tail segments but exhibit different polar headgroups. The surfactants become soluble in water when anionic salts are formed through the deprotonation of the surfactant headgroups by the addition of potassium hydroxide. When either surfactant is exposed to temperature above about 60.degree. C., the retro Diels-Alder reaction occurs, yielding hydrophilic and hydrophobic fragments or the aqueous solutions of the surfactants subsequently exhibit loss of all surface-active behavior.

Thermally cleavable surfactants

DOEpatents

McElhanon, James R [Manteca, CA; Simmons, Blake A [San Francisco, CA; Zifer, Thomas [Manteca, CA; Jamison, Gregory M [Albuquerque, NM; Loy, Douglas A [Albuquerque, NM; Rahimian, Kamyar [Albuquerque, NM; Long, Timothy M [Urbana, IL; Wheeler, David R [Albuquerque, NM; Staiger, Chad L [Albuquerque, NM

2006-04-04

Two new surfactant molecules are reported which contain thermally labile Diels-Alder adducts connecting the polar and non-polar sections of each molecule. The two surfactants possess identical non-polar dodecyl tail segments but exhibit different polar headgroups. The surfactants become soluble in water when anionic salts are formed through the deprotonation of the surfactant headgroups by the addition of potassium hydroxide. When either surfactant is exposed to temperature above about 60.degree. C., the retro Diels-Alder reaction occurs, yielding hydrophilic and hydrophobic fragments and the aqueous solutions of the surfactants subsequently exhibit loss of all surface-active behavior.

Knockout and fragmentation reactions using a broad range of tin isotopes

NASA Astrophysics Data System (ADS)

Rodríguez-Sánchez, J. L.; Benlliure, J.; Bertulani, C. A.; Vargas, J.; Ayyad, Y.; Alvarez-Pol, H.; Atkinson, J.; Aumann, T.; Beceiro-Novo, S.; Boretzky, K.; Caamaño, M.; Casarejos, E.; Cortina-Gil, D.; Díaz-Cortes, J.; Fernández, P. Díaz; Estrade, A.; Geissel, H.; Kelić-Heil, A.; Litvinov, Yu. A.; Mostazo, M.; Paradela, C.; Pérez-Loureiro, D.; Pietri, S.; Prochazka, A.; Takechi, M.; Weick, H.; Winfield, J. S.

2017-09-01

Production cross sections of residual nuclei obtained by knockout and fragmentation reactions of different tin isotopes accelerated at 1 A GeV have been measured with the fragment separator (FRS) at GSI, Darmstadt. The new measurements are used to investigate the neutron-excess dependence of the neutron- and proton-knockout cross sections. These cross sections are compared to Glauber model calculations coupled to a nuclear de-excitation code in order to investigate the role of the remnant excitations. This bench marking shows an overestimation of the cross sections for the removal of deeply bound nucleons. A phenomenological increase in the excitation energy induced in the remnants produced in these cases allows us to reproduce the measured cross sections.

A high burnup model developed for the DIONISIO code

NASA Astrophysics Data System (ADS)

Soba, A.; Denis, A.; Romero, L.; Villarino, E.; Sardella, F.

2013-02-01

A group of subroutines, designed to extend the application range of the fuel performance code DIONISIO to high burn up, has recently been included in the code. The new calculation tools, which are tuned for UO2 fuels in LWR conditions, predict the radial distribution of power density, burnup, and concentration of diverse nuclides within the pellet. The balance equations of all the isotopes involved in the fission process are solved in a simplified manner, and the one-group effective cross sections of all of them are obtained as functions of the radial position in the pellet, burnup, and enrichment in 235U. In this work, the subroutines are described and the results of the simulations performed with DIONISIO are presented. The good agreement with the data provided in the FUMEX II/III NEA data bank can be easily recognized.

Determination of the δ34S of sulfate in water; RSIL lab code 1951

USGS Publications Warehouse

Revesz, Kinga; Qi, Haiping; Coplen, Tyler B.

2006-01-01

The purpose of the Reston Stable Isotope Laboratory (RSIL) lab code 1951 is to determine the δ(34S/32S), abbreviated as δ34S, of dissolved sulfate. Dissolved sulfate is collected in the field and precipitated with BaCl2 at pH 3 to 4 as BaSO4 in the laboratory. However, the dissolved organic sulfur (DOS) is oxidized to SO2, and the carbonate is acidified to CO2. Both are degassed from the water sample before the sulfate is precipitated. The precipitated BaSO4 is filtered and dried before introduction into an elemental analyzer (EA) Carlo Erba NC 2500. The EA is used to convert sulfur in a BaSO4 solid sample into SO2 gas, and the EA is connected to a continuous flow isotope-ratio mass spectrometer (CF-IRMS), which determines the differences in the isotope-amount ratios of stable sulfur isotopes (34S/32S) of the product SO2 gas. The combustion is quantitative; no isotopic fractionation is involved. Samples are placed in a tin capsule and loaded into the Costech Zero Blank Autosampler of the EA. Under computer control, samples are dropped into a heated tube reaction tube that combines the oxidation and reduction reactions. The combustion takes place in a helium atmosphere containing an excess of oxygen gas at the oxidation zone at the top of the reaction tube. Combustion products are transported by a helium carrier through the reduction zone at the bottom of the reaction tube to remove excess oxygen and through a separate drying tube to remove any water. The gas-phase products, mainly CO2, N2, and SO2, are separated by a gas chromatograph. The gas is then introduced into the isotope-ratio mass spectrometer (IRMS) through a Finnigan MAT (now Thermo Scientific) ConFlo II interface, which also is used to inject SO2 reference gas and helium for sample dilution. The IRMS is a Thermo Scientific Delta V Plus CF-IRMS. It has a universal triple collector with two wide cups and a narrow cup in the middle. It is capable of measuring mass/charge (m/z) 64 and 66 simultaneously. The ion beams from SO2 are as follows: m/z 64 = SO2 = 32S16O16O; m/z 66 = SO2 = 34S16O16O primarily.

Microbes encapsulated within crosslinkable polymers

DOEpatents

Chidambaram, Devicharan; Liu, Ying; Rafailovich, Miriam H

2013-02-05

The invention relates to porous films comprising crosslinked electrospun hydrogel fibers. Viable microbes are encapsulated within the crosslinked electrospun hydrogel fibers. The crosslinked electrospun hydrogel fibers are water insoluble and permeable. The invention also relates to methods of making and using such porous films.

Lignin-derived thermoplastic co-polymers and methods of preparation

DOEpatents

Naskar, Amit K.; Saito, Tomonori; Pickel, Joseph M.; Baker, Frederick S.; Eberle, Claude Clifford; Norris, Robert E.; Mielenz, Jonathan Richard

2014-06-10

The present invention relates to a crosslinked lignin comprising a lignin structure having methylene or ethylene linking groups therein crosslinking between phenyl ring carbon atoms, wherein said crosslinked lignin is crosslinked to an extent that it has a number-average molecular weight of at least 10,000 g/mol, is melt-processible, and has either a glass transition temperature of at least 100.degree. C., or is substantially soluble in a polar organic solvent or aqueous alkaline solution. Thermoplastic copolymers containing the crosslinked lignin are also described. Methods for producing the crosslinked lignin and thermoplastic copolymers are also described.

Studies of the permeation properties of glomerular basement membrane: cross-linking renders glomerular basement membrane permeable to protein.

PubMed

Walton, H A; Byrne, J; Robinson, G B

1992-03-20

Cross-linking glomerular basement membrane (GBM) has been shown to render it more permeable to protein. Isolated pig GBM was cross-linked with dimethylmalonimidate which reacts selectively with lysine epsilon-NH2 groups or with glutaraldehyde, a less selective cross-linking agent. Studies of the ultrafiltration properties of these materials in vitro using cytochrome c, myoglobin, bovine serum albumin and immunoglobulin showed that cross-linking had markedly increased solvent and protein fluxes as compared with native membranes particularly at higher pressures. Filtration studies with serum demonstrated that the cross-linked membranes were more permeable to serum proteins. Thickness measurements under pressure indicated that cross-linked membrane was less compressed than native membrane as pressure was increased. Pore theory did not provide a suitable model for analysis of the results, but analysis of the results using the fibre-matrix hypothesis indicated that cross-linking had the effect of bundling together the fibres (type IV collagen) in the GBM matrix. The effect of cross-linking on filtration could be explained by a combination of contraction of the membrane, fibre bundling and increased rigidity compared with native membrane. Cross-linking of GBM might lead to long-term damage of the glomerular capillary wall in nephritis, so promoting proteinuria.

Acetylation and glycation of fibrinogen in vitro occur at specific lysine residues in a concentration dependent manner: A mass spectrometric and isotope labeling study

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

Svensson, Jan, E-mail: jan.svensson@ki.se; Karolinska Institutet, Department of Clinical Sciences, Danderyd Hospital, SE-182 88 Stockholm; Bergman, Ann-Charlotte

Highlights: Black-Right-Pointing-Pointer Fibrinogen was incubated in vitro with glucose or aspirin. Black-Right-Pointing-Pointer Acetylations and glycations were found at twelve lysine sites by mass spectrometry. Black-Right-Pointing-Pointer The labeling by aspirin and glucose occurred dose-dependently. Black-Right-Pointing-Pointer No competition between glucose and aspirin for binding to fibrinogen was found. -- Abstract: Aspirin may exert part of its antithrombotic effects through platelet-independent mechanisms. Diabetes is a condition in which the beneficial effects of aspirin are less prominent or absent - a phenomenon called 'aspirin resistance'. We investigated whether acetylation and glycation occur at specific sites in fibrinogen and if competition between glucose and aspirinmore » in binding to fibrinogen occurs. Our hypothesis was that such competition might be one explanation to 'aspirin resistance' in diabetes. After incubation of fibrinogen in vitro with aspirin (0.8 mM, 24 h) or glucose (100 mM, 5-10 days), we found 12 modified sites with mass spectrometric techniques. Acetylations in the {alpha}-chain: {alpha}K191, {alpha}K208, {alpha}K224, {alpha}K429, {alpha}K457, {alpha}K539, {alpha}K562, in the {beta}-chain: {beta}K233, and in the {gamma}-chain: {gamma}K170 and {gamma}K273. Glycations were found at {beta}K133 and {gamma}K75, alternatively {gamma}K85. Notably, the lysine 539 is a site involved in FXIII-mediated cross-linking of fibrin. With isotope labeling in vitro, using [{sup 14}C-acetyl]salicylic acid and [{sup 14}C]glucose, a labeling of 0.013-0.084 and 0.12-0.5 mol of acetylated and glycated adduct/mol fibrinogen, respectively, was found for clinically (12.9-100 {mu}M aspirin) and physiologically (2-8 mM glucose) relevant plasma concentrations. No competition between acetylation and glycation could be demonstrated. Thus, fibrinogen is acetylated at several lysine residues, some of which are involved in the cross-linking of fibrinogen. This may mechanistically explain why aspirin facilitates fibrin degradation. We find no support for the idea that glycation of fibrin(ogen) interferes with acetylation of fibrinogen.« less

Sensitizing capacity and allergenicity of enzymatically cross-linked sodium caseinate in comparison to sodium caseinate in a mouse model for cow's milk allergy.

PubMed

van Esch, Betty C A M; Gros-van Hest, Marjan; Westerbeek, Hans; Garssen, Johan

2013-03-27

A transglutaminase cross-linked caseinate was designed for use in dairy products to increase the viscosity of food matrices. The difference in structure of cross-linked caseinate might have implications for the risk of developing cow's milk allergy. The sensitizing capacity and the allergenicity (the potency to induce an allergic effector response) of cross-linked sodium caseinate was investigated using a mouse model for cow's milk allergy. Mice were orally sensitized with cross-linked caseinate or caseinate using cholera toxin as adjuvant. Anaphylactic shock reactions, change in body temperature, acute allergic skin response, caseinate-, cross-linked caseinate-IgE and mMCP-1 concentrations were determined after challenge with cross-linked caseinate or caseinate. Sensitization with cross-linked caseinate did not result in anaphylactic shock symptoms, drop in body temperature or release of serum mMCP-1. A tendency toward decreased casein-specific IgE levels was observed. The allergenicity did not differ between both products. These results indicate that in already caseinate-sensitized mice, cross-linked caseinate did not provoke more pronounced allergenic reactions compared to sodium caseinate. On top of that, reduced sensitization to cross-linked caseinate was observed. Cross-linked caseinate might therefore be an interesting new dietary concept for humans at risk for food allergy although more mechanistic studies and clinical trials are needed for validation. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Development of Parallel Computing Framework to Enhance Radiation Transport Code Capabilities for Rare Isotope Beam Facility Design

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

Kostin, Mikhail; Mokhov, Nikolai; Niita, Koji

A parallel computing framework has been developed to use with general-purpose radiation transport codes. The framework was implemented as a C++ module that uses MPI for message passing. It is intended to be used with older radiation transport codes implemented in Fortran77, Fortran 90 or C. The module is significantly independent of radiation transport codes it can be used with, and is connected to the codes by means of a number of interface functions. The framework was developed and tested in conjunction with the MARS15 code. It is possible to use it with other codes such as PHITS, FLUKA andmore » MCNP after certain adjustments. Besides the parallel computing functionality, the framework offers a checkpoint facility that allows restarting calculations with a saved checkpoint file. The checkpoint facility can be used in single process calculations as well as in the parallel regime. The framework corrects some of the known problems with the scheduling and load balancing found in the original implementations of the parallel computing functionality in MARS15 and PHITS. The framework can be used efficiently on homogeneous systems and networks of workstations, where the interference from the other users is possible.« less

J-integral fracture toughness and tearing modulus measurement of radiation cross-linked UHMWPE.

PubMed

Gomoll, A; Wanich, T; Bellare, A

2002-11-01

Radiation and chemical cross-linking of medical grade ultrahigh molecular weight polyethylene (UHMWPE) has recently been utilized in an effort to improve wear performance of total joint replacement components. However, reductions in mechanical properties with cross-linking are cause for concern regarding the use of cross-linked UHMWPE for high-stress applications such as in total knee replacement prostheses. In this study, the fracture behavior of radiation cross-linked UHMWPE was compared to that of uncross-linked UHMWPE. The Rice and Sorensen model that utilizes mechanical parameters obtained from uniaxial tensile and compact tension tests was used to calculate the steady state J-integral fracture toughness, Jss, for radiation cross-linked UHMWPE. Jss decreased monotonically with increase in radiation dose. UHMWPE exhibited tough, ductile tearing behavior with stable crack growth when it was cross-linked using a gamma radiation dose of 0-50 kGy. However, in cross-linked UHMWPE irradiated to a dose of 100 and 200 kGy, unstable fracture occurred spontaneously upon attaining the initial crack driving force, J1c. This indicates that a high degree of cross-linking is less desirable for high-stress applications in orthopaedic implants. However, a substantial increase in J1c, even at a low degree of cross-linking, suggests that a low degree of cross-linking may be beneficial for resistance to delamination and catastrophic failure, both of which require an initiation step for the fracture to propagate in the material. This mechanical test should, however, be considered along with fatigue tests and joint simulator testing before determination of an appropriate amount of cross-linking for total joint replacement prostheses that experience high stresses.

Quantitative Evaluation of Collagen Crosslinks and Corresponding Tensile Mechanical Properties in Mouse Cervical Tissue during Normal Pregnancy

PubMed Central

Yoshida, Kyoko; Jiang, Hongfeng; Kim, MiJung; Vink, Joy; Cremers, Serge; Paik, David; Wapner, Ronald; Mahendroo, Mala; Myers, Kristin

2014-01-01

The changes in the mechanical integrity of the cervix during pregnancy have implications for a successful delivery. Cervical collagens are known to remodel extensively in mice with progressing gestation leading to a soft cervix at term. During this process, mature crosslinked collagens are hypothesized to be replaced with immature less crosslinked collagens to facilitate cervical softening and ripening. To determine the mechanical role of collagen crosslinks during normal mouse cervical remodeling, tensile load-to-break tests were conducted for the following time points: nonpregnant (NP), gestation day (d) 6, 12, 15, 18 and 24 hr postpartum (PP) of the 19-day gestation period. Immature crosslinks (HLNL and DHLNL) and mature crosslinks (DPD and PYD) were measured using ultra performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS). There were no significant changes in the total immature crosslink density (HLNL+DHLNL mol per collagen mol) throughout normal mouse gestation (range: 0.31–0.49). Total mature crosslink density (PYD+DPD mol per collagen mol) decreased significantly in early softening from d6 to d15 (d6: 0.17, d12: 0.097, d15: 0.026) and did not decrease with further gestation. The maturity ratio (total mature to total immature crosslinks) significantly decreased in early softening from d6 to d15 (d6: 0.2, d15: 0.074). All of the measured crosslinks correlated significantly with a measure of tissue stiffness and strength, with the exception of the immature crosslink HLNL. This data provides quantitative evidence to support the hypothesis that as mature crosslinked collagens decline, they are replaced by immature collagens to facilitate increased tissue compliance in the early softening period from d6 to d15. PMID:25397407

Di-isodityrosine is the intermolecular cross-link of isodityrosine-rich extensin analogs cross-linked in vitro.

PubMed

Held, Michael A; Tan, Li; Kamyab, Abdolreza; Hare, Michael; Shpak, Elena; Kieliszewski, Marcia J

2004-12-31

Extensins are cell wall hydroxyproline-rich glycoproteins that form covalent networks putatively involving tyrosyl and lysyl residues in cross-links catalyzed by one or more extensin peroxidases. The precise cross-links remain to be chemically identified both as network components in muro and as enzymic products generated in vitro with native extensin monomers as substrates. However, some extensin monomers contain variations within their putative cross-linking motifs that complicate cross-link identification. Other simpler extensins are recalcitrant to isolation including the ubiquitous P3-type extensin whose major repetitive motif, Hyp)(4)-Ser-Hyp-Ser-(Hyp)(4)-Tyr-Tyr-Tyr-Lys, is of particular interest, not least because its Tyr-Tyr-Tyr intramolecular isodityrosine cross-link motifs are also putative candidates for further intermolecular cross-linking to form di-isodityrosine. Therefore, we designed a set of extensin analogs encoding tandem repeats of the P3 motif, including Tyr --> Phe and Lys --> Leu variations. Expression of these P3 analogs in Nicotiana tabacum cells yielded glycoproteins with virtually all Pro residues hydroxylated and subsequently arabinosylated and with likely galactosylated Ser residues. This was consistent with earlier analyses of P3 glycopeptides isolated from cell wall digests and the predictions of the Hyp contiguity hypothesis. The tyrosine-rich P3 analogs also contained isodityrosine, formed in vivo. Significantly, these isodityrosine-containing analogs were further cross-linked in vitro by an extensin peroxidase to form the tetra-tyrosine intermolecular cross-link amino acid di-isodityrosine. This is the first identification of an inter-molecular cross-link amino acid in an extensin module and corroborates earlier suggestions that di-isodityrosine represents one mechanism for cross-linking extensins in muro.

The Importance of Non-accessible Crosslinks and Solvent Accessible Surface Distance in Modeling Proteins with Restraints From Crosslinking Mass Spectrometry*

PubMed Central

Bullock, Joshua Matthew Allen; Schwab, Jannik; Thalassinos, Konstantinos; Topf, Maya

2016-01-01

Crosslinking mass spectrometry (XL-MS) is becoming an increasingly popular technique for modeling protein monomers and complexes. The distance restraints garnered from these experiments can be used alone or as part of an integrative modeling approach, incorporating data from many sources. However, modeling practices are varied and the difference in their usefulness is not clear. Here, we develop a new scoring procedure for models based on crosslink data—Matched and Nonaccessible Crosslink score (MNXL). We compare its performance with that of other commonly-used scoring functions (Number of Violations and Sum of Violation Distances) on a benchmark of 14 protein domains, each with 300 corresponding models (at various levels of quality) and associated, previously published, experimental crosslinks (XLdb). The distances between crosslinked lysines are calculated either as Euclidean distances or Solvent Accessible Surface Distances (SASD) using a newly-developed method (Jwalk). MNXL takes into account whether a crosslink is nonaccessible, i.e. an experimentally observed crosslink has no corresponding SASD in a model due to buried lysines. This metric alone is shown to have a significant impact on modeling performance and is a concept that is not considered at present if only Euclidean distances are used. Additionally, a comparison between modeling with SASD or Euclidean distance shows that SASD is superior, even when factoring out the effect of the nonaccessible crosslinks. Our benchmarking also shows that MNXL outperforms the other tested scoring functions in terms of precision and correlation to Cα-RMSD from the crystal structure. We finally test the MNXL at different levels of crosslink recovery (i.e. the percentage of crosslinks experimentally observed out of all theoretical ones) and set a target recovery of ∼20% after which the performance plateaus. PMID:27150526

Laser crosslinking of E. coli RNA polymerase and T7 DNA.

PubMed Central

Harrison, C A; Turner, D H; Hinkle, D C

1982-01-01

The first photochemical crosslinking of a protein to a nucleic acid using laser excitation is reported. A single, 120 mJ, 20 ns pulse at 248 nm crosslinks about 10% of bound E. coli RNA polymerase to T7 DNA under the conditions studied. The crosslinking yield depends on mercaptoethanol concentration, and is a linear function of laser intensity. The protein subunits crosslinked to DNA are beta, beta' and sigma. PMID:7045809

Molecular and macro-scale analysis of enzyme-crosslinked silk hydrogels for rational biomaterial design.

PubMed

McGill, Meghan; Coburn, Jeannine M; Partlow, Benjamin P; Mu, Xuan; Kaplan, David L

2017-11-01

Silk fibroin-based hydrogels have exciting applications in tissue engineering and therapeutic molecule delivery; however, their utility is dependent on their diffusive properties. The present study describes a molecular and macro-scale investigation of enzymatically-crosslinked silk fibroin hydrogels, and demonstrates that these systems have tunable crosslink density and diffusivity. We developed a liquid chromatography tandem mass spectroscopy (LC-MS/MS) method to assess the quantity and order of covalent tyrosine crosslinks in the hydrogels. This analysis revealed between 28 and 56% conversion of tyrosine to dityrosine, which was dependent on the silk concentration and reactant concentration. The crosslink density was then correlated with storage modulus, revealing that both crosslinking and protein concentration influenced the mechanical properties of the hydrogels. The diffusive properties of the bulk material were studied by fluorescence recovery after photobleaching (FRAP), which revealed a non-linear relationship between silk concentration and diffusivity. As a result of this work, a model for synthesizing hydrogels with known crosslink densities and diffusive properties has been established, enabling the rational design of silk hydrogels for biomedical applications. Hydrogels from naturally-derived silk polymers offer versitile opportunities in the biomedical field, however, their design has largely been an empirical process. We present a fundamental study of the crosslink density, storage modulus, and diffusion behavior of enzymatically-crosslinked silk hydrogels to better inform scaffold design. These studies revealed unexpected non-linear trends in the crosslink density and diffusivity of silk hydrogels with respect to protein concentration and crosslink reagent concentration. This work demonstrates the tunable diffusivity and crosslinking in silk fibroin hydrogels, and enables the rational design of biomaterials. Further, the characterization methods presented have applications for other materials with dityrosine crosslinks, which are found in nature as post-translational modificaitons, as well as in engineered matrices such as tyramine-substituted hyaluronic acid and recombinant resilin. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

A Single Molecular Diels-Alder Crosslinker for Achieving Recyclable Cross-Linked Polymers.

PubMed

Chen, Shengli; Wang, Fenfen; Peng, Yongjin; Chen, Tiehong; Wu, Qiang; Sun, Pingchuan

2015-09-01

A triol-functional crosslinker combining the thermoreversible properties of Diels-Alder (DA) adducts in one molecule is designed, synthesized, and used as an ideal substitute of a traditional crosslinker to prepare thermal recyclable cross-linked polyurethanes with excellent mechanical properties and recyclability in a very simple and efficient way. The recycle property of these materials achieved by the DA/retro-DA reaction at a suitable temperature is verified by differential scanning calorimetry and in situ variable temperature solid-state NMR experiments during the cyclic heating and cooling processes. The thermal recyclability and remending ability of the bulk polyurethanes is demonstrated by three polymer processing methods, including hot-press molding, injection molding, and solution casting. It is notable that all the recycled cross-linked polymers display nearly invariable elongation/stress at break compared to the as-synthesized samples. Further end-group functionalization of this single molecular DA crosslinker provides the potential in preparing a wide range of recyclable cross-linked polymers. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Porous Cross-Linked Polyimide Networks

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B. (Inventor); Guo, Haiquan (Inventor)

2015-01-01

Porous cross-linked polyimide networks are provided. The networks comprise an anhydride end-capped polyamic acid oligomer. The oligomer (i) comprises a repeating unit of a dianhydride and a diamine and terminal anhydride groups, (ii) has an average degree of polymerization of 10 to 50, (iii) has been cross-linked via a cross-linking agent, comprising three or more amine groups, at a balanced stoichiometry of the amine groups to the terminal anhydride groups, and (iv) has been chemically imidized to yield the porous cross-linked polyimide network. Also provided are porous cross-linked polyimide aerogels comprising a cross-linked and imidized anhydride end-capped polyamic acid oligomer, wherein the oligomer comprises a repeating unit of a dianhydride and a diamine, and the aerogel has a density of 0.10 to 0.333 g/cm.sup.3 and a Young's modulus of 1.7 to 102 MPa. Also provided are thin films comprising aerogels, and methods of making porous cross-linked polyimide networks.

Cross-linking of type I collagen with microbial transglutaminase: identification of cross-linking sites.

PubMed

Stachel, Ines; Schwarzenbolz, Uwe; Henle, Thomas; Meyer, Michael

2010-03-08

Collagen is a popular biomaterial. To deal with its lack of thermal stability and its weak resistance to proteolytic degradation, collagen-based materials are stabilized via different cross-linking procedures. Regarding the potential toxicity of residual cross-linking agents, enzyme-mediated cross-linking would provide an alternative and nontoxic method for collagen stabilization. The results of this study show that type I collagen is a substrate for mTG. However, epsilon-(gamma-glutamyl)lysine cross-links are only incorporated at elevated temperatures when the protein is partially or completely denatured. A maximum number of 5.4 cross-links per collagen monomer were found for heat-denatured collagen. Labeling with the primary amine monodansylcadaverine revealed that at least half of the cross-links are located within the triple helical region of the collagen molecule. Because the triple helix is highly ordered in its native state, this finding might explain why the glutamine residues are inaccessible for mTG under nondenaturing conditions.

A Systematic Evaluation of Collagen Crosslinks in the Human Cervix

PubMed Central

Zork, Noelia M; Myers, Kristin Marie; Yoshida, Ms. Kyoko; Cremers, Serge; Jiang, Hongfeng; Ananth, Cande V; Wapner, Ronald; Kitajewski, Jan; Vink, Joy

2014-01-01

Objective The mechanical strength of the cervix relies on crosslinking of the tissue’s collagen network. Clinically, the internal os is functionally distinct from the external os. We sought to detect specific collagen crosslinks in human cervical tissue and determine if crosslink profiles were similar at the internal and external os. Study Design Transverse slices of cervical tissue were obtained at the internal and external os from 13 non-pregnant, premenopausal women undergoing a benign hysterectomy. To understand how crosslinks were distributed throughout the entire cervix and at the internal and external os, biopsies were obtained from three circumferential zones in four quadrants from each slice. Biopsies were pulverized, lyophilized, reduced with sodium borohydride, hydrolyzed with hydrochloric acid and reconstituted in heptafluorobutyric acid buffer. Hydroxyproline was measured by ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS), converted to total collagen, and normalized by dry weight. Collagen crosslinks pyridinoline (PYD), deoxypyridinoline (DPD), dihydroxylysinonorleucine (DHLNL), and the nonenzymatic advanced glycation end product pentosidine [PEN] were measured by UPLC-ESI-MS/MS and reported as crosslink density ratio (crosslink:total collagen). Generalized estimated equation analysis was used to compare results between the internal and external os and to compare quadrants and zones within slices from the internal and external os to determine if crosslink profiles were similar. Results 592 samples from 13 patients were analyzed. Collagen crosslinks are detectable in the human cervix by UPLC-ESI-MS/MS. When comparing all samples from the internal and external os, similar levels of collagen content, PYD, DHLNL and DPD were found but PEN density was higher at the external os (0.005 vs 0.004, P=0.001). When comparing all internal os samples, significant heterogeneity was found in collagen content and crosslink densities across zones and quadrants. The external os exhibited heterogeneity only across zones. Conclusion Collagen crosslinks (PYD, DPD, DHLNL, and PEN) are detectable by UPLC-ESI-MS/MS in the human cervix. The internal os exhibits significant collagen crosslink heterogeneity compared to the external os. Further studies are needed to evaluate how collagen crosslink heterogeneity correlates to the mechanical strength and function of the human cervix. PMID:25281365

Probing structures of large protein complexes using zero-length cross-linking.

PubMed

Rivera-Santiago, Roland F; Sriswasdi, Sira; Harper, Sandra L; Speicher, David W

2015-11-01

Structural mass spectrometry (MS) is a field with growing applicability for addressing complex biophysical questions regarding proteins and protein complexes. One of the major structural MS approaches involves the use of chemical cross-linking coupled with MS analysis (CX-MS) to identify proximal sites within macromolecules. Identified cross-linked sites can be used to probe novel protein-protein interactions or the derived distance constraints can be used to verify and refine molecular models. This review focuses on recent advances of "zero-length" cross-linking. Zero-length cross-linking reagents do not add any atoms to the cross-linked species due to the lack of a spacer arm. This provides a major advantage in the form of providing more precise distance constraints as the cross-linkable groups must be within salt bridge distances in order to react. However, identification of cross-linked peptides using these reagents presents unique challenges. We discuss recent efforts by our group to minimize these challenges by using multiple cycles of LC-MS/MS analysis and software specifically developed and optimized for identification of zero-length cross-linked peptides. Representative data utilizing our current protocol are presented and discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

Crosslinked polybenzimidazoles containing branching structure as membrane materials with excellent cell performance and durability for fuel cell applications

NASA Astrophysics Data System (ADS)

Hu, Meishao; Ni, Jiangpeng; Zhang, Boping; Neelakandan, Sivasubramaniyan; Wang, Lei

2018-06-01

Crosslinking is an effective method to improve the properties of high temperature proton exchange membranes based on polybenzimidazole. However, the compact structure of crosslinked polybenzimidazole hinders the phosphoric acid absorption of the membranes, resulting in a relatively poor fuel cell performance. Recently, we find that branched polymers can absorb more phosphoric acid with a larger free volume, but suffer from deteriorated mechanical strength. In this work, a new method is proposed to obtain excellent over-all properties of high temperature proton exchange membranes. A series of crosslinked polybenzimidazoles containing branching structure as membrane materials are successfully prepared for the first time. Compared with conventional crosslinked membranes, these crosslinked polybenzimidazole membranes containing branching structure exhibit a higher phosphoric acid doping level and proton conductivity, improved durability, lower swelling rate and comparable mechanical strength. In particular, the fuel cell base on the crosslinked and branched membrane with a 10% ratio of crosslinker in non-humidified hydrogen/air at 160 °C achieves a power density of 404 mW cm-2. The results indicate that the combination of crosslinking and branching is an effective approach to improve the properties of polybenzimidazole membrane materials.

Crosslinking of Chitosan with Dialdehyde Derivatives of Nucleosides and Nucleotides. Mechanism and Comparison with Glutaraldehyde.

PubMed

Mikhailov, Sergey N; Zakharova, Alexandra N; Drenichev, Mikhail S; Ershov, Andrey V; Kasatkina, Mariya A; Vladimirov, Leonid V; Novikov, Valentin V; Kildeeva, Natalia R

2016-01-01

In medical and pharmaceutical applications, chitosan is used as a component of hydrogels-macromolecular networks swollen in water. Chemical hydrogels are formed by covalent links between the crosslinking reagents and amino functionalities of chitosan. To date, the most commonly used chitosan crosslinkers are dialdehydes, such as glutaraldehyde (GA). We have developed novel GA like crosslinkers with additional functional groups-dialdehyde derivatives of uridine (oUrd) and nucleotides (oUMP and oAMP)-leading to chitosan-based biomaterials with new properties. The process of chitosan crosslinking was investigated in details and compared to crosslinking with GA. The rates of crosslinking with oUMP, oAMP, and GA were essentially the same, though much higher than in the case of oUrd. The remarkable difference in the crosslinking properties of nucleoside and nucleotide dialdehydes can be clearly attributed to the presence of the phosphate group in nucleotides that participates in the gelation process through ionic interactions with the amino groups of chitosan. Using NMR spectroscopy, we have not observed the formation of aldimine bonds. It can be concluded that the real number of crosslinks needed to cause gelation of chitosan chains may be less than 1%.

Microrheology of highly crosslinked microtubule networks is dominated by force-induced crosslinker unbinding

PubMed Central

Yang, Yali; Bai, Mo; Klug, William S.; Levine, Alex J.

2012-01-01

We determine the time- and force-dependent viscoelastic responses of reconstituted networks of microtubules that have been strongly crosslinked by biotin-streptavidin bonds. To measure the microscale viscoelasticity of such networks, we use a magnetic tweezers device to apply localized forces. At short time scales, the networks respond nonlinearly to applied force, with stiffening at small forces, followed by a reduction in the stiffening response at high forces, which we attribute to the force-induced unbinding of crosslinks. At long time scales, force-induced bond unbinding leads to local network rearrangement and significant bead creep. Interestingly, the network retains its elastic modulus even under conditions of significant plastic flow, suggesting that crosslinker breakage is balanced by the formation of new bonds. To better understand this effect, we developed a finite element model of such a stiff filament network with labile crosslinkers obeying force-dependent Bell model unbinding dynamics. The coexistence of dissipation, due to bond breakage, and the elastic recovery of the network is possible because each filament has many crosslinkers. Recovery can occur as long as a sufficient number of the original crosslinkers are preserved under the loading period. When these remaining original crosslinkers are broken, plastic flow results. PMID:23577042

Dehydration of an ethanol/water azeotrope through alginate-DNA membranes cross-linked with metal ions by pervaporation.

PubMed

Uragami, Tadashi; Banno, Masashi; Miyata, Takashi

2015-12-10

To obtain high dehydration membranes for an ethanol/water azeotrope, dried blend membranes prepared from mixtures of sodium alginate (Alg-Na) and sodium deoxyribonucleate (DNA-Na) were cross-linked by immersing in a methanol solution of CaCl2 or MaCl2. In the dehydration of an ethanol/water azeotropic mixture by pervaporation, the effects of immersion time in methanol solution of CaCl2 or MaCl2 on the permeation rate and water/ethanol selectivity through Alg-DNA/Ca(2+) and Alg-DNA/Mg(2+) cross-linked membranes were investigated. Alg-DNA/Mg(2+) cross-linked membrane immersed for 12h in methanol solution of MaCl2 exhibited the highest water/ethanol selectivity. This results from depressed swelling of the membranes by formation of a cross-linked structure. However, excess immersion in solution containing cross-linker led to an increase in the hydrophobicity of cross-linked membrane. Therefore, the water/ethanol selectivity of Alg-DNA/Mg(2+) cross-linked membranes with an excess immersion in cross-linking solution was lowered. The relationship between the structure of Alg-DNA/Ca(2+) and Alg-DNA/Mg(2+) cross-linked membranes and their permeation and separation characteristics during pervaporation of an ethanol/water azeotropic mixture is discussed in detail. Copyright © 2015 Elsevier Ltd. All rights reserved.

Genipin-crosslinked silk fibroin/hydroxybutyl chitosan nanofibrous scaffolds for tissue-engineering application.

PubMed

Zhang, Kuihua; Qian, Yongfang; Wang, Hongsheng; Fan, Linpeng; Huang, Chen; Yin, Anlin; Mo, Xiumei

2010-12-01

To improve water-resistant ability and mechanical properties of silk fibroin (SF)/hydroxybutyl chitosan (HBC) nanofibrous scaffolds for tissue-engineering applications, genipin, glutaraldehyde (GTA), and ethanol were used to crosslink electrospun nanofibers, respectively. The mechanical properties of nanofibrous scaffolds were obviously improved after 24 h of crosslinking with genipin and were superior to those crosslinked with GTA and ethanol for 24 h. SEM indicated that crosslinked nanofibers with genipin and GTA vapor had good water-resistant ability. Characterization of the microstructure (porosity and pore structure) demonstrated crosslinked nanofibrous scaffolds with genipin and GTA vapor had lager porosities and mean diameters than those with ethanol. Characterization of FTIR-ATR and (13)C NMR clarified both genipin and GTA acted as crosslinking agents for SF and HBC. Furthermore, genipin could induce SF conformation from random coil or α-helix to β-sheet. Although GTA could also successfully crosslink SF/HBC nanofibrous scaffolds, in long run, genipin maybe a better method due to lower cytotoxicity than GTA. Cell viability studies and wound-healing test in rats clarified that the genipin-crosslinked SF/HBC nanofibrous scaffolds had a good biocompatibility both in vitro and in vivo. These results suggested that genipin-crosslinked SF/HBC nanofibrous scaffolds might be potential candidates for wound dressing and tissue-engineering scaffolds. © 2010 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2010.

Crosslinked Polyamide

DOEpatents

Huang, Zhi H.; McDonald, William F.; Wright, Stacy C.; Taylor, Andrew C.

2002-06-04

A crosslinked polyamide material and a process for preparing the crosslinked polyamide material are disclosed. The crosslinked polyamide material comprises a crosslinked chemical combination of (1) a polyamide of the formula: ##STR1## wherein n is between about 50 and 10,000, wherein each R is between 1 and 50 carbon atoms alone and is optionally substituted with heteroatoms, oxygen, nitrogen, sulfur, or phosphorus and combinations thereof, wherein multiple of the R are in vertically aligned spaced relationship along a backbone forming the polyamide, and wherein two or more of the R contain an amino group; and (2) a crosslinking agent containing at least two functional groups capable of reacting with the amino groups of the polyamide. In one embodiment of the invention, the crosslinking agent is an aliphatic or aromatic isocyanate compound having 2 or more --N.dbd.C.dbd.O groups. In another embodiment of the invention, the crosslinking agent is an aliphatic aldehyde or aromatic aldehyde compound having 2 or more --CHO groups. In still another embodiment of the invention, the crosslinking agent is selected from a phosphine having the general formula (A).sub.2 P(B) and mixtures thereof, wherein A is hydroxyalkyl, and B is hydroxyalkyl, alkyl, or aryl. In yet another embodiment of the invention, the crosslinking agent is selected from the group consisting of epoxy resins having more than one epoxide group per molecule.

Chitosan membranes for tissue engineering: comparison of different crosslinkers.

PubMed

Ruini, F; Tonda-Turo, C; Chiono, V; Ciardelli, G

2015-11-03

Chitosan (CS), a derivative of the naturally occurring biopolymer chitin, is an attractive material for biomedical applications thanks to its biocompatibility, biodegradability, antibacterial properties and ability to enhance cell adhesion and growth compared to other biopolymers. However, the physical and mechanical stability of CS based materials in aqueous solutions is limited and crosslinking agents are required to increase CS performances in a biological environment. In this work, the effect of three highly-biocompatible crosslinkers as genipin (GP), γ-glycidoxypropyltrimethoxysilane (GPTMS), dibasic sodium phosphate (DSP) and a combination of GPTMS and DSP (GPTMS_DSP) on CS physicochemical, thermal, morphological, mechanical properties, swelling and degradation behavior was investigated. Infrared spectroscopy and thermogravimetric analyses confirmed the chemical reaction between CS and the different crosslinkers. CS wettability was enhanced when CS was DSP ionically crosslinked showing contact angle values of about 65° and exhibiting a higher swelling behavior compared to covalently crosslinked films. Moreover, all the crosslinking methods analyzed improved the stability of CS in aqueous media, showed model molecule permeation in time and increased the mechanical properties when compared with non-crosslinked films. The possibility to tailor the final properties of CS scaffolds through crosslinking is a key strategy in applying CS in different biomedical and tissue engineering applications. The obtained results reveal that the optimization of the crosslinking mechanism provides CS membrane properties required in different biomedical applications.

Effect of polyfunctional monomers on properties of radiation crosslinked EPDM/waste tire dust blend

NASA Astrophysics Data System (ADS)

Yasin, Tariq; Khan, Sajid; Nho, Young-Chang; Ahmad, Rashid

2012-04-01

In this study, waste tire dust is recycled as filler and blended with ethylene-propylene diene monomer (EPDM) rubber. Three different polyfuntional monomers (PFMs) are incorporated into the standard formulation and irradiated under electron beam at different doses up to maximum of 100 kGy. The combined effects of PFMs and absorbed dose on the physical properties of EPDM/WTD blend are measured and compared with sulfur crosslinked formulation. Thermogravimetric analysis showed that radiation developed better crosslinked network with higher thermal stability than sulfur crosslinked structure. The physical properties of radiation crosslinked blend are similar to the sulfur crosslinked blend. The absence of toxic chemicals/additives in radiation crosslinked blends made them an ideal candidate for many applications such as roof sealing sheets, water retention pond, playground mat, sealing profile for windows etc.

Determination of the δ2H and δ18O of soil water and water in plant matter; RSIL lab code 1700

USGS Publications Warehouse

Revesz, Kinga M.; Buck, Bryan; Coplen, Tyler B.

2012-01-01

The purpose of the Reston Stable Isotope Laboratory lab code 1700 is to determine the δ2H/1H), abbreviated as δ2H, and the δ18O/16O), abbreviated as δ18O, of soil water and water in plant matter. This method is based on the observation that water and toluene form an azeotropic mixture at 84.1 °C. This temperature is substantially lower than the boiling points of water (100 °C) and toluene (110 °C), but water and toluene are immiscible at ambient temperature. The water content of a soil or plant is determined by weighing, drying, and reweighing a small amount of sample. Sufficient sample to collect 3 to 5 milliliters of water after distillation is loaded into a distillation flask. Sufficient toluene is added so that the sample is immersed throughout the entire distillation to minimize evaporation of water, which would affect the δ2H and δ18O values. The mixture of sample and toluene is heated in a flask to its boiling point (84.1 °C) so that water from the sample and toluene can distill together into a specially designed collection funnel. The temperature of 84.1 °C is maintained until the water has been quantitatively transferred to the collection funnel, at which time the temperature is raised to the boiling point of the remaining component (toluene, 110 °C). The collection funnel is maintained at ambient temperature so that the sample water and toluene can be separated physically. After separation, the sample water is purified by addition of paraffin wax to the container with the sample water, capping the container, and heating to approximately 60 °C to melt the wax. Trace amounts of toluene will dissolve in the wax, purifying the sample water for isotopic analysis. The isotopic composition of the purified water is then determined by equilibration with gaseous hydrogen or carbon dioxide, followed by dual-inlet isotope-ratio mass spectrometry. Because laser-absorption spectrometry is sensitive to organic compounds, such as trace toluene remaining in water samples, water samples should be analyzed for isotopic composition only by mass spectrometry and not by laser-absorption spectrometry.

Ab initio simulations of bond breaking in sulfur crosslinked isoprene oligomer units

NASA Astrophysics Data System (ADS)

Gehrke, Sascha; Alznauer, Hans Tobias; Karimi-Varzaneh, Hossein Ali; Becker, Jörg August

2017-12-01

Sulfur crosslinked polyisoprene (rubber) is used in important material components for a number of technical tasks (e.g., in tires and sealings). If mechanical stress, like tension or shear, is applied on these material components, the sulfur crosslinks suffer from homolytic bond breaking. In this work, we have simulated the bond breaking mechanism of sulfur crosslinks between polyisoprene chains using Car-Parrinello molecular dynamic simulations and investigated the maximum forces which can be resisted by the crosslinks. Small model systems with crosslinks formed by chains of N = 1 to N = 6 sulfur atoms have been simulated with the slow growth-technique, known from the literature. The maximum force can be thereby determined from the calculated energies as a function of strain (elongation). The stability of the crosslink under strain is quantified in terms of the maximum force that can be resisted by the system before the crosslink breaks. As shown by our simulations, this maximum force decreases with the sulfur crosslink length N in a step like manner. Our findings indicate that in bridges with N = 1, 2, and 3 sulfur atoms predominantly, carbon-sulfur bonds break, while in crosslinks with N > 3, the breaking of a sulfur-sulfur bond is the dominant failure mechanism. The results are explained within a simple chemical bond model, which describes how the delocalization of the electrons in the generated radicals can lower their electronic energy and decrease the activation barriers. It is described which of the double bonds in the isoprene units are involved in the mechanochemistry of crosslinked rubber.

Computational investigation of kinetics of cross-linking reactions in proteins: importance in structure prediction.

PubMed

Bandyopadhyay, Pradipta; Kuntz, Irwin D

2009-01-01

The determination of protein structure using distance constraints is a new and promising field of study. One implementation involves attaching residues of a protein using a cross-linking agent, followed by protease digestion, analysis of the resulting peptides by mass spectroscopy, and finally sequence threading to detect the protein folds. In the present work, we carry out computational modeling of the kinetics of cross-linking reactions in proteins using the master equation approach. The rate constants of the cross-linking reactions are estimated using the pKas and the solvent-accessible surface areas of the residues involved. This model is tested with fibroblast growth factor (FGF) and cytochrome C. It is consistent with the initial experimental rate data for individual lysine residues for cytochrome C. Our model captures all observed cross-links for FGF and almost 90% of the observed cross-links for cytochrome C, although it also predicts cross-links that were not observed experimentally (false positives). However, the analysis of the false positive results is complicated by the fact that experimental detection of cross-links can be difficult and may depend on specific experimental conditions such as pH, ionic strength. Receiver operator characteristic plots showed that our model does a good job in predicting the observed cross-links. Molecular dynamics simulations showed that for cytochrome C, in general, the two lysines come closer for the observed cross-links as compared to the false positive ones. For FGF, no such clear pattern exists. The kinetic model and MD simulation can be used to study proposed cross-linking protocols.

Multiscale mechanical effects of native collagen cross-linking in tendon.

PubMed

Eekhoff, Jeremy D; Fang, Fei; Lake, Spencer P

2018-06-06

The hierarchical structure of tendon allows for attenuation of mechanical strain down decreasing length scales. While reorganization of collagen fibers accounts for microscale strain attenuation, cross-linking between collagen molecules contributes to deformation mechanisms at the fibrillar and molecular scales. Divalent and trivalent enzymatic cross-links form during the development of collagen fibrils through the enzymatic activity of lysyl oxidase (LOX). By establishing connections between telopeptidyl and triple-helical domains of adjacent molecules within collagen fibrils, these cross-links stiffen the fibrils by resisting intermolecular sliding. Ultimately, greater enzymatic cross-linking leads to less compliant and stronger tendon as a result of stiffer fibrils. In contrast, nonenzymatic cross-links such as glucosepane and pentosidine are not produced during development but slowly accumulate through glycation of collagen. Therefore, these cross-links are only expected to be present in significant quantities in advanced age, where there has been sufficient time for glycation to occur, and in diabetes, where the presence of more free sugar in the extracellular matrix increases the rate of glycation. Unlike enzymatic cross-links, current evidence suggests that nonenzymatic cross-links are at least partially isolated to the surface of collagen fibers. As a result, glycation has been proposed to primarily impact tendon mechanics by altering molecular interactions at the fiber interface, thereby diminishing sliding between fibers. Thus, increased nonenzymatic cross-linking decreases microscale strain attenuation and the viscous response of tendon. In conclusion, enzymatic and nonenzymatic collagen cross-links have demonstrable and distinct effects on the mechanical properties of tendon across different length scales.

21 CFR 177.1211 - Cross-linked polyacrylate copolymers.

Code of Federal Regulations, 2011 CFR

2011-04-01

... polyacrylate copolymers consist of: (1) The grafted copolymer of cross-linked sodium polyacrylate identified as... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Cross-linked polyacrylate copolymers. 177.1211... Basic Components of Single and Repeated Use Food Contact Surfaces § 177.1211 Cross-linked polyacrylate...

21 CFR 177.1211 - Cross-linked polyacrylate copolymers.

Code of Federal Regulations, 2010 CFR

2010-04-01

... polyacrylate copolymers consist of: (1) The grafted copolymer of cross-linked sodium polyacrylate identified as... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Cross-linked polyacrylate copolymers. 177.1211... Basic Components of Single and Repeated Use Food Contact Surfaces § 177.1211 Cross-linked polyacrylate...

Self-association of short-chain nonionic amphiphiles in binary and ternary systems: comparison between the cleavable ethylene glycol monobutyrate and its ether counterparts.

PubMed

Zhu, Ying; Fournial, Anne-Gaëlle; Molinier, Valérie; Azaroual, Nathalie; Vermeersch, Gaston; Aubry, Jean-Marie

2009-01-20

In the context of environmental concerns for the production of surface active species, the introduction of a carbonyl function into the skeleton of ethyleneglycol-derived solvo-surfactants is a way to access cleavable compounds with presumed enhanced biodegradability. Ethylene glycol monobutyrate (C(3)COE(1)) was synthesized and compared to its ether counterparts, ethylene glycol monopropyl (C(3)E(1)) and monobutyl ethers (C(4)E(1)), to assess the effect of the insertion of a carbonyl function in the skeleton of short-chain ethoxylated amphiphilic compounds. In aqueous solutions, the ester has intermediate behavior between that of the two ethers with regard to surface tension, solubilization of Me-naphtalene in water, and self-diffusion by PGSE NMR. In ternary systems, C(3)COE(1) and C(3)E(1) have the same optimal oil (EACN = 2.8), which is much more polar than that of C(4)E(1) (EACN = 8.5). With regard to the ability to form structured systems, the behavior in water does not differ significantly for the three compounds, and the transition between nonassociating solvents and amphiphilic solvents, sometimes called solvo-surfactants, is gradual. In ternary systems, however, only C(4)E(1) and C(3)COE(1) form a third phase near the optimal formulation, which tends to show that C(3)COE(1) possesses the minimum amphiphilicity to get a structuration. Self-diffusion NMR studies of the one-phase domains do not, however, allow us to distinguish between different degrees of organization in the three systems.

Effective modification of cell death-inducing intracellular peptides by means of a photo-cleavable peptide array-based screening system.

PubMed

Kozaki, Ikko; Shimizu, Kazunori; Honda, Hiroyuki

2017-08-01

Intracellular functional peptides that play a significant role inside cells have been receiving a lot of attention as regulators of cellular activity. Previously, we proposed a novel screening system for intracellular functional peptides; it combined a photo-cleavable peptide array system with cell-penetrating peptides (CPPs). Various peptides can be delivered into cells and intracellular functions of the peptides can be assayed by means of our system. The aim of the present study was to demonstrate that the proposed screening system can be used for assessing the intracellular activity of peptides. The cell death-inducing peptide (LNLISKLF) identified in a mitochondria-targeting domain (MTD) of the Noxa protein served as an original peptide sequence for screening of peptides with higher activity via modification of the peptide sequence. We obtained 4 peptides with higher activity, in which we substituted serine (S) at the fifth position with phenylalanine (F), valine (V), tryptophan (W), or tyrosine (Y). During analysis of the mechanism of action, the modified peptides induced an increase in intracellular calcium concentration, which was caused by the treatment with the original peptide. Higher capacity for cell death induction by the modified peptides may be caused by increased hydrophobicity or an increased number of aromatic residues. Thus, the present work suggests that the intracellular activity of peptides can be assessed using the proposed screening system. It could be used for identifying intracellular functional peptides with higher activity through comprehensive screening. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Magnetic-Fe/Fe(3)O(4)-nanoparticle-bound SN38 as carboxylesterase-cleavable prodrug for the delivery to tumors within monocytes/macrophages.

PubMed

Wang, Hongwang; Shrestha, Tej B; Basel, Matthew T; Dani, Raj Kumar; Seo, Gwi-Moon; Balivada, Sivasai; Pyle, Marla M; Prock, Heidy; Koper, Olga B; Thapa, Prem S; Moore, David; Li, Ping; Chikan, Viktor; Troyer, Deryl L; Bossmann, Stefan H

2012-01-01

The targeted delivery of therapeutics to the tumor site is highly desirable in cancer treatment, because it is capable of minimizing collateral damage. Herein, we report the synthesis of a nanoplatform, which is composed of a 15 ± 1 nm diameter core/shell Fe/Fe(3)O(4) magnetic nanoparticles (MNPs) and the topoisomerase I blocker SN38 bound to the surface of the MNPs via a carboxylesterase cleavable linker. This nanoplatform demonstrated high heating ability (SAR = 522 ± 40 W/g) in an AC-magnetic field. For the purpose of targeted delivery, this nanoplatform was loaded into tumor-homing double-stable RAW264.7 cells (mouse monocyte/macrophage-like cells (Mo/Ma)), which have been engineered to express intracellular carboxylesterase (InCE) upon addition of doxycycline by a Tet-On Advanced system. The nanoplatform was taken up efficiently by these tumor-homing cells. They showed low toxicity even at high nanoplatform concentration. SN38 was released successfully by switching on the Tet-On Advanced system. We have demonstrated that this nanoplatform can be potentially used for thermochemotherapy. We will be able to achieve the following goals: (1) Specifically deliver the SN38 prodrug and magnetic nanoparticles to the cancer site as the payload of tumor-homing double-stable RAW264.7 cells; (2) Release of chemotherapeutic SN38 at the cancer site by means of the self-containing Tet-On Advanced system; (3) Provide localized magnetic hyperthermia to enhance the cancer treatment, both by killing cancer cells through magnetic heating and by activating the immune system.

Identification and Characterization of Botulinum Neurotoxin A Substrate Binding Pockets and Their Re-Engineering for Human SNAP-23.

PubMed

Sikorra, Stefan; Litschko, Christa; Müller, Carina; Thiel, Nadine; Galli, Thierry; Eichner, Timo; Binz, Thomas

2016-01-29

Botulinum neurotoxins (BoNTs) are highly potent bacterial proteins that block neurotransmitter release at the neuromuscular junction by cleaving SNAREs (soluble N-ethyl maleimide sensitive factor attachment protein receptors). However, their serotype A (BoNT/A) that cleaves SNAP-25 (synaptosomal-associated protein of 25 kDa) has also been an established pharmaceutical for treatment of medical conditions that rely on hyperactivity of cholinergic nerve terminals for 25 years. The expansion of its use to a variety of further medical conditions associated with hypersecretion components is prevented partly because the involved SNARE isoforms are not cleaved. Therefore, we examined by mutational analyses the reason for the resistance of human SNAP-23, an isoform of SNAP-25. We show that replacement of 10 SNAP-23 residues with their SNAP-25 counterparts effects SNAP-25-like cleavability. Conversely, transfer of each of the replaced SNAP-23 residues to SNAP-25 drastically decreased the cleavability of SNAP-25. By means of the existing SNAP-25-toxin co-crystal structure, molecular dynamics simulations, and corroborative mutagenesis studies, the appropriate binding pockets for these residues in BoNT/A were characterized. Systematic mutagenesis of two major BoNT/A binding pockets was conducted in order to adapt these pockets to corresponding amino acids of human SNAP-23. Human SNAP-23 cleaving mutants were isolated using a newly established yeast-based screening system. This method may be useful for engineering novel BoNT/A pharmaceuticals for the treatment of diseases that rely on SNAP-23-mediated hypersecretion. Copyright © 2015 Elsevier Ltd. All rights reserved.

Nanoparticle bioconjugate for controlled cellular delivery of doxorubicin

NASA Astrophysics Data System (ADS)

Sangtani, Ajmeeta; Petryayeva, Eleonora; Wu, Miao; Susumu, Kimihiro; Oh, Eunkeu; Huston, Alan L.; Lasarte-Aragones, Guillermo; Medintz, Igor L.; Algar, W. Russ; Delehanty, James B.

2018-02-01

Nanoparticle (NP)-mediated drug delivery offers the potential to overcome limitations of systemic delivery, including the ability to specifically target cargo and control release of NP-associated drug cargo. Doxorubicin (DOX) is a widely used FDA-approved cancer therapeutic; however, multiple side effects limit its utility. Thus, there is wide interest in modulating toxicity after cell delivery. Our goal here was to realize a NP-based DOX-delivery system that can modulate drug toxicity by controlling the release kinetics of DOX from the surface of a hard NP carrier. To achieve this, we employed a quantum dot (QD) as a central scaffold which DOX was appended via three different peptidyl linkages (ester, disulfide, hydrazone) that are cleavable in response to various intracellular conditions. Attachment of a cell penetrating peptide (CPP) containing a positively charged polyarginine sequence facilitates endocytosis of the ensemble. Polyhistidine-driven metal affinity coordination was used to self-assemble both peptides to the QD surface, allowing for fine control over both the ratio of peptides attached to the QD as well as DOX dose delivered to cells. Microplate-based Förster resonance energy transfer assays confirmed the successful ratiometric assembly of the conjugates and functionality of the linkages. Cell delivery experiments and cytotoxicity assays were performed to compare the various cleavable linkages to a control peptide where DOX is attached through an amide bond. The role played by various attachment chemistries used in QD-peptide-drug assemblies and their implications for the rationale in design of NPbased constructs for drug delivery is described here.

Initial Results: An Ultra-Low-Background Germanium Crystal Array

DTIC Science & Technology

2010-09-01

data (focused on γ -γ coincidence signatures) (Smith et al., 2004) and the Multi- Isotope Coincidence Analysis code (MICA) (Warren et al., 2006). The...The follow-on “CASCADES” project aims to develop a multicoincidence data- analysis package and make robust fission-product demonstration measurements...sensitivity. This effort is focused on improving gamma analysis capabilities for nuclear detonation detection (NDD) applications, e.g., nuclear treaty

Prise en compte d'un couplage fin neutronique-thermique dans les calculs d'assemblage pour les reacteurs a eau pressurisee

NASA Astrophysics Data System (ADS)

Greiner, Nathan

Core simulations for Pressurized Water Reactors (PWR) is insured by a set of computer codes which allows, under certain assumptions, to approximate the physical quantities of interest, such as the effective multiplication factor or the power or temperature distributions. The neutronics calculation scheme relies on three great steps : -- the production of an isotopic cross-sections library ; -- the production of a reactor database through the lattice calculation ; -- the full-core calculation. In the lattice calculation, in which Boltzmann's transport equation is solved over an assembly geometry, the temperature distribution is uniform and constant during irradiation. This represents a set of approximations since, on the one hand, the temperature distribution in the assembly is not uniform (strong temperature gradients in the fuel pins, discrepancies between the fuel pins) and on the other hand, irradiation causes the thermal properties of the pins to change, which modifies the temperature distribution. Our work aims at implementing and introducing a neutronics-thermomechanics coupling into the lattice calculation to finely discretize the temperature distribution and to study its effects. To perform the study, CEA (Commissariat a l'Energie Atomique et aux Energies Alternatives) lattice code APOLLO2 was used for neutronics and EDF (Electricite De France) code C3THER was used for the thermal calculations. We show very small effects of the pin-scaled coupling when comparing the use of a temperature profile with the use of an uniform temperature over UOX-type and MOX-type fuels. We next investigate the thermal feedback using an assembly-scaled coupling taking into account the presence of large water gaps on an UOX-type assembly at burnup 0. We show the very small impact on the calculation of the hot spot factor. Finally, the coupling is introduced into the isotopic depletion calculation and we show that reactivity and isotopic number densities deviations remain small albeit not negligible for UOX-type and MOX-type assemblies. The specific behavior of gadolinium-stuffed fuel pins in an UO2Gd2O 3-type assembly is highlighted.

Thermally crosslinked polymeric compositions and methods of making the same

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

Koros, William John; Kratochvil, Adam Michal

2014-03-04

The various embodiments of the present disclosure relate generally to thermally crosslinked polymeric compositions and methods of making thermally crosslinked polymeric compositions. An embodiment of the present invention comprises a composition comprising: a first polymer comprising a first repeat unit, the first repeat unit comprising a carboxyl group, wherein the first polymer crosslinks to a second polymer formed from a second repeat unit, and wherein the first polymer crosslinks to the second polymer without formation of an ester group.

Study on the preparation process of cross-linked porous cassava starch

NASA Astrophysics Data System (ADS)

Yin, Xiulian; You, Qinghong; Wan, Miaomiao; Zhang, Xuejuan; Dai, Chunhua

2017-04-01

Using cassava starch as raw material, preparation process of porous cross-linked cassava starch was studied. Using TSTP as cross-linking agents, Orthogonal design was applied for the optimization of cross-linked porous starch preparation process. The results showed that the opitmal conditions of cross-linked porous cassava starch were as follows: reaction temperature 45°C, reaction time 20 h, 1% of the amount of the enzyme, the enzyme ratio of 1:5, pH 5.50, substrate concentration of 40%.

A new fast-cycling system for AMS at ANU

NASA Astrophysics Data System (ADS)

De Cesare, M.; Fifield, L. K.; Weisser, D. C.; Tsifakis, D.; Cooper, A.; Lobanov, N. R.; Tunningley, T. B.; Tims, S. G.; Wallner, A.

2015-10-01

In order to perform higher precision measurements, an upgrade of the ANU accelerator is underway. Fast switching times on the low-energy side, with maximum settling times of 30 ms, are achieved by holding the injector magnet field constant while changing the energy of the different isotopes by changing the pre-acceleration voltage after the ion source. Because ions of the different isotopes then have different energies before injection, it is necessary to adjust the strength and steering of the electrostatic quadrupole lens that focusses the beam before entry into the accelerator. First tests of the low-energy system will be reported. At the high energy end, a larger vacuum box in the analyzing magnet has been designed, manufactured and installed to allow the transport of differences in mass as large as 10% at constant terminal voltage. For the cases where more than one isotope must be transported to the detector an additional refinement is necessary. If the accelerator voltage is to be kept constant, then the trajectories of the different isotopes around both the analyzing and switching magnets must be modified. This will be achieved using bounced electrostatic steerers before and after the magnets. Simulations have been performed with the ion optic code COSY Infinity to determine the optimal positions and sizes of these steerers.

Fragment emission from the mass-symmetric reactions 58Fe,58Ni +58Fe,58Ni at Ebeam=30 MeV/nucleon

NASA Astrophysics Data System (ADS)

Ramakrishnan, E.; Johnston, H.; Gimeno-Nogues, F.; Rowland, D. J.; Laforest, R.; Lui, Y.-W.; Ferro, S.; Vasal, S.; Yennello, S. J.

1998-04-01

The mass-symmetric reactions 58Fe,58Ni +58Fe,58Ni were studied at a beam energy of Ebeam=30 MeV/nucleon in order to investigate the isospin dependence of fragment emission. Ratios of inclusive yields of isotopic fragments from hydrogen through nitrogen were extracted as a function of laboratory angle. A moving source analysis of the data indicates that at laboratory angles around 40° the yield of intermediate mass fragments (IMF's) beyond Z=3 is predominantly from a midrapidity source. The angular dependence of the relative yields of isotopes beyond Z=3 indicates that the IMF's at more central angles originate from a source which is more neutron deficient than the source responsible for fragments emitted at forward angles. The charge distributions and kinetic energy spectra of the IMF's at various laboratory angles were well reproduced by calculations employing a quantum molecular-dynamics code followed by a statistical multifragmentation model for generating fragments. The calculations indicate that the measured IMF's originate mainly from a single source. The isotopic composition of the emitted fragments is, however, not reproduced by the same calculation. The measured isotopic and isobaric ratios indicate an emitting source that is more neutron rich in comparison to the source predicted by model calculations.

Disk mass determination through CO isotopologues

NASA Astrophysics Data System (ADS)

Miotello, Anna; Kama, Mihkel; van Dishoeck, Ewine

2015-08-01

One of the key properties for understanding how disks evolve to planetary systems is their overall mass, combined with their surface density distribution. So far, virtually all disk mass determinations are based on observations of the millimeter continuum dust emission.To derive the total gas + dust disk mass from these data involves however several big assumptions. The alternative method is to directly derive the gas mass through the detection of carbon monoxide (CO) and its less abundant isotopologues. CO chemistry is well studied and easily implemented in chemical models, provided that isotope-selective processes are properly accounted for.CO isotope-selective photodissociation was implemented for the first time in a full physical-chemical code in Miotello et al. (2014). The main result is that if isotope-selective effects are not considered in the data analysis, disk masses can be underestimated by an order of magnitude or more. For example, the mass discrepancy found for the renowned TW Hya disk may be explained or at least mitigated by this implementation. In this poster, we present new results for a large grid of disk models. We derive mass correction factors for different disk, stellar and grain properties in order to account for isotope-selective effects in analyzing ALMA data of CO isotopologues (Miotello et al., in prep.).

IsoWeb: A Bayesian Isotope Mixing Model for Diet Analysis of the Whole Food Web

PubMed Central

Kadoya, Taku; Osada, Yutaka; Takimoto, Gaku

2012-01-01

Quantitative description of food webs provides fundamental information for the understanding of population, community, and ecosystem dynamics. Recently, stable isotope mixing models have been widely used to quantify dietary proportions of different food resources to a focal consumer. Here we propose a novel mixing model (IsoWeb) that estimates diet proportions of all consumers in a food web based on stable isotope information. IsoWeb requires a topological description of a food web, and stable isotope signatures of all consumers and resources in the web. A merit of IsoWeb is that it takes into account variation in trophic enrichment factors among different consumer-resource links. Sensitivity analysis using realistic hypothetical food webs suggests that IsoWeb is applicable to a wide variety of food webs differing in the number of species, connectance, sample size, and data variability. Sensitivity analysis based on real topological webs showed that IsoWeb can allow for a certain level of topological uncertainty in target food webs, including erroneously assuming false links, omission of existent links and species, and trophic aggregation into trophospecies. Moreover, using an illustrative application to a real food web, we demonstrated that IsoWeb can compare the plausibility of different candidate topologies for a focal web. These results suggest that IsoWeb provides a powerful tool to analyze food-web structure from stable isotope data. We provide R and BUGS codes to aid efficient applications of IsoWeb. PMID:22848427

Small-interfering RNA (siRNA)-based functional micro- and nanostructures for efficient and selective gene silencing.

PubMed

Lee, Soo Hyeon; Chung, Bong Hyun; Park, Tae Gwan; Nam, Yoon Sung; Mok, Hyejung

2012-07-17

Because of RNA's ability to encode structure and functional information, researchers have fabricated diverse geometric structures from this polymer at the micro- and nanoscale. With their tunable structures, rigidity, and biocompatibility, novel two-dimensional and three-dimensional RNA structures can serve as a fundamental platform for biomedical applications, including engineered tissues, biosensors, and drug delivery vehicles. The discovery of the potential of small-interfering RNA (siRNA) has underscored the applications of RNA-based micro- and nanostructures in medicine. Small-interfering RNA (siRNA), synthetic double-stranded RNA consisting of approximately 21 base pairs, suppresses problematic target genes in a sequence-specific manner via inherent RNA interference (RNAi) processing. As a result, siRNA offers a potential strategy for treatment of many human diseases. However, due to inefficient delivery to cells and off-target effects, the clinical application of therapeutic siRNA has been very challenging. To address these issues, researchers have studied a variety of nanocarrier systems for siRNA delivery. In this Account, we describe several strategies for efficient siRNA delivery and selective gene silencing. We took advantage of facile chemical conjugation and complementary hybridization to design novel siRNA-based micro- and nanostructures. Using chemical crosslinkers and hydrophobic/hydrophilic polymers at the end of siRNA, we produced various RNA-based structures, including siRNA block copolymers, micelles, linear siRNA homopolymers, and microhydrogels. Because of their increased charge density and flexibility compared with conventional siRNA, these micro- and nanostructures can form polyelectrolyte complexes with poorly charged and biocompatible cationic carriers that are both more condensed and more homogenous than the complexes formed in other carrier systems. In addition, the fabricated siRNA-based structures are linked by cleavable disulfide bonds for facile generation of original siRNA in the cytosol and for target-specific gene silencing. These newly developed siRNA-based structures greatly enhance intracellular uptake and gene silencing both in vitro and in vivo, making them promising biomaterials for siRNA therapeutics.

Polyvinyl alcohol membranes as alkaline battery separators

NASA Technical Reports Server (NTRS)

Sheibley, D. W.; Gonzalez-Sanabria, O.; Manzo, M. A.

1982-01-01

Polyvinly alcohol (PVA) cross-linked with aldehyde reagents yields membranes that demonstrate properties that make them suitable for use as alkaline battery separators. Film properties can be controlled by the choice of cross-linker, cross-link density and the method of cross-linking. Three methods of cross-linking and their effects on film properties are discussed. Film properties can also be modified by using a copolymer of vinyl alcohol and acrylic acid as the base for the separator and cross-linking it similarly to the PVA. Fillers can be incorporated into the films to further modify film properties. Results of separator screening tests and cell tests for several variations of PBA films are discussed.

Fabrication of patterned calcium cross-linked alginate hydrogel films and coatings through reductive cation exchange.

PubMed

Bruchet, Marion; Melman, Artem

2015-10-20

Calcium cross-linked alginate hydrogels are widely used in targeted drug delivery, tissue engineering, wound treatment, and other biomedical applications. We developed a method for preparing homogeneous alginate hydrogels cross-linked with Ca(2+) cations using reductive cation exchange in homogeneous iron(III) cross-linked alginate hydrogels. Treatment of iron(III) cross-linked alginate hydrogels with calcium salts and sodium ascorbate results in reduction of iron(III) cations to iron(II) that are instantaneously replaced with Ca(2+) cations, producing homogeneous ionically cross-linking hydrogels. Alternatively, the cation exchange can be performed by photochemical reduction in the presence of calcium chloride using a sacrificial photoreductant. This approach allows fabrication of patterned calcium alginate hydrogels through photochemical patterning of iron(III) cross-linked alginate hydrogel followed by the photochemical reductive exchange of iron cations to calcium. Copyright © 2015 Elsevier Ltd. All rights reserved.

Inability of keratinocytes lacking their specific transglutaminase to form cross-linked envelopes: absence of envelopes as a simple diagnostic test for lamellar ichthyosis.

PubMed

Jeon, S; Djian, P; Green, H

1998-01-20

Epidermal keratinocytes, late in their terminal differentiation, form cross-linked envelopes resistant to ionic detergent and reducing agent. Because the cross-linking process is catalyzed by the keratinocyte transglutaminase, the absence of active transglutaminase should result in failure of the keratinocyte to form a cross-linked envelope. Three keratinocyte strains bearing mutations in the keratinocyte transglutaminase were examined: two contained no detectable transglutaminase mRNA and none contained active enzyme. All three were unable to form cross-linked envelopes, either spontaneously in stratified cultures or upon induction with Ca2+. Although stratum corneum of normal humans and scales from patients with different ichthyotic diseases contain cross-linked envelopes, those from patients with transglutaminase-negative lamellar ichthyosis do not. Therefore, the disease due to the absence of transglutaminase may be readily distinguished from other ichthyotic disease by a simple test for cross-linked envelopes.

Synthesis and characterization of a novel hyaluronic acid hydrogel.

PubMed

Zhao, X

2006-01-01

Hyaluronic acid (hyaluronan, HA) has many medical applications as a biomaterial. To enhance its biostability, a novel hydrogel of cross-linked hyaluronic acid was prepared using a double cross-linking process, which involves building cross-linkages between hydroxyl group pairs and carboxyl group pairs. The present study explored a number of cross-linking processes in order to obtain different degrees of cross-linking, which were evaluated by the measurement of water absorption capacity as an index of the gel network density. To gain a better understanding of the stability of the gel, the chemical structure and particularly the rheological behaviour of the cross-linked HA, which included the influences of factors, such as degree of cross-linking, HA concentration and gel particle size, were investigated. The in vitro biostability against hyaluronidase and free radical degradation was tested to show that the cross-linked hydrogel had improved resistance to in vitro hyaluronidase and free radical degradation.

Characterization of the Deoxyguanosine–Lysine Cross-Link of Methylglyoxal

PubMed Central

2015-01-01

Methylglyoxal is a mutagenic bis-electrophile that is produced endogenously from carbohydrate precursors. Methylglyoxal has been reported to induce DNA–protein cross-links (DPCs) in vitro and in cultured cells. Previous work suggests that these cross-links are formed between guanine and either lysine or cysteine side chains. However, the chemical nature of the methylglyoxal induced DPC have not been determined. We have examined the reaction of methylglyoxal, deoxyguanosine (dGuo), and Nα-acetyllysine (AcLys) and determined the structure of the cross-link to be the N2-ethyl-1-carboxamide with the lysine side chain amino group (1). The cross-link was identified by mass spectrometry and the structure confirmed by comparison to a synthetic sample. Further, the cross-link between methylglyoxal, dGuo, and a peptide (AcAVAGKAGAR) was also characterized. The mechanism of cross-link formation is likely to involve an Amadori rearrangement. PMID:24801980

Polymeric micelles with ionic cores containing biodegradable cross-links for delivery of chemotherapeutic agents.

PubMed

Kim, Jong Oh; Sahay, Gaurav; Kabanov, Alexander V; Bronich, Tatiana K

2010-04-12

Novel functional polymeric nanocarriers with ionic cores containing biodegradable cross-links were developed for delivery of chemotherapeutic agents. Block ionomer complexes (BIC) of poly(ethylene oxide)-b-poly(methacylic acid) (PEO-b-PMA) and divalent metal cations (Ca(2+)) were utilized as templates. Disulfide bonds were introduced into the ionic cores by using cystamine as a biodegradable cross-linker. The resulting cross-linked micelles with disulfide bonds represented soft, hydrogel-like nanospheres and demonstrated a time-dependent degradation in the conditions mimicking the intracellular reducing environment. The ionic character of the cores allowed to achieve a very high level of doxorubicin (DOX) loading (50% w/w) into the cross-linked micelles. DOX-loaded degradable cross-linked micelles exhibited more potent cytotoxicity against human A2780 ovarian carcinoma cells as compared to micellar formulations without disulfide linkages. These novel biodegradable cross-linked micelles are expected to be attractive candidates for delivery of anticancer drugs.

Phase Transition in Biopolymer Hydrogels Based on Glycine (g), Valine (v), Proline (p), and Isoleucine (i)

NASA Astrophysics Data System (ADS)

Lee, Jonghwi; Urry, Dan W.; Macosko, Christopher W.

2000-03-01

Selectively modified elastic protein-based polymers demonstrate diverse energy conversions by means of the control of a phase transition resulting from the sensitivity to stimuli of the hydrophobic association. Among these polymers, poly(GVGVP), poly(GVGIP) and analogues of poly(GVGVP) containing carboxylic acid or amino functional groups as side chains were cross-linked and their swelling behavior was studied. Regardless of cross-linking method, reversible phase transitions can be observed in the swelling of all cross-linked polymers by changing temperature and pH, where relevant. Decreased cross-link density leads to increased swelling ratio as the transition becomes more pronounced. Fibers, chemically cross-linked after formation, exhibit anisotropic dimensional changes on changing the temperature. Gamma-irradiation cross-linked poly(GVGVP) exhibited a more distinct phase transition than modified poly(GVGVP) with ion pairs between side chains, which were partially converted to amide cross-links.

Photocontrolled Cargo Release from Dual Cross-Linked Polymer Particles.

PubMed

Tan, Shereen; Cui, Jiwei; Fu, Qiang; Nam, Eunhyung; Ladewig, Katharina; Ren, Jing M; Wong, Edgar H H; Caruso, Frank; Blencowe, Anton; Qiao, Greg G

2016-03-09

Burst release of a payload from polymeric particles upon photoirradiation was engineered by altering the cross-linking density. This was achieved via a dual cross-linking concept whereby noncovalent cross-linking was provided by cyclodextrin host-guest interactions, and irreversible covalent cross-linking was mediated by continuous assembly of polymers (CAP). The dual cross-linked particles (DCPs) were efficiently infiltrated (∼80-93%) by the biomacromolecule dextran (molecular weight up to 500 kDa) to provide high loadings (70-75%). Upon short exposure (5 s) to UV light, the noncovalent cross-links were disrupted resulting in increased permeability and burst release of the cargo (50 mol % within 1 s) as visualized by time-lapse fluorescence microscopy. As sunlight contains UV light at low intensities, the particles can potentially be incorporated into systems used in agriculture, environmental control, and food packaging, whereby sunlight could control the release of nutrients and antimicrobial agents.

Nuclear Resonance Fluorescence for Materials Assay

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

Quiter, Brian; Ludewigt, Bernhard; Mozin, Vladimir

This paper discusses the use of nuclear resonance fluorescence (NRF) techniques for the isotopic and quantitative assaying of radioactive material. Potential applications include age-dating of an unknown radioactive source, pre- and post-detonation nuclear forensics, and safeguards for nuclear fuel cycles Examples of age-dating a strong radioactive source and assaying a spent fuel pin are discussed. The modeling work has ben performed with the Monte Carlo radiation transport computer code MCNPX, and the capability to simulate NRF has bee added to the code. Discussed are the limitations in MCNPX's photon transport physics for accurately describing photon scattering processes that are importantmore » contributions to the background and impact the applicability of the NRF assay technique.« less

Preliminary investigation of parasitic radioisotope production using the LANL IPF secondary neutron flux

NASA Astrophysics Data System (ADS)

Engle, J. W.; Kelsey, C. T.; Bach, H.; Ballard, B. D.; Fassbender, M. E.; John, K. D.; Birnbaum, E. R.; Nortier, F. M.

2012-12-01

In order to ascertain the potential for radioisotope production and material science studies using the Isotope Production Facility at Los Alamos National Lab, a two-pronged investigation has been initiated. The Monte Carlo for Neutral Particles eXtended (MCNPX) code has been used in conjunction with the CINDER 90 burnup code to predict neutron flux energy distributions as a result of routine irradiations and to estimate yields of radioisotopes of interest for hypothetical irradiation conditions. A threshold foil activation experiment is planned to study the neutron flux using measured yields of radioisotopes, quantified by HPGe gamma spectroscopy, from representative nuclear reactions with known thresholds up to 50 MeV.

Combining Amine-Reactive Cross-Linkers and Photo-Reactive Amino Acids for 3D-Structure Analysis of Proteins and Protein Complexes.

PubMed

Lössl, Philip; Sinz, Andrea

2016-01-01

During the last 15 years, the combination of chemical cross-linking and high-resolution mass spectrometry (MS) has matured into an alternative approach for analyzing 3D-structures of proteins and protein complexes. Using the distance constraints imposed by the cross-links, models of the protein or protein complex under investigation can be created. The majority of cross-linking studies are currently conducted with homobifunctional amine-reactive cross-linkers. We extend this "traditional" cross-linking/MS strategy by adding complementary photo-cross-linking data. For this, the diazirine-containing unnatural amino acids photo-leucine and photo-methionine are incorporated into the proteins and cross-link formation is induced by UV-A irradiation. The advantage of the photo-cross-linking strategy is that it is not restricted to lysine residues and that hydrophobic regions in proteins can be targeted, which is advantageous for investigating membrane proteins. We consider the strategy of combining cross-linkers with orthogonal reactivities and distances to be ideally suited for maximizing the amount of structural information that can be gained from a cross-linking experiment.

Macromolecular cross-linked enzyme aggregates (M-CLEAs) of α-amylase.

PubMed

Nadar, Shamraja S; Muley, Abhijeet B; Ladole, Mayur R; Joshi, Pranoti U

2016-03-01

Macromolecular cross-linked enzyme aggregates (M-CLEAs) of α-amylase were prepared by precipitation and subsequent cross-linking. The non-toxic, biodegradable, biocompatible, renewable polysaccharide based macromolecular cross-linkers viz. agar, chitosan, dextran, and gum arabic were used as a substitute for traditional glutaraldehyde to augment activity recovery toward macromolecular substrate. Macromolecular cross-linkers were prepared by periodate mediated controlled oxidation of polysaccharides. The effects of precipitating agent, concentration and different cross-linkers on activity recovery of α-amylase CLEAs were investigated. α-Amylase aggregated with ammonium sulphate and cross-linked by dextran showed 91% activity recovery, whereas glutaraldehyde CLEAs (G-CLEAs) exhibited 42% activity recovery. M-CLEAs exhibited higher thermal stability in correlation with α-amylase and G-CLEAs. Moreover, dextran and chitosan M-CLEAs showed same affinity for starch hydrolysis as of free α-amylase. The changes in secondary structures revealed the enhancements in structural and conformational rigidity attributed by cross-linkers. Finally, after five consecutive cycles dextran M-CLEAs retained 1.25 times higher initial activity than G-CLEAs. Copyright © 2015 Elsevier B.V. All rights reserved.

Recyclable crosslinked polymer networks with full property recovery made via one-step controlled radical polymerization

NASA Astrophysics Data System (ADS)

Jin, Kailong; Li, Lingqiao; Torkelson, John

Rubber tires illustrate well the issues ranging from economic loss to environmental problems and sustainability issues that arise with spent, covalently crosslinked polymers. A nitroxide-mediated polymerization (NMP) strategy has been developed that allows for one-step synthesis of recyclable crosslinked polymers from monomers or polymers that contain carbon-carbon double bonds amenable to radical polymerization. Resulting materials possess dynamic alkoxyamine crosslinks that undergo reversible decrosslinking as a function of temperature. Using polybutadiene as starting material, and styrene, an appropriate nitroxide molecule and bifunctional initiator for initial crosslinking, a model for tire rubber can be produced by reaction at temperatures comparable to those employed in tire molding. Upon cooling, the crosslinks are made permanent due to the extraordinarily strong temperature dependence of the reverisible nitroxide capping and uncapping reaction. Based on thermomechanical property characterization, when the original crosslinked model rubber is chopped into bits and remolded in the melt state, a well-consolidated material is obtained which exhibits full recovery of properties reflecting crosslink density after multiple recycling steps.

Crosslinking to enhance colloidal stability and redispersity of layered double hydroxide nanoparticles.

PubMed

Zuo, Huali; Gu, Zi; Cooper, Helen; Xu, Zhi Ping

2015-12-01

This article introduces a strategy for stabilizing and redispersing layered double hydroxide (LDH) nanoparticles by crosslinking bovine serum albumin (BSA) coated onto the surface. The strategy involves optimization of the amount of the crosslinking agent glutaraldehyde (GTA) to achieve minimal aggregation and ready redispersion. LDH nanoparticles were prepared by co-precipitation and hydrothermal treatment, with subsequent BSA coating at the BSA/LDH mass ratio of 5:2. BSA coated onto LDH nanoparticles was crosslinked with different amounts of GTA. Aggregation studies using dilution assays, dynamic light scattering, and zeta potential analysis indicated that severe aggregation at lower LDH nanoparticle concentrations can be prevented by proper crosslinking of BSA with GTA. The GTA-crosslinked BSA-coated nanoparticles showed excellent redispersity compared to the non-crosslinked nanoparticles. In vitro cytotoxicity and cell uptake were found to be minimally affected by GTA-crosslinking. The new strategy therefore provides a much more effective method for the prevention of LDH nanoparticle aggregation and improved LDH nanoparticle redispersion for use in a wide variety of bio-applications in vitro and in vivo. Copyright © 2015 Elsevier Inc. All rights reserved.

Effect of crosslinking UHMWPE on its tensile and compressive creep performance.

PubMed

Lewis, G; Carroll, M

2001-01-01

The in vitro quasi-static tensile and compressive creep properties of three sets of GUR 1050 ultra-high-molecular-weight polyethylene (UHMWPE) specimens were obtained. These sets were: control (as-received stock); "low-gamma" (specimens were crosslinked using gamma radiation, with a minimum dose of 5 Mrad); and "high-gamma" (specimens were crosslinked using gamma radiation, with a minimum dose of 15 Mrad). The % crystallinity (%C) and crosslink density (rho(x)) of the specimens in the three sets were also obtained. It was found that, in both tension and compression, crosslinking resulted in a significant depreciation in the creep properties, relative to control. The trend in the creep results is explained in terms of the impact of crosslinking on the polymer's %C and rho(x). The present results are in contrast to literature reports that show that crosslinking enhances the wear resistance of the polymer. The implications of the present results, taken together with the aforementioned literature results, are fully discussed vis-a-vis the use of crosslinked UHMWPE for fabricating articular components for arthroplasties.

Optimization of Formaldehyde Cross-Linking for Protein Interaction Analysis of Non-Tagged Integrin β1

PubMed Central

Klockenbusch, Cordula; Kast, Juergen

2010-01-01

Formaldehyde cross-linking of protein complexes combined with immunoprecipitation and mass spectrometry analysis is a promising technique for analysing protein-protein interactions, including those of transient nature. Here we used integrin β1 as a model to describe the application of formaldehyde cross-linking in detail, particularly focusing on the optimal parameters for cross-linking, the detection of formaldehyde cross-linked complexes, the utility of antibodies, and the identification of binding partners. Integrin β1 was found in a high molecular weight complex after formaldehyde cross-linking. Eight different anti-integrin β1 antibodies were used for pull-down experiments and no loss in precipitation efficiency after cross-linking was observed. However, two of the antibodies could not precipitate the complex, probably due to hidden epitopes. Formaldehyde cross-linked complexes, precipitated from Jurkat cells or human platelets and analyzed by mass spectrometry, were found to be composed of integrin β1, α4 and α6 or β1, α6, α2, and α5, respectively. PMID:20634879

Repair of DNA-polypeptide crosslinks by human excision nuclease

NASA Astrophysics Data System (ADS)

Reardon, Joyce T.; Sancar, Aziz

2006-03-01

DNA-protein crosslinks are relatively common DNA lesions that form during the physiological processing of DNA by replication and recombination proteins, by side reactions of base excision repair enzymes, and by cellular exposure to bifunctional DNA-damaging agents such as platinum compounds. The mechanism by which pathological DNA-protein crosslinks are repaired in humans is not known. In this study, we investigated the mechanism of recognition and repair of protein-DNA and oligopeptide-DNA crosslinks by the human excision nuclease. Under our assay conditions, the human nucleotide excision repair system did not remove a 16-kDa protein crosslinked to DNA at a detectable level. However, 4- and 12-aa-long oligopeptides crosslinked to the DNA backbone were recognized by some of the damage recognition factors of the human excision nuclease with moderate selectivity and were excised from DNA at relatively efficient rates. Our data suggest that, if coupled with proteolytic degradation of the crosslinked protein, the human excision nuclease may be the major enzyme system for eliminating protein-DNA crosslinks from the genome. damage recognition | nucleotide excision repair

Characterization of the crosslinking reaction in high performance phenolic resins

NASA Astrophysics Data System (ADS)

Patel, Jigneshkumar; Zou, Guo Xiang; Hsu, Shaw Ling; university of massachusetts/Polymer science; Engineering Team

In this study, a combination of thermal analysis, infrared spectroscopy (near and mid) in conjunction with low field NMR, was used to characterize the crosslinking reaction involving phenol formaldehyde resin and a crosslinking agent, Hexamethylenetetramine (HMTA). The strong hydrogen bonds in the resin and the completely crystalline HMTA (Tm = 280 °C) severely hamper the crosslinking process. Yet the addition of a small amount of plasticizer can induce a highly efficient crosslinking reaction to achieve the desired mechanical properties needed in a number of high performance organic-inorganic composites. The infrared spectroscopy clarifies the dissolution process of the crystalline crosslinker and the specific interactions needed to achieve miscibility of the reactants. The thermal analysis enabled us to follow the changing mobility of the system as a function of temperature. The low field NMR with the T1 inverse recovery technique allowed us to monitor the crosslinking process directly. For the first time, it is now possible to identify the functionality of the plasticizer and correlate the crosslinked structure achieved to the macroscopic performance needed for high performance organic-inorganic composites.

Infrared microspectroscopic determination of collagen cross-links in articular cartilage

NASA Astrophysics Data System (ADS)

Rieppo, Lassi; Kokkonen, Harri T.; Kulmala, Katariina A. M.; Kovanen, Vuokko; Lammi, Mikko J.; Töyräs, Juha; Saarakkala, Simo

2017-03-01

Collagen forms an organized network in articular cartilage to give tensile stiffness to the tissue. Due to its long half-life, collagen is susceptible to cross-links caused by advanced glycation end-products. The current standard method for determination of cross-link concentrations in tissues is the destructive high-performance liquid chromatography (HPLC). The aim of this study was to analyze the cross-link concentrations nondestructively from standard unstained histological articular cartilage sections by using Fourier transform infrared (FTIR) microspectroscopy. Half of the bovine articular cartilage samples (n=27) were treated with threose to increase the collagen cross-linking while the other half (n=27) served as a control group. Partial least squares (PLS) regression with variable selection algorithms was used to predict the cross-link concentrations from the measured average FTIR spectra of the samples, and HPLC was used as the reference method for cross-link concentrations. The correlation coefficients between the PLS regression models and the biochemical reference values were r=0.84 (p<0.001), r=0.87 (p<0.001) and r=0.92 (p<0.001) for hydroxylysyl pyridinoline (HP), lysyl pyridinoline (LP), and pentosidine (Pent) cross-links, respectively. The study demonstrated that FTIR microspectroscopy is a feasible method for investigating cross-link concentrations in articular cartilage.

Sequence-Dependent Diastereospecific and Diastereodivergent Crosslinking of DNA by Decarbamoylmitomycin C.

PubMed

Aguilar, William; Paz, Manuel M; Vargas, Anayatzinc; Clement, Cristina C; Cheng, Shu-Yuan; Champeil, Elise

2018-04-20

Mitomycin C (MC), a potent antitumor drug, and decarbamoylmitomycin C (DMC), a derivative lacking the carbamoyl group, form highly cytotoxic DNA interstrand crosslinks. The major interstrand crosslink formed by DMC is the C1'' epimer of the major crosslink formed by MC. The molecular basis for the stereochemical configuration exhibited by DMC was investigated using biomimetic synthesis. The formation of DNA-DNA crosslinks by DMC is diastereospecific and diastereodivergent: Only the 1''S-diastereomer of the initially formed monoadduct can form crosslinks at GpC sequences, and only the 1''R-diastereomer of the monoadduct can form crosslinks at CpG sequences. We also show that CpG and GpC sequences react with divergent diastereoselectivity in the first alkylation step: 1"S stereochemistry is favored at GpC sequences and 1''R stereochemistry is favored at CpG sequences. Therefore, the first alkylation step results, at each sequence, in the selective formation of the diastereomer able to generate an interstrand DNA-DNA crosslink after the "second arm" alkylation. Examination of the known DNA adduct pattern obtained after treatment of cancer cell cultures with DMC indicates that the GpC sequence is the major target for the formation of DNA-DNA crosslinks in vivo by this drug. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crosslinking of surface antibodies and Fc sub. gamma. receptors: Theory and application

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

Wofsy, C.; Goldstein, B.

1991-03-15

In an immune response, the crosslinking of surface immunoglobulin (sIg) on B cells by multiply-bound ligand activates a range of cell responses, culminating in the production of antibody-secreting cells. However, when the crosslinking agent is itself an antibody, B cell activation is inhibited. Solution antibody (IgG) can bind simultaneously to sIg and to another cell surface receptor, Fc{sub {gamma}}R, co-crosslinking' the distinct receptors. Experiments point to co-crosslinking as the inhibitory signal. It is not clear how co-crosslinking inhibits B cell stimulation. The authors construct and analyze a mathematical model aimed at clarifying the nature and mechanisms of action of themore » separate cell signals controlling B cell responses to antibodies. Basophils and mast cells respond to the crosslinking of cell surface antibody by releasing histamine. Like B cells, basophils also express FC{sub {gamma}}R. They use their model to analyze new data on the effect of antibody-induced co-crosslinking of the two types of receptor on this family of cells. Predictions of the model indicate that an observed difference between the response patterns induced by antibodies and by antibody fragments that cannot bind to FC{sub {gamma}}R can be explained if co-crosslinking is neither inhibitory nor stimulatory in this system.« less

Evaluation of Production Cross Sections of Li, Be, B in CR

NASA Technical Reports Server (NTRS)

Moskalenko, I. V.; Mashnik, S. G.

2003-01-01

Accurate evaluation of the production cross section of light elements is important for models of cosmic ray (CR) propagation, galactic chemical evolution, and cosmological studies. However, the experimental spallation cross section data are scarce and often unavailable to CR community while semi-empirical systematics are frequently wrong by a significant factor. Running sophisticated nuclear codes is not an option of choice for everyone either. We use the Los Alamos versions of the Quark-Gluon String Model code LAQGSM and the improved Cascade-Exciton Model code CEM2k together with all available data from Los Alamos Nuclear Laboratory (LANL) nuclear database to produce evaluated production cross sections of isotopes of Li, Be, and B suitable for astrophysical applications. The LAQGSM and CEM2k models have been shown to reproduce well nuclear reactions and hadronic data in the range 0.01-800 GeV/nucleon.

CEM2k and LAQGSM Codes as Event-Generators for Space Radiation Shield and Cosmic Rays Propagation Applications

NASA Technical Reports Server (NTRS)

Mashnik, S. G.; Gudima, K. K.; Sierk, A. J.; Moskalenko, I. V.

2002-01-01

Space radiation shield applications and studies of cosmic ray propagation in the Galaxy require reliable cross sections to calculate spectra of secondary particles and yields of the isotopes produced in nuclear reactions induced both by particles and nuclei at energies from threshold to hundreds of GeV per nucleon. Since the data often exist in a very limited energy range or sometimes not at all, the only way to obtain an estimate of the production cross sections is to use theoretical models and codes. Recently, we have developed improved versions of the Cascade-Exciton Model (CEM) of nuclear reactions: the codes CEM97 and CEM2k for description of particle-nucleus reactions at energies up to about 5 GeV. In addition, we have developed a LANL version of the Quark-Gluon String Model (LAQGSM) to describe reactions induced both by particles and nuclei at energies up to hundreds of GeVhucleon. We have tested and benchmarked the CEM and LAQGSM codes against a large variety of experimental data and have compared their results with predictions by other currently available models and codes. Our benchmarks show that CEM and LAQGSM codes have predictive powers no worse than other currently used codes and describe many reactions better than other codes; therefore both our codes can be used as reliable event-generators for space radiation shield and cosmic ray propagation applications. The CEM2k code is being incorporated into the transport code MCNPX (and several other transport codes), and we plan to incorporate LAQGSM into MCNPX in the near future. Here, we present the current status of the CEM2k and LAQGSM codes, and show results and applications to studies of cosmic ray propagation in the Galaxy.

Formaldehyde substitute fixatives: effects on nucleic acid preservation.

PubMed

Moelans, Cathy B; Oostenrijk, Daphne; Moons, Michiel J; van Diest, Paul J

2011-11-01

In surgical pathology, formalin-fixed paraffin-embedded tissues are increasingly being used as a source of DNA and RNA for molecular assays in addition to histopathological evaluation. However, the commonly used formalin fixative is carcinogenic, and its crosslinking impairs DNA and RNA quality. The suitability of three new presumably less toxic, crosslinking (F-Solv) and non-crosslinking (FineFIX, RCL2) alcohol-based fixatives was tested for routine molecular pathology in comparison with neutral buffered formalin (NBF) as gold standard. Size ladder PCR, epidermal growth factor receptor sequence analysis, microsatellite instability (MSI), chromogenic (CISH), fluorescence in situ hybridisation (FISH) and qPCR were performed. The alcohol-based non-crosslinking fixatives (FineFIX and RCL2) resulted in a higher DNA yield and quality compared with crosslinking fixatives (NBF and F-Solv). Size ladder PCR resulted in a shorter amplicon size (300 bp) for both crosslinking fixatives compared with the non-crosslinking fixatives (400 bp). All four fixatives were directly applicable for MSI and epidermal growth factor receptor sequence analysis. All fixatives except F-Solv showed clear signals in CISH and FISH. RNA yield and quality were superior after non-crosslinking fixation. qPCR resulted in lower Ct values for RCL2 and FineFIX. The alcohol-based non-crosslinking fixatives performed better than crosslinking fixatives with regard to DNA and RNA yield, quality and applicability in molecular diagnostics. Given the higher yield, less starting material may be necessary, thereby increasing the applicability of biopsies for molecular studies.

A PI 4. 6 peroxidase that specifically crosslinks extensin precursors

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

Upham, B.L; Alizadeh, H.; Ryan, K.J.

1991-05-01

The primary cell wall is a microcomposite of cellulose, pectin, hemicellulose and protein. The warp-weft model of the primary cell wall hypothesize that extensin monomers are intermolecularly crosslinked orthogonal to the cellulose microfibril thus mechanically coupling the major load-bearing polymer: cellulose. Media of tomato cell cultures contains heat labile, peroxide dependent crosslinking activity, as determined by the rate of decrease in monomer concentration analyzed via Superose-6. Isoelectric focusing of tomato cell culture media indicated crosslinking was predominantly in the acidic peroxidase fraction (pI4.6). This peroxidase was partially purified by ultracentrifugation, DEAE-Trisacryl and HPLC-DEAE chromatography techniques resulting in a 90 foldmore » purification and 45% yield. A second acidic peroxidase eluted from the HPLC-DEAE column had 25% of the crosslinking activity of the pI 4.6 peroxidase. Purified basic peroxidase had only 0.7% of the activity of the pI 4.6 peroxidase. The specific activity of the pI 4.6 peroxidase was 5,473 mg extensin crosslinked/min/mg peroxidase. The pI 4.6 peroxidase crosslinked the following extensins: tomato I and II, carrot, Ginkgo II and did not crosslink Ginkgo I, Douglas Fir, Maize, Asparagus I and II, and sugarbeet extensins as well as bovine serum albumin. Comparison of motifs common to extensins that are crosslinked by the pI 4.6 peroxidase may help identify the crosslink domain(s) of extension.« less

Effects of cross-linking on mechanical, biological properties and biodegradation behavior of Nile tilapia skin collagen sponge as a biomedical material.

PubMed

Sun, Leilei; Li, Bafang; Yao, Di; Song, Wenkui; Hou, Hu

2018-04-01

The objective of this study was to explore the effects of dehydrothermal treatment (DHT) and glutaraldehyde (GTA) cross-linking on mechanical, biological properties and biodegradation behavior of Nile tilapia skin collagen sponge fabricated by freeze-drying technology. It was found that the GTA cross-linked collagen sponge exhibited a higher degree of cross-linking in comparison with DHT. The extent of increased tensile strength as well as hygroscopicity indicated that GTA cross-linking was superior to DHT in mechanical properties and liquid absorption, which was attributed to different cross-linking mechanisms. Hygroscopicity assay indicated that cross-linking could improve stability of collagen in solutions. No obvious changes in porosity and blood coagulation time were observed whether cross-linking or not. Results from collagenase biodegradation assay in vitro illustrated that GTA-treated collagen sponge was more resistant to collagenase biodegradation, while DHT exhibited negligible resistance. In addition, photochemical stability of collagen sponge was studied by Fourier transforms infrared spectroscopy (FTIR), which indicated that both cross-linking treatments could not change the backbone structure of collagen. Furthermore, the microstructure of collagen sponge was stable after cross-linking. The highly porous and interconnected structure of collagen sponge was helpful to the absorption of wound exudates, supplement of oxygen and cell proliferation, accompanied with good blood compatibility, which indicated that our fabricated collagen sponge could be applied in biomedical materials field as wound dressings. Copyright © 2018. Published by Elsevier Ltd.

Effects of crosslinking on the mechanical properties, drug release and cytocompatibility of protein polymers.

PubMed

Martinez, Adam W; Caves, Jeffrey M; Ravi, Swathi; Li, Wehnsheng; Chaikof, Elliot L

2014-01-01

Recombinant elastin-like protein polymers are increasingly being investigated as component materials of a variety of implantable medical devices. This is chiefly a result of their favorable biological properties and the ability to tailor their physical and mechanical properties. In this report, we explore the potential of modulating the water content, mechanical properties, and drug release profiles of protein films through the selection of different crosslinking schemes and processing strategies. We find that the selection of crosslinking scheme and processing strategy has a significant influence on all aspects of protein polymer films. Significantly, utilization of a confined, fixed volume, as well as vapor-phase crosslinking strategies, decreased protein polymer equilibrium water content. Specifically, as compared to uncrosslinked protein gels, water content was reduced for genipin (15.5%), glutaraldehyde (GTA, 24.5%), GTA vapor crosslinking (31.6%), disulfide (SS, 18.2%) and SS vapor crosslinking (25.5%) (P<0.05). Distinct crosslinking strategies modulated protein polymer stiffness, strain at failure and ultimate tensile strength (UTS). In all cases, vapor-phase crosslinking produced the stiffest films with the highest UTS. Moreover, both confined, fixed volume and vapor-phase approaches influenced drug delivery rates, resulting in decreased initial drug burst and release rates as compared to solution phase crosslinking. Tailored crosslinking strategies provide an important option for modulating the physical, mechanical and drug delivery properties of protein polymers. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Chemical crosslinking and mass spectrometry studies of the structure and dynamics of membrane proteins and receptors.

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

Haskins, William E.; Leavell, Michael D.; Lane, Pamela

2005-03-01

Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurementmore » using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.« less

An Evaluation of Lysyl Oxidase–Derived Cross-Linking in Keratoconus by Liquid Chromatography/Mass Spectrometry

PubMed Central

Takaoka, Anna; Babar, Natasha; Hogan, Julia; Kim, MiJung; Price, Marianne O.; Price, Francis W.; Trokel, Stephen L.; Paik, David C.

2016-01-01

Purpose Current literature contains scant information regarding the extent of enzymatic collagen cross-linking in the keratoconus (KC) cornea. The aim of the present study was to examine levels of enzymatic lysyl oxidase–derived cross-links in stromal collagen in KC tissue, and to correlate the cross-link levels with collagen fibril stability as determined by thermal denaturation temperature (Tm). Methods Surgical KC samples (n = 17) and Eye-Bank control (n = 11) corneas of age 18 to 68 years were analyzed. The samples were defatted, reduced (NaBH4), hydrolyzed (6N HCl at 110°C for 18 hours), and cellulose enriched before analysis by C8 high-performance liquid chromatography equipped with parallel fluorescent and mass detectors in selective ion monitoring mode (20 mM heptafluorobutyric acid/methanol 70:30 isocratic at 1 mL/min). Nine different cross-links were measured, and the cross-link density was determined relative to collagen content (determined colorimetrically). The Tm was determined by differential scanning calorimetry. Results Cross-links detected were dihydroxylysinonorleucine (DHLNL), hydroxylysinonorleucine, lysinonorleucine (LNL), and histidinohydroxylysinonorleucine in both control and KC samples. Higher DHLNL levels were detected in KC, whereas the dominant cross-link, LNL, was decreased in KC samples. Decreased LNL levels were observed among KC ≤ 40 corneas. There was no difference in total cross-link density between KC samples and the controls. Pyridinolines, desmosines, and pentosidine were not detected. There was no notable correlation between cross-link levels with fibril instability as determined by Tm. Conclusions Lower levels of LNL in the KC cornea suggest that there might be a cross-linking defect either in fibrillar collagen or the microfibrillar elastic network composed of fibrillin. PMID:26780316

The rational design of recognitive polymeric networks for sensing applications

NASA Astrophysics Data System (ADS)

Noss, Kimberly Ryanne Dial

Testosterone recognitive networks were synthesized with varying feed crosslinking percentages and length of the bi-functional crosslinking agent to analyze the effect of changing structural parameters on template binding properties such as affinity, selectivity, capacity, and diffusional transport. The crosslinking percentage of the crosslinking monomer ethylene glycol dimethacrylate was varied from 50% to 90% and associated networks experienced a 2 fold increase in capacity and a 4 fold increase in affinity with the equilibrium association constants, Ka, ranging from 0.32 +/- 0.02 x 10 4 M-1 to 1.3 +/- 0.1 x 104 M -1, respectively. The higher concentration of crosslinking monomer increased the crosslinking points available for inter-chain stabilization creating an increased number of stable cavities for template association. However, by increasing the length of the crosslinking agent and increasing the feed crosslinking percentage from 77% crosslinked poly(methacrylic acid- co-ethylene glycol dimethacrylate) (poly(MAA-co-EGDMA)) to 50% crosslinked poly(methacrylic acid-co-poly(ethylene glycol)200 dimethacrylate) (poly(MAA-co-PEG200DMA)), the mesh size of the network increased resulting in an increased template diffusion coefficient from (2.83 +/- 0.06) x 109 cm2/s to (4.3 +/- 0.06) x 109 cm2/s, respectively, which is approximately a 40% faster template diffussional transport. A 77% crosslinked poly (MAA-co-PEG200DMA) recognitive network had an association constant of (0.20 +/- 0.05) x 104 M -1 and bound (0.72 +/- 0.04) x 10-2 mmol testosterone/g dry polymer, which was less by 6 and 3 fold, respectively, compared to a similarly crosslinked poly(MAA-co-EGDMA) recognitive network. Structural manipulation of the macromolecular architecture illustrates the programmability of recognitive networks for specific template binding parameters and diffusional transport, which may lead to enhanced imprinted sensor materials and successful integration onto sensor platforms.

On the Formation and Properties of Interstrand DNA-DNA Cross-links Forged by Reaction of an Abasic Site With the Opposing Guanine Residue of 5′-CAp Sequences in Duplex DNA

PubMed Central

Johnson, Kevin M.; Price, Nathan E.; Wang, Jin; Fekry, Mostafa I.; Dutta, Sanjay; Seiner, Derrick R.; Wang, Yinsheng; Gates, Kent S.

2014-01-01

We recently reported that the aldehyde residue of an abasic (Ap) site in duplex DNA can generate an interstrand cross-link via reaction with a guanine residue on the opposing strand. This finding is intriguing because the highly deleterious nature of interstrand cross-links suggests that even small amounts of Ap-derived cross-links could make a significant contribution to the biological consequences stemming from the generation of Ap sites in cellular DNA. Incubation of 21-bp duplexes containing a central 5′-CAp sequence under conditions of reductive amination (NaCNBH3, pH 5.2) generated much higher yields of cross-linked DNA than reported previously. At pH 7, in the absence of reducing agents, these Ap-containing duplexes also produced cross-linked duplexes that were readily detected on denaturing polyacrylamide gels. Cross-link formation was not highly sensitive to reaction conditions and, once formed, the cross-link was stable to a variety of work-up conditions. Results of multiple experiments including MALDI-TOF mass spectrometry, gel mobility, methoxyamine capping of the Ap aldehyde, inosine-for-guanine replacement, hydroxyl radical footprinting, and LCMS/MS were consistent with a cross-linking mechanism involving reversible reaction of the Ap aldehyde residue with the N2-amino group of the opposing guanine residue in 5′-CAp sequences to generate hemiaminal, imine, or cyclic hemiaminal cross-links (7-10) that were irreversibly converted under conditions of reductive amination (NaCNBH3/pH 5.2) to a stable amine linkage. Further support for the importance of the exocyclic N2-amino group in this reaction was provided by an experiment showing that installation of a 2-aminopurine-thymine base pair at the cross-linking site produced high yields (15-30%) of a cross-linked duplex at neutral pH, in the absence of NaCNBH3. PMID:23215239

On the Numerical Analysis of Decay Rate Enhancement in Metallic Environment

NASA Astrophysics Data System (ADS)

Mehedinteanu, S.

2007-10-01

Motivated on the very recent experiments to determine the acceleration of the alpha decay of meta-stable radionuclides in metallic environment some work has been done to strengthten the importance in the process of electrons screening in metals. Thus, by combining the Gamow decay theory with electrostatic screening in Debye-Hückel approximation (jellium model) a formula for ``the shift'' in screening energy which enters in the decay enhancement factor expression that copes well with these experiments has been derived. It was established that to simulate the poly-atoms system containing decaying isotopes in QM&MD codes calculations, and to include ``the screening energy shift'' of protons, decay alpha, beta+ particles due to all surrounding interacting effects, it is sufficiently only to substitute the code ruly pseudo-potential input for hydrogen-like atoms (including alpha) by a screened Coulomb potential as from the well-known Gamow alpha decay theory. For demonstration is used the QM&MD code package which usually performs density-functional theory (DFT) total-energy calculations for materials ranging from insulators to transition metals. This package employs first-principles pseudo-potentials and a plane-wave basis-set, and it was used to do a special calculus for some metal environments (Pd) where protons-deuterons are implanted or when it is alloyed with a radionuclide-like isotopes (174Hf72), the results compare well with the existing experiments on the decay enhancement. These works give further arguments for a cheap solution to remove the transuranic waste (involving all alpha-decay) of used-up rods of fission reactors in a time period of a few years.

Cross-sections of residual nuclei from deuteron irradiation of thin thorium target at energy 7 GeV

NASA Astrophysics Data System (ADS)

Vespalec, Radek; Adam, Jindrich; Baldin, Anton Alexandrovich; Khushvaktov, Jurabek; Solnyshkin, Alexander Alexandrovich; Tsoupko-Sitnikov, Vsevolod Mikhailovich; Tyutyunikov, Sergey Ivanovich; Vrzalova, Jitka; Zavorka, Lukas; Zeman, Miroslav

2017-09-01

The residual nuclei yields are of great importance for the estimation of basic radiation-technology characteristics (like a total target activity, production of long-lived nuclides etc.) of accelerator driven systems planned for transmutation of spent nuclear fuel and for a design of radioisotopes production facilities. Experimental data are also essential for validation of nuclear codes describing various stages of a spallation reaction. Therefore, the main aim of this work is to add new experimental data in energy region of relativistic deuterons, as similar data are missing in nuclear databases. The sample made of thin natural thorium foil was irradiated at JINR Nuclotron accelerator with a deuteron beam of the total kinetic energy 7 GeV. Integral number of deuterons was determined with the use of aluminum activation detectors. Products of deuteron induced spallation reaction were qualified and quantified by means of gamma-ray spectroscopy method. Several important spectroscopic corrections were applied to obtain results of high accuracy. Experimental cumulative and independent cross-sections were determined for more than 80 isotopes including meta-stable isomers. The total uncertainty of results rarely exceeded 9%. Experimental results were compared with MCNP6.1 Monte-Carlo code predictions. Generally, experimental and calculated cross-sections are in a reasonably good agreement, with the exception of a few light isotopes in a fragmentation region, where the calculations are highly under-estimated. Measured data will be useful for future development of high-energy nuclear codes. After completion, final data will be added into the EXFOR database.

Geant4 Modifications for Accurate Fission Simulations

NASA Astrophysics Data System (ADS)

Tan, Jiawei; Bendahan, Joseph

Monte Carlo is one of the methods to simulate the generation and transport of radiation through matter. The most widely used radiation simulation codes are MCNP and Geant4. The simulation of fission production and transport by MCNP has been thoroughly benchmarked. There is an increasing number of users that prefer using Geant4 due to the flexibility of adding features. However, it has been found that Geant4 does not have the proper fission-production cross sections and does not produce the correct fission products. To achieve accurate results for studies in fissionable material applications, Geant4 was modified to correct these inaccuracies and to add new capabilities. The fission model developed by the Lawrence Livermore National Laboratory was integrated into the neutron-fission modeling package. The photofission simulation capability was enabled using the same neutron-fission library under the assumption that nuclei fission in the same way, independent of the excitation source. The modified fission code provides the correct multiplicity of prompt neutrons and gamma rays, and produces delayed gamma rays and neutrons with time and energy dependencies that are consistent with ENDF/B-VII. The delayed neutrons are now directly produced by a custom package that bypasses the fragment cascade model. The modifications were made for U-235, U-238 and Pu-239 isotopes; however, the new framework allows adding new isotopes easily. The SLAC nuclear data library is used for simulation of isotopes with an atomic number above 92 because it is not available in Geant4. Results of the modified Geant4.10.1 package of neutron-fission and photofission for prompt and delayed radiation are compared with ENDFB-VII and with results produced with the original package.

Bruyères-le-Châtel Neutron Evaluations of Actinides with the TALYS Code: The Fission Channel

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

Romain, P., E-mail: pascal.romain@cea.fr; Morillon, B.; Duarte, H.

For several years, various neutron evaluations of plutonium and uranium isotopes have been performed at Bruyères-le-Châtel (BRC), from 1 keV up to 30 MeV. Since only nuclear reaction models have been used to produce these evaluations, our approach was named the “Full Model” approach. Total, shape elastic and direct inelastic cross sections were obtained from the coupled channels model using a dispersive optical potential developed for actinides, with a large enough coupling scheme including the lowest octupolar band. All other cross sections were calculated using the Hauser-Feshbach theory (TALYS code) with a pre-equilibrium component above 8–10 MeV. In this paper,more » we focus our attention on the fission channel. More precisely, we will present the BRC contribution to fission modeling and the philosophy adopted in our “Full Model” approach. Performing evaluations with the “Full Model” approach implies the optimization of a large number of model parameters. With increasing neutron incident energy, many residual nuclei produced by nucleon emission also lead to fission. All available experimental data assigned to various fission mechanisms of the same nucleus were used to determine fission barrier parameters. For uranium isotopes, triple-humped fission barriers were required in order to reproduce accurately variations of the experimental fission cross sections. Our BRC fission modeling has shown that the effects of the class II or class III states located in the wells of the fission barrier sometimes provide an anti-resonant transmission rather than a resonant one. Consistent evaluations were produced for a large series of U and Pu isotopes. Resulting files were tested against integral data.« less

Sensitive determination of thiols in wine samples by a stable isotope-coded derivatization reagent d0/d4-acridone-10-ethyl-N-maleimide coupled with high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry analysis.

PubMed

Lv, Zhengxian; You, Jinmao; Lu, Shuaimin; Sun, Weidi; Ji, Zhongyin; Sun, Zhiwei; Song, Cuihua; Chen, Guang; Li, Guoliang; Hu, Na; Zhou, Wu; Suo, Yourui

2017-03-31

As the key aroma compounds, varietal thiols are the crucial odorants responsible for the flavor of wines. Quantitative analysis of thiols can provide crucial information for the aroma profiles of different wine styles. In this study, a rapid and sensitive method for the simultaneous determination of six thiols in wine using d 0 /d 4 -acridone-10-ethyl-N-maleimide (d 0 /d 4 -AENM) as stable isotope-coded derivatization reagent (SICD) by high performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS) has been developed. Quantification of thiols was performed by using d 4 -AENM labeled thiols as the internal standards (IS), followed by stable isotope dilution HPLC-ESI-MS/MS analysis. The AENM derivatization combined with multiple reactions monitoring (MRM) not only allowed trace analysis of thiols due to the extremely high sensitivity, but also efficiently corrected the matrix effects during HPLC-MS/MS and the fluctuation in MS/MS signal intensity due to instrument. The obtained internal standard calibration curves for six thiols were linear over the range of 25-10,000pmol/L (R 2 ≥0.9961). Detection limits (LODs) for most of analytes were below 6.3pmol/L. The proposed method was successfully applied for the simultaneous determination of six kinds of thiols in wine samples with precisions ≤3.5% and recoveries ≥78.1%. In conclusion, the developed method is expected to be a promising tool for detection of trace thiols in wine and also in other complex matrix. Copyright © 2017 Elsevier B.V. All rights reserved.

Development of a pair of differential H/D isotope-coded derivatization reagents d(0)/d(3)-4-(1-methyl-1H-phenanthro[9,10-d]imidazol-2-yl)phenlamine and its application for determination of aldehydes in selected aquatic products by liquid chromatography-tandem mass spectrometry.

PubMed

Sun, Zhiwei; Wang, Xiaoxiang; Cai, Yiping; Fu, Junqing; You, Jinmao

2014-03-01

A new pair of derivatization reagents, d0-4-(1-methyl-1H-phenanthro[9,10-d]imidazol-2-yl)phenlamine (d0-MPIA) and d3-4-(1-methyl-1H-phenanthro[9,10-d]imidazol-2-yl)phenlamine (d3-MPIA) have been designed and synthesized. It was successfully used to label aliphatic aldehydes and the aldehyde derivatives were analyzed by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The new isotope-coded reagents could easily label aldehydes under acidic conditions in the presence of NaCNBH3. The target derivatives exhibited intense [M+H](+) and regular product ions with electrospray ionization source in positive mode. The d0/d3-MPIA-aldehydes were monitored by the transitions of [M+H](+)→m/z 322 and [M+H](+)→m/z 165, and the obtained detection limits were in the range of 0.18-15.9 pg/mL at signal to noise ratio of 3. The global isotope internal standard technology was employed for quantification analysis with d3-MPIA-aldehyde as internal standard for corresponding d0-MPIA-aldehyde. Excellent linear responses for relative quantification were observed in the range of 1/10-10/1 with coefficients >0.998. The developed method has been applied to the quantification of aliphatic aldehydes in selected aquatic products with RSD<3.6% and recoveries >85.2%. © 2013 Elsevier B.V. All rights reserved.

An In Vivo Photo-Cross-Linking Approach Reveals a Homodimerization Domain of Aha1 in S. cerevisiae

PubMed Central

Berg, Michael; Michalowski, Annette; Palzer, Silke; Rupp, Steffen; Sohn, Kai

2014-01-01

Protein-protein interactions play an essential role in almost any biological processes. Therefore, there is a particular need for methods which describe the interactions of a defined target protein in its physiological context. Here we report a method to photo-cross-link interacting proteins in S. cerevisiae by using the non-canonical amino acid p-azido-L-phenylalanine (pAzpa). Based on the expanded genetic code the photoreactive non-canonical amino acid pAzpa was site-specifically incorporated at eight positions into a domain of Aha1 that was previously described to bind Hsp90 in vitro to function as a cochaperone of Hsp90 and activates its ATPase activity. In vivo photo-cross-linking to the cognate binding partner of Aha1 was carried out by irradiation of mutant strains with UV light (365 nm) to induce covalent intermolecular bonds. Surprisingly, an interaction between Aha1 and Hsp90 was not detected, although, we could confirm binding of suppressed pAzpa containing Aha1 to Hsp90 by native co-immunoprecipitation. However, a homodimer consisting of two covalently crosslinked Aha1 monomers was identified by mass spectrometry. This homodimer could also be confirmed using p-benzoyl-L-phenylalanine, another photoreactive non-canonical amino acid. Crosslinking was highly specific as it was dependent on irradiation using UV light, the exact position of the non-canonical amino acid in the protein sequence as well as on the addition of the non-canonical amino acid to the growth medium. Therefore it seems possible that an interaction of Aha1 with Hsp90 takes place at different positions than previously described in vitro highlighting the importance of in vivo techniques to study protein-protein interactions. Accordingly, the expanded genetic code can easily be applied to other S. cerevisiae proteins to study their interaction under physiological relevant conditions in vivo. PMID:24614167

Crosslinking of aromatic polyamides via pendant propargyl groups

NASA Technical Reports Server (NTRS)

St.clair, A. K.; St.clair, T. L.; Barrick, J. D.; Campbell, F. J.

1980-01-01

Methods for crosslinking N-methyl substituted aromatic polyamides were investigated in an effort to improve the applicability of these polymers as matrix resins for Kavlar trademark fiber composites. High molecular weight polymers were prepared from isophthaloyl dichloride and 4,4'- bis(methylamino)diphenylmethane with varying proportions of the N,N'bispropargyl diamine incorporated as a crosslinking agent. The propargylcontaining diamines were crosslinked thermally and characterized by infrared spectroscopy, differential scanning calorimetry, and thermogravimetric analysis. Attempts were also made to crosslink polyamide films by exposure to ultraviolet light, electron beam, and gamma radiation.

Cross-Linked Enzyme Aggregates for Applications in Aqueous and Nonaqueous Media.

PubMed

Roy, Ipsita; Mukherjee, Joyeeta; Gupta, Munishwar N

2017-01-01

Extensive cross-linking of a precipitate of a protein by a cross-linking reagent (glutaraldehyde has been most commonly used) creates an insoluble enzyme preparation called cross-linked enzyme aggregates (CLEAs). CLEAs show high stability and performance in conventional aqueous as well as nonaqueous media. These are also stable at fairly high temperatures. CLEAs with more than one kind of enzyme activity can be prepared, and such CLEAs are called combi-CLEAs or multipurpose CLEAs. Extent of cross-linking often influences their morphology, stability, activity, and enantioselectivity.

Cross-linked polyvinyl alcohol and method of making same

NASA Technical Reports Server (NTRS)

Hsu, L. C.; Sheibley, D. W.; Philipp, W. H. (Inventor)

1981-01-01

A film-forming polyvinyl alcohol polymer is mixed with a polyaldehyde-polysaccharide cross-linking agent having at least two monosaccharide units and a plurality of aldehyde groups per molecule, perferably an average of at least one aldehyde group per monosaccharide units. The cross-linking agent, such as a polydialdehyde starch, is used in an amount of about 2.5 to 20% of the theoretical amount required to cross-link all of the available hydroxyl groups of the polyvinyl alcohol polymer. Reaction between the polymer and cross-linking agent is effected in aqueous acidic solution to produce the cross-linked polymer. The polymer product has low electrical resistivity and other properties rendering it suitable for making separators for alkaline batteries.

A comparison of thiolated and disulfide-crosslinked polyethylenimine for nonviral gene delivery.

PubMed

Aravindan, Latha; Bicknell, Katrina A; Brooks, Gavin; Khutoryanskiy, Vitaliy V; Williams, Adrian C

2013-09-01

Branched polyethylenimine (25 kDa) is thiolated and compared with redox-sensitive crosslinked derivatives. Both polymers thiol contents are assessed; the thiolated polymers have 390-2300 mmol SH groups/mol, whereas the crosslinked polymers have lower thiol contents. Cytotoxicity assays show that both modified polymers give lower hemolysis than unmodified PEI. Increased thiol content increases gene transfer efficiency but also elevates cytotoxicity. Crosslinking improves plasmid DNA condensation and enhances transfection efficiency, but extensive crosslinking overstabilizes the polyplexes and decreases transfection, emphasizing the need to balance polyplex stabilization and unpacking. Thus, at low levels of crosslinking, 25 kDa PEI can be an efficient redox-sensitive carrier system. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Validation of Heavy Ion Transport Capabilities in PHITS

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

Ronningen, Reginald M.

The performance of the Monte Carlo code system PHITS is validated for heavy ion transport capabilities by performing simulations and comparing results against experimental data from heavy ion reactions of benchmark quality. These data are from measurements of secondary neutron production cross sections in reactions of Xe at 400 MeV/u with lithium and lead targets, measurements of neutrons outside of thick concrete and iron shields, and measurements of isotope yields produced in the fragmentation of a 140 MeV/u 48Ca beam on a beryllium target and on a tantalum target. A practical example that tests magnetic field capabilities is shown formore » a simulated 48Ca beam at 500 MeV/u striking a lithium target to produce the rare isotope 44Si, with ion transport through a fragmentation-reaction magnetic pre-separator. The results of this study show that PHITS performs reliably for the simulation of radiation fields that is necessary for designing safe, reliable and cost effective future high-powered heavy-ion accelerators in rare isotope beam facilities.« less

Automated collection and processing of environmental samples

DOEpatents

Troyer, Gary L.; McNeece, Susan G.; Brayton, Darryl D.; Panesar, Amardip K.

1997-01-01

For monitoring an environmental parameter such as the level of nuclear radiation, at distributed sites, bar coded sample collectors are deployed and their codes are read using a portable data entry unit that also records the time of deployment. The time and collector identity are cross referenced in memory in the portable unit. Similarly, when later recovering the collector for testing, the code is again read and the time of collection is stored as indexed to the sample collector, or to a further bar code, for example as provided on a container for the sample. The identity of the operator can also be encoded and stored. After deploying and/or recovering the sample collectors, the data is transmitted to a base processor. The samples are tested, preferably using a test unit coupled to the base processor, and again the time is recorded. The base processor computes the level of radiation at the site during exposure of the sample collector, using the detected radiation level of the sample, the delay between recovery and testing, the duration of exposure and the half life of the isotopes collected. In one embodiment, an identity code and a site code are optically read by an image grabber coupled to the portable data entry unit.

Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by site-specific photoaffinity crosslinking.

PubMed Central

Harris, M E; Kazantsev, A V; Chen, J L; Pace, N R

1997-01-01

Bacterial ribonuclease P (RNase P), an endonuclease involved in tRNA maturation, is a ribonucleoprotein containing a catalytic RNA. The secondary structure of this ribozyme is well-established, and a low-resolution model of the three-dimensional structure of the ribozyme-substrate complex has been proposed based on site-specific crosslinking and phylogenetic comparative data [Harris ME et al., 1994 EMBO J 13:3953-3963]. However, several substructures of that model were poorly constrained by the available data. In the present analysis, additional constraints between elements within the Escherichia coli RNase P RNA-pre-tRNA complex were determined by intra- and intermolecular crosslinking experiments. Circularly permuted RNase P RNAs were used to position an azidophenacyl photoactive crosslinking agent specifically at strategic sites within the ribozyme-substrate complex. Crosslink sites were mapped by primer extension and confirmed by analysis of the mobility of the crosslinked RNA lariats on denaturing acrylamide gels relative to circular and linear RNA standards. Crosslinked species generally retained significant catalytic activity, indicating that the results reflect the native ribozyme structure. The crosslinking results support the general configuration of the structure model and predicate new positions and orientations for helices that were previously poorly constrained by the data set. The expanded library of crosslinking constraints was used, together with secondary and tertiary structure identified by phylogenetic sequence comparisons, to refine significantly the model of RNase P RNA with bound substrate pre-tRNA. The crosslinking results and data from chemical-modification and mutational studies are discussed in the context of the current structural perspective on this ribozyme. PMID:9174092

Influence of cross-link structure, density and mechanical properties in the mesoscale deformation mechanisms of collagen fibrils

PubMed Central

Depalle, Baptiste; Qin, Zhao; Shefelbine, Sandra J.; Buehler, Markus J.

2015-01-01

Collagen is a ubiquitous protein with remarkable mechanical properties. It is highly elastic, shows large fracture strength and enables substantial energy dissipation during deformation. Most of the connective tissue in humans consists of collagen fibrils composed of a staggered array of tropocollagen molecules, which are connected by intermolecular cross-links. In this study, we report a three-dimensional coarse-grained model of collagen and analyze the influence of enzymatic cross-links on the mechanics of collagen fibrils. Two representatives immature and mature cross-links are implemented in the mesoscale model using a bottom-up approach. By varying the number, type and mechanical properties of cross-links in the fibrils and performing tensile test on the models, we systematically investigate the deformation mechanisms of cross-linked collagen fibrils. We find that cross-linked fibrils exhibit a three phase behavior, which agrees closer with experimental results than what was obtained using previous models. The fibril mechanical response is characterized by: (i) an initial elastic deformation corresponding to the collagen molecule uncoiling, (ii) a linear regime dominated by molecule sliding and (iii) the second stiffer elastic regime related to the stretching of the backbone of the tropocollagen molecules until the fibril ruptures. Our results suggest that both cross-link density and type dictate the stiffness of large deformation regime by increasing the number of interconnected molecules while cross-links mechanical properties determine the failure strain and strength of the fibril. These findings reveal that cross-links play an essential role in creating an interconnected fibrillar material of tunable toughness and strength. PMID:25153614

Rational design of molecularly imprinted polymer: the choice of cross-linker.

PubMed

Muhammad, Turghun; Nur, Zohre; Piletska, Elena V; Yimit, Osmanjan; Piletsky, Sergey A

2012-06-07

The paper describes a rational approach for the selection of cross-linkers during the development of molecularly imprinted polymers (MIPs). As a model system for this research MIPs specific for the drug zidovudine (AZT) were designed and tested. Three cross-linkers trimethylolpropane trimethacrylate (TRIM), ethylene glycol dimethacrylate (EGDMA) and divinylbenzene (DVB) were studied. The analogue of zidovudine (AZT) ester (AZT-ES) was used as a dummy template. The imprinting factors for all of the polymers in the static adsorption experiments were calculated. The data on the AZT adsorption by control polymers (CP), which were prepared with different cross-linkers without a functional monomer, was also analyzed. DVB was found to be more inert towards zidovudine than EGDMA and TRIM, which was confirmed by both molecular modelling and adsorption experiments. It was demonstrated that DVB-based polymers had a higher imprinting factor (I = 1.85) compared with other tested cross-linked polymers. It was suggested that the selection of the cross-linker should be based on the strength of the interaction with the template: the cross-linker which displays lower binding of the template should be preferential because it generates MIPs with lower non-specific binding and a higher imprinting factor, and therefore specificity. Which cross-linker to use for the preparation of any particular MIP can be determined by analysis of the interactions between the cross-linker and template. This could be done either virtually using computational modelling or by template adsorption using a small library of polymers prepared using different cross-linkers.

Development and characterization of acrylated palm oil nanoparticles using ionizing radiation

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

Tajau, Rida; Yunus, Wan Md Zin Wan; Dahlan, Khairul Zaman Mohd

2012-11-27

In this study, the utilization of radiation crosslinking methods which are known as intermolecular and intramolecular crosslinking for the formation of nanoparticles of Acrylated Palm Oil (APO) in the microemulsion system that also consists of Pluronic F-127 (PF-127) surfactant was demonstrated. This microemulsion system was subjected to the ionizing radiation i.e. gamma irradiation at different doses to form the crosslinked APO nanoparticles. The effects of radiation doses on the size of APO nanoparticles were investigated using the Dynamic Light Scattering (DLS) method and their images were viewed using the Transmission Electron Microcrospy (TEM). The Fourier Transform Infra-Red (FTIR) spectroscopy wasmore » used to characterize the chemical structure and the crosslinking conversion of carbon-carbon double bond (-C = C-) of the APO nanoparticles after irradiation. As a result, the size of the APO nanoparticle decreased when the irradiation dose increased. Reduce in size might be due to the effect of intramolecular crosslinking reaction of the APO nanoparticles during irradiation process. Meanwhile, the intramolecular -C C- crosslinking conversion percentage was increased at doses below 1kGy before decreasing at the higher dose that might due to the intermolecular crosslinking of the macromolecules. This study showed that radiation crosslinking methods of polymerization and crosslinking in the microemulsion were found to be promising for the synthesis of nanoparticles.« less

Visible Light Crosslinking of Methacrylated Hyaluronan Hydrogels for Injectable Tissue Repair

PubMed Central

Fenn, Spencer L.; Oldinski, Rachael A.

2015-01-01

Tissue engineering hydrogels are primarily cured in situ using ultraviolet (UV) radiation which limits the use of hydrogels as drug or cell carriers. Visible green light activated crosslinking systems are presented as a safe alternative to UV photocrosslinked hydrogels, without compromising material properties such as viscosity and stiffness. The objective of this study was to fabricate and characterize photocrosslinked hydrogels with well-regulated gelation kinetics and mechanical properties for the repair or replacement of soft tissue. An anhydrous methacrylation of hyaluronan (HA) was performed to control the degree of modification (DOM) of HA, verified by 1H-NMR spectroscopy. UV activated crosslinking was compared to visible green light activated crosslinking. While the different photocrosslinking techniques resulted in varied crosslinking times, comparable mechanical properties of UV and green light activated crosslinked hydrogels were achieved using each photocrosslinking method by adjusting time of light exposure. Methacrylated HA (HA-MA) hydrogels of varying molecular weight, DOM and concentration exhibited compressive moduli ranging from 1 kPa to 116 kPa, for UV crosslinking, and 3 kPa to 146 kPa, for green light crosslinking. HA-MA molecular weight and concentration were found to significantly influence moduli values. HA-MA hydrogels did not exhibit any significant cytotoxic affects towards human mesenchymal stem cells. Green light activated crosslinking systems are presented as a viable method to form natural-based hydrogels in situ. PMID:26097172

Chemical crosslinking of the subunits of HIV-1 reverse transcriptase.

PubMed Central

Debyser, Z.; De Clercq, E.

1996-01-01

The reverse transcriptase (RT) of the human immunodeficiency virus type 1 (HIV-1) is composed of two subunits of 66 and 51 kDa in a 1 to 1 ratio. Because dimerization is a prerequisite for enzymatic activity, interference with the dimerization process could constitute an alternative antiviral strategy for RT inhibition. Here we describe an in vitro assay for the study of the dimerization state of HIV-1 reverse transcriptase based on chemical crosslinking of the subunits with dimethylsuberimidate. Crosslinking results in the formation of covalent bonds between the subunits, so that the crosslinked species can be resolved by denaturing gel electrophoresis. Crosslinked RT species with molecular weight greater than that of the dimeric form accumulate during a 1-15-min time course. Initial evidence suggests that those high molecular weight species represent trimers and tetramers and may be the result of intramolecular crosslinking of the subunits of a higher-order RT oligomer. A peptide that corresponds to part of the tryptophan repeat motif in the connection domain of HIV-1 RT inhibits crosslink formation as well as enzymatic activity. The crosslinking assay thus allows the investigation of the effect of inhibitors on the dimerization of HIV-1 RT. PMID:8745406

Structure of neutron-rich nuclei around the N = 50 shell-gap closure

NASA Astrophysics Data System (ADS)

Faul, T.; Duchêne, G.; Thomas, J.-C.; Nowacki, F.; Huyse, M.; Van Duppen, P.

2010-04-01

The structure of neutron-rich nuclei in the vicinity of 78Ni have been investigated via the β-decay of 71,73,75Cu isotopes (ISOLDE, CERN). Experimental results have been compared with shell-model calculations performed with the ANTOINE code using a large (2p3/21f5/22p1/21g9/2) valence space and a 56/28Ni28 core.

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages

PubMed Central

Yu, Ying; Fuscoe, James C.; Zhao, Chen; Guo, Chao; Jia, Meiwen; Qing, Tao; Bannon, Desmond I.; Lancashire, Lee; Bao, Wenjun; Du, Tingting; Luo, Heng; Su, Zhenqiang; Jones, Wendell D.; Moland, Carrie L.; Branham, William S.; Qian, Feng; Ning, Baitang; Li, Yan; Hong, Huixiao; Guo, Lei; Mei, Nan; Shi, Tieliu; Wang, Kevin Y.; Wolfinger, Russell D.; Nikolsky, Yuri; Walker, Stephen J.; Duerksen-Hughes, Penelope; Mason, Christopher E.; Tong, Weida; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Shi, Leming; Wang, Charles

2014-01-01

The rat has been used extensively as a model for evaluating chemical toxicities and for understanding drug mechanisms. However, its transcriptome across multiple organs, or developmental stages, has not yet been reported. Here we show, as part of the SEQC consortium efforts, a comprehensive rat transcriptomic BodyMap created by performing RNA-Seq on 320 samples from 11 organs of both sexes of juvenile, adolescent, adult and aged Fischer 344 rats. We catalogue the expression profiles of 40,064 genes, 65,167 transcripts, 31,909 alternatively spliced transcript variants and 2,367 non-coding genes/non-coding RNAs (ncRNAs) annotated in AceView. We find that organ-enriched, differentially expressed genes reflect the known organ-specific biological activities. A large number of transcripts show organ-specific, age-dependent or sex-specific differential expression patterns. We create a web-based, open-access rat BodyMap database of expression profiles with crosslinks to other widely used databases, anticipating that it will serve as a primary resource for biomedical research using the rat model. PMID:24510058

Comparison of short-lived medical isotopes activation by laser thin target induced protons and conventional cyclotron proton beams

NASA Astrophysics Data System (ADS)

Murray, Joseph; Dudnikova, Galina; Liu, Tung-Chang; Papadopoulos, Dennis; Sagdeev, Roald; Su, J. J.; UMD MicroPET Team

2014-10-01

Production diagnostic or therapeutic nuclear medicines are either by nuclear reactors or by ion accelerators. In general, diagnostic nuclear radioisotopes have a very short half-life varying from tens of minutes for PET tracers and few hours for SPECT tracers. Thus supplies of PET and SPECT radiotracers are limited by regional production facilities. For example 18F-fluorodeoxyglucose (FDG) is the most desired tracer for positron emission tomography because its 110 minutes half-life is sufficient long for transport from production facilities to nearby users. From nuclear activation to completing image taking must be done within 4 hours. Decentralized production of diagnostic radioisotopes will be idea to make high specific activity radiotracers available to researches and clinicians. 11 C, 13 N, 15 O and 18 F can be produced in the energy range from 10-20 MeV by protons. Protons of energies up to tens of MeV generated by intense laser interacting with hydrogen containing targets have been demonstrated by many groups in the past decade. We use 2D PIC code for proton acceleration, Geant4 Monte Carlo code for nuclei activation to compare the yields and specific activities of short-lived isotopes produced by cyclotron proton beams and laser driven protons.

Isotope-coded, iodoacetamide-based reagent to determine individual cysteine pKa values by MALDI-TOF mass spectrometry

PubMed Central

Nelson, Kimberly J.; Day, Amanda E.; Zeng, Bubing B.; King, S. Bruce; Poole, Leslie B.

2008-01-01

Cysteine reactivity in enzymes is imparted to a large extent by the stabilization of the deprotonated form of the reduced cysteine (i.e. the thiolate) within the active site. While this is likely to be an important chemical attribute of many thiol-based enzymes including cysteine-dependent peroxidases (peroxiredoxins) and proteases, only relatively few pKa values have been determined experimentally. Presented here is a new technique for determining the pKa value of cysteine residues through quantitative mass spectrometry following chemical modification with an iodoacetamide-based reagent over a range of pH buffers. This isotope-coded reagent, N-phenyl iodoacetamide (iodoacetanilide), is readily prepared in deuterated (d5) and protiated (d0) versions and is more reactive toward free cysteine than is iodoacetamide. Using this approach, the pKa values for the two cysteine residues in Escherichia coli thioredoxin were determined to be 6.5 and > 10, in good agreement with previous reports using chemical modification approaches. This technique allows the pKa of specific cysteine residues to be determined in a clear, fast, and simple manner and, because cysteine residues on separate tryptic peptides are measured separately, is not complicated by the presence of multiple cysteines within the protein of interest. PMID:18162165

Crosslinked anion exchange membranes with primary diamine-based crosslinkers for vanadium redox flow battery application

NASA Astrophysics Data System (ADS)

Cha, Min Suc; Jeong, Hwan Yeop; Shin, Hee Young; Hong, Soo Hyun; Kim, Tae-Ho; Oh, Seong-Geun; Lee, Jang Yong; Hong, Young Taik

2017-09-01

A series of polysulfone-based crosslinked anion exchange membranes (AEMs) with primary diamine-based crosslinkers has been prepared via simple a crosslinking process as low-cost and durable membranes for vanadium redox flow batteries (VRFBs). Chloromethylated polysulfone is used as a precursor polymer for crosslinked AEMs (CAPSU-x) with different degrees of crosslinking. Among the developed AEMs, CAPSU-2.5 shows outstanding dimensional stability and anion (Cl-, SO42-, and OH-) conductivity. Moreover, CAPSU-2.5 exhibits much lower vanadium ion permeability (2.72 × 10-8 cm2 min-1) than Nafion 115 (2.88 × 10-6 cm2 min-1), which results in an excellent coulombic efficiency of 100%. The chemical and operational stabilities of the membranes have been investigated via ex situ soaking tests in 0.1 M VO2+ solution and in situ operation tests for 100 cycles, respectively. The excellent chemical, physical, and electrochemical properties of the CAPSU-2.5 membrane make it suitable for use in VRFBs.

Crosslinking transcription factors to their recognition sequences with PtII complexes

NASA Technical Reports Server (NTRS)

Chu, B. C.; Orgel, L. E.

1992-01-01

We have prepared phosphorothioate-containing cyclic oligodeoxynucleotides that fold into 'dumbbells' containing CRE and TRE sequences, the binding sequences for the CREB and JUN proteins, respectively. Six phosphorothioate residues were introduced into each of the recognition sequences. K2PtCl4 crosslinks CRE to CREB and TRE to JUN. The extent of crosslinking is about eight times greater than that observed with standard oligodeoxynucleotides and amounts to 30-50% of the efficiency of non-covalent association as estimated by gel-shift assays. Crosslinking is reversed by incubation with NaCN. The crosslinking reaction is specific--a dumbbell oligonucleotide with six phosphorothioate groups introduced into the Sp1 recognition sequence could not be crosslinked efficiently to CREB or JUN proteins with K2PtCl4. The binding of TRE to CREB is not strong enough for effective detection by gel-shift assays, but the TRE-CREB complex is crosslinked efficiently by K2PtCl4 and can then readily be detected.

Inability of keratinocytes lacking their specific transglutaminase to form cross-linked envelopes: Absence of envelopes as a simple diagnostic test for lamellar ichthyosis

PubMed Central

Jeon, Saewha; Djian, Philippe; Green, Howard

1998-01-01

Epidermal keratinocytes, late in their terminal differentiation, form cross-linked envelopes resistant to ionic detergent and reducing agent. Because the cross-linking process is catalyzed by the keratinocyte transglutaminase, the absence of active transglutaminase should result in failure of the keratinocyte to form a cross-linked envelope. Three keratinocyte strains bearing mutations in the keratinocyte transglutaminase were examined: two contained no detectable transglutaminase mRNA and none contained active enzyme. All three were unable to form cross-linked envelopes, either spontaneously in stratified cultures or upon induction with Ca2+. Although stratum corneum of normal humans and scales from patients with different ichthyotic diseases contain cross-linked envelopes, those from patients with transglutaminase-negative lamellar ichthyosis do not. Therefore, the disease due to the absence of transglutaminase may be readily distinguished from other ichthyotic diseases by a simple test for cross-linked envelopes. PMID:9435253

Development and evaluation of polyvinyl-alcohol blend polymer films as battery separators

NASA Technical Reports Server (NTRS)

Manzo, M. A.

1982-01-01

Several dialdehydes and epoxies were evaluated for their suitability as cross-linkers. Optium concentrations of several cross-linking reagents were determined. A two-step method of cross-linking, which involves treatment of the film in an acid or acid periodate bath, was investigated and dropped in favor of a one-step method in which the acid catalyst, which initiates cross-linking, is added to the PVA - cross-linker solution before casting. The cross-linking was thus achieved during the drying step. This one-step method was much more adaptable to commercial processing. Cross-linked films were characterized as alkaline battery separators. Films were prepared in the lab and tested in cells in order to evaluate the effect of film composition and a number of processing parameters on cell performance. These tests were conducted in order to provide a broader data base from which to select optimum processing parameters. Results of the separator screening tests and the cell tests are discussed.

Mechanical and spectroscopic characterization of crosslinked zein films cast from solutions of acetic acid leading to a new mechanism for the crosslinking of oleic acid plasticized zein films.

PubMed

Turasan, Hazal; Barber, Emma A; Malm, Morgan; Kokini, Jozef L

2018-06-01

This study discovered through FTIR, FT-Raman and rheological measurements that glutaraldehyde binds to zein through the amine groups of glutamine turns by replacing the already-bonded oleic acid molecules and forming imine structures. As a secondary crosslinking mechanism, glutaraldehyde unfolds some of the α-helices and turns them into β-sheets. While crosslinking resulted in stiffer and less ductile zein films, it made the surface of the films rougher, measured using AFM, and more hydrophilic, measured using WCA. In the crosslinking conditions in this study, the number of crosslinks estimated from rubber elasticity theory were not enough to change the water vapor permeability of the films significantly. Improving the understanding of crosslinking mechanism and its effects on physical and chemical properties of zein films can be useful to develop stiffer, stronger and more durable platforms for biodegradable biosensors, microfluidic devices or scaffolds. Copyright © 2018 Elsevier Ltd. All rights reserved.

Cross-linking and the molecular packing of corneal collagen

NASA Technical Reports Server (NTRS)

Yamauchi, M.; Chandler, G. S.; Tanzawa, H.; Katz, E. P.

1996-01-01

We have quantitatively characterized, for the first time, the cross-linking in bovine cornea collagen as a function of age. The major iminium reducible cross-links were dehydro-hydroxylysinonorleucine (deH-HLNL) and dehydro-histidinohydroxymerodesmosine (deH-HHMD). The former rapidly diminished after birth; however, the latter persisted in mature animals at a level of 0.3 - 0.4 moles/mole of collagen. A nonreducible cross-link, histidinohydroxylysinonorleucine (HHL), previously found only in skin, was also found to be a major mature cross-link in cornea. The presence of HHL indicates that cornea fibrils have a molecular packing similar to skin collagen. However, like deH-HHMD, the HHL content in corneal fibrils only reaches a maximum value with time about half that of skin. These data suggest that the corneal fibrils are comprised of discrete filaments that are internally stabilized by HHL and deH-HHMD cross-links. This pattern of intermolecular cross-linking would facilitate the special collagen swelling property required for corneal transparency.

Organization of photosystem I polypeptides examined by chemical cross-linking

NASA Technical Reports Server (NTRS)

Armbrust, T. S.; Chitnis, P. R.; Guikema, J. A.; Spooner, B. S. (Principal Investigator)

1996-01-01

Photosystem I from the cyanobacterium Synechocystis sp. PCC 6803 was examined using the chemical cross-linkers glutaraldehyde and N-ethyl-1-3-[3-(dimethylamino)propyl]carbodiimide to investigate the organization of the polypeptide subunits. Thylakoid membranes and photosystem I, which was isolated by Triton X-100 fractionation, were treated with cross-linking reagents and were resolved using a Tricine/urea low-molecular-weight resolution gel system. Subunit-specific antibodies and western blotting analysis were used to identify the components of cross-linked species. These analyses identified glutaraldehyde-dependent cross-linking products composed of small amounts of PsaD and PsaC, PsaC and PsaE, and PsaE and PsaF. The novel cross-link between PsaE and PsaF was also observed following treatment with N-ethyl-1-3-[3-(dimethylamino)propyl]carbodiimide. These cross-linking results suggest a structural interaction between PsaE and PsaF and predict a transmembrane topology for PsaF.

Fabrication and characterization of electrospun gelatin nanofibers crosslinked with oxidized phenolic compounds.

PubMed

Tavassoli-Kafrani, Elham; Goli, Sayed Amir Hossein; Fathi, Milad

2017-10-01

In this study, the ability of oxidized phenolic compounds of tannic, gallic, ferulic and caffeic acids to crosslink gelatin (G) was investigated. The electrospun crosslinked gelatin nanofibers were assessed in terms of gelatin solution properties, fiber morphology, thermal properties, FTIR spectra, XRD pattern and antioxidant activity. Tannic acid showed the most crosslinking activity towards gelatin (13.3 vs 7.44, 4.65, and 3.45% for caffeic, gallic and ferulic, respectively). Crosslinking enhanced roughly electrical conductivity of gelatin solution while the surface tension and viscosity reduced. According to scanning electron microscopy (SEM) results, the fibrous structure of crosslinked gelatin nanofibers didn't change while their diameter increased to the highest value of 280nm for gelatin-tannic. Gelatin-gallic sample showed the highest total phenolic content (86.3mg gallic acid equivalent/g) and antioxidant activity (86.5%). Surprisingly, from differential scanning calorimetry (DSC) curves, it was found that crosslinking led to the reduction of thermal stability of gelatin nanofibers. Copyright © 2017 Elsevier B.V. All rights reserved.

Structure of starch aerogel as affected by crosslinking and feasibility assessment of the aerogel for an anti-fungal volatile release.

PubMed

Abhari, Negar; Madadlou, Ashkan; Dini, Ali

2017-04-15

Starch suspensions were crosslinked with trisodium citrate for either 0 or 17h, gelled and then freeze-dried to corresponding aerogels. The aerogel from the 17h-crosslinked suspension was loaded with the antifungal compound, trans-2-hexenal, and coated with the surfactant, sorbitan monooleate. Aerogel hardness was increased by the citrate-mediated crosslinking, whereas its adhesiveness decreased. Starch gelation decreased the crystallinity index (CrI) from 59% to ≈23%; however, the pre-gelation crosslinking resulted in a higher CrI value (i.e. ≈38%) for the aerogel. The voids at the internal microstructure of the 17h-crosslinked aerogel were more uniform and coating with surfactant closed the surface openings. The latter accordingly resulted in a more sustained release of the volatile, trans-2-hexenal, from the crosslinked starch aerogel and led to slower lethality of Aspergillus parasiticus cells inoculated on pistachio nuts compared with the non-coated condition. Copyright © 2016 Elsevier Ltd. All rights reserved.

Physicochemical properties and micro-structural characteristics in starch from kudzu root as affected by cross-linking.

PubMed

Chen, Boru; Dang, Leping; Zhang, Xiao; Fang, Wenzhi; Hou, Mengna; Liu, Tiankuo; Wang, Zhanzhong

2017-03-15

Kudzu starch was cross-linked with sodium trimetaphosphate (STMP) at different temperatures, time and of STMP concentrations in this work. The cross-linked starches (CLSs) were fractionated further into cross-linked amylose and amylopectin in order to compare the effect of cross-linking on the microstructure. According to scanning electron microscope (SEM), CLSs displayed the resemble appearance of spherical and polygonal shapes like NS. X-ray diffraction (XRD) revealed that amylose of native starch (A), NS and CLS displayed a combination of A-type and B-type structure, while that was not found in amylose of cross-linked starch (CLA). The deconvoluted fourier transform infrared (FT-IR) indicated that crystal structure of kudzu starch was losing with the proceeding of cross-linking reaction. The CLSs exhibited a higher retrogradation and freeze-thaw stability than NS. This was accompanied by a significant decrease in sedimentation, transparency, swelling power and solubility. Copyright © 2016 Elsevier Ltd. All rights reserved.

Transglutaminase catalyzed cross-linking of sodium caseinate improves oxidative stability of flaxseed oil emulsion.

PubMed

Ma, Hairan; Forssell, Pirkko; Kylli, Petri; Lampi, Anna-Maija; Buchert, Johanna; Boer, Harry; Partanen, Riitta

2012-06-20

Sodium caseinate was modified by transglutaminase catalyzed cross-linking reaction prior to the emulsification process in order to study the effect of cross-linking on the oxidative stability of protein stabilized emulsions. The extent of the cross-linking catalyzed by different dosages of transglutaminase was investigated by following the ammonia production during the reaction and using SDS-PAGE gel. O/W emulsions prepared with the cross-linked and non-cross-linked sodium caseinates were stored for 30 days under the same conditions. Peroxide value measurement, oxygen consumption measurement, and headspace gas chromatography analysis were used to study the oxidative stability of the emulsions. The emulsion made of the cross-linked sodium caseinate showed an improved oxidative stability with reduced formation of fatty acid hydroperoxides and volatiles and a longer period of low rate oxygen consumption. The improving effect of transglutaminase catalyzed cross-linking could be most likely attributed to the enhanced physical stability of the interfacial protein layer against competitive adsorption by oil oxidation products.

Interactions of collagen molecules in the presence of N-hydroxysuccinimide activated adipic acid (NHS-AA) as a crosslinking agent.

PubMed

Zhang, Min; Wu, Kun; Li, Guoying

2011-11-01

The effect of crosslinking agent on pepsin-soluble bovine collagen solution was examined using N-hydroxysuccinimide activated adipic acid (NHS-AA) as a crosslinker. Electrophoretic patterns indicated that crosslinks formed when NHS-AA was added. A higher polarity level deduced from the changes in the fluorescence emission spectrum of pyrene in the crosslinked collagen solution indicated that the formation of well-ordered aggregates was suppressed. The random aggregation of collagens was also observed by atomic force microscopy (AFM). Furthermore, the association of collagens into fibrils was influenced by crosslinking. Self-assembly was suppressed at 37°C; however, as temperature was increased to 39°C, a small amount of NHS-AA leaded to an improvement in the ability of self-aggregation. Although more random structure was brought about by crosslinking, self-aggregation might still be promoted as temperature was increased, accompanying by the thermal stability improvement of fibrils. Copyright © 2011 Elsevier B.V. All rights reserved.

Degradation Analysis of NBR and Epichlorohydrin Rubber by New Micro Analysis Method

NASA Astrophysics Data System (ADS)

Katoh, Hisao; Kamoto, Ritsu; Murata, Jun

The degradation analysis of NBR and Epichlorohydrin rubber was carried out by infrared micro spectroscopy (μ-IR) and micro sampling mass spectrometry (μ-MS) which gives information on the scission and crosslinking of rubber molecules. Samples were prepared by three different treatments, heat as well as ultra violet (UV) and electron beam (EB) irradiations. It was found for NBR vulcanizates that the heat treatment induced the oxidation, scission and crosslinking of rubber molecules. By the UV treatment, chain scission and crosslinking accompanied by a slight oxidation were induced. The EB treatment enhanced the crosslinking, however, the extent of oxidation was negligible. For Epichlorohydrin rubber vulcanizates, the heat treatment accelerated chain scission rather than crosslinking. On the other hand, the oxidation and crosslinking were induced by the UV and EB treatments.

Stereocomplexation of low molecular weight poly(L-lactic acid) and high molecular weight poly(D-lactic acid), radiation crosslinking PLLA/PDLA stereocomplexes and their characterization

NASA Astrophysics Data System (ADS)

Quynh, Tran Minh; Mai, Hoang Hoa; Lan, Pham Ngoc

2013-02-01

Poly(L-lactic acid)s (PLLAx) were synthesized from L-lactic acid by polycondensation. Different stereocomplexes were also obtained with equimolar mixtures of synthesized PLLAx and a commercial PDLA. The stereocomplexes were crosslinked with triallyl isocyanurate (TAIC) by gamma irradiation. Crosslinking density increased with radiation doses, the heavier the crosslinking network, the lower its swelling degree. The crosslinking structures were introduced in the stereocomplexes inhibiting the mobility for crystallization of PLLA molecules. Thermal and mechanical properties of PLA stereocomplexes were remarkably enhanced by radiation induced crosslinking. PLA stereocomplex does not seem to be degraded by PLLA degrading microorganisms existing in compost at room temperature, but the synthesized PLLA was significantly degraded.

Recycling and processing of several typical crosslinked polymer scraps with enhanced mechanical properties based on solid-state mechanochemical milling

NASA Astrophysics Data System (ADS)

Lu, Canhui; Zhang, Xinxing; Zhang, Wei

2015-05-01

The partially devulcanization or de-crosslinking of ground tire rubber (GTR), post-vulcanized fluororubber scraps and crosslinked polyethylene from cable scraps through high-shear mechanochemical milling (HSMM) was conducted by a modified solid-state mechanochemical reactor. The results indicated that the HSMM treated crosslinked polymer scraps can be reprocessed as virgin rubbers or thermoplastics to produce materials with high performance. The foamed composites of low density polyethylene/GTR and the blend of post-vulcanized flurorubber (FKM) with polyacrylate rubber (ACM) with better processability and mechanical properties were obtained. The morphology observation showed that the dispersion and compatibility between de-crosslinked polymer scraps and matrix were enhanced. The results demonstrated that HSMM is a feasible alternative technology for recycling post-vulcanized or crosslinked polymer scraps.

An interactive code (NETPATH) for modeling NET geochemical reactions along a flow PATH, version 2.0

USGS Publications Warehouse

Plummer, Niel; Prestemon, Eric C.; Parkhurst, David L.

1994-01-01

NETPATH is an interactive Fortran 77 computer program used to interpret net geochemical mass-balance reactions between an initial and final water along a hydrologic flow path. Alternatively, NETPATH computes the mixing proportions of two to five initial waters and net geochemical reactions that can account for the observed composition of a final water. The program utilizes previously defined chemical and isotopic data for waters from a hydrochemical system. For a set of mineral and (or) gas phases hypothesized to be the reactive phases in the system, NETPATH calculates the mass transfers in every possible combination of the selected phases that accounts for the observed changes in the selected chemical and (or) isotopic compositions observed along the flow path. The calculations are of use in interpreting geochemical reactions, mixing proportions, evaporation and (or) dilution of waters, and mineral mass transfer in the chemical and isotopic evolution of natural and environmental waters. Rayleigh distillation calculations are applied to each mass-balance model that satisfies the constraints to predict carbon, sulfur, nitrogen, and strontium isotopic compositions at the end point, including radiocarbon dating. DB is an interactive Fortran 77 computer program used to enter analytical data into NETPATH, and calculate the distribution of species in aqueous solution. This report describes the types of problems that can be solved, the methods used to solve problems, and the features available in the program to facilitate these solutions. Examples are presented to demonstrate most of the applications and features of NETPATH. The codes DB and NETPATH can be executed in the UNIX or DOS1 environment. This report replaces U.S. Geological Survey Water-Resources Investigations Report 91-4078, by Plummer and others, which described the original release of NETPATH, version 1.0 (dated December, 1991), and documents revisions and enhancements that are included in version 2.0. 1 The use of trade, brand or product names in this report is for identification purposes only and does not constitute endorsement by the U.S. Geological Survey.

Quantitative analysis of N-glycans from human alfa-acid-glycoprotein using stable isotope labeling and zwitterionic hydrophilic interaction capillary liquid chromatography electrospray mass spectrometry as tool for pancreatic disease diagnosis.

PubMed

Giménez, Estela; Balmaña, Meritxell; Figueras, Joan; Fort, Esther; de Bolós, Carme; Sanz-Nebot, Victòria; Peracaula, Rosa; Rizzi, Andreas

2015-03-25

In this work we demonstrate the potential of glycan reductive isotope labeling (GRIL) using [(12)C]- and [(13)C]-coded aniline and zwitterionic hydrophilic interaction capillary liquid chromatography electrospray mass spectrometry (μZIC-HILIC-ESI-MS) for relative quantitation of glycosylation variants in selected glycoproteins present in samples from cancer patients. Human α1-acid-glycoprotein (hAGP) is an acute phase serum glycoprotein whose glycosylation has been described to be altered in cancer and chronic inflammation. However, it is not clear yet whether some particular glycans in hAGP can be used as biomarker for differentiating between these two pathologies. In this work, hAGP was isolated by immunoaffinity chromatography (IAC) from serum samples of healthy individuals and from those suffering chronic pancreatitis and different stages of pancreatic cancer, respectively. After de-N-glycosylation, relative quantitation of the hAGP glycans was carried out using stable isotope labeling and μZIC-HILIC-ESI-MS analysis. First, protein denaturing conditions prior to PNGase F digestion were optimized to achieve quantitative digestion yields, and the reproducibility of the established methodology was evaluated with standard hAGP. Then, the proposed method was applied to the analysis of the clinical samples (control vs. pathological). Pancreatic cancer samples clearly showed an increase in the abundance of fucosylated glycans as the stage of the disease increases and this was unlike to samples from chronic pancreatitis. The results gained here indicate the mentioned glycan in hAGP as a candidate structure worth to be corroborated by an extended study including more clinical cases; especially those with chronic pancreatitis and initial stages of pancreatic cancer. Importantly, the results demonstrate that the presented methodology combining an enrichment of a target protein by IAC with isotope coded relative quantitation of N-glycans can be successfully used for targeted glycomics studies. The methodology is assumed being suitable as well for other such studies aimed at finding novel cancer associated glycoprotein biomarkers. Copyright © 2015 Elsevier B.V. All rights reserved.

Determination of the δ15N and δ13C of total nitrogen and carbon in solids; RSIL lab code 1832

USGS Publications Warehouse

Revesz, Kinga; Qi, Haiping; Coplan, Tyler B.

2006-01-01

The purpose of the Reston Stable Isotope Laboratory (RSIL) lab code 1832 is to determine the δ(15N/14N), abbreviated as δ15N, and the δ(13C/12C), abbreviated as δ13C, of total nitrogen and carbon in a solid sample. A Carlo Erba NC 2500 elemental analyzer (EA) is used to convert total nitrogen and carbon in a solid sample into N2 and CO2 gas. The EA is connected to a continuous flow isotope-ratio mass spectrometer (CF-IRMS), which determines the relative difference in stable nitrogen isotope-amount ratio (15N/14N) of the product N2 gas and the relative difference in stable carbon isotope-amount ratio (13C/12C) of the product CO2 gas. The combustion is quantitative; no isotopic fractionation is involved. Samples are placed in tin capsules and loaded into a Costech Zero Blank Autosampler on the EA. Under computer control, samples then are dropped into a heated reaction tube that contains an oxidant, where combustion takes place in a helium atmosphere containing an excess of oxygen gas. Combustion products are transported by a helium carrier through a reduction furnace to remove excess oxygen and to convert all nitrous oxides into N2 and through a drying tube to remove water. The gas-phase products, mainly CO2 and N2, are separated by a gas chromatograph. The gas is then introduced into the IRMS through a Finnigan MAT (now Thermo Scientific) ConFlo II interface. The Finnigan MAT ConFlo II interface is used for introducing not only sample into the IRMS but also N2 and CO2 reference gases and helium for sample dilution. The flash combustion is quantitative; no isotopic fractionation is involved. The IRMS is a Thermo Scientific Delta V CF-IRMS. It has a universal triple collector, two wide cups with a narrow cup in the middle; it is capable of measuring mass/charge (m/z) 28, 29, 30 or with a magnet current change 44, 45, 46, simultaneously. The ion beams from these m/z values are as follows: m/z 28 = N2 = 14N/14N; m/z 29 = N2 = 14N/15N primarily; m/z 30 = NO = 14N/16O primarily, which is a sign of contamination or incomplete reduction; m/z 44 = CO2 = 12C16O16O; m/z 45 = CO2 = 13C16O16O primarily; and m/z 46 = CO2 = 12C16O18O primarily.

Two DD-carboxypeptidases from Mycobacterium smegmatis affect cell surface properties through regulation of peptidoglycan cross-linking and glycopeptidolipids.

PubMed

Pandey, Satya Deo; Pal, Shilpa; Kumar N, Ganesh; Bansal, Ankita; Mallick, Sathi; Ghosh, Anindya S

2018-05-07

During the peptidoglycan (PG) maturation of mycobacteria, the glycan strands are interlinked by both 3-3 (between two meso-DAP) and 4-3 cross-links (between D-ala and meso-DAP), though there is a predominance (60-80%) of 3-3 cross-links. The DD-CPases act on pentapeptides to generate tetrapeptides that are used by LD-transpeptidases as substrates to form 3-3 cross-links. Therefore, DD-CPases play a crucial role in mycobacterial PG cross-link formation. However, the physiology of DD-CPases in mycobacteria is relatively unexplored. Here, we deleted two DD-CPase genes, msmeg_2433 , and msmeg_2432 , both individually and in combination, from Mycobacterium smegmatis mc 2 155. Though the single DD-CPase deletions had no significant impact on the mycobacterial physiology, many interesting functional alterations were observed in the double deletion mutant, viz. , a predominance in PG cross-link formation was shifted from 3-3 cross-links to 4-3, cell surface glycopeptidolipid (GPL) expression was reduced and susceptibility towards β-lactams and anti-tubercular agents was enhanced. Moreover, the existence of the double mutant within murine macrophages was better as compared to the parent. Interestingly, the complementation with any one of the DD-CPase genes could restore the wild-type phenotype. In a nutshell, we infer that the altered ratio of 4-3: 3-3 PG cross-links might have influenced the expression of surface GPLs, colony morphology, biofilm formation,, drug susceptibility and subsistence of the cells within macrophages. Importance The glycan strands in mycobacterial peptidoglycan (PG) are interlinked by both 3-3 and 4-3 cross-links. The DD-CPases generate tetrapeptides by acting on the pentapeptides, and LD-transpeptidases use tetrapeptides as substrates to form 3-3 cross-links. Here, we showed that simultaneous deletions of two DD-CPases alter the nature of PG cross-linking from 3-3 cross-links to 4-3 cross-links. The deletions subsequently decrease the expression of Glycopeptidolipids (a significant surface lipid present in many non-tuberculous mycobacteria including Mycobacterium smegmatis ) and affect other physiological parameters like cell morphology, growth rate, biofilm formation, antibiotic susceptibility and existence within murine macrophages. Thus, unraveling the physiology of DD-CPases might help us design anti-mycobacterial therapeutics in future. Copyright © 2018 American Society for Microbiology.

Contributions to the study of the mechanisms of photodynamic cross-linking of proteins

NASA Astrophysics Data System (ADS)

Shen, Hui-Rong

The illumination of proteins in solution and in cells in the presence of photosensitizers may lead to the inter- and/or intramolecular crosslinking of the proteins (photosensitized or photodynamic crosslinking). This phenomenon appears to be involved in the photohemolysis of red cells, cataract development, skin photoaging, photodynamic therapy for cancers, laser welding of tissues, biomaterial modification, and other biological situations. Although the processes involved in the photocrosslinking of proteins have been extensively studied, the mechanisms involved are still largely unknown. The main objectives of the studies reported in this dissertation were to investigate the detailed mechanisms involved in the photocrosslinking of proteins and to determine the chemical nature of the crosslinks formed. The first part of this study was devoted to the verification of the roles of His, Lys and Tyr in the photodynamic crosslinking of proteins. The crosslinking reaction was modeled using tailor-made water-soluble synthetic N-(2-hydroxypropyl)methacrylamide (HPMA) copolymers containing epsilon-aminocaproic acid side chains terminating in His, Lys or tyrosinamide residues photosensitized by rose bengal (RB) and flavin mononucleotide (FMN). RB typically produces singlet oxygen, whereas FMN produces both singlet oxygen and radicals. His-His and His-Lys crosslinks were formed with RB as the sensitizer. RB-sensitization did not crosslink Tyr residues, whereas FMN coupled two Tyr residues via a radical pathway. Protection of the His and/or Lys residues in ribonuclease A (RNase A) significantly inhibited the extent of intermolecular crosslinking, and confirmed the key roles played by His and Lys in crosslinking reactions. The second part of this study involved the elucidation of the detailed reaction mechanisms and the chemical structures of His-His and Tyr-Tyr crosslinks. N-benzoyl-histidine (Bz-His) and N-acetyl-tyrosine (Ac-Tyr) were used to model the photosensitized crosslinking of proteins involving His and Tyr residues. Photocrosslinking of Bz-His was performed in phosphate buffer at pH 7.4 with immobilized RB beads as sensitizer. The main dimerized product was isolated and characterized. Its chemical structure was established by MS and NMR methods. Ac-Tyr was photocrosslinked with FMN as the sensitizer at pH 6.0; oxygen was necessary. Three main crosslinked dimers were obtained. Their chemical structures were determined by MS and NMR data.

Synthesis and characterization of drug loaded albumin mesospheres for intratumoral chemotherapy

NASA Astrophysics Data System (ADS)

Freeman, Shema Taian

Conventional chemotherapy is problematic due to toxic complications. Intratumoral (IT) drug delivery, offers a new, less toxic, potentially more effective treatment concept. The objectives of this research encompassed (1) an investigation of the synthesis of BSA mesospheres (MS) employing genipin (GEN) as a novel crosslinking agent, (2) comparison with glutaraldehyde (GTA) crosslinked mesosphere, (3) a study of process parameters to define conditions for the synthesis of 1-10microm drug loaded mesospheres, and (4) investigation of the drug delivery properties of such mesospheres for IT chemotherapy. Smooth, spherical BSA-MS, crosslinked with glutaraldehyde and genipin, were prepared in a dry particle size range of 1microm to 10microm. It was shown that increasing dispersion stirring rate, crosslinking time and GEN/BSA ratio led to a decrease in particle size and a narrower particle distribution. It was also shown that increasing crosslinking time, GEN/BSA ratio, BSA concentrations, GEN concentration slowed enzymatic degradation. Post-loading and in situ drug loading methods were studied for the incorporation of cyclophosphamide and cisplatin into mesospheres. Maximum post loading of cisplatin was 3.2% (w/w) and 2.6% (w/w) with GEN and with GTA crosslinking. For cyclophosphamide 8.2% (w/w) and 7.1% (w/w) loading was achieved with GEN and GTA respectively. In situ drug loaded MS genipin and glutaraldehyde crosslinked mesospheres were also synthesized with 1.8% (w/w) cisplatin (using GEN) and 1.2% (w/w) (using GTA). Maximum loading of 13.3% (w/w) was achieved for cyclophosphamide in genipin crosslinked mesospheres. The cytotoxicity of in situ loaded genipin and glutaraldehyde crosslinked cisplatin mesospheres was evaluated using a murine Lewis lung model. Both genipin and glutaraldehyde crosslinked BSA-cisplatin mesospheres proved to be cytotoxic during a 48 hour test. Ultimately a standard set of processing parameters (BSA concentration, CAB concentration, GEN concentration, GEN/BSA ratio, stabilization stirring rate and crosslinking time) were defined to produce both GEN and GTA crosslinked cisplatin and cyclophosphamide BSA mesospheres. In vitro analysis confirmed the utility of mesosphere bound drug. In several related studies, (1) IT delivered dispersions of mitoxantrone loaded albumin microspheres were shown to afford an effective treatment, with significantly prolonging animal survival and (2) genipin and gadolinium crosslinked MS were prepared from HA and BSA/HA.

Benchmarking Heavy Ion Transport Codes FLUKA, HETC-HEDS MARS15, MCNPX, and PHITS

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

Ronningen, Reginald Martin; Remec, Igor; Heilbronn, Lawrence H.

Powerful accelerators such as spallation neutron sources, muon-collider/neutrino facilities, and rare isotope beam facilities must be designed with the consideration that they handle the beam power reliably and safely, and they must be optimized to yield maximum performance relative to their design requirements. The simulation codes used for design purposes must produce reliable results. If not, component and facility designs can become costly, have limited lifetime and usefulness, and could even be unsafe. The objective of this proposal is to assess the performance of the currently available codes PHITS, FLUKA, MARS15, MCNPX, and HETC-HEDS that could be used for designmore » simulations involving heavy ion transport. We plan to access their performance by performing simulations and comparing results against experimental data of benchmark quality. Quantitative knowledge of the biases and the uncertainties of the simulations is essential as this potentially impacts the safe, reliable and cost effective design of any future radioactive ion beam facility. Further benchmarking of heavy-ion transport codes was one of the actions recommended in the Report of the 2003 RIA R&D Workshop".« less

Improvements of MCOR: A Monte Carlo depletion code system for fuel assembly reference calculations

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

Tippayakul, C.; Ivanov, K.; Misu, S.

2006-07-01

This paper presents the improvements of MCOR, a Monte Carlo depletion code system for fuel assembly reference calculations. The improvements of MCOR were initiated by the cooperation between the Penn State Univ. and AREVA NP to enhance the original Penn State Univ. MCOR version in order to be used as a new Monte Carlo depletion analysis tool. Essentially, a new depletion module using KORIGEN is utilized to replace the existing ORIGEN-S depletion module in MCOR. Furthermore, the online burnup cross section generation by the Monte Carlo calculation is implemented in the improved version instead of using the burnup cross sectionmore » library pre-generated by a transport code. Other code features have also been added to make the new MCOR version easier to use. This paper, in addition, presents the result comparisons of the original and the improved MCOR versions against CASMO-4 and OCTOPUS. It was observed in the comparisons that there were quite significant improvements of the results in terms of k{sub inf}, fission rate distributions and isotopic contents. (authors)« less

Photocrosslinking approaches to interactome mapping

PubMed Central

Pham, Nam D.; Parker, Randy B.; Kohler, Jennifer J.

2012-01-01

Photocrosslinking approaches can be used to map interactome networks within the context of living cells. Photocrosslinking methods rely on use of metabolic engineering or genetic code expansion to incorporate photocrosslinking analogs of amino acids or sugars into cellular biomolecules. Immunological and mass spectrometry techniques are used to analyze crosslinked complexes, thereby defining specific interactomes. Because photocrosslinking can be conducted in native, cellular settings, it can be used to define context-dependent interactions. Photocrosslinking methods are also ideally suited for determining interactome dynamics, mapping interaction interfaces, and identifying transient interactions in which intrinsically disordered proteins and glycoproteins engage. Here we discuss the application of cell-based photocrosslinking to the study of specific problems in immune cell signaling, transcription, membrane protein dynamics, nucleocytoplasmic transport, and chaperone-assisted protein folding. PMID:23149092

A single miR390 targeting event is sufficient for triggering TAS3-tasiRNA biogenesis in Arabidopsis

PubMed Central

Marchais, Antonin; Sarazin, Alexis; Oberlin, Stefan; Voinnet, Olivier

2017-01-01

Abstract In plants, tasiRNAs form a class of endogenous secondary siRNAs produced through the action of RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6) upon microRNA-mediated cleavage of non-coding TAS RNAs. In Arabidopsis thaliana, TAS1, TAS2 and TAS4 tasiRNA production proceeds via a single cleavage event mediated by 22nt-long or/and asymmetric miRNAs in an ARGONAUTE-1 (AGO1)-dependent manner. By contrast, tasiRNA production from TAS3 seems to follow the so-called ‘two-hit’ process, where dual targeting of TAS3, specifically mediated by the 21nt-long, symmetric miR390, initiates AGO7-dependent tasiRNA production. Interestingly, features for TAS3 tasiRNA production differ in other plant species and we show here that such features also enable TAS3 tasiRNA biogenesis in Arabidopsis, and that a single miR390 targeting event is, in fact, sufficient for this process, suggesting that the ‘one-hit’ model underpins all the necessary rudiments of secondary siRNA biogenesis from plant TAS transcripts. Further results suggest that the two-hit configuration likely enhances the fidelity of tasiRNA production and, hence, the accuracy of downstream gene regulation. Finally, we show that a ‘non-cleavable one-hit’ process allows tasiRNA production from both TAS1 and TAS3 transcripts, indicating that RDR6 recruitment does not require miRNA cleavage, nor does the recruitment, as we further show, of SUPRRESSOR-OF-GENE-SILENCING-3, indispensable for tasiRNA generation. PMID:28334969

Assessment of collagen quality associated with non-enzymatic cross-links in human bone using Fourier-transform infrared imaging.

PubMed

Schmidt, F N; Zimmermann, E A; Campbell, G M; Sroga, G E; Püschel, K; Amling, M; Tang, S Y; Vashishth, D; Busse, B

2017-04-01

Aging and many disease conditions, most notably diabetes, are associated with the accumulation of non-enzymatic cross-links in the bone matrix. The non-enzymatic cross-links, also known as advanced glycation end products (AGEs), occur at the collagen tissue level, where they are associated with reduced plasticity and increased fracture risk. In this study, Fourier-transform infrared (FTIR) imaging was used to detect spectroscopic changes associated with the formation of non-enzymatic cross-links in human bone collagen. Here, the non-enzymatic cross-link profile was investigated in one cohort with an in vitro ribose treatment as well as another cohort with an in vivo bisphosphonate treatment. With FTIR imaging, the two-dimensional (2D) spatial distribution of collagen quality associated with non-enzymatic cross-links was measured through the area ratio of the 1678/1692cm -1 subbands within the amide I peak, termed the non-enzymatic crosslink-ratio (NE-xLR). The NE-xLR increased by 35% in the ribation treatment group in comparison to controls (p<0.005), with interstitial bone tissue being more susceptible to the formation of non-enzymatic cross-links. Ultra high-performance liquid chromatography, fluorescence microscopy, and fluorometric assay confirm a correlation between the non-enzymatic cross-link content and the NE-xLR ratio in the control and ribated groups. High resolution FTIR imaging of the 2D bone microstructure revealed enhanced accumulation of non-enzymatic cross-links in bone regions with higher tissue age (i.e., interstitial bone). This non-enzymatic cross-link ratio (NE-xLR) enables researchers to study not only the overall content of AGEs in the bone but also its spatial distribution, which varies with skeletal aging and diabetes mellitus and provides an additional measure of bone's propensity to fracture. Copyright © 2017 Elsevier Inc. All rights reserved.

Assessment of collagen quality associated with non-enzymatic cross-links in human bone using Fourier-transform infrared imaging

PubMed Central

Schmidt, F.N.; Zimmermann, E.A.; Campbell, G.M.; Sroga, G.E.; Püschel, K.; Amling, M.; Tang, S. Y.; Vashishth, D.; Busse, B.

2017-01-01

Aging and many disease conditions, most notably diabetes, are associated with the accumulation of non-enzymatic cross-links in the bone matrix. The non-enzymatic crosslinks, also known as advanced glycation end products (AGEs), occur at the collagen tissue level, where they are associated with reduced plasticity and increased fracture risk. In this study, Fourier-transform infrared (FTIR) imaging was used to detect spectroscopic changes associated with the formation of non-enzymatic cross-links in human bone collagen. Here, the non-enzymatic cross-link profile was investigated in one cohort with an in vitro ribose treatment as well as another cohort with an in vivo bisphosphonate treatment. With FTIR imaging, the two-dimensional (2D) spatial distribution of collagen quality associated with non-enzymatic cross-links was measured through the area ratio of the 1678/1692 cm−1 subbands within the amide I peak, termed the non-enzymatic crosslink-ratio (NE-xLR). The NE-xLR increased by 35% in the ribation treatment group in comparison to controls (p< 0.005), with interstitial bone tissue being more susceptible to the formation of non-enzymatic cross-links. Ultra high performance liquid chromatography, fluorescence microscopy, and fluorometric assay confirm a correlation between the non-enzymatic cross-link content and the NE-xLR ratio in the control and ribated groups. High resolution FTIR imaging of the 2D bone microstructure revealed enhanced accumulation of non-enzymatic cross-links in bone regions with higher tissue age (i.e., interstitial bone). This non-enzymatic cross-link ratio (NE-xLR) enables researchers to study not only the overall content of AGEs in the bone but also its spatial distribution, which varies with skeletal aging and diabetes mellitus and provides an additional measure of bone's propensity to fracture. PMID:28109917

Nitric oxide-induced interstrand cross-links in DNA.

PubMed

Caulfield, Jennifer L; Wishnok, John S; Tannenbaum, Steven R

2003-05-01

The DNA damaging effects of nitrous acid have been extensively studied, and the formation of interstrand cross-links have been observed. The potential for this cross-linking to occur through a common nitrosating intermediate derived from nitric oxide is investigated here. Using a HPLC laser-induced fluorescence (LIF) system, the amount of interstrand cross-link formed on nitric oxide treatment of the 5'-fluorescein-labeled oligomer ATATCGATCGATAT was determined. This self-complimentary sequence contains two 5'-CG sequences, which is the preferred site for nitrous acid-induced cross-linking. Nitric oxide was delivered to an 0.5 mM oligomer solution at 15 nmol/mL/min to give a final nitrite concentration of 652 microM. The resulting concentration of the deamination product, xanthine, in this sample was found to be 211 +/- 39 nM, using GC/MS, and the amount of interstrand cross-link was determined to be 13 +/- 2.5 nM. Therefore, upon nitric oxide treatment, the cross-link is found at approximately 6% of the amount of the deamination product. Using this system, detection of the cross-link is also possible for significantly lower doses of nitric oxide, as demonstrated by treatment of the same oligomer with NO at a rate of 18 nmol/mL/min resulting in a final nitrite concentration of 126 microM. The concentration of interstrand cross-link was determined to be 3.6 +/- 0.1 nM in this sample. Therefore, using the same dose rate, when the total nitric oxide concentration delivered drops by a factor of approximately 5, the concentration of cross-link drops by a factor of about 4-indicating a qausi-linear response. It may now be possible to predict the number of cross-links in a small genome based on the number of CpG sequences and the yield of xanthine derived from nitrosative deamination.

Nanomechanics of layer-by-layer polyelectrolyte complexes: a manifestation of ionic cross-links and fixed charges.

PubMed

Han, Biao; Chery, Daphney R; Yin, Jie; Lu, X Lucas; Lee, Daeyeon; Han, Lin

2016-01-28

This study investigates the roles of two distinct features of ionically cross-linked polyelectrolyte networks - ionic cross-links and fixed charges - in determining their nanomechanical properties. The layer-by-layer assembled poly(allylamine hydrochloride)/poly(acrylic acid) (PAH/PAA) network is used as the model material. The densities of ionic cross-links and fixed charges are modulated through solution pH and ionic strength (IS), and the swelling ratio, elastic and viscoelastic properties are quantified via an array of atomic force microscopy (AFM)-based nanomechanical tools. The roles of ionic cross-links are underscored by the distinctive elastic and viscoelastic nanomechanical characters observed here. First, as ionic cross-links are highly sensitive to solution conditions, the instantaneous modulus, E0, exhibits orders-of-magnitude changes upon pH- and IS-governed swelling, distinctive from the rubber elasticity prediction based on permanent covalent cross-links. Second, ionic cross-links can break and self-re-form, and this mechanism dominates force relaxation of PAH/PAA under a constant indentation depth. In most states, the degree of relaxation is >90%, independent of ionic cross-link density. The importance of fixed charges is highlighted by the unexpectedly more elastic nature of the network despite low ionic cross-link density at pH 2.0, IS 0.01 M. Here, the complex is a net charged, loosely cross-linked, where the degree of relaxation is attenuated to ≈50% due to increased elastic contribution arising from fixed charge-induced Donnan osmotic pressure. In addition, this study develops a new method for quantifying the thickness of highly swollen polymer hydrogel films. It also underscores important technical considerations when performing nanomechanical tests on highly rate-dependent polymer hydrogel networks. These results provide new insights into the nanomechanical characters of ionic polyelectrolyte complexes, and lay the ground for further investigation of their unique time-dependent properties.

Optimisation of UV irradiation as a binding site conserving method for crosslinking collagen-based scaffolds.

PubMed

Davidenko, Natalia; Bax, Daniel V; Schuster, Carlos F; Farndale, Richard W; Hamaia, Samir W; Best, Serena M; Cameron, Ruth E

2016-01-01

Short wavelength (λ = 254 nm) UV irradiation was evaluated over a range of intensities (0.06 to 0.96 J/cm(2)) as a means of cross-linking collagen- and gelatin-based scaffolds, to tailor their material characteristics whilst retaining biological functionality. Zero-link carbodiimide treatments are commonly applied to collagen-based materials, forming cross-links from carboxylate anions (for example the acidic E of GFOGER) that are an essential part of integrin binding sites on collagen. Cross-linking these amino acids therefore disrupts the bioactivity of collagen. In contrast, UV irradiation forms bonds from less important aromatic tyrosine and phenylalanine residues. We therefore hypothesised that UV cross-linking would not compromise collagen cell reactivity. Here, highly porous (~99 %) isotropic, collagen-based scaffolds were produced via ice-templating. A series of scaffolds (pore diameters ranging from 130-260 μm) with ascending stability in water was made from gelatin, two different sources of collagen I, or blends of these materials. Glucose, known to aid UV crosslinking of collagen, was added to some lower-stability formulations. These scaffolds were exposed to different doses of UV irradiation, and the scaffold morphology, dissolution stability in water, resistance to compression and cell reactivity was assessed. Stabilisation in aqueous media varied with both the nature of the collagen-based material employed and the UV intensity. Scaffolds made from the most stable materials showed the greatest stability after irradiation, although the levels of cross-linking in all cases were relatively low. Scaffolds made from pure collagen from the two different sources showed different optimum levels of irradiation, suggesting altered balance between stabilisation from cross-linking and destabilisation from denaturation. The introduction of glucose into the scaffold enhanced the efficacy of UV cross-linking. Finally, as hypothesized, cell attachment, spreading and proliferation on collagen materials were unaffected by UV cross-linking. UV irradiation may therefore be used to provide relatively low level cross-linking of collagen without loss of biological functionality.

Role of solvent-mediated carbodiimide cross-linking in fabrication of electrospun gelatin nanofibrous membranes as ophthalmic biomaterials.

PubMed

Chou, Shih-Feng; Luo, Li-Jyuan; Lai, Jui-Yang; Ma, David Hui-Kang

2017-02-01

Due to their ability to mimic the structure of extracellular matrix, electrospun gelatin nanofibers are promising cell scaffolding materials for tissue engineering applications. However, the hydrophilic gelatin molecules usually need stabilization before use in aqueous physiological environment. Considering that biomaterials cross-linked via film immersion technique may have a more homogeneous cross-linked structure than vapor phase cross-linking, this work aims to investigate the chemical modification of electrospun gelatin nanofibrous membranes by liquid phase carbodiimide in the presence of ethanol/water co-solvents with varying ethanol concentrations ranging from 80 to 99.5vol%. The results of characterization showed that increasing water content in the binary reaction solvent system increases the extent of cross-linking of gelatin nanofibers, but simultaneously promotes the effect of biopolymer swelling and distortion in fiber mat structure. As compared to non-cross-linked counterparts, carbodiimide treated gelatin nanofibrous mats exhibited better thermal and biological stability where the shrinkage temperature and resistance to enzymatic degradation varied in response to ethanol/water solvent composition-mediated generation of cross-links. Irrespective of their cross-linking density, all studied membrane samples did not induce any responses in ocular epithelial cell cultures derived from cornea, lens, and retina. Unlike many other cross-linking agents and/or methods (e.g., excessive vapor phase cross-linking) that may pose a risk of toxicity, our study demonstrated that these nanofibrous materials are well tolerated by anterior segment tissues. These findings also indicate the safety of using ethanol/water co-solvents for chemical cross-linking of gelatin to engineer nanofibrous materials with negligible biological effects. In summary, the present results suggest the importance of solvent-mediated carbodiimide cross-linking in modulating structure-property relationship without compromising in vitro and in vivo biocompatibility of electrospun gelatin nanofibers for future ophthalmic applications. Copyright © 2016 Elsevier B.V. All rights reserved.

Influence of cross-link structure, density and mechanical properties in the mesoscale deformation mechanisms of collagen fibrils.

PubMed

Depalle, Baptiste; Qin, Zhao; Shefelbine, Sandra J; Buehler, Markus J

2015-12-01

Collagen is a ubiquitous protein with remarkable mechanical properties. It is highly elastic, shows large fracture strength and enables substantial energy dissipation during deformation. Most of the connective tissue in humans consists of collagen fibrils composed of a staggered array of tropocollagen molecules, which are connected by intermolecular cross-links. In this study, we report a three-dimensional coarse-grained model of collagen and analyze the influence of enzymatic cross-links on the mechanics of collagen fibrils. Two representatives immature and mature cross-links are implemented in the mesoscale model using a bottom-up approach. By varying the number, type and mechanical properties of cross-links in the fibrils and performing tensile test on the models, we systematically investigate the deformation mechanisms of cross-linked collagen fibrils. We find that cross-linked fibrils exhibit a three phase behavior, which agrees closer with experimental results than what was obtained using previous models. The fibril mechanical response is characterized by: (i) an initial elastic deformation corresponding to the collagen molecule uncoiling, (ii) a linear regime dominated by molecule sliding and (iii) the second stiffer elastic regime related to the stretching of the backbone of the tropocollagen molecules until the fibril ruptures. Our results suggest that both cross-link density and type dictate the stiffness of large deformation regime by increasing the number of interconnected molecules while cross-links mechanical properties determine the failure strain and strength of the fibril. These findings reveal that cross-links play an essential role in creating an interconnected fibrillar material of tunable toughness and strength. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Induction and repair of DNA cross-links induced by sulfur mustard in the A-549 cell line followed by a comet assay.

PubMed

Jost, Petr; Svobodova, Hana; Stetina, Rudolf

2015-07-25

Sulfur mustard is a highly toxic chemical warfare agent with devastating impact on intoxicated tissues. DNA cross-links are probably the most toxic DNA lesions induced in the cell by sulfur mustard. The comet assay is a very sensitive method for measuring DNA damage. In the present study using the A-549 lung cell line, the comet assay protocol was optimized for indirect detection of DNA cross-links induced by sulfur mustard. The method is based on the additional treatment of the assayed cells containing cross-links with the chemical mutagen, styrene oxide. Alkali-labile adducts of styrene oxide cause DNA breaks leading to the formation of comets. A significant dose-dependent reduction of DNA migration of the comet's tail was found after exposing cells to sulfur mustard, indicative of the amount of sulfur mustard induced cross-links. The remarkable decrease of % tail DNA could be observed as early as 5min following exposure to sulfur mustard and the maximal effect was found after 30min, when DNA migration was reduced to the minimum. Sulfur mustard preincubated in culture medium without cells lost its ability to induce cross-links and had a half-life of about 15min. Pre-incubation longer than 30min does not lead to a significant increase in cross-links when applied to cells. However, the amount of cross-links is decreased during further incubation due to repair. The current modification of the comet assay provides a useful tool for detecting DNA cross-links induced by sulfur mustard and could be used for detection of other DNA cross-linking agents such as chemotherapeutic drugs. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Identification of cross-linked amino acids in the protein pair HmaL23-HmaL29 from the 50S ribosomal subunit of the archaebacterium Haloarcula marismortui.

PubMed

Bergmann, U; Wittmann-Liebold, B

1993-03-23

50S ribosomal subunits from the extreme halophilic archaebacterium Haloarcula marismortui were treated with the homobifunctional protein-protein cross-linking reagents diepoxybutane (4 A) and dithiobis(succinimidyl propionate) (12 A). The dominant product with both cross-linking reagents was identified on the protein level as HmaL23-HmaL29, which is homologous to the protein pair L23-L29 from Escherichia coli [Walleczek, J., Martin, T., Redl, B., Stöffler-Meilicke, M., & Stöffler, G. (1989) Biochemistry 28, 4099-4105] and from Bacillus stearothermophilus [Brockmöller, J., & Kamp, R. M. (1986) Biol. Chem. Hoppe-Seyler 367, 925-935]. To reveal the exact cross-linking site in HmaL23-HmaL29, the cross-linked complex was purified on a preparative scale by conventional and high-performance liquid chromatography. After endoproteolytic fragmentation of the protein pair, the amino acids engaged in cross-link formation were unambiguously identified by N-terminal sequence analysis and mass spectrometry of the cross-linked peptides. The cross-link is formed between lysine-57 in the C-terminal region of HmaL29 and the alpha-amino group of the N-terminal serine in protein HmaL23, irrespective of the cross-linking reagent. This result demonstrates that the N-terminal region of protein HmaL23 and the C-terminal domain of HmaL29 are highly flexible so that the distance between the two polypeptide chains can vary by at least 8 A. Comparison of our cross-linking results with those obtained with B. stearothermophilus revealed that the fine structure within this ribosomal domain is at least partially conserved.

Genipin-crosslinked O-carboxymethyl chitosan-gum Arabic coacervate as a pH-sensitive delivery system and microstructure characterization.

PubMed

Huang, Guo-Qing; Cheng, Ling-Yun; Xiao, Jun-Xia; Wang, Shi-Qing; Han, Xiao-Na

2016-08-01

The possibility of genipin-crosslinked O-carboxymethyl chitosan-gum Arabic coacervate as a pH-sensitive delivery vehicle was investigated. O-carboxymethyl chitosan-gum Arabic coacervates separated in pH 3.0, 4.5, and 6.0 were crosslinked by genipin for different durations and the crosslinked products were subjected to crosslinking degree, swelling behavior, bovine serum albumin release profile, and microstructure characterization. Genipin-crosslinking greatly improved the stability of the coacervates against the simulated gastric solution and created certain pH-sensitivity. The coacervates displayed higher swelling ratios in the simulated gastric solution than in the simulated intestine and colon solutions; meanwhile, the coacervates prepared in pH 4.5 and 6.0 swelled more severely than the complex separated in pH 3.0. Nevertheless, the bovine serum albumin release in the simulated gastric solution from the microcapsules prepared in pH 6.0 was much lower than those prepared in pH 4.5 and 3.0, whose cumulative release percentages in the three simulated solutions were 17.14%, 55.23%, and 79.79%, respectively, in crosslinking duration 2 h. X-ray diffraction, scanning electron microscopy, and transmission electron microscopy analysis revealed that genipin-crosslinking improved the regularity and compactness of coacervate structure, whereas confocal laser scanning microscopy observation indicated that O-carboxymethyl chitosan content was possibly the major reason for the different swelling and bovine serum albumin release behavior of the coacervates. It was concluded that the genipin-crosslinked O-carboxymethyl chitosan-gum Arabic coacervate was a potential intestine-targeted delivery system and its delivery performance could be tailored by varying the crosslinking degree and coacervation acidity. © The Author(s) 2016.

Mapping of contact sites in complex formation between transducin and light-activated rhodopsin by covalent crosslinking: Use of a photoactivatable reagent

PubMed Central

Cai, Kewen; Itoh, Yoshiki; Khorana, H. Gobind

2001-01-01

Interaction of light-activated rhodopsin with transducin (T) is the first event in visual signal transduction. We use covalent crosslinking approaches to map the contact sites in interaction between the two proteins. Here we use a photoactivatable reagent, N-[(2-pyridyldithio)-ethyl], 4-azido salicylamide. The reagent is attached to the SH group of cytoplasmic monocysteine rhodopsin mutants by a disulfide-exchange reaction with the pyridylthio group, and the derivatized rhodopsin then is complexed with T by illumination at λ >495 nm. Subsequent irradiation of the complex at λ310 nm generates covalent crosslinks between the two proteins. Crosslinking was demonstrated between T and a number of single cysteine rhodopsin mutants. However, sites of crosslinks were investigated in detail only between T and the rhodopsin mutant S240C (cytoplasmic loop V-VI). Crosslinking occurred predominantly with Tα. For identification of the sites of crosslinks in Tα, the strategy used involved: (i) derivatization of all of the free cysteines in the crosslinked proteins with N-ethylmaleimide; (ii) reduction of the disulfide bond linking the two proteins and isolation of all of the Tα species carrying the crosslinked moiety with a free SH group; (iii) adduct formation of the latter with the N-maleimide moiety of the reagent, maleimido-butyryl-biocytin, containing a biotinyl group; (iv) trypsin degradation of the resulting Tα derivatives and isolation of Tα peptides carrying maleimido-butyryl-biocytin by avidin-agarose chromatography; and (v) identification of the isolated peptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. We found that crosslinking occurred mainly to two C-terminal peptides in Tα containing the amino acid sequences 310–313 and 342–345. PMID:11320237

In situ crosslinking of surface-initiated ring opening metathesis polymerization of polynorbornene for improved stability.

PubMed

Fursule, Ishan A; Abtahi, Ashkan; Watkins, Charles B; Graham, Kenneth R; Berron, Brad J

2018-01-15

In situ crosslinking is expected to increase the solvent stability of coatings formed by surface-initiated ring opening metathesis polymerization (SI ROMP). Solvent-associated degradation limits the utility of SI ROMP coatings. SI ROMP coatings have a unique capacity for post-functionalization through reaction of the unsaturated site on the polymer backbone. Any post-reaction scheme which requires a liquid solvent has the potential to degrade the coating and lower the thickness of the resulting film. We designed a macromolecular crosslinking group based on PEG dinorbornene. The PEG length is tailored to the expected mean chain to chain distance during surface-initiated polymerization. This crosslinking macromer is randomly copolymerized with norbornene through SI ROMP on a gold coated substrate. The solvent stability of polynorbornene coatings with and without PEG dinorbornene is quantitatively determined, and the mechanism of degradation is further supported through XPS and AFM analyses. The addition of the 0.25mol% PEG dinorbornene significantly increases the solvent stability of the SI ROMP coatings. The crosslinker presence in the more stable films is supported with observable PEG absorbances by FTIR and an increase in contact angle hysteresis when compared to non-crosslinked coatings. The oxidation of the SI ROMP coatings is supported by the observation of carbonyl oxygen in the polynorbornene coatings. The rapid loss of the non-crosslinked SI ROMP coating corresponds to nanoscale pitting across the surface and micron-scale regions of widespread film loss. The crosslinked coatings have uniform nanoscale pitting, but the crosslinked films show no evidence of micron-scale film damage. In all, the incorporation of minimal crosslinking content is a simple strategy for improving the solvent stability of SI ROMP coatings. Copyright © 2017 Elsevier Inc. All rights reserved.

Phase Inversion of EPDM/PP Blends: Effect of Viscosity Ratio

NASA Astrophysics Data System (ADS)

Machado, Ana Vera; Antunes, Carla Filipa; van Duin, Martin

2011-07-01

EPDM/PP blends and TPVs with and without crosslinking, respectively, were prepared, in a batch mixer, using three different EPDM rubbers. EPDM/PP based TPVs were dynamic vulcanised using the resol/SnCl2 system. Samples were collected along the time in order to get information on the morphology evolution and crosslinking density during dynamic vulcanisation. The morphology was studied by SEM and the crosslink density by gel content. In the case of low viscosity EPDMs, crosslinking of the EPDM phase was retarded due to its low crosslinking efficiency. This delay on crosslinking reaction enables the observation of the various stages of the morphological mechanism that takes place during dynamic vulcanisation. It could be observed that phase inversion takes place via lamellar mechanism. More detailed insight on phase inversion mechanism during dynamic vulcanisation was accomplished.

Recycling and processing of several typical crosslinked polymer scraps with enhanced mechanical properties based on solid-state mechanochemical milling

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

Lu, Canhui; Zhang, Xinxing; Zhang, Wei

The partially devulcanization or de-crosslinking of ground tire rubber (GTR), post-vulcanized fluororubber scraps and crosslinked polyethylene from cable scraps through high-shear mechanochemical milling (HSMM) was conducted by a modified solid-state mechanochemical reactor. The results indicated that the HSMM treated crosslinked polymer scraps can be reprocessed as virgin rubbers or thermoplastics to produce materials with high performance. The foamed composites of low density polyethylene/GTR and the blend of post-vulcanized flurorubber (FKM) with polyacrylate rubber (ACM) with better processability and mechanical properties were obtained. The morphology observation showed that the dispersion and compatibility between de-crosslinked polymer scraps and matrix were enhanced. Themore » results demonstrated that HSMM is a feasible alternative technology for recycling post-vulcanized or crosslinked polymer scraps.« less

In-situ cross linking of polyvinyl alcohol. [application to battery separator films

NASA Technical Reports Server (NTRS)

Philipp, W. H.; Hsu, L. C.; Sheibley, D. W. (Inventor)

1981-01-01

A method of producing a crosslinked polyvinyl alcohol structure, such as a battery separator membrane or electrode envelope is described. An aqueous solution of a film-forming polyvinyl alcohol is admixed with an aldehyde crosslinking agent a basic pH to inhibit crosslinking. The crosslinking agent, perferably a dialdehyde such as glutaraldehyde, is used in an amount of from about 1/2 to about 20% of the theoretical amount required to crosslink all of the hydroxyl groups of the polymer. The aqueous admixture is formed into a desired physical shape, such as by casting a sheet of the solution. The sheet is then dried to form a self-supporting film. Crosslinking is then effected by immersing the film in aqueous acid solution. The resultant product has excellent properties for use as a battery separator.

Actin Cross-link Assembly and Disassembly Mechanics for α-Actinin and Fascin*

PubMed Central

Courson, David S.; Rock, Ronald S.

2010-01-01

Self-assembly of complex structures is commonplace in biology but often poorly understood. In the case of the actin cytoskeleton, a great deal is known about the components that include higher order structures, such as lamellar meshes, filopodial bundles, and stress fibers. Each of these cytoskeletal structures contains actin filaments and cross-linking proteins, but the role of cross-linking proteins in the initial steps of structure formation has not been clearly elucidated. We employ an optical trapping assay to investigate the behaviors of two actin cross-linking proteins, fascin and α-actinin, during the first steps of structure assembly. Here, we show that these proteins have distinct binding characteristics that cause them to recognize and cross-link filaments that are arranged with specific geometries. α-Actinin is a promiscuous cross-linker, linking filaments over all angles. It retains this flexibility after cross-links are formed, maintaining a connection even when the link is rotated. Conversely, fascin is extremely selective, only cross-linking filaments in a parallel orientation. Surprisingly, bundles formed by either protein are extremely stable, persisting for over 0.5 h in a continuous wash. However, using fluorescence recovery after photobleaching and fluorescence decay experiments, we find that the stable fascin population can be rapidly competed away by free fascin. We present a simple avidity model for this cross-link dissociation behavior. Together, these results place constraints on how cytoskeletal structures assemble, organize, and disassemble in vivo. PMID:20551315

CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization.

PubMed

Courcelles, Mathieu; Coulombe-Huntington, Jasmin; Cossette, Émilie; Gingras, Anne-Claude; Thibault, Pierre; Tyers, Mike

2017-07-07

Protein cross-linking mass spectrometry (CL-MS) enables the sensitive detection of protein interactions and the inference of protein complex topology. The detection of chemical cross-links between protein residues can identify intra- and interprotein contact sites or provide physical constraints for molecular modeling of protein structure. Recent innovations in cross-linker design, sample preparation, mass spectrometry, and software tools have significantly improved CL-MS approaches. Although a number of algorithms now exist for the identification of cross-linked peptides from mass spectral data, a dearth of user-friendly analysis tools represent a practical bottleneck to the broad adoption of the approach. To facilitate the analysis of CL-MS data, we developed CLMSVault, a software suite designed to leverage existing CL-MS algorithms and provide intuitive and flexible tools for cross-platform data interpretation. CLMSVault stores and combines complementary information obtained from different cross-linkers and search algorithms. CLMSVault provides filtering, comparison, and visualization tools to support CL-MS analyses and includes a workflow for label-free quantification of cross-linked peptides. An embedded 3D viewer enables the visualization of quantitative data and the mapping of cross-linked sites onto PDB structural models. We demonstrate the application of CLMSVault for the analysis of a noncovalent Cdc34-ubiquitin protein complex cross-linked under different conditions. CLMSVault is open-source software (available at https://gitlab.com/courcelm/clmsvault.git ), and a live demo is available at http://democlmsvault.tyerslab.com/ .

The effect of collagen crosslinking on the biphasic poroviscoelastic cartilage properties determined from a semi-automated microindentation protocol for stress relaxation.

PubMed

McGann, Megan E; Bonitsky, Craig M; Ovaert, Timothy C; Wagner, Diane R

2014-06-01

Given the important role of the collagenous structure in cartilage mechanics, there is considerable interest in the relationship between collagen crosslinking and the mechanical behavior of the cartilage matrix. While crosslink-induced alterations to the elastic modulus of cartilage have been described, changes to time-dependent behavior have not yet been determined. The objective of the study was to quantify changes to cartilage material properties, including viscoelastic coefficients, with crosslinking via indentation. To accomplish this, a semi-autonomous microindentation stress relaxation protocol was first developed, validated and then applied to cartilage specimens before and after crosslinking. The change in mechanical properties with crosslinking was analyzed both in the unloading portions of the test via the Oliver-Pharr method and in the holding portion with an inverse iterative finite element model that represented cartilage as a biphasic poroviscoelastic material. Although both techniques suggested a similar increase in equilibrium modulus in the crosslinked specimens as compared to the controls, distinct differences in the control specimens were apparent, suggesting that the two different techniques may be capturing different aspects of the material behavior. No differences in time-dependent properties were observed between the crosslinked and the control specimens. These results give further insight into the effects of crosslinking in cartilage mechanical behavior. Additionally, the microindentation stress relaxation protocol may enable increased automation for high-throughput testing. Copyright © 2014 Elsevier Ltd. All rights reserved.

Selective Detection of Peptide-Oligonucleotide Heteroconjugates Utilizing Capillary HPLC-ICPMS

NASA Astrophysics Data System (ADS)

Catron, Brittany; Caruso, Joseph A.; Limbach, Patrick A.

2012-06-01

A method for the selective detection and quantification of peptide:oligonucleotide heteroconjugates, such as those generated by protein:nucleic acid cross-links, using capillary reversed-phase high performance liquid chromatography (cap-RPHPLC) coupled with inductively coupled plasma mass spectrometry detection (ICPMS) is described. The selective detection of phosphorus as 31P+, the only natural isotope, in peptide-oligonucleotide heteroconjugates is enabled by the elemental detection capabilities of the ICPMS. Mobile phase conditions that allow separation of heteroconjugates while maintaining ICPMS compatibility were investigated. We found that trifluoroacetic acid (TFA) mobile phases, used in conventional peptide separations, and hexafluoroisopropanol/triethylamine (HFIP/TEA) mobile phases, used in conventional oligonucleotide separations, both are compatible with ICPMS and enable heteroconjugate separation. The TFA-based separations yielded limits of detection (LOD) of ~40 ppb phosphorus, which is nearly seven times lower than the LOD for HFIP/TEA-based separations. Using the TFA mobile phase, 1-2 pmol of a model heteroconjugate were routinely separated and detected by this optimized capLC-ICPMS method.

A quantitative telomeric chromatin isolation protocol identifies different telomeric states

NASA Astrophysics Data System (ADS)

Grolimund, Larissa; Aeby, Eric; Hamelin, Romain; Armand, Florence; Chiappe, Diego; Moniatte, Marc; Lingner, Joachim

2013-11-01

Telomere composition changes during tumourigenesis, aging and in telomere syndromes in a poorly defined manner. Here we develop a quantitative telomeric chromatin isolation protocol (QTIP) for human cells, in which chromatin is cross-linked, immunopurified and analysed by mass spectrometry. QTIP involves stable isotope labelling by amino acids in cell culture (SILAC) to compare and identify quantitative differences in telomere protein composition of cells from various states. With QTIP, we specifically enrich telomeric DNA and all shelterin components. We validate the method characterizing changes at dysfunctional telomeres, and identify and validate known, as well as novel telomere-associated polypeptides including all THO subunits, SMCHD1 and LRIF1. We apply QTIP to long and short telomeres and detect increased density of SMCHD1 and LRIF1 and increased association of the shelterins TRF1, TIN2, TPP1 and POT1 with long telomeres. Our results validate QTIP to study telomeric states during normal development and in disease.

Vision Restoration with a Collagen Crosslinked Boston Keratoprosthesis Unit

DTIC Science & Technology

2016-09-01

AWARD NUMBER: W81XWH-15-2-0044 TITLE: Vision Restoration with a Collagen Crosslinked Boston Keratoprosthesis Unit PRINCIPAL INVESTIGATOR: Joseph B...TITLE AND SUBTITLE 5a. CONTRACT NUMBER Vision Restoration with a Collagen Cross-linked Boston Keratoprosthesis Unit 5b. GRANT NUMBER W81XWH-15-2-0044...the incidence or potentially eliminate corneal melts by strengthening the keratoprosthesis carrier tissue by collagen -crosslinking the cornea graft

Nuclear Resonance Fluorescence for Materials Assay

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

Quiter, Brian J.; Ludewigt, Bernhard; Mozin, Vladimir

This paper discusses the use of nuclear resonance fluorescence (NRF) techniques for the isotopic and quantitative assaying of radioactive material. Potential applications include age-dating of an unknown radioactive source, pre- and post-detonation nuclear forensics, and safeguards for nuclear fuel cycles Examples of age-dating a strong radioactive source and assaying a spent fuel pin are discussed. The modeling work has ben performed with the Monte Carlo radiation transport computer code MCNPX, and the capability to simulate NRF has bee added to the code. Discussed are the limitations in MCNPX?s photon transport physics for accurately describing photon scattering processes that are importantmore » contributions to the background and impact the applicability of the NRF assay technique.« less

Automated Installation Verification of COMSOL via LiveLink for MATLAB

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

Crowell, Michael W

Verifying that a local software installation performs as the developer intends is a potentially time-consuming but necessary step for nuclear safety-related codes. Automating this process not only saves time, but can increase reliability and scope of verification compared to ‘hand’ comparisons. While COMSOL does not include automatic installation verification as many commercial codes do, it does provide tools such as LiveLink™ for MATLAB® and the COMSOL API for use with Java® through which the user can automate the process. Here we present a successful automated verification example of a local COMSOL 5.0 installation for nuclear safety-related calculations at the Oakmore » Ridge National Laboratory’s High Flux Isotope Reactor (HFIR).« less

Accelerated healing of full-thickness wounds by genipin-crosslinked silk sericin/PVA scaffolds.

PubMed

Aramwit, Pornanong; Siritienthong, Tippawan; Srichana, Teerapol; Ratanavaraporn, Juthamas

2013-01-01

Silk sericin has recently been studied for its advantageous biological properties, including its ability to promote wound healing. This study developed a delivery system to accelerate the healing of full-thickness wounds. Three-dimensional scaffolds were fabricated from poly(vinyl alcohol) (PVA), glycerin (as a plasticizer) and genipin (as a crosslinking agent), with or without sericin. The physical and biological properties of the genipin-crosslinked sericin/PVA scaffolds were investigated and compared with those of scaffolds without sericin. The genipin-crosslinked sericin/PVA scaffolds exhibited a higher compressive modulus and greater swelling in water than the scaffolds without sericin. Sericin also exhibited controlled release from the scaffolds. The genipin-crosslinked sericin/PVA scaffolds promoted the attachment and proliferation of L929 mouse fibroblasts. After application to full-thickness rat wounds, the wounds treated with genipin-crosslinked sericin/PVA scaffolds showed a significantly greater reduction in wound size, collagen formation and epithelialization compared with the control scaffolds without sericin but lower numbers of macrophages and multinucleated giant cells. These results indicate that the delivery of sericin from the novel genipin-crosslinked scaffolds efficiently healed the wound. Therefore, these genipin-crosslinked sericin/PVA scaffolds represent a promising candidate for the accelerated healing of full-thickness wounds. Copyright © 2013 S. Karger AG, Basel.

The Preparation and Properties of Thermo-reversibly Cross-linked Rubber Via Diels-Alder Chemistry.

PubMed

Polgar, Lorenzo Massimo; van Duin, Martin; Picchioni, Francesco

2016-08-25

A method for using Diels Alder thermo-reversible chemistry as cross-linking tool for rubber products is demonstrated. In this work, a commercial ethylene-propylene rubber, grafted with maleic anhydride, is thermo-reversibly cross-linked in two steps. The pending anhydride moieties are first modified with furfurylamine to graft furan groups to the rubber backbone. These pendant furan groups are then cross-linked with a bis-maleimide via a Diels-Alder coupling reaction. Both reactions can be performed under a broad range of experimental conditions and can easily be applied on a large scale. The material properties of the resulting Diels-Alder cross-linked rubbers are similar to a peroxide-cured ethylene/propylene/diene rubber (EPDM) reference. The cross-links break at elevated temperatures (> 150 °C) via the retro-Diels-Alder reaction and can be reformed by thermal annealing at lower temperatures (50-70 °C). Reversibility of the system was proven with infrared spectroscopy, solubility tests and mechanical properties. Recyclability of the material was also shown in a practical way, i.e., by cutting a cross-linked sample into small parts and compression molding them into new samples displaying comparable mechanical properties, which is not possible for conventionally cross-linked rubbers.

Lysyl hydroxylase 2 induces a collagen cross-link switch in tumor stroma

PubMed Central

Chen, Yulong; Terajima, Masahiko; Yang, Yanan; Sun, Li; Ahn, Young-Ho; Pankova, Daniela; Puperi, Daniel S.; Watanabe, Takeshi; Kim, Min P.; Blackmon, Shanda H.; Rodriguez, Jaime; Liu, Hui; Behrens, Carmen; Wistuba, Ignacio I.; Minelli, Rosalba; Scott, Kenneth L.; Sanchez-Adams, Johannah; Guilak, Farshid; Pati, Debananda; Thilaganathan, Nishan; Burns, Alan R.; Creighton, Chad J.; Martinez, Elisabeth D.; Zal, Tomasz; Grande-Allen, K. Jane; Yamauchi, Mitsuo; Kurie, Jonathan M.

2015-01-01

Epithelial tumor metastasis is preceded by an accumulation of collagen cross-links that heighten stromal stiffness and stimulate the invasive properties of tumor cells. However, the biochemical nature of collagen cross-links in cancer is still unclear. Here, we postulated that epithelial tumorigenesis is accompanied by changes in the biochemical type of collagen cross-links. Utilizing resected human lung cancer tissues and a p21CIP1/WAF1-deficient, K-rasG12D-expressing murine metastatic lung cancer model, we showed that, relative to normal lung tissues, tumor stroma contains higher levels of hydroxylysine aldehyde–derived collagen cross-links (HLCCs) and lower levels of lysine aldehyde–derived cross-links (LCCs), which are the predominant types of collagen cross-links in skeletal tissues and soft tissues, respectively. Gain- and loss-of-function studies in tumor cells showed that lysyl hydroxylase 2 (LH2), which hydroxylates telopeptidyl lysine residues on collagen, shifted the tumor stroma toward a high-HLCC, low-LCC state, increased tumor stiffness, and enhanced tumor cell invasion and metastasis. Together, our data indicate that LH2 enhances the metastatic properties of tumor cells and functions as a regulatory switch that controls the relative abundance of biochemically distinct types of collagen cross-links in the tumor stroma. PMID:25664850

Ara h 2 cross-linking catalyzed by MTGase decreases its allergenicity.

PubMed

Wu, Zhihua; Lian, Jun; Zhao, Ruifang; Li, Kun; Li, Xin; Yang, Anshu; Tong, Ping; Chen, Hongbing

2017-03-22

Peanuts, whose major allergen is Ara h 2, are included among the eight major food allergens. After reduction using dithiothreitol (DTT), cross-linking of Ara h 2 could be catalyzed by microbial transglutaminase (MTGase), a widely used enzyme in the food industry. In this study, Ara h 2 cross-linking was catalyzed by MTGase after it was reduced by DTT. Using mass spectrometry and PLINK software, five cross-linkers were identified, and five linear allergen epitopes were found to be involved in the reactions. The IgE binding capacity of cross-linked Ara h 2 was found to be significantly lower compared to that of native and reduced Ara h 2. After simulated gastric fluid (SGF) digestion, the digested products of the cross-linked Ara h 2, again, had a significantly lower IgE binding capacity compared to untreated and reduced Ara h 2. Furthermore, reduced and cross-linked Ara h 2 (RC-Ara h 2) induced lower sensitization in mice, indicating its lower allergenicity. Reduction and MTGase-catalyzed cross-linking are effective methods to decrease the allergenicity of Ara h 2. The reactions involved linear allergen epitopes destroying the material basis of the allergenicity, and this might develop a new direction for protein desensitization processes.

Preparation, characterization, and evaluation of genipin crosslinked chitosan/gelatin three-dimensional scaffolds for liver tissue engineering applications.

PubMed

Zhang, Yi; Wang, Qiang-Song; Yan, Kuo; Qi, Yun; Wang, Gui-Fang; Cui, Yuan-Lu

2016-08-01

In liver tissue engineering, scaffolds with porous structure desgined to supply nutrient and oxygen exchange for three-dimensional (3-D) cells culture, and maintain liver functions. Meanwhile, genipin, as a natural crosslinker, is widely used to crosslink biomaterials in tissue engineering, with lower cytotoxicity and better biocompatibility. In present study, chitosan/gelatin 3-D scaffolds crosslinked by genipin, glutaraldehyde or 1-(3-dimethylaminopropyl)-3-ethyl-carbodimide hydrochloride (EDC) were prepared and characterized by Fourier-transform infrared (FT-IR) and scanning electron microscopy (SEM). The biocompatibility of chitosan/gelatin scaffolds corsslinked with different crosslinkers was investigated by cell viability, morphology and liver specific functions. The result showed that the 1% and 2% genipin crosslinked chitosan/gelatin scaffolds possess ideal porosity. The genipin crosslinked 3-D scaffolds possessed the best biocompatibility than that of the others, and maintained liver specific functions when HepG2 cells seeded on scaffolds. The cellular morphology of HepG2 cells seeded on scaffolds showed that cells could penetrate into the scaffolds and proliferate significantly. Therefore, genipin crosslinked chitosan/gelatin scaffolds could be a promising biomaterial used in liver tissue engineering. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1863-1870, 2016. © 2016 Wiley Periodicals, Inc.

Improved performance of collagen scaffolds crosslinked by Traut's reagent and Sulfo-SMCC.

PubMed

Li, Yiming; He, Qifen; Hu, Xiucheng; Liu, Yun; Cheng, Xiaohui; Li, Xiachen; Deng, Feilong

2017-05-01

Collagen scaffolds are frequently employed for applications in regenerative medicine. In previous studies, we affirmed that Traut's reagent (2-Iminothiolane hydrochloride) and Sulfo-SMCC (4-(N-Maleimidomethyl) cyclohexane-1-carboxylic acid 3-sulpho-N-hydroxysuccinimide ester sodium salt) could covalently bind growth factors on collagen scaffolds. We also observed that crosslinking formed within the collagen scaffolds with excess dosage of Sulfo-SMCC, which improved the biological performance of collagen scaffolds together with growth factors. In order to evaluate changes in capacity caused by crosslinking, Traut's reagent and adjusted different concentrations of Sulfo-SMCC (0.263, 1.315, 2.63 and 5.26 mM) were used to construct collagen scaffolds with differing extents of crosslinking in this study. The results demonstrated that resistance of collagen scaffolds to enzymatic digestion, cellularization and vascularization in vivo were enhanced by the crosslinking procedure. The cell culture studies indicated that the crosslinking procedure did not influence biocompatibility. Moreover, there were no statistical differences in the degradation rate, cellularization or vascularization among 1.315, 2.63 and 5.26 mM crosslinked groups. These results demonstrated that crosslinking collagen scaffolds with an appropriate amount of Traut's reagent and Sulfo-SMCC was an effective and safe method to modify naturally derived collagen scaffolds with notable potential uses in tissue regeneration.

Comparison of femtosecond laser and continuous wave UV sources for protein-nucleic acid crosslinking.

PubMed

Fecko, Christopher J; Munson, Katherine M; Saunders, Abbie; Sun, Guangxing; Begley, Tadhg P; Lis, John T; Webb, Watt W

2007-01-01

Crosslinking proteins to the nucleic acids they bind affords stable access to otherwise transient regulatory interactions. Photochemical crosslinking provides an attractive alternative to formaldehyde-based protocols, but irradiation with conventional UV sources typically yields inadequate product amounts. Crosslinking with pulsed UV lasers has been heralded as a revolutionary technique to increase photochemical yield, but this method had only been tested on a few protein-nucleic acid complexes. To test the generality of the yield enhancement, we have investigated the benefits of using approximately 150 fs UV pulses to crosslink TATA-binding protein, glucocorticoid receptor and heat shock factor to oligonucleotides in vitro. For these proteins, we find that the quantum yields (and saturating yields) for forming crosslinks using the high-peak intensity femtosecond laser do not improve on those obtained with low-intensity continuous wave (CW) UV sources. The photodamage to the oligonucleotides and proteins also has comparable quantum yields. Measurements of the photochemical reaction yields of several small molecules selected to model the crosslinking reactions also exhibit nearly linear dependences on UV intensity instead of the previously predicted quadratic dependence. Unfortunately, these results disprove earlier assertions that femtosecond pulsed laser sources provide significant advantages over CW radiation for protein-nucleic acid crosslinking.

Improved thermal-stability and mechanical properties of type I collagen by crosslinking with casein, keratin and soy protein isolate using transglutaminase.

PubMed

Wu, Xiaomeng; Liu, Yaowei; Liu, Anjun; Wang, Wenhang

2017-05-01

The inferior thermal- stability of collagen hinders its extensive application in food industry, including edible packaging. To improve the thermal- stability and mechanical properties of collagen, we attempted to crosslink collagen with some proteins possessing excellent thermal stability (i. e., casein, keratin and soy protein isolate (SPI)). Observed from the SDS- PAGE and particle size distribution, some complexes with higher molecule weight and relative bigger size particle occurred in the protein mixture, especially after TGase crosslinking. Importantly, the crosslinking greatly improved the thermal- stable property of protein complex, especially that of the collagen- casein complex judged from differential scanning calorimetric (DSC). Moreover, the crosslinking enhanced the mechanical properties of the combined films in terms of tensile strength (TS) and elongation at break (EAB). Also, some obvious differences in morphology of proteins before and after TGase crosslinking were observed by scanning electron microscopy (SEM). These impacts of TGase crosslinking with heat- resistant proteins on collagen features were associated with the conformational changes of the protein complex analyzed by Fourier transform infrared spectroscopy (FTIR). In conclusion, TGase crosslinking with higher thermally stable proteins could be an effective method to contribute to collagen' application in food packaging field. Copyright © 2017 Elsevier B.V. All rights reserved.

Intramolecularly Protein-Crosslinked DNA Gels: New Biohybrid Nanomaterials with Controllable Size and Catalytic Activity.

PubMed

Zhou, Li; Morel, Mathieu; Rudiuk, Sergii; Baigl, Damien

2017-07-01

DNA micro- and nanogels-small-sized hydrogels made of a crosslinked DNA backbone-constitute new promising materials, but their functions have mainly been limited to those brought by DNA. Here a new way is described to prepare sub-micrometer-sized DNA gels of controllable crosslinking density that are able to embed novel functions, such as an enzymatic activity. It consists of using proteins, instead of traditional base-pairing assembly or covalent approaches, to form crosslinks inside individual DNA molecules, resulting in structures referred to as intramolecularly protein-crosslinked DNA gels (IPDGs). It is first shown that the addition of streptavidin to biotinylated T4DNA results in the successful formation of thermally stable IPDGs with a controllable crosslinking density, forming structures ranging from elongated to raspberry-shaped and pearl-necklace-like morphologies. Using reversible DNA condensation strategies, this paper shows that the gels can be reversibly actuated at a low crosslinking density, or further stabilized when they are highly crosslinked. Finally, by using streptavidin-protein conjugates, IPDGs with various enzymes are successfully functionalized. It is demonstrated that the enzymes keep their catalytic activity upon their incorporation into the gels, opening perspectives ranging from biotechnologies (e.g., enzyme manipulation) to nanomedicine (e.g., vectorization). © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of carbon nanotube dispersion on glass transition in cross-linked epoxy-carbon nanotube nanocomposites: role of interfacial interactions.

PubMed

Khare, Ketan S; Khare, Rajesh

2013-06-20

We have used atomistic molecular simulations to study the effect of nanofiller dispersion on the glass transition behavior of cross-linked epoxy-carbon nanotube (CNT) nanocomposites. Specific chemical interactions at the interface of CNTs and cross-linked epoxy create an interphase region, whose impact on the properties of their nanocomposites increases with an increasing extent of dispersion. To investigate this aspect, we have compared the volumetric, structural, and dynamical properties of three systems: neat cross-linked epoxy, cross-linked epoxy nanocomposite containing dispersed CNTs, and cross-linked epoxy nanocomposite containing aggregated CNTs. We find that the nanocomposite containing dispersed CNTs shows a depression in the glass transition temperature (Tg) by ~66 K as compared to the neat cross-linked epoxy, whereas such a large depression is absent in the nanocomposite containing aggregated CNTs. Our results suggest that the poor interfacial interactions between the CNTs and the cross-linked epoxy matrix lead to a more compressible interphase region between the CNTs and the bulk matrix. An analysis of the resulting dynamic heterogeneity shows that the probability of percolation of immobile domains becomes unity near the Tg calculated from volumetric properties. Our observations also lend support to the conceptual analogy between polymer nanocomposites and the nanoconfinement of polymer thin films.

An Improved Method for Measuring Chromatin-binding Dynamics Using Time-dependent Formaldehyde Crosslinking

PubMed Central

Hoffman, Elizabeth A.; Zaidi, Hussain; Shetty, Savera J.; Bekiranov, Stefan; Auble, David T.

2018-01-01

Formaldehyde crosslinking is widely used in combination with chromatin immunoprecipitation (ChIP) to measure the locations along DNA and relative levels of transcription factor (TF)-DNA interactions in vivo. However, the measurements that are typically made do not provide unambiguous information about the dynamic properties of these interactions. We have developed a method to estimate binding kinetic parameters from time-dependent formaldehyde crosslinking data, called crosslinking kinetics (CLK) analysis. Cultures of yeast cells are crosslinked with formaldehyde for various periods of time, yielding the relative ChIP signal at particular loci. We fit the data using the mass-action CLK model to extract kinetic parameters of the TF-chromatin interaction, including the on- and off-rates and crosslinking rate. From the on- and off-rate we obtain the occupancy and residence time. The following protocol is the second iteration of this method, CLKv2, updated with improved crosslinking and quenching conditions, more information about crosslinking rates, and systematic procedures for modeling the observed kinetic regimes. CLKv2 analysis has been applied to investigate the binding behavior of the TATA-binding protein (TBP), and a selected subset of other TFs. The protocol was developed using yeast cells, but may be applicable to cells from other organisms as well. PMID:29682595

Light-induced cross-linking and post-cross-linking modification of polyglycidol.

PubMed

Marquardt, F; Bruns, M; Keul, H; Yagci, Y; Möller, M

2018-02-08

The photoinduced radical generation process has received renewed interest due to its economic and ecological appeal. Herein the light-induced cross-linking of functional polyglycidol and its post-cross-linking modification are presented. Linear polyglycidol was first functionalized with a tertiary amine in a two-step reaction. Dimethylaminopropyl functional polyglycidol was cross-linked in a UV-light mediated reaction with camphorquinone as a type II photoinitiator. The cross-linked polyglycidol was further functionalized by quaternization with various organoiodine compounds. Aqueous dispersions of the cross-linked polymers were investigated by means of DLS and zeta potential measurements. Polymer films were evaluated by DSC and XPS.

Poly(4-vinylphenol) gate insulator with cross-linking using a rapid low-power microwave induction heating scheme for organic thin-film-transistors

NASA Astrophysics Data System (ADS)

Fan, Ching-Lin; Shang, Ming-Chi; Hsia, Mao-Yuan; Wang, Shea-Jue; Huang, Bohr-Ran; Lee, Win-Der

2016-03-01

A Microwave-Induction Heating (MIH) scheme is proposed for the poly(4-vinylphenol) (PVP) gate insulator cross-linking process to replace the traditional oven heating cross-linking process. The cross-linking time is significantly decreased from 1 h to 5 min by heating the metal below the PVP layer using microwave irradiation. The necessary microwave power was substantially reduced to about 50 W by decreasing the chamber pressure. The MIH scheme is a good candidate to replace traditional thermal heating for cross-linking of PVP as the gate insulator for organic thin-film-transistors.

Enhanced wear performance of ultra high molecular weight polyethylene crosslinked by organosilane.

PubMed

Tang, C Y; Xie, X L; Wu, X C; Li, R K Y; Mai, Y W

2002-11-01

Ultra high molecular weight polyethylene (UHMWPE) crosslinked by organosilane was thermal compression molded. The organosilane used was the tri-ethyloxyl vinyl silane. Its gelation, melting behavior, crystallinity, mechanical and wear-resisting properties were systematically investigated. The results showed that the gel ratio of UHMWPE increases with the incorporation of organosilane. At a low content of organosilane, the melting point and crystallinity of the crosslinked UHMWPE increase, and hence the mechanical and wear-resisting properties are improved. However, at a high content of organosilane, these performances of the crosslinked UHMWPE become worse. At 0.4 phr silane, the wear resistance of crosslinked UHMWPE reaches its optimum value.

Antibacterial effect of novel synthesized sulfated β-cyclodextrin crosslinked cotton fabric and its improved antibacterial activities with ZnO, TiO2 and Ag nanoparticles coating.

PubMed

Selvam, S; Rajiv Gandhi, R; Suresh, J; Gowri, S; Ravikumar, S; Sundrarajan, M

2012-09-15

Sulfated β-cyclodextrin was synthesized from sulfonation of β-cyclodextrin and sulfated polymer was crosslinked with cotton fabric using ethylenediaminetetraacetic acid as crosslinker. ZnO, TiO(2) and Ag nanoparticles were prepared and characterized by XRD, UV, DLS, SEM and PSA. The prepared nanoparticles were coated on crosslinked cotton fabric. The crosslinking and nanoparticles coating effects of cotton fabrics were studied by FTIR and SEM analysis. The antibacterial test was done against gram positive Staphylococcus aureus and gram negative Escherichia coli bacterium. Copyright © 2012 Elsevier B.V. All rights reserved.

Role of (n,2n) reactions in transmutation of long-lived fission products

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

Apse, V. A.; Kulikov, G. G., E-mail: ggkulikov@mephi.ru; Kulikov, E. G.

2016-12-15

The conditions under which (n,γ) and (n,2n) reactions can help or hinder each other in neutron transmutation of long-lived fission products (LLFPs) are considered. Isotopic and elemental transmutation for the main long-lived fission products, {sup 79}Se, {sup 93}Zr, {sup 99}Tc, {sup 107}Pd, {sup 126}Sn, {sup 129}I, and {sup 135}Cs, are considered. The effect of (n,2n) reactions on the equilibrium amount of nuclei of the transmuted isotope and the neutron consumption required for the isotope processing is estimated. The aim of the study is to estimate the influence of (n,2n) reactions on efficiency of neutron LLFP transmutation. The code TIME26 andmore » the libraries of evaluated nuclear data ABBN-93, JEF-PC, and JANIS system are applied. The following results are obtained: (1) The effect of (n,2n) reactions on the minimum number of neutrons required for transmutation and the equilibrium amount of LLFP nuclei is estimated. (2) It is demonstrated that, for three LLFP isotopes ({sup 126}Sn, {sup 129}I, and {sup 135}Cs), (n,γ) and (n,2n) reactions are partners facilitating neutron transmutation. The strongest effect of (n,2n) reaction is found for {sup 126}Sn transmutation (reduction of the neutron consumption by 49% and the equilibrium amount of nuclei by 19%).« less

Lesson from the stoichiometry determination of the cohesin complex: a short protease mediated elution increases the recovery from cross-linked antibody-conjugated beads.

PubMed

Holzmann, Johann; Fuchs, Johannes; Pichler, Peter; Peters, Jan-Michael; Mechtler, Karl

2011-02-04

Affinity purification of proteins using antibodies coupled to beads and subsequent mass spectrometric analysis has become a standard technique for the identification of protein complexes. With the recent transfer of the isotope dilution mass spectrometry principle (IDMS) to the field of proteomics, quantitative analyses-such as the stoichiometry determination of protein complexes-have become achievable. Traditionally proteins were eluted from antibody-conjugated beads using glycine at low pH or using diluted acids such as HCl, TFA, or FA, but elution was often found to be incomplete. Using the cohesin complex and the anaphase promoting complex/cyclosome (APC/C) as examples, we show that a short 15-60 min predigestion with a protease such as LysC (modified on-bead digest termed protease elution) increases the elution efficiency 2- to 3-fold compared to standard acid elution protocols. While longer incubation periods-as performed in standard on-bead digestion-led to partial proteolysis of the cross-linked antibodies, no or only insignificant cleavage was observed after 15-60 min protease mediated elution. Using the protease elution method, we successfully determined the stoichiometry of the cohesin complex by absolute quantification of the four core subunits using LC-SRM analysis and 19 reference peptides generated with the EtEP strategy. Protease elution was 3-fold more efficient compared to HCl elution, but measurements using both elution techniques are in agreement with a 1:1:1:1 stoichiometry. Furthermore, using isoform specific reference peptides, we determined the exact STAG1:STAG2 stoichiometry within the population of cohesin complexes. In summary, we show that the protease elution protocol increases the recovery from affinity beads and is compatible with quantitative measurements such as the stoichiometry determination of protein complexes.

Matrix metalloproteinase-9 (MMP-9) as an activator of nanosystems for targeted drug delivery in pancreatic cancer.

PubMed

Grünwald, Barbara; Vandooren, Jennifer; Locatelli, Erica; Fiten, Pierre; Opdenakker, Ghislain; Proost, Paul; Krüger, Achim; Lellouche, Jean Paul; Israel, Liron Limor; Shenkman, Louis; Comes Franchini, Mauro

2016-10-10

Specific cancer cell targeting is a pre-requisite for efficient drug delivery as well as for high-resolution imaging and still represents a major technical challenge. Tumor-associated enzyme-assisted targeting is a new concept that takes advantage of the presence of a specific activity in the tumor entity. MMP-9 is a protease found to be upregulated in virtually all malignant tumors. Consequently, we hypothesized that its presence can provide a de-shielding activity for targeted delivery of drugs by nanoparticles (NPs) in pancreatic cancer. Here, we describe synthesis and characterization of an optimized MMP-9-cleavable linker mediating specific removal of a PEG shield from a PLGA-b-PEG-based polymeric nanocarrier (Magh@PNPs-PEG-RegaCP-PEG) leading to specific uptake of the smaller PNPs with their cargo into cells. The specific MMP-9-cleavable linker was designed based on the degradation efficiency of peptides derived from the collagen type II sequence. MMP-9-dependent uptake of the Magh@PNPs-PEG-RegaCP-PEG was demonstrated in pancreatic cancer cells in vitro. Accumulation of the Magh@PNPs-PEG-RegaCP-PEG in pancreatic tissues in the clinically relevant KPC mouse model of pancreatic cancer, as a proof-of-concept, was tumor-specific and MMP-9-dependent, indicating that MMP-9 has a strong potential as a specific mediator of PNP de-shielding for tumor-specific uptake. Pre-treatment of mice with Magh@PNPs-PEG-RegaCP-PEG led to reduction of liver metastasis and drastically decreased average colony size. In conclusion, the increased tumor-specific presence and activity of MMP-9 can be exploited to deliver an MMP-9-activatable NP to pancreatic tumors specifically, effectively, and safely. Copyright © 2016 Elsevier B.V. All rights reserved.

Induction of apoptosis by plumbagin through reactive oxygen species-mediated inhibition of topoisomerase II

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

Kawiak, Anna; Piosik, Jacek; Stasilojc, Grzegorz

2007-09-15

Reactive oxygen species (ROS) have been recognized as key molecules, which can selectively modify proteins and therefore regulate cellular signalling including apoptosis. Plumbagin, a naphthoquinone exhibiting antitumor activity, is known to generate ROS and has been found to inhibit the activity of topoisomerase II (Topo II) through the stabilization of the Topo II-DNA cleavable complex. The objective of this research was to clarify the role of ROS and Topo II inhibition in the induction of apoptosis mediated by plumbagin. As determined by the comet assay, plumbagin induced DNA cleavage in HL-60 cells, whereas in a cell line with reduced Topomore » II activity-HL-60/MX2, the level of DNA damage was significantly decreased. The onset of DNA strand break formation in HL-60 cells was delayed in comparison with the generation of intracellular ROS. In HL-60/MX2 cells, ROS were generated at a similar rate, whereas a significant reduction in the level of DNA damage was detected. The pretreatment of cells with N-acetylcysteine (NAC) attenuated plumbagin-induced DNA damage, pointing out to the involvement of ROS generation in cleavable complex formation. These results suggest that plumbagin-induced ROS does not directly damage DNA but requires the involvement of Topo II. Furthermore, experiments carried out using light spectroscopy indicated no direct interactions between plumbagin and DNA. The induction of apoptosis was significantly delayed in HL-60/MX2 cells indicating the involvement of Topo II inhibition in plumbagin-mediated apoptosis. Thus, these findings strongly suggest ROS-mediated inhibition of Topo II as an important mechanism contributing to the apoptosis-inducing properties of plumbagin.« less

Ultra-sensitive EUV resists based on acid-catalyzed polymer backbone breaking

NASA Astrophysics Data System (ADS)

Manouras, Theodoros; Kazazis, Dimitrios; Koufakis, Eleftherios; Ekinci, Yasin; Vamvakaki, Maria; Argitis, Panagiotis

2018-03-01

The main target of the current work was to develop new sensitive polymeric materials for lithographic applications, focusing in particular to EUV lithography, the main chain of which is cleaved under the influence of photogenerated acid. Resist materials based on the cleavage of polymer main chain are in principle capable to create very small structures, to the dimensions of the monomers that they consist of. Nevertheless, in the case of the commonly used nonchemically amplified materials of this type issues like sensitivity and poor etch resistance limit their areas of application, whereas inadequate etch resistance and non- satisfactory process reliability are the usual problems encountered in acid catalysed materials based on main chain scission. In our material design the acid catalyzed chain cleavable polymers contain very sensitive moieties in their backbone while they remain intact in alkaline ambient. These newly synthesized polymers bear in addition suitable functional groups for the achievement of desirable lithographic characteristics (thermal stability, acceptable glass transition temperature, etch resistance, proper dissolution behavior, adhesion to the substrate). Our approach for achieving acceptable etch resistance, a main drawback in other main chain cleavable resists, is based on the introduction of polyaromatic hydrocarbons in the polymeric backbone, whereas the incorporation of an inorganic component further enhances the etch resistance. Single component systems can also be designed following the proposed approach by the incorporation of suitable PAGs and base quencher molecules in the main chain. Resist formulations based on a random copolymer designed according to the described rules evaluated in EUV exhibit ultrahigh sensitivity, capability for high resolution patterning and overall processing characteristics that make them strong candidates for industrial use upon further optimization.

Magnetic-Fe/Fe3O4-nanoparticle-bound SN38 as carboxylesterase-cleavable prodrug for the delivery to tumors within monocytes/macrophages

PubMed Central

Shrestha, Tej B; Basel, Matthew T; Dani, Raj Kumar; Seo, Gwi-Moon; Balivada, Sivasai; Pyle, Marla M; Prock, Heidy; Koper, Olga B; Thapa, Prem S; Moore, David; Li, Ping; Chikan, Viktor

2012-01-01

Summary The targeted delivery of therapeutics to the tumor site is highly desirable in cancer treatment, because it is capable of minimizing collateral damage. Herein, we report the synthesis of a nanoplatform, which is composed of a 15 ± 1 nm diameter core/shell Fe/Fe3O4 magnetic nanoparticles (MNPs) and the topoisomerase I blocker SN38 bound to the surface of the MNPs via a carboxylesterase cleavable linker. This nanoplatform demonstrated high heating ability (SAR = 522 ± 40 W/g) in an AC-magnetic field. For the purpose of targeted delivery, this nanoplatform was loaded into tumor-homing double-stable RAW264.7 cells (mouse monocyte/macrophage-like cells (Mo/Ma)), which have been engineered to express intracellular carboxylesterase (InCE) upon addition of doxycycline by a Tet-On Advanced system. The nanoplatform was taken up efficiently by these tumor-homing cells. They showed low toxicity even at high nanoplatform concentration. SN38 was released successfully by switching on the Tet-On Advanced system. We have demonstrated that this nanoplatform can be potentially used for thermochemotherapy. We will be able to achieve the following goals: (1) Specifically deliver the SN38 prodrug and magnetic nanoparticles to the cancer site as the payload of tumor-homing double-stable RAW264.7 cells; (2) Release of chemotherapeutic SN38 at the cancer site by means of the self-containing Tet-On Advanced system; (3) Provide localized magnetic hyperthermia to enhance the cancer treatment, both by killing cancer cells through magnetic heating and by activating the immune system. PMID:23016149

Identification of yeast DNA topoisomerase II mutants resistant to the antitumor drug doxorubicin: implications for the mechanisms of doxorubicin action and cytotoxicity.

PubMed

Patel, S; Sprung, A U; Keller, B A; Heaton, V J; Fisher, L M

1997-10-01

Doxorubicin is a therapeutically useful anticancer drug that exerts multiple biological effects. Its antitumor and cardiotoxic properties have been ascribed to anthracycline-mediated free radical damage to DNA and membranes. Evidence for this idea comes in part from the selection by doxorubicin from stationary phase yeast cells of mutants (petites) deficient in mitochondrial respiration and therefore defective in free radical generation. However, doxorubicin also binds to DNA topoisomerase II, converting the enzyme into a DNA damaging agent through the trapping of a covalent enzyme-DNA complex termed the 'cleavable complex.' We have used yeast to determine whether stabilization of cleavable complexes plays a role in doxorubicin action and cytotoxicity. A plasmid-borne yeast TOP2 gene was mutagenized with hydroxylamine and used to transform drug-permeable yeast strain JN394t2-4, which carries a temperature-sensitive top2-4 mutation in its chromosomal TOP2 gene. Selection in growth medium at the nonpermissive temperature of 35 degrees in the presence of doxorubicin resulted in the isolation of plasmid-borne top2 mutants specifying functional doxorubicin-resistant DNA topoisomerase II. Single-point changes of Gly748 to Glu or Ala642 to Ser in yeast topoisomerase II, which lie in and adjacent to the CAP-like DNA binding domain, respectively, were identified as responsible for resistance to doxorubicin, implicating these regions in drug action. None of the mutants selected in JN394t2-4, which has a rad52 defect in double-strand DNA break repair, was respiration-deficient. We conclude that topoisomerase II is an intracellular target for doxorubicin and that the genetic background and/or cell proliferation status can determine the relative importance of topoisomerase II- versus free radical-killing.