Apparatus for producing diamond-like carbon flakes

NASA Technical Reports Server (NTRS)

Banks, Bruce A. (Inventor)

1986-01-01

A vacuum arc from a spot at the face of a graphite cathode to a graphite anode produces a beam of carbon ions and atoms. A carbon coating from this beam is deposited on an ion beam sputtered target to produce diamond-like carbon flakes. A graphite tube encloses the cathode, and electrical isolation is provided by an insulating sleeve. The tube forces the vacuum arc spot to be confined to the surface on the outermost end of the cathode. Without the tube the arc spot will wander to the side of the cathode. This spot movement results in low rates of carbon deposition, and the properties of the deposited flakes are more graphite-like than diamond-like.

Spatial fragment distribution from a therapeutic pencil-like carbon beam in water.

PubMed

Matsufuji, Naruhiro; Komori, Masataka; Sasaki, Hitomi; Akiu, Kengo; Ogawa, Masako; Fukumura, Akifumi; Urakabe, Eriko; Inaniwa, Taku; Nishio, Teiji; Kohno, Toshiyuki; Kanai, Tatsuaki

2005-07-21

The latest heavy ion therapy tends to require information about the spatial distribution of the quality of radiation in a patient's body in order to make the best use of any potential advantage of swift heavy ions for the therapeutic treatment of a tumour. The deflection of incident particles is described well by Molière's multiple-scattering theory of primary particles; however, the deflection of projectile fragments is not yet thoroughly understood. This paper reports on our investigation of the spatial distribution of fragments produced from a therapeutic carbon beam through nuclear reactions in thick water. A DeltaE-E counter telescope system, composed of a plastic scintillator, a gas-flow proportional counter and a BGO scintillator, was rotated around a water target in order to measure the spatial distribution of the radiation quality. The results revealed that the observed deflection of fragment particles exceeded the multiple scattering effect estimated by Molière's theory. However, the difference can be sufficiently accounted for by considering one term involved in the multiple-scattering formula; this term corresponds to a lateral 'kick' at the point of production of the fragment. This kick is successfully explained as a transfer of the intra-nucleus Fermi momentum of a projectile to the fragment; the extent of the kick obeys the expectation derived from the Goldhaber model.

Optical model calculations of heavy-ion target fragmentation

NASA Technical Reports Server (NTRS)

Townsend, L. W.; Wilson, J. W.; Cucinotta, F. A.; Norbury, J. W.

1986-01-01

The fragmentation of target nuclei by relativistic protons and heavy ions is described within the context of a simple abrasion-ablation-final-state interaction model. Abrasion is described by a quantum mechanical formalism utilizing an optical model potential approximation. Nuclear charge distributions of the excited prefragments are calculated by both a hypergeometric distribution and a method based upon the zero-point oscillations of the giant dipole resonance. Excitation energies are estimated from the excess surface energy resulting from the abrasion process and the additional energy deposited by frictional spectator interactions of the abraded nucleons. The ablation probabilities are obtained from the EVA-3 computer program. Isotope production cross sections for the spallation of copper targets by relativistic protons and for the fragmenting of carbon targets by relativistic carbon, neon, and iron projectiles are calculated and compared with available experimental data.

Targeting incentives to reduce habitat fragmentation

Treesearch

David Lewis; Andrew Plantinga; Junjie Wu

2009-01-01

This article develops a theoretical model to analyze the spatial targeting of incentives for the restoration of forested landscapes when wildlife habitat can be enhanced by reducing fragmentation. The key theoretical result is that the marginal net benefits of increasing forest can be convex, in which case corner solutions--converting either none or all of the...

Virtual Screening of Peptide and Peptidomimetic Fragments Targeted to Inhibit Bacterial Dithiol Oxidase DsbA.

PubMed

Duprez, Wilko; Bachu, Prabhakar; Stoermer, Martin J; Tay, Stephanie; McMahon, Róisín M; Fairlie, David P; Martin, Jennifer L

2015-01-01

Antibacterial drugs with novel scaffolds and new mechanisms of action are desperately needed to address the growing problem of antibiotic resistance. The periplasmic oxidative folding system in Gram-negative bacteria represents a possible target for anti-virulence antibacterials. By targeting virulence rather than viability, development of resistance and side effects (through killing host native microbiota) might be minimized. Here, we undertook the design of peptidomimetic inhibitors targeting the interaction between the two key enzymes of oxidative folding, DsbA and DsbB, with the ultimate goal of preventing virulence factor assembly. Structures of DsbB--or peptides--complexed with DsbA revealed key interactions with the DsbA active site cysteine, and with a hydrophobic groove adjacent to the active site. The present work aimed to discover peptidomimetics that target the hydrophobic groove to generate non-covalent DsbA inhibitors. The previously reported structure of a Proteus mirabilis DsbA active site cysteine mutant, in a non-covalent complex with the heptapeptide PWATCDS, was used as an in silico template for virtual screening of a peptidomimetic fragment library. The highest scoring fragment compound and nine derivatives were synthesized and evaluated for DsbA binding and inhibition. These experiments discovered peptidomimetic fragments with inhibitory activity at millimolar concentrations. Although only weakly potent relative to larger covalent peptide inhibitors that interact through the active site cysteine, these fragments offer new opportunities as templates to build non-covalent inhibitors. The results suggest that non-covalent peptidomimetics may need to interact with sites beyond the hydrophobic groove in order to produce potent DsbA inhibitors.

Momentum distributions of isotopes produced by fragmentation of relativistic C-12 and O-16 projectiles

NASA Technical Reports Server (NTRS)

Greiner, D. E.; Lindstrom, P. J.; Heckman, H. H.; Cork, B.; Bieser, F. S.

1975-01-01

The fragment momentum distributions in the projectile rest frame are, typically, Gaussian shaped, narrow, consistent with isotropy, depend on fragment and projectile, and have no significant correlation with target mass or beam energy. The nuclear temperature is inferred from the momentum distributions of the fragments and is approximately equal to the projectile nuclear binding energy, indicative of small energy transfer between target and fragment.

Site Identification by Ligand Competitive Saturation (SILCS) Simulations for Fragment-Based Drug Design

PubMed Central

Faller, Christina E.; Raman, E. Prabhu; MacKerell, Alexander D.; Guvench, Olgun

2015-01-01

Fragment-based drug design (FBDD) involves screening low molecular weight molecules (“fragments”) that correspond to functional groups found in larger drug-like molecules to determine their binding to target proteins or nucleic acids. Based on the principle of thermodynamic additivity, two fragments that bind non-overlapping nearby sites on the target can be combined to yield a new molecule whose binding free energy is the sum of those of the fragments. Experimental FBDD approaches, like NMR and X-ray crystallography, have proven very useful but can be expensive in terms of time, materials, and labor. Accordingly, a variety of computational FBDD approaches have been developed that provide different levels of detail and accuracy. The Site Identification by Ligand Competitive Saturation (SILCS) method of computational FBDD uses all-atom explicit-solvent molecular dynamics (MD) simulations to identify fragment binding. The target is “soaked” in an aqueous solution with multiple fragments having different identities. The resulting computational competition assay reveals what small molecule types are most likely to bind which regions of the target. From SILCS simulations, 3D probability maps of fragment binding called “FragMaps” can be produced. Based on the probabilities relative to bulk, SILCS FragMaps can be used to determine “Grid Free Energies (GFEs),” which provide per-atom contributions to fragment binding affinities. For essentially no additional computational overhead relative to the production of the FragMaps, GFEs can be used to compute Ligand Grid Free Energies (LGFEs) for arbitrarily complex molecules, and these LGFEs can be used to rank-order the molecules in accordance with binding affinities. PMID:25709034

Recombinant human antibody fragment against tetanus toxoid produced by phage display

PubMed Central

Neelakantam, B.; Sridevi, N. V.; Shukra, A. M.; Sugumar, P.; Samuel, S.

2014-01-01

Phage display technology is a powerful in vitro method for the identification of specific monoclonal antibodies (antibody fragments) to an antigenic target and allows the rapid generation and selection of high affinity, fully human antibodies directed toward any disease target appropriate for antibody therapy. In the present study, we exploited the phage display technology for the selection of an antigen binding fragment (Fabs) toward tetanus toxoid using human naïve phage antibody library constructed from peripheral blood lymphocytes of naïve human donors. The phages displaying Fab were subjected to three rounds of bio-panning with tetanus toxoid as antigen on a solid phase. The high affinity antibody fragments were expressed in HB2151 strain of Escherichia coli and purified by immobilized metal affinity chromatography. The binding activity and specificity of the antibody fragment was established by its reactivity toward tetanus toxoid and non-reactivity toward other related toxins as determined by enzyme-linked immunosorbent assay and immunoblot analysis. The selected Fab fragment forming the antigen-binding complexes with the toxoid in flocculation assay indicates that the Fab may have a potential neutralizing ability toward antigen. PMID:24678405

Recombinant human antibody fragment against tetanus toxoid produced by phage display.

PubMed

Neelakantam, B; Sridevi, N V; Shukra, A M; Sugumar, P; Samuel, S; Rajendra, L

2014-03-01

Phage display technology is a powerful in vitro method for the identification of specific monoclonal antibodies (antibody fragments) to an antigenic target and allows the rapid generation and selection of high affinity, fully human antibodies directed toward any disease target appropriate for antibody therapy. In the present study, we exploited the phage display technology for the selection of an antigen binding fragment (Fabs) toward tetanus toxoid using human naïve phage antibody library constructed from peripheral blood lymphocytes of naïve human donors. The phages displaying Fab were subjected to three rounds of bio-panning with tetanus toxoid as antigen on a solid phase. The high affinity antibody fragments were expressed in HB2151 strain of Escherichia coli and purified by immobilized metal affinity chromatography. The binding activity and specificity of the antibody fragment was established by its reactivity toward tetanus toxoid and non-reactivity toward other related toxins as determined by enzyme-linked immunosorbent assay and immunoblot analysis. The selected Fab fragment forming the antigen-binding complexes with the toxoid in flocculation assay indicates that the Fab may have a potential neutralizing ability toward antigen.

Elaboration of a fragment library hit produces potent and selective aspartate semialdehyde dehydrogenase inhibitors.

PubMed

Thangavelu, Bharani; Bhansali, Pravin; Viola, Ronald E

2015-10-15

Aspartate-β-semialdehyde dehydrogenase (ASADH) lies at the first branch point in the aspartate metabolic pathway which leads to the biosynthesis of several essential amino acids and some important metabolites. This pathway is crucial for many metabolic processes in plants and microbes like bacteria and fungi, but is absent in mammals. Therefore, the key microbial enzymes involved in this pathway are attractive potential targets for development of new antibiotics with novel modes of action. The ASADH enzyme family shares the same substrate binding and active site catalytic groups; however, the enzymes from representative bacterial and fungal species show different inhibition patterns when previously screened against low molecular weight inhibitors identified from fragment library screening. In the present study several approaches, including fragment based drug discovery (FBDD), inhibitor docking, kinetic, and structure-activity relationship (SAR) studies have been used to guide ASADH inhibitor development. Elaboration of a core structure identified by FBDD has led to the synthesis of low micromolar inhibitors of the target enzyme, with high selectivity introduced between the Gram-negative and Gram-positive orthologs of ASADH. This new set of structures open a novel direction for the development of inhibitors against this validated drug-target enzyme. Copyright © 2015 Elsevier Ltd. All rights reserved.

Knowledge-based fragment binding prediction.

PubMed

Tang, Grace W; Altman, Russ B

2014-04-01

Target-based drug discovery must assess many drug-like compounds for potential activity. Focusing on low-molecular-weight compounds (fragments) can dramatically reduce the chemical search space. However, approaches for determining protein-fragment interactions have limitations. Experimental assays are time-consuming, expensive, and not always applicable. At the same time, computational approaches using physics-based methods have limited accuracy. With increasing high-resolution structural data for protein-ligand complexes, there is now an opportunity for data-driven approaches to fragment binding prediction. We present FragFEATURE, a machine learning approach to predict small molecule fragments preferred by a target protein structure. We first create a knowledge base of protein structural environments annotated with the small molecule substructures they bind. These substructures have low-molecular weight and serve as a proxy for fragments. FragFEATURE then compares the structural environments within a target protein to those in the knowledge base to retrieve statistically preferred fragments. It merges information across diverse ligands with shared substructures to generate predictions. Our results demonstrate FragFEATURE's ability to rediscover fragments corresponding to the ligand bound with 74% precision and 82% recall on average. For many protein targets, it identifies high scoring fragments that are substructures of known inhibitors. FragFEATURE thus predicts fragments that can serve as inputs to fragment-based drug design or serve as refinement criteria for creating target-specific compound libraries for experimental or computational screening.

Knowledge-based Fragment Binding Prediction

PubMed Central

Tang, Grace W.; Altman, Russ B.

2014-01-01

Target-based drug discovery must assess many drug-like compounds for potential activity. Focusing on low-molecular-weight compounds (fragments) can dramatically reduce the chemical search space. However, approaches for determining protein-fragment interactions have limitations. Experimental assays are time-consuming, expensive, and not always applicable. At the same time, computational approaches using physics-based methods have limited accuracy. With increasing high-resolution structural data for protein-ligand complexes, there is now an opportunity for data-driven approaches to fragment binding prediction. We present FragFEATURE, a machine learning approach to predict small molecule fragments preferred by a target protein structure. We first create a knowledge base of protein structural environments annotated with the small molecule substructures they bind. These substructures have low-molecular weight and serve as a proxy for fragments. FragFEATURE then compares the structural environments within a target protein to those in the knowledge base to retrieve statistically preferred fragments. It merges information across diverse ligands with shared substructures to generate predictions. Our results demonstrate FragFEATURE's ability to rediscover fragments corresponding to the ligand bound with 74% precision and 82% recall on average. For many protein targets, it identifies high scoring fragments that are substructures of known inhibitors. FragFEATURE thus predicts fragments that can serve as inputs to fragment-based drug design or serve as refinement criteria for creating target-specific compound libraries for experimental or computational screening. PMID:24762971

Fission fragment yields from heavy-ion-induced reactions measured with a fragment separator

NASA Astrophysics Data System (ADS)

Tarasov, O. B.; Delaune, O.; Farget, F.; Morrissey, D. J.; Amthor, A. M.; Bastin, B.; Bazin, D.; Blank, B.; Cacéres, L.; Chbihi, A.; Fernández-Dominguez, B.; Grévy, S.; Kamalou, O.; Lukyanov, S. M.; Mittig, W.; Pereira, J.; Perrot, L.; Saint-Laurent, M.-G.; Savajols, H.; Sherrill, B. M.; Stodel, C.; Thomas, J. C.; Villari, A. C.

2018-04-01

The systematic study of fission fragment yields under different initial conditions has provided valuable experimental data for benchmarking models of fission product yields. Nuclear reactions using inverse kinematics coupled to the use of a high-resolution spectrometer with good fragment identification are shown here to be a powerful tool to measure the inclusive isotopic yields of fission fragments. In-flight fusion-fission was used in this work to produce secondary beams of neutron-rich isotopes in the collisions of a 238U beam at 24 MeV/u with 9Be and 12C targets at GANIL using the LISE3 fragment separator. Unique identification of the A, Z, and atomic charge state, q, of fission products was attained with the Δ E- TKE-B ρ- ToF measurement technique. Mass, and atomic number distributions are reported for the two reactions. The results show the importance of different reaction mechanisms in the two cases. The optimal target material for higher yields of neutron-rich high- Z isotopes produced in fusion-fission reactions as a function of projectile energy is discussed.

Proteolysis of the Matricellular Protein Hevin by Matrix Metalloproteinase-3 Produces a SPARC-like Fragment (SLF) Associated with Neovasculature in a Murine Glioma Model

PubMed Central

Weaver, Matt; Workman, Gail; Schultz, Chad R.; Lemke, Nancy; Rempel, Sandra A.; Sage, E. Helene

2011-01-01

The matricellular SPARC-family member hevin (Sparc-like 1/SPARCL-1/SC1/Mast9) contributes to neural development and alters tumor progression in a range of mammalian models. Based on sequence similarity, we hypothesized that proteolytic digestion of hevin would result in SPARC-like fragments (SLF) that affect the activity and/or location of these proteins. Incubation of hevin with matrix metalloproteinase-3 (MMP-3), a protease known to cleave SPARC, produced a limited number of peptides. Sequencing revealed the major proteolytic products to be SPARC-like in primary structure. In gliomas implanted into murine brain, a SLF was associated with SPARC in the neovasculature but not with hevin, the latter prominent in the astrocytes encompassed by infiltrating tumor. In this model of invasive glioma that involves MMP-3 activity, host-derived SLF was not observed in the extracellular matrix adjacent to tumor cells. In contrast, it occurred with its homolog SPARC in the angiogenic response to the tumor. We conclude that MMP-3-derived SLF is a marker of neovessels in glioma, where it could influence the activity of SPARC. PMID:21688302

Design of Chemical Conjugate for Targeted Therapy of Multiple Sclerosis Based of Constant Fragment of Human Antibody Heavy Chain and Peptoid Analog of Autoantigen MOG35-55.

PubMed

Lomakin, Y A; Stepanov, A V; Balabashin, D S; Ponomarenko, N A; Smirnov, I V; Belogurov, A A

2017-04-01

Elimination of B cells producing autoantibodies to neuroantigens is considered as beneficial in the treatment of multiple sclerosis. Myelin oligodendrocyte glycoprotein (MOG) is a significant autoantigen in multiple sclerosis. It was shown that MOG-like peptoid AMogP3 can bind autoantibodies produced by pathological lymphocytes. We propose a structure of an innovative drug for targeted elimination of the pool of autoreactive B cells responsible for multiple sclerosis pathogenesis; this compound is a complex of peptoid AMogP3 with Fc fragment of human immunoglobulin. The obtained Fc-PEG-AMogP3 conjugate effectively interact with autoreactive antibodies, which attests to their high therapeutic potential.

An endogenously produced fragment of cardiac myosin-binding protein C is pathogenic and can lead to heart failure.

PubMed

Razzaque, Md Abdur; Gupta, Manish; Osinska, Hanna; Gulick, James; Blaxall, Burns C; Robbins, Jeffrey

2013-08-16

A stable 40-kDa fragment is produced from cardiac myosin-binding protein C when the heart is stressed using a stimulus, such as ischemia-reperfusion injury. Elevated levels of the fragment can be detected in the diseased mouse and human heart, but its ability to interfere with normal cardiac function in the intact animal is unexplored. To understand the potential pathogenicity of the 40-kDa fragment in vivo and to investigate the molecular pathways that could be targeted for potential therapeutic intervention. We generated cardiac myocyte-specific transgenic mice using a Tet-Off inducible system to permit controlled expression of the 40-kDa fragment in cardiomyocytes. When expression of the 40-kDa protein is induced by crossing the responder animals with tetracycline transactivator mice under conditions in which substantial quantities approximating those observed in diseased hearts are reached, the double-transgenic mice subsequently experience development of sarcomere dysgenesis and altered cardiac geometry, and the heart fails between 12 and 17 weeks of age. The induced double-transgenic mice had development of cardiac hypertrophy with myofibrillar disarray and fibrosis, in addition to activation of pathogenic MEK-ERK pathways. Inhibition of MEK-ERK signaling was achieved by injection of the mitogen-activated protein kinase (MAPK)/ERK inhibitor U0126. The drug effectively improved cardiac function, normalized heart size, and increased probability of survival. These results suggest that the 40-kDa cardiac myosin-binding protein C fragment, which is produced at elevated levels during human cardiac disease, is a pathogenic fragment that is sufficient to cause hypertrophic cardiomyopathy and heart failure.

Route to three-dimensional fragments using diversity-oriented synthesis

PubMed Central

Hung, Alvin W.; Ramek, Alex; Wang, Yikai; Kaya, Taner; Wilson, J. Anthony; Clemons, Paul A.; Young, Damian W.

2011-01-01

Fragment-based drug discovery (FBDD) has proven to be an effective means of producing high-quality chemical ligands as starting points for drug-discovery pursuits. The increasing number of clinical candidate drugs developed using FBDD approaches is a testament of the efficacy of this approach. The success of fragment-based methods is highly dependent on the identity of the fragment library used for screening. The vast majority of FBDD has centered on the use of sp2-rich aromatic compounds. An expanded set of fragments that possess more 3D character would provide access to a larger chemical space of fragments than those currently used. Diversity-oriented synthesis (DOS) aims to efficiently generate a set of molecules diverse in skeletal and stereochemical properties. Molecules derived from DOS have also displayed significant success in the modulation of function of various “difficult” targets. Herein, we describe the application of DOS toward the construction of a unique set of fragments containing highly sp3-rich skeletons for fragment-based screening. Using cheminformatic analysis, we quantified the shapes and physical properties of the new 3D fragments and compared them with a database containing known fragment-like molecules. PMID:21482811

Route to three-dimensional fragments using diversity-oriented synthesis.

PubMed

Hung, Alvin W; Ramek, Alex; Wang, Yikai; Kaya, Taner; Wilson, J Anthony; Clemons, Paul A; Young, Damian W

2011-04-26

Fragment-based drug discovery (FBDD) has proven to be an effective means of producing high-quality chemical ligands as starting points for drug-discovery pursuits. The increasing number of clinical candidate drugs developed using FBDD approaches is a testament of the efficacy of this approach. The success of fragment-based methods is highly dependent on the identity of the fragment library used for screening. The vast majority of FBDD has centered on the use of sp(2)-rich aromatic compounds. An expanded set of fragments that possess more 3D character would provide access to a larger chemical space of fragments than those currently used. Diversity-oriented synthesis (DOS) aims to efficiently generate a set of molecules diverse in skeletal and stereochemical properties. Molecules derived from DOS have also displayed significant success in the modulation of function of various "difficult" targets. Herein, we describe the application of DOS toward the construction of a unique set of fragments containing highly sp(3)-rich skeletons for fragment-based screening. Using cheminformatic analysis, we quantified the shapes and physical properties of the new 3D fragments and compared them with a database containing known fragment-like molecules.

Target fragmentation in proton-nucleus and16O-nucleus reactions at 60 and 200 GeV/nucleon

NASA Astrophysics Data System (ADS)

Albrecht, R.; Awes, T. C.; Baktash, C.; Beckmann, P.; Claesson, G.; Berger, F.; Bock, R.; Dragon, L.; Ferguson, R. L.; Franz, A.; Garpman, S.; Glasow, R.; Gustafsson, H. Å.; Gutbrod, H. H.; Kampert, K. H.; Kolb, B. W.; Kristiansson, P.; Lee, I. Y.; Löhner, H.; Lund, I.; Obenshain, F. E.; Oskarsson, A.; Otterlund, I.; Peitzmann, T.; Persson, S.; Plasil, F.; Poskanzer, A. M.; Purschke, M.; Ritter, H. G.; Santo, R.; Schmidt, H. R.; Siemiarczuk, T.; Sorensen, S. P.; Stenlund, E.; Young, G. R.

1988-03-01

Target remnants with Z<3 from proton-nucleus and16O-nucleus reactions at 60 and 200 GeV/nucleon were measured in the angular range from 30° to 160° (-1.7<η<1.3) employing the Plastic Ball detector. The excitation energy of the target spectator matter in central oxygen-induced collisions is found to be high enough to allow for complete disintegration of the target nucleus into fragments with Z<3. The average longitudinal momentum transfer per proton to the target in central collisions is considerably higher in the case of16O-induced reactions (≈300 MeV/c) than in proton-induced reactions (≈130 MeV/c). The baryon rapidity distributions are roughly in agreement with one-fluid hydrodynamical calculations at 60 GeV/nucleon16O+Au but are in disagreement at 200 GeV/nucleon, indicating the higher degree of transparency at the higher bombarding energy. Both, the transverse momenta of target spectators and the entropy produced in the target fragmentation region are compared to those attained in head-on collisions of two heavy nuclei at Bevalac energies. They are found to be comparable or do even exceed the values for the participant matter at beam energies of about 1 2 GeV/nucleon.

Identification of potential glutaminyl cyclase inhibitors from lead-like libraries by in silico and in vitro fragment-based screening.

PubMed

Szaszkó, Mária; Hajdú, István; Flachner, Beáta; Dobi, Krisztina; Magyar, Csaba; Simon, István; Lőrincz, Zsolt; Kapui, Zoltán; Pázmány, Tamás; Cseh, Sándor; Dormán, György

2017-02-01

A glutaminyl cyclase (QC) fragment library was in silico selected by disconnection of the structure of known QC inhibitors and by lead-like 2D virtual screening of the same set. The resulting fragment library (204 compounds) was acquired from commercial suppliers and pre-screened by differential scanning fluorimetry followed by functional in vitro assays. In this way, 10 fragment hits were identified ([Formula: see text]5 % hit rate, best inhibitory activity: 16 [Formula: see text]). The in vitro hits were then docked to the active site of QC, and the best scoring compounds were analyzed for binding interactions. Two fragments bound to different regions in a complementary manner, and thus, linking those fragments offered a rational strategy to generate novel QC inhibitors. Based on the structure of the virtual linked fragment, a 77-membered QC target focused library was selected from vendor databases and docked to the active site of QC. A PubChem search confirmed that the best scoring analogues are novel, potential QC inhibitors.

Recombinant GDNF: Tetanus toxin fragment C fusion protein produced from insect cells

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

Li, Jianhong; Chian, Ru-Ju; Ay, Ilknur

2009-07-31

Glial cell line-derived neurotrophic factor (GDNF) has potent survival-promoting effects on CNS motor neurons in experimental animals. Its therapeutic efficacy in humans, however, may have been limited by poor bioavailability to the brain and spinal cord. With a view toward improving delivery of GDNF to CNS motor neurons in vivo, we generated a recombinant fusion protein comprised of rat GDNF linked to the non-toxic, neuron-binding fragment of tetanus toxin. Recombinant GDNF:TTC produced from insect cells was a soluble homodimer like wild-type GDNF and was bi-functional with respect to GDNF and TTC activity. Like recombinant rat GDNF, the fusion protein increasedmore » levels of immunoreactive phosphoAkt in treated NB41A3-hGFR{alpha}-1 neuroblastoma cells. Like TTC, GDNF:TTC bound to immobilized ganglioside GT1b in vitro with high affinity and selectivity. These results support further testing of recombinant GDNF:TTC as a non-viral vector to improve delivery of GDNF to brain and spinal cord in vivo.« less

Effects of Target Fragmentation on Evaluation of LET Spectra From Space Radiation in Low-Earth Orbit (LEO) Environment: Impact on SEU Predictions

NASA Technical Reports Server (NTRS)

Shinn, J. L.; Cucinotta, F. A.; Badhwar, G. D.; ONeill, P. M.; Badavi, F. F.

1995-01-01

Recent improvements in the radiation transport code HZETRN/BRYNTRN and galactic cosmic ray environmental model have provided an opportunity to investigate the effects of target fragmentation on estimates of single event upset (SEU) rates for spacecraft memory devices. Since target fragments are mostly of very low energy, an SEU prediction model has been derived in terms of particle energy rather than linear energy transfer (LET) to account for nonlinear relationship between range and energy. Predictions are made for SEU rates observed on two Shuttle flights, each at low and high inclination orbit. Corrections due to track structure effects are made for both high energy ions with track structure larger than device sensitive volume and for low energy ions with dense track where charge recombination is important. Results indicate contributions from target fragments are relatively important at large shield depths (or any thick structure material) and at low inclination orbit. Consequently, a more consistent set of predictions for upset rates observed in these two flights is reached when compared to an earlier analysis with CREME model. It is also observed that the errors produced by assuming linear relationship in range and energy in the earlier analysis have fortuitously canceled out the errors for not considering target fragmentation and track structure effects.

SKI2 mediates degradation of RISC 5'-cleavage fragments and prevents secondary siRNA production from miRNA targets in Arabidopsis.

PubMed

Branscheid, Anja; Marchais, Antonin; Schott, Gregory; Lange, Heike; Gagliardi, Dominique; Andersen, Stig Uggerhøj; Voinnet, Olivier; Brodersen, Peter

2015-12-15

Small regulatory RNAs are fundamental in eukaryotic and prokaryotic gene regulation. In plants, an important element of post-transcriptional control is effected by 20-24 nt microRNAs (miRNAs) and short interfering RNAs (siRNAs) bound to the ARGONAUTE1 (AGO1) protein in an RNA induced silencing complex (RISC). AGO1 may cleave target mRNAs with small RNA complementarity, but the fate of the resulting cleavage fragments remains incompletely understood. Here, we show that SKI2, SKI3 and SKI8, subunits of a cytoplasmic cofactor of the RNA exosome, are required for degradation of RISC 5', but not 3'-cleavage fragments in Arabidopsis. In the absence of SKI2 activity, many miRNA targets produce siRNAs via the RNA-dependent RNA polymerase 6 (RDR6) pathway. These siRNAs are low-abundant, and map close to the cleavage site. In most cases, siRNAs were produced 5' to the cleavage site, but several examples of 3'-spreading were also identified. These observations suggest that siRNAs do not simply derive from RDR6 action on stable 5'-cleavage fragments and hence that SKI2 has a direct role in limiting secondary siRNA production in addition to its function in mediating degradation of 5'-cleavage fragments. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

SKI2 mediates degradation of RISC 5′-cleavage fragments and prevents secondary siRNA production from miRNA targets in Arabidopsis

PubMed Central

Branscheid, Anja; Marchais, Antonin; Schott, Gregory; Lange, Heike; Gagliardi, Dominique; Andersen, Stig Uggerhøj; Voinnet, Olivier; Brodersen, Peter

2015-01-01

Small regulatory RNAs are fundamental in eukaryotic and prokaryotic gene regulation. In plants, an important element of post-transcriptional control is effected by 20–24 nt microRNAs (miRNAs) and short interfering RNAs (siRNAs) bound to the ARGONAUTE1 (AGO1) protein in an RNA induced silencing complex (RISC). AGO1 may cleave target mRNAs with small RNA complementarity, but the fate of the resulting cleavage fragments remains incompletely understood. Here, we show that SKI2, SKI3 and SKI8, subunits of a cytoplasmic cofactor of the RNA exosome, are required for degradation of RISC 5′, but not 3′-cleavage fragments in Arabidopsis. In the absence of SKI2 activity, many miRNA targets produce siRNAs via the RNA-dependent RNA polymerase 6 (RDR6) pathway. These siRNAs are low-abundant, and map close to the cleavage site. In most cases, siRNAs were produced 5′ to the cleavage site, but several examples of 3′-spreading were also identified. These observations suggest that siRNAs do not simply derive from RDR6 action on stable 5′-cleavage fragments and hence that SKI2 has a direct role in limiting secondary siRNA production in addition to its function in mediating degradation of 5′-cleavage fragments. PMID:26464441

Optical model analyses of galactic cosmic ray fragmentation in hydrogen targets

NASA Technical Reports Server (NTRS)

Townsend, Lawrence W.

1993-01-01

Quantum-mechanical optical model methods for calculating cross sections for the fragmentation of galactic cosmic ray nuclei by hydrogen targets are presented. The fragmentation cross sections are calculated with an abrasion-ablation collision formalism. Elemental and isotopic cross sections are estimated and compared with measured values for neon, sulfur, and calcium ions at incident energies between 400A MeV and 910A MeV. Good agreement between theory and experiment is obtained.

Progress on the chemical separation of fission fragments from 236Np produced by proton irradiation of natural uranium target

NASA Astrophysics Data System (ADS)

Larijani, C.; Jerome, S. M.; Lorusso, G.; Ivanov, P.; Russell, B.; Pearce, A. K.; Regan, P. H.

2017-11-01

The aim of the current work is to develop and validate a radiochemical separation scheme capable of separating both 236gNp and 236Pu from a uranium target of natural isotopic composition ( 1 g uranium) and 200 MBq of fission decay products. A target containing 1.2 g of UO2 was irradiated with a beam of 25 MeV protons with a typical beam current of 30 μA for 19 h in December 2013 at the University of Birmingham Cyclotron facility. Using literature values for the production cross-section for fusion of protons with uranium targets, we estimate that an upper limit of approximately 250 Bq of activity from the 236Np ground state was produced in this experiment. Using a radiochemical separation scheme, Np and Pu fractions were separated from the produced fission decay products, with analyses of the target-based final reaction products made using Inductively Couple Plasma Mass Spectrometry (ICP-MS) and high-resolution α particle and γ-ray spectrometry.

Fragment-Based Screening of a Natural Product Library against 62 Potential Malaria Drug Targets Employing Native Mass Spectrometry

PubMed Central

2018-01-01

Natural products are well known for their biological relevance, high degree of three-dimensionality, and access to areas of largely unexplored chemical space. To shape our understanding of the interaction between natural products and protein targets in the postgenomic era, we have used native mass spectrometry to investigate 62 potential protein targets for malaria using a natural-product-based fragment library. We reveal here 96 low-molecular-weight natural products identified as binding partners of 32 of the putative malarial targets. Seventy-nine (79) fragments have direct growth inhibition on Plasmodium falciparum at concentrations that are promising for the development of fragment hits against these protein targets. This adds a fragment library to the published HTS active libraries in the public domain. PMID:29436819

Fragment-Based Screening of a Natural Product Library against 62 Potential Malaria Drug Targets Employing Native Mass Spectrometry.

PubMed

Vu, Hoan; Pedro, Liliana; Mak, Tin; McCormick, Brendan; Rowley, Jessica; Liu, Miaomiao; Di Capua, Angela; Williams-Noonan, Billy; Pham, Ngoc B; Pouwer, Rebecca; Nguyen, Bao; Andrews, Katherine T; Skinner-Adams, Tina; Kim, Jessica; Hol, Wim G J; Hui, Raymond; Crowther, Gregory J; Van Voorhis, Wesley C; Quinn, Ronald J

2018-04-13

Natural products are well known for their biological relevance, high degree of three-dimensionality, and access to areas of largely unexplored chemical space. To shape our understanding of the interaction between natural products and protein targets in the postgenomic era, we have used native mass spectrometry to investigate 62 potential protein targets for malaria using a natural-product-based fragment library. We reveal here 96 low-molecular-weight natural products identified as binding partners of 32 of the putative malarial targets. Seventy-nine (79) fragments have direct growth inhibition on Plasmodium falciparum at concentrations that are promising for the development of fragment hits against these protein targets. This adds a fragment library to the published HTS active libraries in the public domain.

Accurate Mass Fragment Library for Rapid Analysis of Pesticides on Produce Using Ambient Pressure Desorption Ionization with High-Resolution Mass Spectrometry

NASA Astrophysics Data System (ADS)

Kern, Sara E.; Lin, Lora A.; Fricke, Frederick L.

2014-08-01

U.S. food imports have been increasing steadily for decades, intensifying the need for a rapid and sensitive screening technique. A method has been developed that uses foam disks to sample the surface of incoming produce. This work provides complimentary information to the extensive amount of published pesticide fragmentation data collected using LCMS systems (Sack et al. Journal of Agricultural and Food Chemistry, 59, 6383-6411, 2011; Mol et al. Analytical and Bioanalytical Chemistry, 403, 2891-2908, 2012). The disks are directly analyzed using transmission-mode direct analysis in real time (DART) ambient pressure desorption ionization coupled to a high resolution accurate mass-mass spectrometer (HRAM-MS). In order to provide more certainty in the identification of the pesticides detected, a library of accurate mass fragments and isotopes of the protonated parent molecular ion (the [M+H]+) has been developed. The HRAM-MS is equipped with a quadrupole mass filter, providing the capability of "data-dependent" fragmentation, as opposed to "all -ion" fragmentation (where all of the ions enter a collision chamber and are fragmented at once). A temperature gradient for the DART helium stream and multiple collision energies were employed to detect and fragment 164 pesticides of varying chemical classes, sizes, and polarities. The accurate mass information of precursor ([M+H]+ ion) and fragment ions is essential in correctly identifying chemical contaminants on the surface of imported produce. Additionally, the inclusion of isotopes of the [M+H]+ in the database adds another metric to the confirmation process. The fragmentation data were collected using a Q-Exactive mass spectrometer and were added to a database used to process data collected with an Exactive mass spectrometer, an instrument that is more readily available for this screening application. The commodities investigated range from smooth-skinned produce such as apples to rougher surfaces like broccoli. The

Synchronous detection of ebolavirus conserved RNA sequences and ebolavirus-encoded miRNA-like fragment based on a zwitterionic copper (II) metal-organic framework.

PubMed

Qiu, Gui-Hua; Weng, Zi-Hua; Hu, Pei-Pei; Duan, Wen-Jun; Xie, Bao-Ping; Sun, Bin; Tang, Xiao-Yan; Chen, Jin-Xiang

2018-04-01

From a three-dimensional (3D) metal-organic framework (MOF) of {[Cu(Cmdcp)(phen)(H 2 O)] 2 ·9H 2 O} n (1, H 3 CmdcpBr = N-carboxymethyl-(3,5-dicarboxyl)pyridinium bromide, phen = phenanthroline), a sensitive and selective fluorescence sensor has been developed for the simultaneous detection of ebolavirus conserved RNA sequences and ebolavirus-encoded microRNA-like (miRNA-like) fragment. The results from molecular dynamics simulation confirmed that MOF 1 absorbs carboxyfluorescein (FAM)-tagged and 5(6)-carboxyrhodamine, triethylammonium salt (ROX)-tagged probe ss-DNA (probe DNA, P-DNA) by π … π stacking and hydrogen bonding, as well as additional electrostatic interactions to form a sensing platform of P-DNAs@1 with quenched FAM and ROX fluorescence. In the presence of targeted ebolavirus conserved RNA sequences or ebolavirus-encoded miRNA-like fragment, the fluorophore-labeled P-DNA hybridizes with the analyte to give a P-DNA@RNA duplex and released from MOF 1, triggering a fluorescence recovery. Simultaneous detection of two target RNAs has also been realized by single and synchronous fluorescence analysis. The formed sensing platform shows high sensitivity for ebolavirus conserved RNA sequences and ebolavirus-encoded miRNA-like fragment with detection limits at the picomolar level and high selectivity without cross-reaction between the two probes. MOF 1 thus shows the potential as an effective fluorescent sensing platform for the synchronous detection of two ebolavirus-related sequences, and offer improved diagnostic accuracy of Ebola virus disease. Copyright © 2017 Elsevier B.V. All rights reserved.

Diversity-Oriented Synthesis as a Strategy for Fragment Evolution against GSK3β.

PubMed

Wang, Yikai; Wach, Jean-Yves; Sheehan, Patrick; Zhong, Cheng; Zhan, Chenyang; Harris, Richard; Almo, Steven C; Bishop, Joshua; Haggarty, Stephen J; Ramek, Alexander; Berry, Kayla N; O'Herin, Conor; Koehler, Angela N; Hung, Alvin W; Young, Damian W

2016-09-08

Traditional fragment-based drug discovery (FBDD) relies heavily on structural analysis of the hits bound to their targets. Herein, we present a complementary approach based on diversity-oriented synthesis (DOS). A DOS-based fragment collection was able to produce initial hit compounds against the target GSK3β, allow the systematic synthesis of related fragment analogues to explore fragment-level structure-activity relationship, and finally lead to the synthesis of a more potent compound.

Fragmentation Cross Sections of 290 and 400 MeV/nucleon 12C Beamson Elemental Targets

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

Zeitlin, C.; Guetersloh, S.; Heilbronn, L.

Charge-changing and fragment production cross sections at 0circ have been obtained for interactions of 290 MeV/nucleon and 400MeV/nucleon carbon beams with C, CH2, Al, Cu, Sn, and Pb targets. Thesebeams are relevant to cancer therapy, space radiation, and the productionof radioactive beams. We compare to previously published results using Cand CH2 targets at similar beam energies. Due to ambiguities arising fromthe presence of multiple fragments on many events, previous publicationshave reported only cross sections for B and Be fragments. In this work wehave extracted cross sections for all fragment species, using dataobtained at three distinct values of angular acceptance, supplementedmore » bydata taken with the detector stack placed off the beam axis. A simulationof the experiment with the PHITS Monte Carlo code shows fair agreementwith the data obtained with the large acceptance detectors, but agreementis poor at small acceptance. The measured cross sections are alsocompared to the predictions of the one-dimensional cross section modelsEPAX2 and NUCFRG2; the latter is presently used in NASA's space radiationtransport calculations. Though PHITS and NUCFRG2 reproduce thecharge-changing cross sections with reasonable accuracy, none of themodels is able to accurately predict the fragment cross sections for allfragment species and target materials.« less

Apoptosis-like programmed cell death induces antisense ribosomal RNA (rRNA) fragmentation and rRNA degradation in Leishmania.

PubMed

Padmanabhan, P K; Samant, M; Cloutier, S; Simard, M J; Papadopoulou, B

2012-12-01

Few natural antisense (as) RNAs have been reported as yet in the unicellular protozoan Leishmania. Here, we describe that Leishmania produces natural asRNAs complementary to all ribosomal RNA (rRNA) species. Interestingly, we show that drug-induced apoptosis-like programmed cell death triggers fragmentation of asRNA complementary to the large subunit gamma (LSU-γ) rRNA, one of the six 28S rRNA processed fragments in Leishmania. Heat and oxidative stress also induce fragmentation of asrRNA, but to a lesser extent. Extensive asrRNA cleavage correlates with rRNA breakdown and translation inhibition. Indeed, overexpression of asLSU-γ rRNA accelerates rRNA degradation upon induction of apoptosis. In addition, we provide mechanistic insight into the regulation of apoptosis-induced asrRNA fragmentation by a 67 kDa ATP-dependent RNA helicase of the DEAD-box subfamily. This helicase binds both sense (s)LSU-γ and asLSU-γ rRNAs, and appears to have a key role in protecting rRNA from degradation by preventing asrRNA cleavage and thus cell death. Remarkably, the asrRNA fragmentation process operates not only in trypanosomatid protozoa but also in mammals. Our findings uncover a novel mechanism of regulation involving asrRNA fragmentation and rRNA breakdown, that is triggered by apoptosis and conditions of reduced translation under stress, and seems to be evolutionary conserved.

Apoptosis-like programmed cell death induces antisense ribosomal RNA (rRNA) fragmentation and rRNA degradation in Leishmania

PubMed Central

Padmanabhan, P K; Samant, M; Cloutier, S; Simard, M J; Papadopoulou, B

2012-01-01

Few natural antisense (as) RNAs have been reported as yet in the unicellular protozoan Leishmania. Here, we describe that Leishmania produces natural asRNAs complementary to all ribosomal RNA (rRNA) species. Interestingly, we show that drug-induced apoptosis-like programmed cell death triggers fragmentation of asRNA complementary to the large subunit gamma (LSU-γ) rRNA, one of the six 28S rRNA processed fragments in Leishmania. Heat and oxidative stress also induce fragmentation of asrRNA, but to a lesser extent. Extensive asrRNA cleavage correlates with rRNA breakdown and translation inhibition. Indeed, overexpression of asLSU-γ rRNA accelerates rRNA degradation upon induction of apoptosis. In addition, we provide mechanistic insight into the regulation of apoptosis-induced asrRNA fragmentation by a 67 kDa ATP-dependent RNA helicase of the DEAD-box subfamily. This helicase binds both sense (s)LSU-γ and asLSU-γ rRNAs, and appears to have a key role in protecting rRNA from degradation by preventing asrRNA cleavage and thus cell death. Remarkably, the asrRNA fragmentation process operates not only in trypanosomatid protozoa but also in mammals. Our findings uncover a novel mechanism of regulation involving asrRNA fragmentation and rRNA breakdown, that is triggered by apoptosis and conditions of reduced translation under stress, and seems to be evolutionary conserved. PMID:22767185

Diversity-Oriented Synthesis as a Strategy for Fragment Evolution against GSK3β

PubMed Central

2016-01-01

Traditional fragment-based drug discovery (FBDD) relies heavily on structural analysis of the hits bound to their targets. Herein, we present a complementary approach based on diversity-oriented synthesis (DOS). A DOS-based fragment collection was able to produce initial hit compounds against the target GSK3β, allow the systematic synthesis of related fragment analogues to explore fragment-level structure–activity relationship, and finally lead to the synthesis of a more potent compound. PMID:27660690

Binding-Site Assessment by Virtual Fragment Screening

PubMed Central

Huang, Niu; Jacobson, Matthew P.

2010-01-01

The accurate prediction of protein druggability (propensity to bind high-affinity drug-like small molecules) would greatly benefit the fields of chemical genomics and drug discovery. We have developed a novel approach to quantitatively assess protein druggability by computationally screening a fragment-like compound library. In analogy to NMR-based fragment screening, we dock ∼11000 fragments against a given binding site and compute a computational hit rate based on the fraction of molecules that exceed an empirically chosen score cutoff. We perform a large-scale evaluation of the approach on four datasets, totaling 152 binding sites. We demonstrate that computed hit rates correlate with hit rates measured experimentally in a previously published NMR-based screening method. Secondly, we show that the in silico fragment screening method can be used to distinguish known druggable and non-druggable targets, including both enzymes and protein-protein interaction sites. Finally, we explore the sensitivity of the results to different receptor conformations, including flexible protein-protein interaction sites. Besides its original aim to assess druggability of different protein targets, this method could be used to identifying druggable conformations of flexible binding site for lead discovery, and suggesting strategies for growing or joining initial fragment hits to obtain more potent inhibitors. PMID:20404926

A Bioinorganic Approach to Fragment-Based Drug Discovery Targeting Metalloenzymes.

PubMed

Cohen, Seth M

2017-08-15

Metal-dependent enzymes (i.e., metalloenzymes) make up a large fraction of all enzymes and are critically important in a wide range of biological processes, including DNA modification, protein homeostasis, antibiotic resistance, and many others. Consequently, metalloenzymes represent a vast and largely untapped space for drug development. The discovery of effective therapeutics that target metalloenzymes lies squarely at the interface of bioinorganic and medicinal chemistry and requires expertise, methods, and strategies from both fields to mount an effective campaign. In this Account, our research program that brings together the principles and methods of bioinorganic and medicinal chemistry are described, in an effort to bridge the gap between these fields and address an important class of medicinal targets. Fragment-based drug discovery (FBDD) is an important drug discovery approach that is particularly well suited for metalloenzyme inhibitor development. FBDD uses relatively small but diverse chemical structures that allow for the assembly of privileged molecular collections that focus on a specific feature of the target enzyme. For metalloenzyme inhibition, the specific feature is rather obvious, namely, a metal-dependent active site. Surprisingly, prior to our work, the exploration of diverse molecular fragments for binding the metal active sites of metalloenzymes was largely unexplored. By assembling a modest library of metal-binding pharmacophores (MBPs), we have been able to find lead hits for many metalloenzymes and, from these hits, develop inhibitors that act via novel mechanisms of action. A specific case study on the use of this strategy to identify a first-in-class inhibitor of zinc-dependent Rpn11 (a component of the proteasome) is highlighted. The application of FBDD for the development of metalloenzyme inhibitors has raised several other compelling questions, such as how the metalloenzyme active site influences the coordination chemistry of bound

Heavy fragment production cross sections from 1.05 GeV/nucleon 56Fe in C, Al, Cu, Pb, and CH2 targets

NASA Technical Reports Server (NTRS)

Zeitlin, C.; Heilbronn, L.; Miller, J.; Rademacher, S. E.; Borak, T.; Carter, T. R.; Frankel, K. A.; Schimmerling, W.; Stronach, C. E.; Chatterjee, A. (Principal Investigator)

1997-01-01

We have obtained charge-changing cross sections and partial cross sections for fragmentation of 1.05 GeV/nucleon Fe projectiles incident on H, C, Al, Cu, and Pb nuclei. The energy region covered by this experiment is critical for an understanding of galactic cosmic ray propagation and space radiation biophysics. Surviving primary beam particles and fragments with charges from 12 to 25 produced within a forward cone of half-angle 61 mrad were detected using a silicon detector telescope to identify their charge and the cross sections were calculated after correction of the measured yields for finite target thickness effects. The cross sections are compared to model calculations and to previous measurements. Cross sections for the production of fragments with even-numbered nuclear charges are seen to be enhanced in almost all cases.

Apparatus for producing laser targets

DOEpatents

Jarboe, T.R.; Baker, W.R.

1975-09-23

This patent relates to an apparatus and method for producing deuterium targets or pellets of 25u to 75u diameter. The pellets are sliced from a continuously spun solid deuterium thread at a rate of up to 10 pellets/second. The pellets after being sliced from the continuous thread of deuterium are collimated and directed to a point of use, such as a laser activated combustion or explosion chamber wherein the pellets are imploded by laser energy or laser produced target plasmas for neutral beam injection. (auth)

Antipodal fragment velocities for porous and weak targets at catastrophic impacts

NASA Technical Reports Server (NTRS)

Yanagisawa, M.; Itoi, T.

1993-01-01

Mortar, porous alumina, and sand targets, which were spherical in shape and from 11 to 15 cm in diameter, were impacted normally by plastic (polycarbonate) projectiles of nearly 1 g in mass at velocities about 6 km/s. Fragment velocity at the antipole of impact site (antipodal velocity, V(sub a)), for each experiment, was obtained from two Flash X-ray images recorded prior to and at predetermined delayed time after impact event. It has been revealed that the velocities for the same E/M(sub t) (impact energy divided by target mass) depend strongly on target material, and differ about an order of magnitude between the sand and basalt.

Antipodal fragment velocities for porous and weak targets at catastrophic impacts

NASA Astrophysics Data System (ADS)

Yanagisawa, M.; Itoi, T.

1993-03-01

Mortar, porous alumina, and sand targets, which were spherical in shape and from 11 to 15 cm in diameter, were impacted normally by plastic (polycarbonate) projectiles of nearly 1 g in mass at velocities about 6 km/s. Fragment velocity at the antipole of impact site (antipodal velocity, V(sub a)), for each experiment, was obtained from two Flash X-ray images recorded prior to and at predetermined delayed time after impact event. It has been revealed that the velocities for the same E/M(sub t) (impact energy divided by target mass) depend strongly on target material, and differ about an order of magnitude between the sand and basalt.

The Effect of Fragmented Pathogenic α-Synuclein Seeds on Prion-like Propagation*

PubMed Central

Tarutani, Airi; Suzuki, Genjiro; Shimozawa, Aki; Nonaka, Takashi; Akiyama, Haruhiko; Hisanaga, Shin-ichi; Hasegawa, Masato

2016-01-01

Aggregates of abnormal proteins are widely observed in neuronal and glial cells of patients with various neurodegenerative diseases, and it has been proposed that prion-like behavior of these proteins can account for not only the onset but also the progression of these diseases. However, it is not yet clear which abnormal protein structures function most efficiently as seeds for prion-like propagation. In this study, we aimed to identify the most pathogenic species of α-synuclein (α-syn), the main component of the Lewy bodies and Lewy neurites that are observed in α-synucleinopathies. We prepared various forms of α-syn protein and examined their seeding properties in vitro in cells and in mouse experimental models. We also characterized these α-syn species by means of electron microscopy and thioflavin fluorescence assays and found that fragmented β sheet-rich fibrous structures of α-syn with a length of 50 nm or less are the most efficient promoters of accumulation of phosphorylated α-syn, which is the hallmark of α-synucleinopathies. These results indicate that fragmented amyloid-like aggregates of short α-syn fibrils are the key pathogenic seeds that trigger prion-like conversion. PMID:27382062

Is semantic priming (ir)rational? Insights from the speeded word fragment completion task.

PubMed

Heyman, Tom; Hutchison, Keith A; Storms, Gert

2016-10-01

Semantic priming, the phenomenon that a target is recognized faster if it is preceded by a semantically related prime, is a well-established effect. However, the mechanisms producing semantic priming are subject of debate. Several theories assume that the underlying processes are controllable and tuned to prime utility. In contrast, purely automatic processes, like automatic spreading activation, should be independent of the prime's usefulness. The present study sought to disentangle both accounts by creating a situation where prime processing is actually detrimental. Specifically, participants were asked to quickly complete word fragments with either the letter a or e (e.g., sh_ve to be completed as shave). Critical fragments were preceded by a prime that was either related (e.g., push) or unrelated (write) to a prohibited completion of the target (e.g., shove). In 2 experiments, we found a significant inhibitory priming effect, which is inconsistent with purely "rational" explanations of semantic priming. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

A Role for Fragment-Based Drug Design in Developing Novel Lead Compounds for Central Nervous System Targets.

PubMed

Wasko, Michael J; Pellegrene, Kendy A; Madura, Jeffry D; Surratt, Christopher K

2015-01-01

Hundreds of millions of U.S. dollars are invested in the research and development of a single drug. Lead compound development is an area ripe for new design strategies. Therapeutic lead candidates have been traditionally found using high-throughput in vitro pharmacological screening, a costly method for assaying thousands of compounds. This approach has recently been augmented by virtual screening (VS), which employs computer models of the target protein to narrow the search for possible leads. A variant of VS is fragment-based drug design (FBDD), an emerging in silico lead discovery method that introduces low-molecular weight fragments, rather than intact compounds, into the binding pocket of the receptor model. These fragments serve as starting points for "growing" the lead candidate. Current efforts in virtual FBDD within central nervous system (CNS) targets are reviewed, as is a recent rule-based optimization strategy in which new molecules are generated within a 3D receptor-binding pocket using the fragment as a scaffold. This process not only places special emphasis on creating synthesizable molecules but also exposes computational questions worth addressing. Fragment-based methods provide a viable, relatively low-cost alternative for therapeutic lead discovery and optimization that can be applied to CNS targets to augment current design strategies.

A Role for Fragment-Based Drug Design in Developing Novel Lead Compounds for Central Nervous System Targets

PubMed Central

Wasko, Michael J.; Pellegrene, Kendy A.; Madura, Jeffry D.; Surratt, Christopher K.

2015-01-01

Hundreds of millions of U.S. dollars are invested in the research and development of a single drug. Lead compound development is an area ripe for new design strategies. Therapeutic lead candidates have been traditionally found using high-throughput in vitro pharmacological screening, a costly method for assaying thousands of compounds. This approach has recently been augmented by virtual screening (VS), which employs computer models of the target protein to narrow the search for possible leads. A variant of VS is fragment-based drug design (FBDD), an emerging in silico lead discovery method that introduces low-molecular weight fragments, rather than intact compounds, into the binding pocket of the receptor model. These fragments serve as starting points for “growing” the lead candidate. Current efforts in virtual FBDD within central nervous system (CNS) targets are reviewed, as is a recent rule-based optimization strategy in which new molecules are generated within a 3D receptor-binding pocket using the fragment as a scaffold. This process not only places special emphasis on creating synthesizable molecules but also exposes computational questions worth addressing. Fragment-based methods provide a viable, relatively low-cost alternative for therapeutic lead discovery and optimization that can be applied to CNS targets to augment current design strategies. PMID:26441817

RISC-interacting clearing 3'- 5' exoribonucleases (RICEs) degrade uridylated cleavage fragments to maintain functional RISC in Arabidopsis thaliana.

PubMed

Zhang, Zhonghui; Hu, Fuqu; Sung, Min Woo; Shu, Chang; Castillo-González, Claudia; Koiwa, Hisashi; Tang, Guiliang; Dickman, Martin; Li, Pingwei; Zhang, Xiuren

2017-05-02

RNA-induced silencing complex (RISC) is composed of miRNAs and AGO proteins. AGOs use miRNAs as guides to slice target mRNAs to produce truncated 5' and 3' RNA fragments. The 5' cleaved RNA fragments are marked with uridylation for degradation. Here, we identified novel cofactors of Arabidopsis AGOs, named RICE1 and RICE2. RICE proteins specifically degraded single-strand (ss) RNAs in vitro; but neither miRNAs nor miRNA*s in vivo. RICE1 exhibited a DnaQ-like exonuclease fold and formed a homohexamer with the active sites located at the interfaces between RICE1 subunits. Notably, ectopic expression of catalytically-inactive RICE1 not only significantly reduced miRNA levels; but also increased 5' cleavage RISC fragments with extended uridine tails. We conclude that RICEs act to degrade uridylated 5' products of AGO cleavage to maintain functional RISC. Our study also suggests a possible link between decay of cleaved target mRNAs and miRNA stability in RISC.

Shape Distribution of Fragments from Microsatellite Impact Tests

NASA Technical Reports Server (NTRS)

Liou, J.C.; Hanada, T.

2009-01-01

Fragment shape is an important factor for conducting reliable orbital debris damage assessments for critical space assets, such as the International Space Station. To date, seven microsatellite impact tests have been completed as part of an ongoing collaboration between Kyushu University and the NASA Orbital Debris Program Office. The target satellites ranged in size from 15 cm 15 cm 15 cm to 20 cm 20 cm 20 cm. Each target satellite was equipped with fully functional electronics, including circuits, battery, and transmitter. Solar panels and multi-layer insulation (MLI) were added to the target satellites of the last two tests. The impact tests were carried out with projectiles of different sizes and impact speeds. All fragments down to about 2 mm in size were collected and analyzed based on their three orthogonal dimensions, x, y, and z, where x is the longest dimension, y is the longest dimension in the plane perpendicular to x, and z is the longest dimension perpendicular to both x and y. Each fragment was also photographed and classified by shape and material composition. This data set serves as the basis of our effort to develop a fragment shape distribution. Two distinct groups can be observed in the x/y versus y/z distribution of the fragments. Objects in the first group typically have large x/y values. Many of them are needle-like objects originating from the fragmentation of carbon fiber reinforced plastic materials used to construct the satellites. Objects in the second group tend to have small x/y values, and many of them are box-like or plate-like objects, depending on their y/z values. Each group forms the corresponding peak in the x/y distribution. However, only one peak can be observed in the y/z distribution. These distributions and how they vary with size, material type, and impact parameters will be described in detail within the paper.

Multiplicity distributions of shower particles and target fragments in 84 Kr 36-emulsion interactions at 1 GeV per nucleon

NASA Astrophysics Data System (ADS)

Singh, M. K.; Soma, A. K.; Pathak, Ramji; Singh, V.

2014-03-01

This article focuses on multiplicity distributions of shower particles and target fragments for interaction of 84 Kr 36 with NIKFI BR-2 nuclear emulsion target at kinetic energy of 1 GeV per nucleon. Experimental multiplicity distributions of shower particles, grey particles, black particles and heavily ionization particles are well described by multi-component Erlang distribution of multi-source thermal model. We have observed a linear correlation in multiplicities for the above mentioned particles or fragments. Further experimental studies have shown a saturation phenomenon in shower particle multiplicity with the increase of target fragment multiplicity.

Growth and structure of fullerene-like CNx thin films produced by pulsed laser ablation of graphite in nitrogen

NASA Astrophysics Data System (ADS)

Voevodin, A. A.; Jones, J. G.; Zabinski, J. S.; Czigany, Zs.; Hultman, L.

2002-11-01

The growth and structure of fullerene-like CNx films produced by laser ablation of graphite in low pressure nitrogen were investigated. Deposition conditions were selected based on investigations of CN and C2 concentration at the condensation surface, vibrational temperature of CN radicals, and kinetic energies of atomic and molecular species. Films were characterized with x-ray photoelectron spectroscopy, Raman spectroscopy, high-resolution transmission electron microscopy, nanoindentation, and stress analyses. The nitrogen content in CNx films directly depended on the concentration of CN radicals at the condensation surface. Formation of fullerene-like structures required a high vibrational temperature of these radicals, which was maximized at about 4 eV for depositions at 10 mTorr N2 and laser fluences of approx7 J/cm2. The presence of C2 had only a minor effect on film composition and structure. Optimization of plasma characteristics and a substrate temperature of 300 degC helped to produce about 1-mum-thick solid films of CNx (N/C ratioapproximately0.2-0.3) and pure carbon consisting of fullerene-like fragments and packages. In contrast to carbon films, fullerene-like CNx films exhibited a high elastic recovery of about 80% in using a Berkovich tip at 5 mN load and indentation depths up to 150 nm. Their elastic modulus was about 160 GPa measured from the unloading portion of an indentation curve, and about 250 GPa measured with a 40 Hz tip oscillation during nanoindentation tests. The difference was related to time dependent processes of shape restoration of fullerene-like fragments, and an analogy was made to the behavior of elastomer polymers. However, unlike elastomers, CNx film hardness was as high as 30 GPa, which was twice that of fullerene-like carbon films. The unusual combination of high elasticity and hardness of CNx films was explained by crosslinking of fullerene fragments induced by the incorporated nitrogen and stored compressive stress. The

Targeting Ligandable Pockets on Plant Homeodomain (PHD) Zinc Finger Domains by a Fragment-Based Approach.

PubMed

Amato, Anastasia; Lucas, Xavier; Bortoluzzi, Alessio; Wright, David; Ciulli, Alessio

2018-04-20

Plant homeodomain (PHD) zinc fingers are histone reader domains that are often associated with human diseases. Despite this, they constitute a poorly targeted class of readers, suggesting low ligandability. Here, we describe a successful fragment-based campaign targeting PHD fingers from the proteins BAZ2A and BAZ2B as model systems. We validated a pool of in silico fragments both biophysically and structurally and solved the first crystal structures of PHD zinc fingers in complex with fragments bound to an anchoring pocket at the histone binding site. The best-validated hits were found to displace a histone H3 tail peptide in competition assays. This work identifies new chemical scaffolds that provide suitable starting points for future ligand optimization using structure-guided approaches. The demonstrated ligandability of the PHD reader domains could pave the way for the development of chemical probes to drug this family of epigenetic readers.

Study the fragment size distribution in dynamic fragmentation of laser shock loding tin

NASA Astrophysics Data System (ADS)

He, Weihua; Xin, Jianting; Chu, Genbai; Shui, Min; Xi, Tao; Zhao, Yongqiang; Gu, Yuqiu

2017-06-01

Characterizing the distribution of fragment size produced from dynamic fragmentation process is very important for fundamental science like predicting material dymanic response performance and for a variety of engineering applications. However, only a few data about fragment mass or size have been obtained due to its great challenge in its dynamic measurement. This paper would focus on investigating the fragment size distribution from the dynamic fragmentation of laser shock-loaded metal. Material ejection of tin sample with wedge shape groove in the free surface is collected with soft recovery technique. Via fine post-shot analysis techniques including X-ray micro-tomography and the improved watershed method, it is found that fragments can be well detected. To characterize their size distributions, a random geometric statistics method based on Poisson mixtures was derived for dynamic heterogeneous fragmentation problem, which leads to a linear combinational exponential distribution. Finally we examined the size distribution of laser shock-loaded tin with the derived model, and provided comparisons with other state-of-art models. The resulting comparisons prove that our proposed model can provide more reasonable fitting result for laser shock-loaded metal.

Heavy Ion Fragmentation Experiments at the Bevatron

NASA Technical Reports Server (NTRS)

Heckman, H. H.

1975-01-01

Fragmentation processes of heavy nuclei in matter using the heavy-ion capability of the Bevatron were studied. The purpose was to obtain the single particle inclusive spectra of secondary nuclei produced at 0 deg by the fragmentation of heavy ion beam projectiles. The process being examined is B+T yields F + anything, where B is the beam nucleus, T is the target nucleus, and F is the detected fragment. The fragments F are isotopically identified by experimental procedures involving magnetic analysis, energy loss and time-of-flight measurements. Attempts were also made to: (1) measure the total and partial production cross section for all isotopes, (2) test the applicability of high-energy multi-particle interaction theory to nuclear fragmentation, (3) apply the cross-section data and fragmentation probabilities to cosmic ray transport theory, and (4) search for systematic behavior of fragment production as a means to improve existing semi-empirical theories of cross sections.

Target immobilization as a strategy for NMR-based fragment screening: comparison of TINS, STD, and SPR for fragment hit identification.

PubMed

Kobayashi, Masakazu; Retra, Kim; Figaroa, Francis; Hollander, Johan G; Ab, Eiso; Heetebrij, Robert J; Irth, Hubertus; Siegal, Gregg

2010-09-01

Fragment-based drug discovery (FBDD) has become a widely accepted tool that is complementary to high-throughput screening (HTS) in developing small-molecule inhibitors of pharmaceutical targets. Because a fragment campaign can only be as successful as the hit matter found, it is critical that the first stage of the process be optimized. Here the authors compare the 3 most commonly used methods for hit discovery in FBDD: high concentration screening (HCS), solution ligand-observed nuclear magnetic resonance (NMR), and surface plasmon resonance (SPR). They selected the commonly used saturation transfer difference (STD) NMR spectroscopy and the proprietary target immobilized NMR screening (TINS) as representative of the array of possible NMR methods. Using a target typical of FBDD campaigns, the authors find that HCS and TINS are the most sensitive to weak interactions. They also find a good correlation between TINS and STD for tighter binding ligands, but the ability of STD to detect ligands with affinity weaker than 1 mM K(D) is limited. Similarly, they find that SPR detection is most suited to ligands that bind with K(D) better than 1 mM. However, the good correlation between SPR and potency in a bioassay makes this a good method for hit validation and characterization studies.

Targeting Ligandable Pockets on Plant Homeodomain (PHD) Zinc Finger Domains by a Fragment-Based Approach

PubMed Central

2018-01-01

Plant homeodomain (PHD) zinc fingers are histone reader domains that are often associated with human diseases. Despite this, they constitute a poorly targeted class of readers, suggesting low ligandability. Here, we describe a successful fragment-based campaign targeting PHD fingers from the proteins BAZ2A and BAZ2B as model systems. We validated a pool of in silico fragments both biophysically and structurally and solved the first crystal structures of PHD zinc fingers in complex with fragments bound to an anchoring pocket at the histone binding site. The best-validated hits were found to displace a histone H3 tail peptide in competition assays. This work identifies new chemical scaffolds that provide suitable starting points for future ligand optimization using structure-guided approaches. The demonstrated ligandability of the PHD reader domains could pave the way for the development of chemical probes to drug this family of epigenetic readers. PMID:29529862

Measurement of fragmentation cross sections of 12C ions on a thin gold target with the FIRST apparatus

NASA Astrophysics Data System (ADS)

Toppi, M.; Abou-Haidar, Z.; Agodi, C.; Alvarez, M. A. G.; Aumann, T.; Balestra, F.; Battistoni, G.; Bocci, A.; Böhlen, T. T.; Boudard, A.; Brunetti, A.; Carpinelli, M.; Cirio, R.; Cirrone, G. A. P.; Cortes-Giraldo, M. A.; Cuttone, G.; de Napoli, M.; Durante, M.; Fernández-García, J. P.; Finck, Ch.; Golosio, B.; Iarocci, E.; Iazzi, F.; Ickert, G.; Introzzi, R.; Juliani, D.; Krimmer, J.; Kummali, A. H.; Kurz, N.; Labalme, M.; Leifels, Y.; Le Fèvre, A.; Leray, S.; Marchetto, F.; Monaco, V.; Morone, M. C.; Nicolosi, D.; Oliva, P.; Paoloni, A.; Piersanti, L.; Pleskac, R.; Randazzo, N.; Rescigno, R.; Romano, F.; Rossi, D.; Rosso, V.; Rousseau, M.; Sacchi, R.; Sala, P.; Salvador, S.; Sarti, A.; Scheidenberger, C.; Schuy, C.; Sciubba, A.; Sfienti, C.; Simon, H.; Sipala, V.; Spiriti, E.; Tropea, S.; Vanstalle, M.; Younis, H.; Patera, V.; FIRST Collaboration

2016-06-01

A detailed knowledge of the light ions interaction processes with matter is of great interest in basic and applied physics. As an example, particle therapy and space radioprotection require highly accurate fragmentation cross-section measurements to develop shielding materials and estimate acute and late health risks for manned missions in space and for treatment planning in particle therapy. The Fragmentation of Ions Relevant for Space and Therapy experiment at the Helmholtz Center for Heavy Ion research (GSI) was designed and built by an international collaboration from France, Germany, Italy, and Spain for studying the collisions of a 12C ion beam with thin targets. The collaboration's main purpose is to provide the double-differential cross-section measurement of carbon-ion fragmentation at energies that are relevant for both tumor therapy and space radiation protection applications. Fragmentation cross sections of light ions impinging on a wide range of thin targets are also essential to validate the nuclear models implemented in MC simulations that, in such an energy range, fail to reproduce the data with the required accuracy. This paper presents the single differential carbon-ion fragmentation cross sections on a thin gold target, measured as a function of the fragment angle and kinetic energy in the forward angular region (θ ≲6° ), aiming to provide useful data for the benchmarking of the simulation softwares used in light ions fragmentation applications. The 12C ions used in the measurement were accelerated at the energy of 400 MeV/nucleon by the SIS (heavy ion synchrotron) GSI facility.

A Fragment-Based Method of Creating Small-Molecule Libraries to Target the Aggregation of Intrinsically Disordered Proteins.

PubMed

Joshi, Priyanka; Chia, Sean; Habchi, Johnny; Knowles, Tuomas P J; Dobson, Christopher M; Vendruscolo, Michele

2016-03-14

The aggregation process of intrinsically disordered proteins (IDPs) has been associated with a wide range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Currently, however, no drug in clinical use targets IDP aggregation. To facilitate drug discovery programs in this important and challenging area, we describe a fragment-based approach of generating small-molecule libraries that target specific IDPs. The method is based on the use of molecular fragments extracted from compounds reported in the literature to inhibit of the aggregation of IDPs. These fragments are used to screen existing large generic libraries of small molecules to form smaller libraries specific for given IDPs. We illustrate this approach by describing three distinct small-molecule libraries to target, Aβ, tau, and α-synuclein, which are three IDPs implicated in Alzheimer's and Parkinson's diseases. The strategy described here offers novel opportunities for the identification of effective molecular scaffolds for drug discovery for neurodegenerative disorders and to provide insights into the mechanism of small-molecule binding to IDPs.

NMR-based platform for fragment-based lead discovery used in screening BRD4-targeted compounds

PubMed Central

Yu, Jun-lan; Chen, Tian-tian; Zhou, Chen; Lian, Fu-lin; Tang, Xu-long; Wen, Yi; Shen, Jing-kang; Xu, Ye-chun; Xiong, Bing; Zhang, Nai-xia

2016-01-01

Aim: Fragment-based lead discovery (FBLD) is a complementary approach in drug research and development. In this study, we established an NMR-based FBLD platform that was used to screen novel scaffolds targeting human bromodomain of BRD4, and investigated the binding interactions between hit compounds and the target protein. Methods: 1D NMR techniques were primarily used to generate the fragment library and to screen compounds. The inhibitory activity of hits on the first bromodomain of BRD4 [BRD4(I)] was examined using fluorescence anisotropy binding assay. 2D NMR and X-ray crystallography were applied to characterize the binding interactions between hit compounds and the target protein. Results: An NMR-based fragment library containing 539 compounds was established, which were clustered into 56 groups (8–10 compounds in each group). Eight hits with new scaffolds were found to inhibit BRD4(I). Four out of the 8 hits (compounds 1, 2, 8 and 9) had IC50 values of 100–260 μmol/L, demonstrating their potential for further BRD4-targeted hit-to-lead optimization. Analysis of the binding interactions revealed that compounds 1 and 2 shared a common quinazolin core structure and bound to BRD4(I) in a non-acetylated lysine mimetic mode. Conclusion: An NMR-based platform for FBLD was established and used in discovery of BRD4-targeted compounds. Four potential hit-to-lead optimization candidates have been found, two of them bound to BRD4(I) in a non-acetylated lysine mimetic mode, being selective BRD4(I) inhibitors. PMID:27238211

Structure-Based Identification of Inhibitory Fragments Targeting the p300/CBP-Associated Factor Bromodomain

PubMed Central

2016-01-01

The P300/CBP-associated factor plays a central role in retroviral infection and cancer development, and the C-terminal bromodomain provides an opportunity for selective targeting. Here, we report several new classes of acetyl-lysine mimetic ligands ranging from mM to low micromolar affinity that were identified using fragment screening approaches. The binding modes of the most attractive fragments were determined using high resolution crystal structures providing chemical starting points and structural models for the development of potent and selective PCAF inhibitors. PMID:26731131

Search for unbound nuclides and beam/fragment optics with the MoNA/LISA segmented target at NSCL

NASA Astrophysics Data System (ADS)

Gueye, Paul; Frank, Nathan; Thoennessen, Michael; Redpath, Thomas; MoNA Collaboration

2017-09-01

A multi-layered Si/Be segmented target consisting of three 700 mg/cm2 thick Be9 slabs and four 140 microns Si detectors was used by the MoNA Collaboration at the National Superconducting Cyclotron Laboratory of Michigan State University to study the O26 lifetime. This target provides unprecedented information on the incident beams and fragments (energy loss and position), thus allowing for better determination of the incident and outgoing energies and momenta of the detected particles compare to previous experiments conducted at this facility. With the availability of a newly developed Geant4 Monte Carlo simulation of the full N2 vault, we will present and discuss the performances of this target. Search for unbound nuclides and beam/fragment optics with the MoNA/LISA segmented target at NSCL.

Large scale meta-analysis of fragment-based screening campaigns: privileged fragments and complementary technologies.

PubMed

Kutchukian, Peter S; Wassermann, Anne Mai; Lindvall, Mika K; Wright, S Kirk; Ottl, Johannes; Jacob, Jaison; Scheufler, Clemens; Marzinzik, Andreas; Brooijmans, Natasja; Glick, Meir

2015-06-01

A first step in fragment-based drug discovery (FBDD) often entails a fragment-based screen (FBS) to identify fragment "hits." However, the integration of conflicting results from orthogonal screens remains a challenge. Here we present a meta-analysis of 35 fragment-based campaigns at Novartis, which employed a generic 1400-fragment library against diverse target families using various biophysical and biochemical techniques. By statistically interrogating the multidimensional FBS data, we sought to investigate three questions: (1) What makes a fragment amenable for FBS? (2) How do hits from different fragment screening technologies and target classes compare with each other? (3) What is the best way to pair FBS assay technologies? In doing so, we identified substructures that were privileged for specific target classes, as well as fragments that were privileged for authentic activity against many targets. We also revealed some of the discrepancies between technologies. Finally, we uncovered a simple rule of thumb in screening strategy: when choosing two technologies for a campaign, pairing a biochemical and biophysical screen tends to yield the greatest coverage of authentic hits. © 2014 Society for Laboratory Automation and Screening.

A collagen-binding EGFR antibody fragment targeting tumors with a collagen-rich extracellular matrix.

PubMed

Liang, Hui; Li, Xiaoran; Wang, Bin; Chen, Bing; Zhao, Yannan; Sun, Jie; Zhuang, Yan; Shi, Jiajia; Shen, He; Zhang, Zhijun; Dai, Jianwu

2016-02-17

Many tumors over-express collagen, which constitutes the physical scaffold of tumor microenvironment. Collagen has been considered to be a target for cancer therapy. The collagen-binding domain (CBD) is a short peptide, which could bind to collagen and achieve the sustained release of CBD-fused proteins in collagen scaffold. Here, a collagen-binding EGFR antibody fragment was designed and expressed for targeting the collagen-rich extracellular matrix in tumors. The antibody fragment (Fab) of cetuximab was fused with CBD (CBD-Fab) and expressed in Pichia pastoris. CBD-Fab maintained antigen binding and anti-tumor activity of cetuximab and obtained a collagen-binding ability in vitro. The results also showed CBD-Fab was mainly enriched in tumors and had longer retention time in tumors in A431 s.c. xenografts. Furthermore, CBD-Fab showed a similar therapeutic efficacy as cetuximab in A431 xenografts. Although CBD-Fab hasn't showed better therapeutic effects than cetuximab, its smaller molecular and special target may be applicable as antibody-drug conjugates (ADC) or immunotoxins.

A collagen-binding EGFR antibody fragment targeting tumors with a collagen-rich extracellular matrix

PubMed Central

Liang, Hui; Li, Xiaoran; Wang, Bin; Chen, Bing; Zhao, Yannan; Sun, Jie; Zhuang, Yan; Shi, Jiajia; Shen, He; Zhang, Zhijun; Dai, Jianwu

2016-01-01

Many tumors over-express collagen, which constitutes the physical scaffold of tumor microenvironment. Collagen has been considered to be a target for cancer therapy. The collagen-binding domain (CBD) is a short peptide, which could bind to collagen and achieve the sustained release of CBD-fused proteins in collagen scaffold. Here, a collagen-binding EGFR antibody fragment was designed and expressed for targeting the collagen-rich extracellular matrix in tumors. The antibody fragment (Fab) of cetuximab was fused with CBD (CBD-Fab) and expressed in Pichia pastoris. CBD-Fab maintained antigen binding and anti-tumor activity of cetuximab and obtained a collagen-binding ability in vitro. The results also showed CBD-Fab was mainly enriched in tumors and had longer retention time in tumors in A431 s.c. xenografts. Furthermore, CBD-Fab showed a similar therapeutic efficacy as cetuximab in A431 xenografts. Although CBD-Fab hasn’t showed better therapeutic effects than cetuximab, its smaller molecular and special target may be applicable as antibody–drug conjugates (ADC) or immunotoxins. PMID:26883295

Heavy ion fragmentation experiments at the bevatron

NASA Technical Reports Server (NTRS)

Heckman, H. H.

1976-01-01

Collaborative research efforts to study the fragmentation processes of heavy nuclei in matter using heavy ion beams of the Bevatron/Bevalac are described. The goal of the program is to obtain the single particle inclusive spectra of secondary nuclei produced at 0 deg by the fragmentation of heavy ion beam projectiles. The process being examined is B+T yields F + anything, where B is the beam nucleus, T is the target nucleus, and F is the detected fragment. The fragments F are isotopically identified by experimental procedures involving magnetic analysis, energy loss and time-of-flight measurements. Effects were also made to: (a) study processes of heavy nuclei in matter, (b) measure the total and partial production cross section for all isotopes, (c) test the applicability of high energy multiparticle interaction theory to nuclear fragmentation, (d) apply the cross section data and fragmentation probabilities to cosmic ray transport theory, and (e) search for systematic behavior of fragment production as a means to improve existing semi-empirical theories of cross-sections.

Method to separate and determine the amount of ejecta produced in a second-shock material-fragmentation event

NASA Astrophysics Data System (ADS)

Buttler, W. T.; Hixson, R. S.; King, N. S. P.; Olson, R. T.; Rigg, P. A.; Zellner, M. B.; Routley, N.; Rimmer, A.

2007-04-01

The authors consider a mathematical method to separate and determine the amount of ejecta produced in a second-shock material-fragmentation process. The technique is theoretical and assumes that a material undergoing a shock release at a vacuum interface ejects particulate material or fragments as the initial shock unloads and reflects at the vacuum-surface interface. In this case it is thought that the reflected shock may reflect again at the source of the shock and return to the vacuum-surface interface and eject another amount of fragments or particulate material.

Micro-Satellite Impact Tests to Investigate Multi-Layer Insulation Fragments

NASA Astrophysics Data System (ADS)

Murakami, Junko; Hanada, Toshiya; Liou, J.-C.; Stansbery, Eugene

2009-03-01

This paper summarizes two satellite impact experiments completed in 2008. The objective of the experiments is to investigate the physical properties of satellite fragments, including those originated from Multi-Layer Insulation and a solar panel. One test generated approximately 1,800 fragments while the other produced only 1,000 fragments. This difference came from the number of needle-like fragments from carbon fiber reinforced plastics. All collected fragments were analyzed using the same method as described in the NASA standard breakup model and compared with the breakup model. This paper will present: (1) the area-to-mass ratio, size, and mass distributions of the fragments, and (2) the differences in fragment properties between the two tests.

Repurposing Suzuki Coupling Reagents as a Directed Fragment Library Targeting Serine Hydrolases and Related Enzymes.

PubMed

Lanier, Marion; Cole, Derek C; Istratiy, Yelena; Klein, Michael G; Schwartz, Phillip A; Tjhen, Richard; Jennings, Andy; Hixon, Mark S

2017-06-22

Serine hydrolases are susceptible to potent reversible inhibition by boronic acids. Large collections of chemically diverse boronic acid fragments are commercially available because of their utility in coupling chemistry. We repurposed the approximately 650 boronic acid reagents in our collection as a directed fragment library targeting serine hydrolases and related enzymes. Highly efficient hits (LE > 0.6) often result. The utility of the approach is illustrated with the results against autotaxin, a phospholipase implicated in cardiovascular disease.

Energy deposition at the bone-tissue interface from nuclear fragments produced by high-energy nucleons

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Hajnal, Ferenc; Wilson, John W.

1990-01-01

The transport of nuclear fragmentation recoils produced by high-energy nucleons in the region of the bone-tissue interface is considered. Results for the different flux and absorbed dose for recoils produced by 1 GeV protons are presented in a bidirectional transport model. The energy deposition in marrow cavities is seen to be enhanced by recoils produced in bone. Approximate analytic formulae for absorbed dose near the interface region are also presented for a simplified range-energy model.

Effects of target shape and impact speed on the outcome of catastrophic disruptions

NASA Astrophysics Data System (ADS)

Campo~Bagatin, A.; Durda, D.; Alemañ, R.; Flynn, G.; Strait, M.; Clayton, A.; Patmore, E.

2014-07-01

Because of the propensity of previous laboratory investigations to focus on idealized spherical targets, there is a bit of ambiguity in decoupling the relative importance/influence of low speed or spherical shape in producing the 'onion shell' fragment shape outcomes found in impacts into spherical targets [1,2]. If due primarily to impact speed/energy density as suggested by [3], this could play an important role in main-belt impacts due to the presence of non-spherical targets and non-negligible probability of low-speed (i.e., below about 3-4 km/s, subsonic in rock) impacts [4]. Also, [5] and [6] suggested that the shape of targets may affect the outcome of shattering processes, both in terms of fragment shape and mass distribution. To examine explicitly the effects of target shape in impact outcomes, we chose to conduct impact experiments on both spherical and naturally-occurring irregularly-shaped basalt targets. We impacted a total of six targets (two spheres and four irregular targets). We focused on shots with impact speeds in the ˜4 to 6 km/s range by 3/16th-inch diameter Al-sphere projectiles fired at the NASA AVGR. Following each shot, the debris were recovered (>95 %) and large fragments (>0.20 g) were individually weighed, allowing us to carefully measure the mass-frequency distribution from each impact experiment. The 36 largest fragments of each shot were photographed and their largest axes accurately measured by the program ''ImageJ''. Their shortest axes were measured by means of a digital caliber. High-speed video of each impact was obtained to aid interpretation of the fragmentation mode of the targets. Images clearly show that shell-like fragments can be produced in shattering events not in the target's surface. Instead, those fragments may form around the core, well inside the target structure, independently on the target shape itself. This is a feature not reported to date. In order to understand what the bulk macro-porosity of a non

Fragmentation targeted at preferred discontinuities: A new concept in endolithotripsy with Holmium laser:YAG.

PubMed

Sánchez-Martín, F M; Emiliani, E; Pueyo-Morer, E; Angerri-Feu, O; Sanguedolce, F; Millán, F; Villavicencio, H

2018-04-17

There are currently 3holmium laser, YAG (Ho:YAG) endolithotripsy procedures that are considered basic (fragmentation, pulverisation, "pop-corn" technique). We present the technique of fragmentation targeted at preferred discontinuities (FTPD), a new concept of endolithotripsy by Ho:YAG laser. The FTPD technique is based on the selective application of energy (targeting a specific preselected point) to an area that is visually prone to the formation of a fracture line or preferred discontinuity (conditioned by the anisotropy of the urolithiasis). The ideal energy regimen (setting) is a high range of working energy (2-3J) with a very low frequency range (5-8Hz) and short pulse width. Between January 2015 to February 2017, the FTPD technique was used in 37 procedures (7 NLP, 16 RIRS, 12 URS, 2 cystolithotomies), with a Ho:YAG laser (Lumenis Pulse 120H ® , Tel-Aviv, Israel). Maximum power used: 24W (3J/8Hz) with fibres of 365μ and 273μ (URS, RIRS), and 32W (4J/8Hz) with fibres of 550μ (NLP, cystolithotomy). Strategic improvement was achieved in all cases using the TFPD technique to continue the endolithotripsy or remove fragments. No complications were recorded after the use of this method. FTPD can be considered a complementary option in combination with the basic methods of fragmentation and pulverisation. In our experience, it constitutes significant progress in optimising the performance of Ho:YAG laser endolithotripsy. Copyright © 2018 AEU. Publicado por Elsevier España, S.L.U. All rights reserved.

Effects of target plasma electron-electron collisions on correlated motion of fragmented protons.

PubMed

Barriga-Carrasco, Manuel D

2006-02-01

The objective of the present work is to examined the effects of plasma target electron-electron collisions on H2 + protons traversing it. Specifically, the target is deuterium in a plasma state with temperature Te=10 eV and density n=10(23) cm(-3), and proton velocities are vp=vth, vp=2vth, and vp=3vth, where vth is the electron thermal velocity of the target plasma. Proton interactions with plasma electrons are treated by means of the dielectric formalism. The interactions among close protons through plasma electronic medium are called vicinage forces. It is checked that these forces always screen the Coulomb explosions of the two fragmented protons from the same H2 + ion decreasing their relative distance. They also align the interproton vector along the motion direction, and increase the energy loss of the two protons at early dwell times while for longer times the energy loss tends to the value of two isolated protons. Nevertheless, vicinage forces and effects are modified by the target electron collisions. These collisions enhance the calculated self-stopping and vicinage forces over the collisionless results. Regarding proton correlated motion, when these collisions are included, the interproton vector along the motion direction overaligns at slower proton velocities (vp=vth) and misaligns for faster ones (vp=2vth, vp=3vth). They also contribute to a great extend to increase the energy loss of the fragmented H2 + ion. This later effect is more significant in reducing projectile velocity.

Fragmenting networks by targeting collective influencers at a mesoscopic level.

PubMed

Kobayashi, Teruyoshi; Masuda, Naoki

2016-11-25

A practical approach to protecting networks against epidemic processes such as spreading of infectious diseases, malware, and harmful viral information is to remove some influential nodes beforehand to fragment the network into small components. Because determining the optimal order to remove nodes is a computationally hard problem, various approximate algorithms have been proposed to efficiently fragment networks by sequential node removal. Morone and Makse proposed an algorithm employing the non-backtracking matrix of given networks, which outperforms various existing algorithms. In fact, many empirical networks have community structure, compromising the assumption of local tree-like structure on which the original algorithm is based. We develop an immunization algorithm by synergistically combining the Morone-Makse algorithm and coarse graining of the network in which we regard a community as a supernode. In this way, we aim to identify nodes that connect different communities at a reasonable computational cost. The proposed algorithm works more efficiently than the Morone-Makse and other algorithms on networks with community structure.

Fragmenting networks by targeting collective influencers at a mesoscopic level

NASA Astrophysics Data System (ADS)

Kobayashi, Teruyoshi; Masuda, Naoki

2016-11-01

A practical approach to protecting networks against epidemic processes such as spreading of infectious diseases, malware, and harmful viral information is to remove some influential nodes beforehand to fragment the network into small components. Because determining the optimal order to remove nodes is a computationally hard problem, various approximate algorithms have been proposed to efficiently fragment networks by sequential node removal. Morone and Makse proposed an algorithm employing the non-backtracking matrix of given networks, which outperforms various existing algorithms. In fact, many empirical networks have community structure, compromising the assumption of local tree-like structure on which the original algorithm is based. We develop an immunization algorithm by synergistically combining the Morone-Makse algorithm and coarse graining of the network in which we regard a community as a supernode. In this way, we aim to identify nodes that connect different communities at a reasonable computational cost. The proposed algorithm works more efficiently than the Morone-Makse and other algorithms on networks with community structure.

Fragmenting networks by targeting collective influencers at a mesoscopic level

PubMed Central

Kobayashi, Teruyoshi; Masuda, Naoki

2016-01-01

A practical approach to protecting networks against epidemic processes such as spreading of infectious diseases, malware, and harmful viral information is to remove some influential nodes beforehand to fragment the network into small components. Because determining the optimal order to remove nodes is a computationally hard problem, various approximate algorithms have been proposed to efficiently fragment networks by sequential node removal. Morone and Makse proposed an algorithm employing the non-backtracking matrix of given networks, which outperforms various existing algorithms. In fact, many empirical networks have community structure, compromising the assumption of local tree-like structure on which the original algorithm is based. We develop an immunization algorithm by synergistically combining the Morone-Makse algorithm and coarse graining of the network in which we regard a community as a supernode. In this way, we aim to identify nodes that connect different communities at a reasonable computational cost. The proposed algorithm works more efficiently than the Morone-Makse and other algorithms on networks with community structure. PMID:27886251

Crystallographic Fragment Based Drug Discovery: Use of a Brominated Fragment Library Targeting HIV Protease

PubMed Central

Tiefenbrunn, Theresa; Forli, Stefano; Happer, Meaghan; Gonzalez, Ana; Tsai, Yingssu; Soltis, Michael; Elder, John H.; Olson, Arthur J.; Stout, C. David

2013-01-01

A library of 68 brominated fragments was screened against a new crystal form of inhibited HIV-1 protease in order to probe surface sites in soaking experiments. Often fragments are weak binders with partial occupancy, resulting in weak, difficult-to-fit electron density. The use of a brominated fragment library addresses this challenge, as bromine can be located unequivocally via anomalous scattering. Data collection was carried out in an automated fashion using AutoDrug at SSRL. Novel hits were identified in the known surface sites: 3-bromo-2,6-dimethoxybenzoic acid (Br6) in the flap site, and 1-bromo-2-naphthoic acid (Br27) in the exosite, expanding the chemistry of known fragments for development of higher affinity potential allosteric inhibitors. At the same time, mapping the binding sites of a number of weaker binding Br-fragments provides further insight into the nature of these surface pockets. PMID:23998903

RISC-interacting clearing 3’- 5’ exoribonucleases (RICEs) degrade uridylated cleavage fragments to maintain functional RISC in Arabidopsis thaliana

PubMed Central

Zhang, Zhonghui; Hu, Fuqu; Sung, Min Woo; Shu, Chang; Castillo-González, Claudia; Koiwa, Hisashi; Tang, Guiliang; Dickman, Martin; Li, Pingwei; Zhang, Xiuren

2017-01-01

RNA-induced silencing complex (RISC) is composed of miRNAs and AGO proteins. AGOs use miRNAs as guides to slice target mRNAs to produce truncated 5' and 3' RNA fragments. The 5' cleaved RNA fragments are marked with uridylation for degradation. Here, we identified novel cofactors of Arabidopsis AGOs, named RICE1 and RICE2. RICE proteins specifically degraded single-strand (ss) RNAs in vitro; but neither miRNAs nor miRNA*s in vivo. RICE1 exhibited a DnaQ-like exonuclease fold and formed a homohexamer with the active sites located at the interfaces between RICE1 subunits. Notably, ectopic expression of catalytically-inactive RICE1 not only significantly reduced miRNA levels; but also increased 5' cleavage RISC fragments with extended uridine tails. We conclude that RICEs act to degrade uridylated 5’ products of AGO cleavage to maintain functional RISC. Our study also suggests a possible link between decay of cleaved target mRNAs and miRNA stability in RISC. DOI: http://dx.doi.org/10.7554/eLife.24466.001 PMID:28463111

Mass Spectrometry Based Ultrasensitive DNA Methylation Profiling Using Target Fragmentation Assay.

PubMed

Lin, Xiang-Cheng; Zhang, Ting; Liu, Lan; Tang, Hao; Yu, Ru-Qin; Jiang, Jian-Hui

2016-01-19

Efficient tools for profiling DNA methylation in specific genes are essential for epigenetics and clinical diagnostics. Current DNA methylation profiling techniques have been limited by inconvenient implementation, requirements of specific reagents, and inferior accuracy in quantifying methylation degree. We develop a novel mass spectrometry method, target fragmentation assay (TFA), which enable to profile methylation in specific sequences. This method combines selective capture of DNA target from restricted cleavage of genomic DNA using magnetic separation with MS detection of the nonenzymatic hydrolysates of target DNA. This method is shown to be highly sensitive with a detection limit as low as 0.056 amol, allowing direct profiling of methylation using genome DNA without preamplification. Moreover, this method offers a unique advantage in accurately determining DNA methylation level. The clinical applicability was demonstrated by DNA methylation analysis using prostate tissue samples, implying the potential of this method as a useful tool for DNA methylation profiling in early detection of related diseases.

Crystallographic fragment-based drug discovery: use of a brominated fragment library targeting HIV protease.

PubMed

Tiefenbrunn, Theresa; Forli, Stefano; Happer, Meaghan; Gonzalez, Ana; Tsai, Yingssu; Soltis, Michael; Elder, John H; Olson, Arthur J; Stout, Charles D

2014-02-01

A library of 68 brominated fragments was screened against a new crystal form of inhibited HIV-1 protease in order to probe surface sites in soaking experiments. Often, fragments are weak binders with partial occupancy, resulting in weak, difficult-to-fit electron density. The use of a brominated fragment library addresses this challenge, as bromine can be located unequivocally via anomalous scattering. Data collection was carried out in an automated fashion using AutoDrug at SSRL. Novel hits were identified in the known surface sites: 3-bromo-2,6-dimethoxybenzoic acid (Br6) in the flap site and 1-bromo-2-naphthoic acid (Br27) in the exosite, expanding the chemistry of known fragments for development of higher affinity potential allosteric inhibitors. At the same time, mapping the binding sites of a number of weaker binding Br-fragments provides further insight into the nature of these surface pockets. © 2013 John Wiley & Sons A/S.

A preliminary assessment of asteroid shapes produced by impact disruption and re-creation: Application to the AIDA target.

NASA Astrophysics Data System (ADS)

Barnouin, Olivier; Michel, Patrick; Richardson, Derek

2016-04-01

In order to understand the origin of the 65803 Didymos, the target of the Asteroid Impact and Deflection Assessment mission, and gain insights on the origin and evolution of the asteroid's162173 Ryugu and 101955 Bennu, we investigate systematically the shapes of all re-accumulated fragments produced by the catastrophic disruption of a parent body that is 1 km in diameter or larger. These new fragments eventually become new asteroids of the size that current sample-return missions plan to explore. We choose a range of impact conditions by varying the parent bodies' strength, size and porosity, and the velocity and size of the projectile. Impact conditions range from near the catastrophic threshold, usually designated by Q*, where half of the target's mass escapes, to far greater values above this threshold. Our numerical investigations of the catastrophic disruption, which are undertaken using an SPH hydrocode, include a model of fragmentation for porous materials. The gravitationally dominated phase of reaccumulation of our asteroids is computed using the N-body code pkdgrav. At sufficiently slow impact speeds in the N-body model, particles are permitted to stick, forming irregular, competent pieces that can gather into non-idealized rubble piles as a result of re-accumulation. Shape and spin information of re-accumulated bodies are thus preserved. Due to numerical expense, this first study uses what we call a hard-sphere model, rather than a soft-sphere spring and dashpot model. This latter model is more commonly used in granular flow simulations for which detailed treatment of the multicontact physics is needed, which is not the case here, and comes at the expense of much smaller timesteps. With the hard-sphere model, there are three supported collision outcomes for bonded aggregates: sticking on contact (to grow the aggregate); bouncing (computed for these generally non-central impacts); and fragmentation (wherein the particles involved become detached from

[Fragment-based drug discovery: concept and aim].

PubMed

Tanaka, Daisuke

2010-03-01

Fragment-Based Drug Discovery (FBDD) has been recognized as a newly emerging lead discovery methodology that involves biophysical fragment screening and chemistry-driven fragment-to-lead stages. Although fragments, defined as structurally simple and small compounds (typically <300 Da), have not been employed in conventional high-throughput screening (HTS), the recent significant progress in the biophysical screening methods enables fragment screening at a practical level. The intention of FBDD primarily turns our attention to weakly but specifically binding fragments (hit fragments) as the starting point of medicinal chemistry. Hit fragments are then promoted to more potent lead compounds through linking or merging with another hit fragment and/or attaching functional groups. Another positive aspect of FBDD is ligand efficiency. Ligand efficiency is a useful guide in screening hit selection and hit-to-lead phases to achieve lead-likeness. Owing to these features, a number of successful applications of FBDD to "undruggable targets" (where HTS and other lead identification methods failed to identify useful lead compounds) have been reported. As a result, FBDD is now expected to complement more conventional methodologies. This review, as an introduction of the following articles, will summarize the fundamental concepts of FBDD and will discuss its advantages over other conventional drug discovery approaches.

The rise of fragment-based drug discovery.

PubMed

Murray, Christopher W; Rees, David C

2009-06-01

The search for new drugs is plagued by high attrition rates at all stages in research and development. Chemists have an opportunity to tackle this problem because attrition can be traced back, in part, to the quality of the chemical leads. Fragment-based drug discovery (FBDD) is a new approach, increasingly used in the pharmaceutical industry, for reducing attrition and providing leads for previously intractable biological targets. FBDD identifies low-molecular-weight ligands (∼150 Da) that bind to biologically important macromolecules. The three-dimensional experimental binding mode of these fragments is determined using X-ray crystallography or NMR spectroscopy, and is used to facilitate their optimization into potent molecules with drug-like properties. Compared with high-throughput-screening, the fragment approach requires fewer compounds to be screened, and, despite the lower initial potency of the screening hits, offers more efficient and fruitful optimization campaigns. Here, we review the rise of FBDD, including its application to discovering clinical candidates against targets for which other chemistry approaches have struggled.

Luminal epithelium in endometrial fragments affects their vascularization, growth and morphological development into endometriosis-like lesions in mice.

PubMed

Feng, Dilu; Menger, Michael D; Wang, Hongbo; Laschke, Matthias W

2014-02-01

In endometriosis research, endometriosis-like lesions are usually induced in rodents by transplantation of isolated endometrial tissue fragments to ectopic sites. In the present study, we investigated whether this approach is affected by the cellular composition of the grafts. For this purpose, endometrial tissue fragments covered with luminal epithelium (LE(+)) and without luminal epithelium (LE(-)) were transplanted from transgenic green-fluorescent-protein-positive (GFP(+)) donor mice into the dorsal skinfold chamber of GFP(-) wild-type recipient animals to analyze their vascularization, growth and morphology by means of repetitive intravital fluorescence microscopy, histology and immunohistochemistry during a 14-day observation period. LE(-) fragments developed into typical endometriosis-like lesions with cyst-like dilated endometrial glands and a well-vascularized endometrial stroma. In contrast, LE(+) fragments exhibited a polypoid morphology and a significantly reduced blood perfusion after engraftment, because the luminal epithelium prevented the vascular interconnection with the microvasculature of the surrounding host tissue. This was associated with a markedly decreased growth rate of LE(+) lesions compared with LE(-) lesions. In addition, we found that many GFP(+) microvessels grew outside the LE(-) lesions and developed interconnections to the host microvasculature, indicating that inosculation is an important mechanism in the vascularization process of endometriosis-like lesions. Our findings demonstrate that the luminal epithelium crucially affects the vascularization, growth and morphology of endometriosis-like lesions. Therefore, it is of major importance to standardize the cellular composition of endometrial grafts in order to increase the validity and reliability of pre-clinical rodent studies in endometriosis research.

Identification of Multiple Druggable Secondary Sites by Fragment Screening against DC-SIGN.

PubMed

Aretz, Jonas; Baukmann, Hannes; Shanina, Elena; Hanske, Jonas; Wawrzinek, Robert; Zapol'skii, Viktor A; Seeberger, Peter H; Kaufmann, Dieter E; Rademacher, Christoph

2017-06-12

DC-SIGN is a cell-surface receptor for several pathogenic threats, such as HIV, Ebola virus, or Mycobacterium tuberculosis. Multiple attempts to develop inhibitors of the underlying carbohydrate-protein interactions have been undertaken in the past fifteen years. Still, drug-like DC-SIGN ligands are sparse, which is most likely due to its hydrophilic, solvent-exposed carbohydrate-binding site. Herein, we report on a parallel fragment screening against DC-SIGN applying SPR and a reporter displacement assay, which complements previous screenings using 19 F NMR spectroscopy and chemical fragment microarrays. Hit validation by SPR and 1 H- 15 N HSQC NMR spectroscopy revealed that although no fragment bound in the primary carbohydrate site, five secondary sites are available to harbor drug-like molecules. Building on key interactions of the reported fragment hits, these pockets will be targeted in future approaches to accelerate the development of DC-SIGN inhibitors. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fusion of small unilamellar vesicles induced by bovine serum albumin fragments.

PubMed

Garcia, L A; Schenkman, S; Araujo, P S; Chaimovich, H

1983-07-01

The limited pepsin proteolysis products of bovine serum albumin, fragment A (residues 307-586) and fragment B (residues 1-306), induced the fusion of small unilamellar vesicles of egg phosphatidyl choline at concentrations near 5 microM. Fusion was demonstrated and analyzed on the basis of: a) time-dependent changes in absorbance; b) dilution of the fluorescent label 2-(10-(1-pyrene)decanoyl) phosphatidyl choline, incorporated into a small percentage of the vesicles, as measured by the decrease in the excimer to monomer (E/M) ratio; c) increase of the average hydrodynamic radius of the liposomes, estimated by Sepharose 4B filtration, and d) the strict inverse relationship between the size of the liposomes and their E/M ratios. Albumin fragment B, like albumin, induced the formation of large aggregates in which rapid cooperative fusion produced vesicles having a large hydrodynamic radius. Fragment A did not produce large aggregates and the initial fusion products exhibited a hydrodynamic radius. Fragment A did not produce large aggregates and the initial fusion products exhibited a hydrodynamic radius smaller than those obtained with fragment B. Albumin and fragments A and B are fusogenic only at pH below 4.0. These data discussed in terms of a general model for a signal-dependent protein-induced membrane fusion.

Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei

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

Begley, Darren W.; Hartley, Robert C.; Davies, Douglas R.

As part of the Seattle Structural Genomics Center for Infectious Disease, we seek to enhance structural genomics with ligand-bound structure data which can serve as a blueprint for structure-based drug design. We have adapted fragment-based screening methods to our structural genomics pipeline to generate multiple ligand-bound structures of high priority drug targets from pathogenic organisms. In this study, we report fragment screening methods and structure determination results for 2C-methyl-D-erythritol-2,4-cyclo-diphosphate (MECP) synthase from Burkholderia pseudomallei, the gram-negative bacterium which causes melioidosis. Screening by nuclear magnetic resonance spectroscopy as well as crystal soaking followed by X-ray diffraction led to the identification ofmore » several small molecules which bind this enzyme in a critical metabolic pathway. A series of complex structures obtained with screening hits reveal distinct binding pockets and a range of small molecules which form complexes with the target. Additional soaks with these compounds further demonstrate a subset of fragments to only bind the protein when present in specific combinations. This ensemble of fragment-bound complexes illuminates several characteristics of MECP synthase, including a previously unknown binding surface external to the catalytic active site. These ligand-bound structures now serve to guide medicinal chemists and structural biologists in rational design of novel inhibitors for this enzyme.« less

Fragment-based screening in tandem with phenotypic screening provides novel antiparasitic hits.

PubMed

Blaazer, Antoni R; Orrling, Kristina M; Shanmugham, Anitha; Jansen, Chimed; Maes, Louis; Edink, Ewald; Sterk, Geert Jan; Siderius, Marco; England, Paul; Bailey, David; de Esch, Iwan J P; Leurs, Rob

2015-01-01

Methods to discover biologically active small molecules include target-based and phenotypic screening approaches. One of the main difficulties in drug discovery is elucidating and exploiting the relationship between drug activity at the protein target and disease modification, a phenotypic endpoint. Fragment-based drug discovery is a target-based approach that typically involves the screening of a relatively small number of fragment-like (molecular weight <300) molecules that efficiently cover chemical space. Here, we report a fragment screening on TbrPDEB1, an essential cyclic nucleotide phosphodiesterase (PDE) from Trypanosoma brucei, and human PDE4D, an off-target, in a workflow in which fragment hits and a series of close analogs are subsequently screened for antiparasitic activity in a phenotypic panel. The phenotypic panel contained T. brucei, Trypanosoma cruzi, Leishmania infantum, and Plasmodium falciparum, the causative agents of human African trypanosomiasis (sleeping sickness), Chagas disease, leishmaniasis, and malaria, respectively, as well as MRC-5 human lung cells. This hybrid screening workflow has resulted in the discovery of various benzhydryl ethers with antiprotozoal activity and low toxicity, representing interesting starting points for further antiparasitic optimization. © 2014 Society for Laboratory Automation and Screening.

Targeting YAP/TAZ-TEAD protein-protein interactions using fragment-based and computational modeling approaches

PubMed Central

Verma, Chandra

2017-01-01

The Hippo signaling pathway, which is implicated in the regulation of organ size, has emerged as a potential target for the development of cancer therapeutics. YAP, TAZ (transcription co-activators) and TEAD (transcription factor) are the downstream transcriptional machinery and effectors of the pathway. Formation of the YAP/TAZ-TEAD complex leads to transcription of growth-promoting genes. Conversely, disrupting the interactions of the complex decreases cell proliferation. Herein, we screened a 1000-member fragment library using Thermal Shift Assay and identified a hit fragment. We confirmed its binding at the YAP/TAZ-TEAD interface by X-ray crystallography, and showed that it occupies the same hydrophobic pocket as a conserved phenylalanine of YAP/TAZ. This hit fragment serves as a scaffold for the development of compounds that have the potential to disrupt YAP/TAZ-TEAD interactions. Structure-activity relationship studies and computational modeling were also carried out to identify more potent compounds that may bind at this validated druggable binding site. PMID:28570566

Fragment-based lead generation: identification of seed fragments by a highly efficient fragment screening technology

NASA Astrophysics Data System (ADS)

Neumann, Lars; Ritscher, Allegra; Müller, Gerhard; Hafenbradl, Doris

2009-08-01

For the detection of the precise and unambiguous binding of fragments to a specific binding site on the target protein, we have developed a novel reporter displacement binding assay technology. The application of this technology for the fragment screening as well as the fragment evolution process with a specific modelling based design strategy is demonstrated for inhibitors of the protein kinase p38alpha. In a fragment screening approach seed fragments were identified which were then used to build compounds from the deep-pocket towards the hinge binding area of the protein kinase p38alpha based on a modelling approach. BIRB796 was used as a blueprint for the alignment of the fragments. The fragment evolution of these deep-pocket binding fragments towards the fully optimized inhibitor BIRB796 included the modulation of the residence time as well as the affinity. The goal of our study was to evaluate the robustness and efficiency of our novel fragment screening technology at high fragment concentrations, compare the screening data with biochemical activity data and to demonstrate the evolution of the hit fragments with fast kinetics, into slow kinetic inhibitors in an in silico approach.

Cftr gene targeting in mouse embryonic stem cells mediated by Small Fragment Homologous Replacement (SFHR).

PubMed

Sangiuolo, Federica; Scaldaferri, Maria Lucia; Filareto, Antonio; Spitalieri, Paola; Guerra, Lorenzo; Favia, Maria; Caroppo, Rosa; Mango, Ruggiero; Bruscia, Emanuela; Gruenert, Dieter C; Casavola, Valeria; De Felici, Massimo; Novelli, Giuseppe

2008-01-01

Different gene targeting approaches have been developed to modify endogenous genomic DNA in both human and mouse cells. Briefly, the process involves the targeting of a specific mutation in situ leading to the gene correction and the restoration of a normal gene function. Most of these protocols with therapeutic potential are oligonucleotide based, and rely on endogenous enzymatic pathways. One gene targeting approach, "Small Fragment Homologous Replacement (SFHR)", has been found to be effective in modifying genomic DNA. This approach uses small DNA fragments (SDF) to target specific genomic loci and induce sequence and subsequent phenotypic alterations. This study shows that SFHR can stably introduce a 3-bp deletion (deltaF508, the most frequent cystic fibrosis (CF) mutation) into the Cftr (CF Transmembrane Conductance Regulator) locus in the mouse embryonic stem (ES) cell genome. After transfection of deltaF508-SDF into murine ES cells, SFHR-mediated modification was evaluated at the molecular levels on DNA and mRNA obtained from transfected ES cells. About 12% of transcript corresponding to deleted allele was detected, while 60% of the electroporated cells completely lost any measurable CFTR-dependent chloride efflux. The data indicate that the SFHR technique can be used to effectively target and modify genomic sequences in ES cells. Once the SFHR-modified ES cells differentiate into different cell lineages they can be useful for elucidating tissue-specific gene function and for the development of transplantation-based cellular and therapeutic protocols.

Erlotinib induced target-like purpura.

PubMed

Rungtrakulchai, R; Rerknimitr, P

2014-02-18

Erlotinib is an epidermal growth factor receptor (EGFR) inhibitor, used as a treatment for advanced stage cancer. The most common side effect is cutaneous toxicity including the already known papulopustular reaction. We herein report a case of erlotinib induced target-like purpura, a peculiar cutaneous adverse event. A 57-year-old patient with advanced non-small cell lung cancer was treated by erolotinib 150 mg daily. After taking the drug for three days, an unusual target-like purpura developed on her lower legs. Skin biopsy specimen taken from the lesion revealed an extravasation of erythrocytes in the upper dermis without destruction of blood vessel walls. This skin eruption cleared after the drug was withdrawn and recurred after erlotinib was re-challenged. The mechanism underlying this cutaneous adverse event remains to be elucidated. Physicians should be aware of the rare side effect of this increasingly used drug.

In silico design of fragment-based drug targeting host processing α-glucosidase i for dengue fever

NASA Astrophysics Data System (ADS)

Toepak, E. P.; Tambunan, U. S. F.

2017-02-01

Dengue is a major health problem in the tropical and sub-tropical regions. The development of antiviral that targeting dengue’s host enzyme can be more effective and efficient treatment than the viral enzyme. Host enzyme processing α-glucosidase I has an important role in the maturation process of dengue virus envelope glycoprotein. The inhibition of processing α-glucosidase I can become a promising target for dengue fever treatment. The antiviral approach using in silico fragment-based drug design can generate drug candidates with high binding affinity. In this research, 198.621 compounds were obtained from ZINC15 Biogenic Database. These compounds were screened to find the favorable fragments according to Rules of Three and pharmacological properties. The screening fragments were docked into the active site of processing α-glucosidase I. The potential fragment candidates from the molecular docking simulation were linked with castanospermine (CAST) to generate ligands with a better binding affinity. The Analysis of ligand - enzyme interaction showed ligands with code LRS 22, 28, and 47 have the better binding free energy than the standard ligand. Ligand LRS 28 (N-2-4-methyl-5-((1S,3S,6S,7R,8R,8aR)-1,6,7,8-tetrahydroxyoctahydroindolizin-3-yl) pentyl) indolin-1-yl) propionamide) itself among the other ligands has the lowest binding free energy. Pharmacological properties prediction also showed the ligands LRS 22, 28, and 47 can be promising as the dengue fever drug candidates.

Bacterial production and structure-functional validation of a recombinant antigen-binding fragment (Fab) of an anti-cancer therapeutic antibody targeting epidermal growth factor receptor.

PubMed

Kim, Ji-Hun; Sim, Dae-Won; Park, Dongsun; Jung, Tai-Geun; Lee, Seonghwan; Oh, Taeheun; Ha, Jong-Ryul; Seok, Seung-Hyeon; Seo, Min-Duk; Kang, Ho Chul; Kim, Young Pil; Won, Hyung-Sik

2016-12-01

Fragment engineering of monoclonal antibodies (mAbs) has emerged as an excellent paradigm to develop highly efficient therapeutic and/or diagnostic agents. Engineered mAb fragments can be economically produced in bacterial systems using recombinant DNA technologies. In this work, we established recombinant production in Escherichia coli for monovalent antigen-binding fragment (Fab) adopted from a clinically used anticancer mAB drug cetuximab targeting epidermal growth factor receptor (EGFR). Recombinant DNA constructs were designed to express both polypeptide chains comprising Fab in a single vector and to secrete them to bacterial periplasmic space for efficient folding. Particularly, a C-terminal engineering to confer an interchain disulfide bond appeared to be able to enhance its heterodimeric integrity and EGFR-binding activity. Conformational relevance of the purified final product was validated by mass spectrometry and crystal structure at 1.9 Å resolution. Finally, our recombinant cetuximab-Fab was found to have strong binding affinity to EGFR overexpressed in human squamous carcinoma model (A431) cells. Its binding ability was comparable to that of cetuximab. Its EGFR-binding affinity was estimated at approximately 0.7 nM of Kd in vitro, which was quite stronger than the binding affinity of natural ligand EGF. Hence, the results validate that our construction could serve as an efficient platform to produce a recombinant cetuximab-Fab with a retained antigen-binding functionality.

Targeting α-synuclein oligomers by protein-fragment complementation for drug discovery in synucleinopathies.

PubMed

Moussaud, Simon; Malany, Siobhan; Mehta, Alka; Vasile, Stefan; Smith, Layton H; McLean, Pamela J

2015-05-01

Reducing the burden of α-synuclein oligomeric species represents a promising approach for disease-modifying therapies against synucleinopathies such as Parkinson's disease and dementia with Lewy bodies. However, the lack of efficient drug discovery strategies that specifically target α-synuclein oligomers has been a limitation to drug discovery programs. Here we describe an innovative strategy that harnesses the power of bimolecular protein-fragment complementation to monitor synuclein-synuclein interactions. We have developed two robust models to monitor α-synuclein oligomerization by generating novel stable cell lines expressing α-synuclein fusion proteins for either fluorescent or bioluminescent protein-fragment complementation under the tetracycline-controlled transcriptional activation system. A pilot screen was performed resulting in the identification of two potential hits, a p38 MAPK inhibitor and a casein kinase 2 inhibitor, thereby demonstrating the suitability of our protein-fragment complementation assay for the measurement of α-synuclein oligomerization in living cells at high throughput. The application of the strategy described herein to monitor α-synuclein oligomer formation in living cells with high throughput will facilitate drug discovery efforts for disease-modifying therapies against synucleinopathies and other proteinopathies.

Fragment size distribution statistics in dynamic fragmentation of laser shock-loaded tin

NASA Astrophysics Data System (ADS)

He, Weihua; Xin, Jianting; Zhao, Yongqiang; Chu, Genbai; Xi, Tao; Shui, Min; Lu, Feng; Gu, Yuqiu

2017-06-01

This work investigates the geometric statistics method to characterize the size distribution of tin fragments produced in the laser shock-loaded dynamic fragmentation process. In the shock experiments, the ejection of the tin sample with etched V-shape groove in the free surface are collected by the soft recovery technique. Subsequently, the produced fragments are automatically detected with the fine post-shot analysis techniques including the X-ray micro-tomography and the improved watershed method. To characterize the size distributions of the fragments, a theoretical random geometric statistics model based on Poisson mixtures is derived for dynamic heterogeneous fragmentation problem, which reveals linear combinational exponential distribution. The experimental data related to fragment size distributions of the laser shock-loaded tin sample are examined with the proposed theoretical model, and its fitting performance is compared with that of other state-of-the-art fragment size distribution models. The comparison results prove that our proposed model can provide far more reasonable fitting result for the laser shock-loaded tin.

Fragment Screening and HIV Therapeutics

PubMed Central

Bauman, Joseph D.; Patel, Disha; Arnold, Eddy

2013-01-01

Fragment screening has proven to be a powerful alternative to traditional methods for drug discovery. Biophysical methods, such as X-ray crystallography, NMR spectroscopy, and surface plasmon resonance, are used to screen a diverse library of small molecule compounds. Although compounds identified via this approach have relatively weak affinity, they provide a good platform for lead development and are highly efficient binders with respect to their size. Fragment screening has been utilized for a wide-range of targets, including HIV-1 proteins. Here, we review the fragment screening studies targeting HIV-1 proteins using X-ray crystallography or surface plasmon resonance. These studies have successfully detected binding of novel fragments to either previously established or new sites on HIV-1 protease and reverse transcriptase. In addition, fragment screening against HIV-1 reverse transcriptase has been used as a tool to better understand the complex nature of ligand binding to a flexible target. PMID:21972022

Fast metastable fragments produced by dissociative excitation of carbonyl sulfide

NASA Technical Reports Server (NTRS)

Van Brunt, R. J.; Mumma, M. J.

1975-01-01

Dissociative excitation of OCS by electron impact has been studied using the method of translational spectroscopy. Time-of-flight distributions and excitation functions of the fast metastable fragments have been measured. The results are compared with similar measurements on CO2 and show that a variety of metastable fragments including CO(a 3Pi), S(5S), O(5S) as well as long-lived high-lying atomic and molecular Rydberg fragments can contribute to dissociation.

Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library.

PubMed

Huschmann, Franziska U; Linnik, Janina; Sparta, Karine; Ühlein, Monika; Wang, Xiaojie; Metz, Alexander; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard; Weiss, Manfred S; Mueller, Uwe

2016-05-01

Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein-ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin-fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity.

Structures of endothiapepsin–fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library

PubMed Central

Huschmann, Franziska U.; Linnik, Janina; Sparta, Karine; Ühlein, Monika; Wang, Xiaojie; Metz, Alexander; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard; Weiss, Manfred S.; Mueller, Uwe

2016-01-01

Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein–ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin–fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity. PMID:27139825

Intestinal epithelial cells as producers but not targets of chronic TNF suffice to cause murine Crohn-like pathology

PubMed Central

Roulis, Manolis; Armaka, Maria; Manoloukos, Menelaos; Apostolaki, Maria; Kollias, George

2011-01-01

TNF plays a crucial role in the pathogenesis of Crohn disease. Dysregulated TNF production in mice that bear the genetic deletion of the TNF AU-rich regulatory elements (ARE) (TnfΔARE/+ mice) results in TNF receptor I (TNFRI)-dependent spontaneous Crohn-like pathology. Current concepts consider intestinal epithelial cell (IEC) responses to TNF to be critical for intestinal pathology, but the potential contribution of IEC-derived TNF in disease pathogenesis has not been addressed. In this study we examined whether IEC are sufficient as cellular targets or sources of TNF in the development of intestinal pathology. Using IEC-specific reactivation of a hypomorphic TnfΔAREneo allele in mice, we show that selective chronic overproduction of TNF by IEC suffices to cause full development of Crohn-like pathology. Epithelial TNF overexpression leads to early activation of the underlying intestinal myofibroblast, a cell type previously identified as a sufficient target of TNF for disease development in the TnfΔARE model. By contrast, restricted TNFRI expression on IEC although sufficient to confer IEC apoptosis after acute exogenous TNF administration, fails to induce pathology following chronic specific targeting of IEC by endogenous TNF in TnfΔARE/+ mice. Our results argue against IEC being early and sufficient responders to chronic TNF-mediated pathogenic signals and suggest that proinflammatory aberrations leading to chronic TNF production by IEC may initiate pathology in Crohn disease. PMID:21402942

Study of nuclear fragmentation at MPD/NICA

NASA Astrophysics Data System (ADS)

Golubeva, M. B.; Ivashkin, A. P.; Kurepin, A. B.

2017-03-01

Due to the much lower beam energy of NICA compared to the RHIC and LHC hadron colliders and the fixed target experiments at SPS the role and performance of the forward detectors of NICA are quite different. The Neutron Zero Degree Calorimeter could be used for the measurement and monitoring of luminosity, however with lower efficiency of neutron detection produced in ultra-peripheral collisions. The use of Forward Hadron Calorimeter for the determination of centrality is impossible by simply counting the number of spectators because of the ambiguity of the impact parameter dependence. This ambiguity could be removed if the angular distribution of the spectators will be taken into account. It is shown by the simulation with LAQGSM model that the forward multiplicity detector like V0 of ALICE could not be used for the determination of centrality. However it could provide the valuable information on the nuclear fragmentation of heavy ions.

Method and apparatus for producing cryogenic targets

DOEpatents

Murphy, James T.; Miller, John R.

1984-01-01

An improved method and apparatus are given for producing cryogenic inertially driven fusion targets in the fast isothermal freezing (FIF) method. Improved coupling efficiency and greater availability of volume near the target for diagnostic purposes and for fusion driver beam propagation result. Other embodiments include a new electrical switch and a new explosive detonator, all embodiments making use of a purposeful heating by means of optical fibers.

Forward-Backward Emission of Target Evaporated Fragments at High Energy Nucleus-Nucleus Collisions

NASA Astrophysics Data System (ADS)

Zhang, Zhi; Ma, Tian-Li; Zhang, Dong-Hai

The multiplicity distribution, multiplicity moments, scaled variance and entropy of target evaporated fragment emitted in forward and backward hemispheres in relativistic heavy ions induced emulsion heavy targets (AgBr) interactions are investigated. It is found that the multiplicity distribution can be fitted by the Gaussian distribution, and the fitting parameters are different between two hemispheres for all the interactions. The multiplicity moment increases with the order of the moment q, and second-order multiplicity moment is energy independent over the entire energy for all the interactions. The scaled variance is close to one for all the interactions. The entropy in forward hemisphere is greater than that in backward hemisphere for all the interactions.

Renal targeted delivery of triptolide by conjugation to the fragment peptide of human serum albumin.

PubMed

Yuan, Zhi-xiang; Wu, Xiao-juan; Mo, Jingxin; Wang, Yan-li; Xu, Chao-qun; Lim, Lee Yong

2015-08-01

We have previously demonstrated that peptide fragments (PFs) of the human serum albumin could be developed as potential renal targeting carriers, in particular, the peptide fragment, PF-A299-585 (A299-585 representing the amino acid sequence of the human serum albumin). In this paper, we conjugated triptolide (TP), the anti-inflammatory Chinese traditional medicine, to PF-A299-585 via a succinic acid spacer to give TPS-PF-A299-585 (TP loading 2.2% w/w). Compared with the free TP, TPS-PF-A299-585 exhibited comparable anti-inflammatory activity in the lipopolysaccharide stimulated MDCK cells, but was significantly less cytotoxic than the free drug. Accumulation of TPS-PF-A299-585 in the MDCK cells in vitro and in rodent kidneys in vivo was demonstrated using FITC-labeled TPS-PF-A299-585. Renal targeting was confirmed in vivo in a membranous nephropathic (MN) rodent model, where optical imaging and analyses of biochemical markers were combined to show that TPS-PF-A299-585 was capable of alleviating the characteristic symptoms of MN. The collective data affirm PF-A299-585 to be a useful carrier for targeting TP to the kidney. Copyright © 2015 Elsevier B.V. All rights reserved.

Signature of the Fragmentation of a Color Flux Tube

DOE PAGES

Wong, Cheuk-Yin

2015-10-07

The production of quark-antiquark pairs along a color flux tube precedes the fragmentation of the tube. Because of the local conservation of momentum and charge, the production of amore » $q$-$$\\bar q$$ pair will lead to correlations of adjacently produced mesons (mostly pions). Adjacently produced pions however can be signalled by the their rapidity difference $$\\Delta y$$ falling within the window of $$|\\Delta y | < 1/(dN_\\pi/dy)$$, on account of the space-time-rapidity ordering of produced pions in a flux tube fragmentation. Therefore, the local conservation of momentum will lead to a suppression of azimuthal two-pion correlation $$dN/(d\\Delta \\phi\\, d\\Delta y)$$ on the near side at $$(\\Delta \\phi, \\Delta y) \\sim 0$$, but an enhanced azimuthal correlation on the back-to-back, away side at $$(\\Delta \\phi$$$\\sim$$$ \\pi,\\Delta y$$$\\sim$$0). Similarly, in a flux tube fragmentation, the local conservation of charge will forbid the production of like charge pions within $$|\\Delta y | < 1/(dN_\\pi/dy)$$, but there is no such prohibition for $$|\\Delta y| >1/(dN_\\pi/dy)$$. These properties may be used as the signature for the fragmentation of a color flux tube.« less

Evaluating Fragment Construction Policies for SDT Systems

DTIC Science & Technology

2006-01-01

allocates a fragment and begins translation. Once a termination condition is met, Strata emits any trampolines that are necessary. Trampolines are pieces... trampolines (unless its target previously exists in the fragment cache). Once a CTI’s target instruction becomes available in the fragment cache, the CTI is...linked directly to the destination, avoiding future uses of the trampoline . This mechanism is called Fragment Linking and avoids significant overhead

Impact fragmentation of a brittle metal compact

NASA Astrophysics Data System (ADS)

Tang, Megan; Hooper, Joseph P.

2018-05-01

The fragmentation behavior of a metal powder compact which is ductile in compression but brittle in tension is studied via impact experiments and analytical models. Consolidated metal compacts were prepared via cold-isostatic pressing of <10 μm zinc powder at 380 MPa followed by moderate annealing at 365 °C. The resulting zinc material is ductile and strain-hardening in high-rate uniaxial compression like a traditional metal, but is elastic-brittle in tension with a fracture toughness comparable to a ceramic. Cylindrical samples were launched up to 800 m/s in a gas gun into thin aluminum perforation targets, subjecting the projectile to a complex multiaxial and time-dependent stress state that leads to catastrophic fracture. A soft-catch mechanism using low-density artificial snow was developed to recover the impact debris, and collected fragments were analyzed to determine their size distribution down to 30 μm. Though brittle fracture occurs along original particle boundaries, no power-law fragmentation behavior was observed as is seen in other low-toughness materials. An analytical theory is developed to predict the characteristic fragment size accounting for both the sharp onset of fragmentation and the effect of increasing impact velocity.

Method and apparatus for producing cryogenic targets

DOEpatents

Murphy, J.T.; Miller, J.R.

1984-08-07

An improved method and apparatus are given for producing cryogenic inertially driven fusion targets in the fast isothermal freezing (FIF) method. Improved coupling efficiency and greater availability of volume near the target for diagnostic purposes and for fusion driver beam propagation result. Other embodiments include a new electrical switch and a new explosive detonator, all embodiments making use of a purposeful heating by means of optical fibers. 6 figs.

Zhamanshin and Aouelloul - Craters produced by impact of tektite-like glasses?

NASA Technical Reports Server (NTRS)

O'Keefe, John A.

1987-01-01

It is shown that the enhanced abundance of siderophile elements and chromium in tektite-like glasses from the two impact craters of Zhamanshin and Aouelloul cannot be explained as a result of contamination of the country rock by meteorites nor, probably, comets. The pattern is, however, like that found in certain Australasian tektites, and in Ivory Coast tektites. It is concluded, in agreement with earlier suggestions by Campbell-Smith and Hey, that these craters were formed by the impact of large masses of tektite-like glass, of which the glasses which were studied are fragments. It follows that it is necessary, in considering an impact crater, to bear in mind that the projectile may have been a glass.

Zhamanshin and Aouelloul - Craters produced by impact of tektite-like glasses?

NASA Astrophysics Data System (ADS)

O'Keefe, John A.

1987-09-01

It is shown that the enhanced abundance of siderophile elements and chromium in tektite-like glasses from the two impact craters of Zhamanshin and Aouelloul cannot be explained as a result of contamination of the country rock by meteorites nor, probably, comets. The pattern is, however, like that found in certain Australasian tektites, and in Ivory Coast tektites. It is concluded, in agreement with earlier suggestions by Campbell-Smith and Hey, that these craters were formed by the impact of large masses of tektite-like glass, of which the glasses which were studied are fragments. It follows that it is necessary, in considering an impact crater, to bear in mind that the projectile may have been a glass.

Integration of fragment screening and library design.

PubMed

Siegal, Gregg; Ab, Eiso; Schultz, Jan

2007-12-01

With more than 10 years of practical experience and theoretical analysis, fragment-based drug discovery (FBDD) has entered the mainstream of the pharmaceutical and biotech industries. An array of biophysical techniques has been used to detect the weak interaction between a fragment and the target. Each technique presents its own requirements regarding the fragment collection and the target; therefore, in order to optimize the potential of FBDD, the nature of the target should be a driving factor for simultaneous development of both the library and the screening technology. A roadmap is now available to guide fragment-to-lead evolution when structural information is available. The next challenge is to apply FBDD to targets for which high-resolution structural information is not available.

Like-sign dimuon charge asymmetry at the Tevatron: Corrections from B meson fragmentation

NASA Astrophysics Data System (ADS)

Mitov, Alexander

2011-07-01

The existing predictions for the like-sign dimuon charge asymmetry at the Tevatron are expressed in terms of parameters related to B mesons’ mixing and inclusive production fractions. We show that in the realistic case when phase-space cuts are applied, the asymmetry depends also on the details of the production mechanism for the B mesons. In particular, it is sensitive to the difference in the fragmentation functions of Bd0 and Bs0 mesons. We estimate these fragmentation effects and find that they shift the theory prediction for this observable by approximately 10%. We also point out the approximately 20% sensitivity of the asymmetry depending on which set of values for the B meson production fractions is used: as measured at the Z pole or at the Tevatron. The impact of these effects on the extraction of ASLs from the D0 measurement is presented.

Fragment-based approaches to TB drugs.

PubMed

Marchetti, Chiara; Chan, Daniel S H; Coyne, Anthony G; Abell, Chris

2018-02-01

Tuberculosis is an infectious disease associated with significant mortality and morbidity worldwide, particularly in developing countries. The rise of antibiotic resistance in Mycobacterium tuberculosis (Mtb) urgently demands the development of new drug leads to tackle resistant strains. Fragment-based methods have recently emerged at the forefront of pharmaceutical development as a means to generate more effective lead structures, via the identification of fragment molecules that form weak but high quality interactions with the target biomolecule and subsequent fragment optimization. This review highlights a number of novel inhibitors of Mtb targets that have been developed through fragment-based approaches in recent years.

Targets for producing high purity I-123

NASA Technical Reports Server (NTRS)

Blue, J. W. (Inventor)

1978-01-01

Tellurium powder in improved targets is bombarded with a cyclotron beam to produce Xe-123. Flowing gas streams carry the Xe-123 through one cold trap which removes Xe-123 that subsequently decays to I-123. During this bombardment energy is deposited in the target material causing its temperature to rise. Some of the tellurium vaporizes and subsequently condenses on surfaces that are cooler than the vaporization temperature. Provision is made for the repeated bombardment of this condensed tellurium.

Optimization of a binding fragment targeting the "enlarged methionine pocket" leads to potent Trypanosoma brucei methionyl-tRNA synthetase inhibitors.

PubMed

Huang, Wenlin; Zhang, Zhongsheng; Ranade, Ranae M; Gillespie, J Robert; Barros-Álvarez, Ximena; Creason, Sharon A; Shibata, Sayaka; Verlinde, Christophe L M J; Hol, Wim G J; Buckner, Frederick S; Fan, Erkang

2017-06-15

Potent inhibitors of Trypanosoma brucei methionyl-tRNA synthetase were previously designed using a structure-guided approach. Compounds 1 and 2 were the most active compounds in the cyclic and linear linker series, respectively. To further improve cellular potency, SAR investigation of a binding fragment targeting the "enlarged methionine pocket" (EMP) was performed. The optimization led to the identification of a 6,8-dichloro-tetrahydroquinoline ring as a favorable fragment to bind the EMP. Replacement of 3,5-dichloro-benzyl group (the EMP binding fragment) of inhibitor 2 using this tetrahydroquinoline fragment resulted in compound 13, that exhibited an EC 50 of 4nM. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bcl-2-like protein 13 is a mammalian Atg32 homologue that mediates mitophagy and mitochondrial fragmentation

PubMed Central

Murakawa, Tomokazu; Yamaguchi, Osamu; Hashimoto, Ayako; Hikoso, Shungo; Takeda, Toshihiro; Oka, Takafumi; Yasui, Hiroki; Ueda, Hiromichi; Akazawa, Yasuhiro; Nakayama, Hiroyuki; Taneike, Manabu; Misaka, Tomofumi; Omiya, Shigemiki; Shah, Ajay M.; Yamamoto, Akitsugu; Nishida, Kazuhiko; Ohsumi, Yoshinori; Okamoto, Koji; Sakata, Yasushi; Otsu, Kinya

2015-01-01

Damaged mitochondria are removed by mitophagy. Although Atg32 is essential for mitophagy in yeast, no Atg32 homologue has been identified in mammalian cells. Here, we show that Bcl-2-like protein 13 (Bcl2-L-13) induces mitochondrial fragmentation and mitophagy in mammalian cells. First, we hypothesized that unidentified mammalian mitophagy receptors would share molecular features of Atg32. By screening the public protein database for Atg32 homologues, we identify Bcl2-L-13. Bcl2-L-13 binds to LC3 through the WXXI motif and induces mitochondrial fragmentation and mitophagy in HEK293 cells. In Bcl2-L-13, the BH domains are important for the fragmentation, while the WXXI motif facilitates mitophagy. Bcl2-L-13 induces mitochondrial fragmentation in the absence of Drp1, while it induces mitophagy in Parkin-deficient cells. Knockdown of Bcl2-L-13 attenuates mitochondrial damage-induced fragmentation and mitophagy. Bcl2-L-13 induces mitophagy in Atg32-deficient yeast cells. Induction and/or phosphorylation of Bcl2-L-13 may regulate its activity. Our findings offer insights into mitochondrial quality control in mammalian cells. PMID:26146385

Novel avian single-chain fragment variable (scFv) targets dietary gluten and related natural grain prolamins, toxic entities of celiac disease.

PubMed

Stadlmann, Valerie; Harant, Hanna; Korschineck, Irina; Hermann, Marcela; Forster, Florian; Missbichler, Albert

2015-12-01

Celiac disease (CD) is a chronic, small intestinal inflammatory disease mediated by dietary gluten and related prolamins. The only current therapeutic option is maintenance of a strict life-long gluten-free diet, which implies substantial burden for CD patients. Different treatment regimes might be feasible, including masking of toxic celiac peptides with blocking antibodies or fragments thereof. The objective of this study was therefore to select and produce a recombinant avian single-chain fragment variable (scFv) directed against peptic-tryptic digested gliadin (PT-Gliadin) and related celiac toxic entities. Gluten-free raised chicken of same age were immunized with PT-Gliadin. Chicken splenic lymphocytes, selected with antigen-coated magnetic beads, served as RNA source for the generation of cDNA. Chicken VH and VL genes were amplified from the cDNA by PCR to generate full-length scFv constructs consisting of VH and VL fragments joined by a linker sequence. ScFv constructs were ligated in a prokaryotic expression vector, which provides a C-terminal hexahistidine tag. ScFvs from several bacterial clones were expressed in soluble form and crude cell lysates screened for binding to PT-Gliadin by ELISA. We identified an enriched scFv motif, which showed reactivity to PT-Gliadin. One selected scFv candidate was expressed and purified to homogeneity. Polyclonal anti-PT-Gliadin IgY, purified from egg yolk of immunized chicken, served as control. ScFv binds in a dose-dependent manner to PT-Gliadin, comparable to IgY. Furthermore, IgY competitively displaces scFv from PT-Gliadin and natural wheat flour digest, indicating a common epitope of scFv and IgY. ScFv was tested for reactivity to different gastric digested dietary grain flours. ScFv detects common and khorasan wheat comparably with binding affinities in the high nanomolar range, while rye is detected to a lesser extent. Notably, barley and cereals which are part of the gluten-free diet, like corn and rice, are

Targeted habitat restoration can reduce extinction rates in fragmented forests.

PubMed

Newmark, William D; Jenkins, Clinton N; Pimm, Stuart L; McNeally, Phoebe B; Halley, John M

2017-09-05

The Eastern Arc Mountains of Tanzania and the Atlantic Forest of Brazil are two of the most fragmented biodiversity hotspots. Species-area relationships predict that their habitat fragments will experience a substantial loss of species. Most of these extinctions will occur over an extended time, and therefore, reconnecting fragments could prevent species losses and allow locally extinct species to recolonize former habitats. An empirical relaxation half-life vs. area relationship for tropical bird communities estimates the time that it takes to lose one-half of all species that will be eventually lost. We use it to estimate the increase in species persistence by regenerating a forest connection 1 km in width among the largest and closest fragments at 11 locations. In the Eastern Arc Mountains, regenerating 8,134 ha of forest would create >316,000 ha in total of restored contiguous forest. More importantly, it would increase the persistence time for species by a factor of 6.8 per location or ∼2,272 years, on average, relative to individual fragments. In the Atlantic Forest, regenerating 6,452 ha of forest would create >251,000 ha in total of restored contiguous forest and enhance species persistence by a factor of 13.0 per location or ∼5,102 years, on average, relative to individual fragments. Rapidly regenerating forest among fragments is important, because mean time to the first determined extinction across all fragments is 7 years. We estimate the cost of forest regeneration at $21-$49 million dollars. It could provide one of the highest returns on investment for biodiversity conservation worldwide.

Fragmentation Cross Sections of Medium-Energy 35Cl, 40Ar, and 48TiBeams on Elemental Targets

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

Zeitlin, C.; Guetersloh, S.; Heilbronn, L.

Charge-changing and fragment production cross sections at 0degrees have been obtained for interactions of 290, 400, and 650MeV/nucleon 40Ar beams, 650 and 1000 MeV/nucleon 35Cl beams, and a 1000MeV/nucleon 48Ti beam. Targets of C, CH2, Al, Cu, Sn, and Pb were used.Using standard analysis methods, we obtain fragment cross sections forcharges as low as 8 for Cl and Ar beams, and as low as 10 for the Tibeam. Using data obtained with small-acceptance detectors, we reportfragment production cross sections for charges as low as 5, corrected foracceptance using a simple model of fragment angular distributions. Withthe lower-charged fragment cross sections,more » we cancompare the data topredictions from several models (including NUCFRG2, EPAX2, and PHITS) ina region largely unexplored in earlier work. As found in earlier workwith other beams, NUCFRG2 and PHITS predictions agree reasonably wellwith the data for charge-changing cross sections, but do not accuratelypredict the fragment production cross sections. The cross sections forthe lightest fragments demonstrate the inadequacy of several models inwhich the cross sections fall monotonically with the charge of thefragment. PHITS, despite not agreeing particularly well with the fragmentproduction cross sections on average, nonetheless qualitativelyreproduces somesignificant features of the data that are missing from theother models.« less

Species identification in mixed tuna samples with next-generation sequencing targeting two short cytochrome b gene fragments.

PubMed

Kappel, Kristina; Haase, Ilka; Käppel, Christine; Sotelo, Carmen G; Schröder, Ute

2017-11-01

Conventional Sanger sequencing of PCR products is the gold standard for species authentication of seafood products. However, this method is inappropriate for the analysis of products that might contain mixtures of species, such as tinned tuna. The purpose of this study was to test whether next-generation sequencing (NGS) can be a solution for the authentication of mixed products. Nine tuna samples containing mixtures of up to four species were prepared and subjected to an NGS approach targeting two short cytochrome b gene (cytb) fragments on the Illumina MiSeq platform. Sequence recovery was precise and admixtures of as low as 1% could be identified, depending on the species composition of the mixtures. Duplicate samples as well as two individual NGS runs produced very similar results. A first test of three commercial tinned tuna samples indicated the presence of different species in the same tin, although this is forbidden by EU law. Copyright © 2017 Elsevier Ltd. All rights reserved.

In silico fragment-based drug discovery: setup and validation of a fragment-to-lead computational protocol using S4MPLE.

PubMed

Hoffer, Laurent; Renaud, Jean-Paul; Horvath, Dragos

2013-04-22

This paper describes the use and validation of S4MPLE in Fragment-Based Drug Design (FBDD)--a strategy to build drug-like ligands starting from small compounds called fragments. S4MPLE is a conformational sampling tool based on a hybrid genetic algorithm that is able to simulate one (conformer enumeration) or more molecules (docking). The goal of the current paper is to show that due to the judicious design of genetic operators, S4MPLE may be used without any specific adaptation as an in silico FBDD tool. Such fragment-to-lead evolution involves either growing of one or linking of several fragment-like binder(s). The native ability to specifically "dock" a substructure that is covalently anchored to its target (here, some prepositioned fragment formally part of the binding site) enables it to act like dedicated de novo builders and differentiates it from most classical docking tools, which may only cope with non-covalent interactions. Besides, S4MPLE may address growing/linking scenarios involving protein site flexibility, and it might also suggest "growth" moves by bridging the ligand to the site via water-mediated interactions if H2O molecules are simply appended to the input files. Therefore, the only development overhead required to build a virtual fragment→ligand growing/linking strategy based on S4MPLE were two chemoinformatics programs meant to provide a minimalistic management of the linker library. The first creates a duplicate-free library by fragmenting a compound database, whereas the second builds new compounds, attaching chemically compatible linkers to the starting fragments. S4MPLE is subsequently used to probe the optimal placement of the linkers within the binding site, with initial restraints on atoms from initial fragments, followed by an optimization of all kept poses after restraint removal. Ranking is mainly based on two criteria: force-field potential energy and RMSD shifts of the original fragment moieties. This strategy was applied to

Targeted habitat restoration can reduce extinction rates in fragmented forests

PubMed Central

Newmark, William D.; Pimm, Stuart L.; McNeally, Phoebe B.; Halley, John M.

2017-01-01

The Eastern Arc Mountains of Tanzania and the Atlantic Forest of Brazil are two of the most fragmented biodiversity hotspots. Species–area relationships predict that their habitat fragments will experience a substantial loss of species. Most of these extinctions will occur over an extended time, and therefore, reconnecting fragments could prevent species losses and allow locally extinct species to recolonize former habitats. An empirical relaxation half-life vs. area relationship for tropical bird communities estimates the time that it takes to lose one-half of all species that will be eventually lost. We use it to estimate the increase in species persistence by regenerating a forest connection 1 km in width among the largest and closest fragments at 11 locations. In the Eastern Arc Mountains, regenerating 8,134 ha of forest would create >316,000 ha in total of restored contiguous forest. More importantly, it would increase the persistence time for species by a factor of 6.8 per location or ∼2,272 years, on average, relative to individual fragments. In the Atlantic Forest, regenerating 6,452 ha of forest would create >251,000 ha in total of restored contiguous forest and enhance species persistence by a factor of 13.0 per location or ∼5,102 years, on average, relative to individual fragments. Rapidly regenerating forest among fragments is important, because mean time to the first determined extinction across all fragments is 7 years. We estimate the cost of forest regeneration at $21–$49 million dollars. It could provide one of the highest returns on investment for biodiversity conservation worldwide. PMID:28827340

Linkage map of the fragments of herpesvirus papio DNA.

PubMed Central

Lee, Y S; Tanaka, A; Lau, R Y; Nonoyama, M; Rabin, H

1981-01-01

Herpesvirus papio (HVP), an Epstein-Barr-like virus, causes lymphoblastoid disease in baboons. The physical map of HVP DNA was constructed for the fragments produced by cleavage of HVP DNA with restriction endonucleases EcoRI, HindIII, SalI, and PvuI, which produced 12, 12, 10, and 4 fragments, respectively. The total molecular size of HVP DNA was calculated as close to 110 megadaltons. The following methods were used for construction of the map; (i) fragments near the ends of HVP DNA were identified by treating viral DNA with lambda exonuclease before restriction enzyme digestion; (ii) fragments containing nucleotide sequences in common with fragments from the second enzyme digest of HVP DNA were examined by Southern blot hybridization; and (iii) the location of some fragments was determined by isolating individual fragments from agarose gels and redigesting the isolated fragments with a second restriction enzyme. Terminal heterogeneity and internal repeats were found to be unique features of HVP DNA molecule. One to five repeats of 0.8 megadaltons were found at both terminal ends. Although the repeats of both ends shared a certain degree of homology, it was not determined whether they were identical repeats. The internal repeat sequence of HVP DNA was found in the EcoRI-C region, which extended from 8.4 to 23 megadaltons from the left end of the molecule. The average number of the repeats was calculated to be seven, and the molecular size was determined to be 1.8 megadaltons. Similar unique features have been reported in EBV DNA (D. Given and E. Kieff, J. Virol. 28:524-542, 1978). Images PMID:6261015

Fragment informatics and computational fragment-based drug design: an overview and update.

PubMed

Sheng, Chunquan; Zhang, Wannian

2013-05-01

Fragment-based drug design (FBDD) is a promising approach for the discovery and optimization of lead compounds. Despite its successes, FBDD also faces some internal limitations and challenges. FBDD requires a high quality of target protein and good solubility of fragments. Biophysical techniques for fragment screening necessitate expensive detection equipment and the strategies for evolving fragment hits to leads remain to be improved. Regardless, FBDD is necessary for investigating larger chemical space and can be applied to challenging biological targets. In this scenario, cheminformatics and computational chemistry can be used as alternative approaches that can significantly improve the efficiency and success rate of lead discovery and optimization. Cheminformatics and computational tools assist FBDD in a very flexible manner. Computational FBDD can be used independently or in parallel with experimental FBDD for efficiently generating and optimizing leads. Computational FBDD can also be integrated into each step of experimental FBDD and help to play a synergistic role by maximizing its performance. This review will provide critical analysis of the complementarity between computational and experimental FBDD and highlight recent advances in new algorithms and successful examples of their applications. In particular, fragment-based cheminformatics tools, high-throughput fragment docking, and fragment-based de novo drug design will provide the focus of this review. We will also discuss the advantages and limitations of different methods and the trends in new developments that should inspire future research. © 2012 Wiley Periodicals, Inc.

Efficient production of soluble recombinant single chain Fv fragments by a Pseudomonas putida strain KT2440 cell factory.

PubMed

Dammeyer, Thorben; Steinwand, Miriam; Krüger, Sarah-C; Dübel, Stefan; Hust, Michael; Timmis, Kenneth N

2011-02-21

Recombinant antibody fragments have a wide range of applications in research, diagnostics and therapy. For many of these, small fragments like single chain fragment variables (scFv) function well and can be produced inexpensively in bacterial expression systems. Although Escherichia coli K-12 production systems are convenient, yields of different fragments, even those produced from codon-optimized expression systems, vary significantly. Where yields are inadequate, alternative production systems are needed. Pseudomonas putida strain KT2440 is a versatile biosafety strain known for good expression of heterologous genes, so we have explored its utility as a cell factory for production of scFvs. We have generated new broad host range scFv expression constructs and assessed their production in the Pseudomonas putida KT2440 host. Two scFvs bind either to human C-reactive protein or to mucin1, proteins of significant medical diagnostic and therapeutic interest, whereas a third is a model anti-lysozyme scFv. The KT2440 antibody expression systems produce scFvs targeted to the periplasmic space that were processed precisely and were easily recovered and purified by single-step or tandem affinity chromatography. The influence of promoter system, codon optimization for P. putida, and medium on scFv yield was examined. Yields of up to 3.5 mg/l of pure, soluble, active scFv fragments were obtained from shake flask cultures of constructs based on the original codon usage and expressed from the Ptac expression system, yields that were 2.5-4 times higher than those from equivalent cultures of an E. coli K-12 expression host. Pseudomonas putida KT2440 is a good cell factory for the production of scFvs, and the broad host range constructs we have produced allow yield assessment in a number of different expression hosts when yields in one initially selected are insufficient. High cell density cultivation and further optimization and refinement of the KT2440 cell factory will achieve

Two-proton correlations in the target fragmentation region of nuclear collisions at 200 A GeV

NASA Astrophysics Data System (ADS)

Awes, T. C.; Barlag, C.; Berger, F.; Bloomer, M. A.; Blume, C.; Bock, D.; Bock, R.; Bohne, E.-M.; Bucher, D.; Claussen, A.; Clewing, G.; Dragon, L.; Eklund, A.; Garpman, S.; Glasow, R.; Gustafsson, H.; Gutbrod, H. H.; Hölker, G.; Idh, J.; Jacobs, P.; Kampert, K. H.; Kolb, B. W.; Löhner, H.; Lund, I.; Obenshain, F. E.; Oskarsson, A.; Otterlund, I.; Peitzmann, T.; Plasil, F.; Poskanzer, A. M.; Purschke, M.; Roters, B.; Saini, S.; Santo, R.; Schmidt, H. R.; Sørensen, S. P.; Steffens, K.; Steinhaeuser, P.; Stenlund, E.; Stüken, D.; Young, G. R.

1995-06-01

Correlations between protons are studied in the target fragmentation region of reactions of protons and16O with C, Cu, Ag, Au and of32S with Al and Au at 200 A GeV. The emitted protons were measured with the Plastic Ball detector in the WA80 experiment at the CERN SPS. The comparison of the correlation function with calculations, assuming a spherical, gaussian shaped source with a lifetime τ=0 fm/ c, allows the extraction of radius parameters. The values are very close to those expected from the geometry of the target nuclei and increase with the target mass as α A {Target/1/3}. Even in proton induced reactions the whole target nucleus is involved. The dependence of the radii on centrality, polar angle θ lab, and energy, and their relation to measured proton yields are presented.

Universal odd-even staggering in isotopic fragmentation and spallation cross sections of neutron-rich fragments

NASA Astrophysics Data System (ADS)

Mei, B.; Tu, X. L.; Wang, M.

2018-04-01

An evident odd-even staggering (OES) in fragment cross sections has been experimentally observed in many fragmentation and spallation reactions. However, quantitative comparisons of this OES effect in different reaction systems are still scarce for neutron-rich nuclei near the neutron drip line. By employing a third-order difference formula, the magnitudes of this OES in extensive experimental cross sections are systematically investigated for many neutron-rich nuclei with (N -Z ) from 1 to 23 over a broad range of atomic numbers (Z ≈3 -50 ). A comparison of these magnitude values extracted from fragment cross sections measured in different fragmentation and spallation reactions with a large variety of projectile-target combinations over a wide energy range reveals that the OES magnitude is almost independent of the projectile-target combinations and the projectile energy. The weighted average of these OES magnitudes derived from cross sections accurately measured in different reaction systems is adopted as the evaluation value of the OES magnitude. These evaluated OES magnitudes are recommended to be used in fragmentation and spallation models to improve their predictions for fragment cross sections.

Fragment-based approaches to the discovery of kinase inhibitors.

PubMed

Mortenson, Paul N; Berdini, Valerio; O'Reilly, Marc

2014-01-01

Protein kinases are one of the most important families of drug targets, and aberrant kinase activity has been linked to a large number of disease areas. Although eminently targetable using small molecules, kinases present a number of challenges as drug targets, not least obtaining selectivity across such a large and relatively closely related target family. Fragment-based drug discovery involves screening simple, low-molecular weight compounds to generate initial hits against a target. These hits are then optimized to more potent compounds via medicinal chemistry, usually facilitated by structural biology. Here, we will present a number of recent examples of fragment-based approaches to the discovery of kinase inhibitors, detailing the construction of fragment-screening libraries, the identification and validation of fragment hits, and their optimization into potent and selective lead compounds. The advantages of fragment-based methodologies will be discussed, along with some of the challenges associated with using this route. Finally, we will present a number of key lessons derived both from our own experience running fragment screens against kinases and from a large number of published studies.

Ultra-pure, water-dispersed Au nanoparticles produced by femtosecond laser ablation and fragmentation

PubMed Central

Kubiliūtė, Reda; Maximova, Ksenia A; Lajevardipour, Alireza; Yong, Jiawey; Hartley, Jennifer S; Mohsin, Abu SM; Blandin, Pierre; Chon, James WM; Sentis, Marc; Stoddart, Paul R; Kabashin, Andrei; Rotomskis, Ričardas; Clayton, Andrew HA; Juodkazis, Saulius

2013-01-01

Aqueous solutions of ultra-pure gold nanoparticles have been prepared by methods of femtosecond laser ablation from a solid target and fragmentation from already formed colloids. Despite the absence of protecting ligands, the solutions could be (1) fairly stable and poly size-dispersed; or (2) very stable and monodispersed, for the two fabrication modalities, respectively. Fluorescence quenching behavior and its intricacies were revealed by fluorescence lifetime imaging microscopy in rhodamine 6G water solution. We show that surface-enhanced Raman scattering of rhodamine 6G on gold nanoparticles can be detected with high fidelity down to micromolar concentrations using the nanoparticles. Application potential of pure gold nanoparticles with polydispersed and nearly monodispersed size distributions are discussed. PMID:23888114

D meson production asymmetry, unfavored fragmentation, and consequences for prompt atmospheric neutrino production

NASA Astrophysics Data System (ADS)

Maciuła, Rafał; Szczurek, Antoni

2018-04-01

We consider unfavored light quark/antiquark to D meson fragmentation. We discuss nonperturbative effects for small transverse momenta. The asymmetry for D+ and D- production measured by the LHCb collaboration provides natural constraints on the parton (quark/antiquark) fragmentation functions. We find that already a fraction of q /q ¯→D fragmentation probability is sufficient to account for the measured asymmetry. We make predictions for similar asymmetry for neutral D mesons. Large D -meson production asymmetries are found for large xF which is related to dominance of light quark/antiquark q /q ¯→D fragmentation over the standard c →D fragmentation. As a consequence, prompt atmospheric neutrino flux at high neutrino energies can be much larger than for the conventional c →D fragmentation. The latter can constitute a sizeable background for the cosmic neutrinos claimed to be observed recently by the IceCube Observatory. Large rapidity-dependent D+/D- and D0/D¯0 asymmetries are predicted for low (√{s }=20 - 100 GeV ) energies. The q /q ¯→D fragmentation leads to enhanced production of D mesons at low energies. At √{s }=20 GeV the enhancement factor with respect to the conventional contribution is larger than a factor of five. In the considered picture the large-xF D mesons are produced dominantly via fragmentation of light quarks/antiquarks. Predictions for fixed target p + 4He collisions relevant for a fixed target LHCb experiment are presented.

Binding of Soluble Natural Ligands to a Soluble Human T-Cell Receptor Fragment Produced in Escherichia coli

NASA Astrophysics Data System (ADS)

Hilyard, Katherine L.; Reyburn, Hugh; Chung, Shan; Bell, John I.; Strominger, Jack L.

1994-09-01

An Escherichia coli expression system has been developed to produce milligram quantities of the variable domains of a human T-cell receptor from a cytotoxic T cell that recognizes the HLA-A2-influenza matrix peptide complex as a single polypeptide chain. The recombinant protein was purified by metal-chelate chromatography and then refolded in a redox buffer system. The refolded protein was shown to directly bind both Staphylococcus aureus enterotoxin B and the major histocompatibility complex protein-peptide complex using a BIAcore biosensor. Thus this preparation of a single-chain, variable-domain, T-cell receptor fragment can bind both of its natural ligands and some of it is therefore a functional fragment of the receptor molecule.

Targeting lysine specific demethylase 4A (KDM4A) tandem TUDOR domain - A fragment based approach.

PubMed

Upadhyay, Anup K; Judge, Russell A; Li, Leiming; Pithawalla, Ron; Simanis, Justin; Bodelle, Pierre M; Marin, Violeta L; Henry, Rodger F; Petros, Andrew M; Sun, Chaohong

2018-06-01

The tandem TUDOR domains present in the non-catalytic C-terminal half of the KDM4A, 4B and 4C enzymes play important roles in regulating their chromatin localizations and substrate specificities. They achieve this regulatory role by binding to different tri-methylated lysine residues on histone H3 (H3-K4me3, H3-K23me3) and histone H4 (H4-K20me3) depending upon the specific chromatin environment. In this work, we have used a 2D-NMR based fragment screening approach to identify a novel fragment (1a), which binds to the KDM4A-TUDOR domain and shows modest competition with H3-K4me3 binding in biochemical as well as in vitro cell based assays. A co-crystal structure of KDM4A TUDOR domain in complex with 1a shows that the fragment binds stereo-specifically to the methyl lysine binding pocket forming a network of strong hydrogen bonds and hydrophobic interactions. We anticipate that the fragment 1a can be further developed into a novel allosteric inhibitor of the KDM4 family of enzymes through targeting their C-terminal tandem TUDOR domain. Copyright © 2018 Elsevier Ltd. All rights reserved.

Cyanobacteria as efficient producers of mycosporine-like amino acids.

PubMed

Jain, Shikha; Prajapat, Ganshyam; Abrar, Mustari; Ledwani, Lalita; Singh, Anoop; Agrawal, Akhil

2017-09-01

Mycosporine-like amino acids are the most common group of transparent ultraviolet radiation absorbing intracellular secondary metabolites. These molecules absorb light in the range of ultraviolet-A and -B with a maximum absorbance between 310 and 362 nm. Cyanobacteria might have faced the most deleterious ultraviolet radiation, which leads to an evolution of ultraviolet protecting mycosporine-like amino acids for efficient selection in the environment. In the last 30 years, scientists have investigated various cyanobacteria for novel mycosporine-like amino acids, applying different induction techniques. This review organizes all the cyanobacterial groups that produce various mycosporine-like amino acids. We found out that cyanobacteria belonging to orders Synechococcales, Chroococcales, Oscillatoriales, and Nostocales are frequently studied for the presence of mycosporine-like amino acids, while orders Gloeobacterales, Spirulinales, Pleurocapsales, and Chroococcidiopsidales are still need to be investigated. Nostoc and Anabaena strains are major studied genus for the mycosporine-like amino acids production. Hence, this review will give further insight to the readers about potential mycosporine-like amino acid producing cyanobacterial groups in future investigations. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The soluble extracellular fragment of neuroligin-1 targets Aβ oligomers to the postsynaptic region of excitatory synapses.

PubMed

Dinamarca, Margarita C; Di Luca, Monica; Godoy, Juan A; Inestrosa, Nibaldo C

2015-10-09

Amyloid-β oligomers (Aβo) play a major role in the synaptic dysfunction of Alzheimer's disease (AD). Neuroligins are postsynaptic cell-adhesion molecules, that share an extracellular domain with high degree of similarity to acetylcholinesterase (AChE), one of the first putative Aβo receptors. We recently found that Aβo interact with the soluble N-terminal fragment of neuroligin-1 (NL-1). We report here that Aβo associate with NL-1 at excitatory hippocampal synapses, whereas almost no association was observed with neuroligin-2, an isoform present at inhibitory synapses. Studies using purified hippocampal postsynaptic densities indicate that NL-1 interacts with Aβo in a complex with GluN2B-containing NMDA receptors. Additionally, the soluble fragment of NL-1 was used as a scavenger for Aβo. Field excitatory postsynaptic potentials indicate that fragments of NL-1 protect hippocampal neurons from the impairment induced by Aβo. To our knowledge, this is the first report of the interaction between this extracellular fragment of NL-1 and Aβo, strongly suggest that NL-1 facilitates the targeting of Aβo to the postsynaptic regions of excitatory synapses. Copyright © 2015 Elsevier Inc. All rights reserved.

Polymer-based adsorption medium prepared using a fragment imprinting technique for homologues of chlorinated bisphenol A produced in the environment.

PubMed

Kubo, Takuya; Hosoya, Ken; Watabe, Yoshiyuki; Ikegami, Tohru; Tanaka, Nobuo; Sano, Tomoharu; Kaya, Kunimitsu

2004-03-12

A polymer-based adsorption medium having molecular recognition ability for homologues of chlorinated bisphenol A produced in environment was prepared using a fragment imprinting technique. 2,6-Dimethyl phenol was utilized as a pseudo-template molecule and the adsorption media prepared was evaluated by high performance liquid chromatography (HPLC) and solid-phase extraction (SPE). As results, the adsorption medium showed preferable chromatographic retention and specific adsorption ability for the chlorinated bisphenol As having chlorine substituents at 3,5-positions through fragment imprinting effect.

Microbials for the production of monoclonal antibodies and antibody fragments.

PubMed

Spadiut, Oliver; Capone, Simona; Krainer, Florian; Glieder, Anton; Herwig, Christoph

2014-01-01

Monoclonal antibodies (mAbs) and antibody fragments represent the most important biopharmaceutical products today. Because full length antibodies are glycosylated, mammalian cells, which allow human-like N-glycosylation, are currently used for their production. However, mammalian cells have several drawbacks when it comes to bioprocessing and scale-up, resulting in long processing times and elevated costs. By contrast, antibody fragments, that are not glycosylated but still exhibit antigen binding properties, can be produced in microbial organisms, which are easy to manipulate and cultivate. In this review, we summarize recent advances in the expression systems, strain engineering, and production processes for the three main microbials used in antibody and antibody fragment production, namely Saccharomyces cerevisiae, Pichia pastoris, and Escherichia coli. Copyright © 2013 Elsevier Ltd. All rights reserved.

Study of Projectile Fragmentation Reactions at Intermediate Energies

NASA Astrophysics Data System (ADS)

Souliotis, George A.

The experimental measurements of the present work represent a first attempt towards obtaining systematic data of projectile fragment distributions near 0 degrees produced by intermediate-energy beams delivered by the K1200 cyclotron at the NSCL. The measurements were performed with two different devices operated as 0-degree spectrometers: the K1200 interim beamline and the A1200 mass separator. Momentum distributions and limited angular distributions of projectile -like fragments (PLFs) from a ^{14} N (75 MeV/u) beam with ^{27 }Al and ^{181}Ta targets were measured using the interim K1200 beamline, but the results were of limited quality. In a first series of measurements with the A1200, the 0-degree momentum distributions of PLFs from several beams (^{20} Ne (85 MeV/u), ^{15}N (70 MeV/u) and ^{18}O (70 Mev/u)) were measured, but only a limited number of complete momentum spectra were obtained. In a second series, a detailed measurement of neutron-rich PLFs from the reaction ^{18}O (80 MeV/u) + ^{27}Al was successfully performed. Accurate measurements of 0-degree momentum distributions and relative yields of PLFs were obtained and analysed. Analysis of the centroids of the momentum-per -nucleon (velocity) distributions of the fragments indicated that, along with the fragmentation (break-up) channels, direct stripping and/or pick-up channels contribute significantly to the production of the fragments. Interestingly, the mean velocities of nucleon pick-up products were considerably lower than that of the beam, consistent with momentum conservation and the additional assumption that the nucleon(s) picked -up from the target have preferentially momenta (on average) equal to the nuclear Fermi momentum oriented in the direction of the projectile motion. The widths of the momentum distributions of both nucleon-removal and nucleon pick-up products were in agreement with the independent-particle model of Goldhaber and the cluster stripping model of Friedman. In the case of

Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment-Based Drug Design Facilitated by Dynamic Combinatorial Chemistry.

PubMed

Mondal, Milon; Radeva, Nedyalka; Fanlo-Virgós, Hugo; Otto, Sijbren; Klebe, Gerhard; Hirsch, Anna K H

2016-08-01

Fragment-based drug design (FBDD) affords active compounds for biological targets. While there are numerous reports on FBDD by fragment growing/optimization, fragment linking has rarely been reported. Dynamic combinatorial chemistry (DCC) has become a powerful hit-identification strategy for biological targets. We report the synergistic combination of fragment linking and DCC to identify inhibitors of the aspartic protease endothiapepsin. Based on X-ray crystal structures of endothiapepsin in complex with fragments, we designed a library of bis-acylhydrazones and used DCC to identify potent inhibitors. The most potent inhibitor exhibits an IC50 value of 54 nm, which represents a 240-fold improvement in potency compared to the parent hits. Subsequent X-ray crystallography validated the predicted binding mode, thus demonstrating the efficiency of the combination of fragment linking and DCC as a hit-identification strategy. This approach could be applied to a range of biological targets, and holds the potential to facilitate hit-to-lead optimization. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Developments in SPR Fragment Screening.

PubMed

Chavanieu, Alain; Pugnière, Martine

2016-01-01

Fragment-based approaches have played an increasing role alongside high-throughput screening in drug discovery for 15 years. The label-free biosensor technology based on surface plasmon resonance (SPR) is now sensitive and informative enough to serve during primary screens and validation steps. In this review, the authors discuss the role of SPR in fragment screening. After a brief description of the underlying principles of the technique and main device developments, they evaluate the advantages and adaptations of SPR for fragment-based drug discovery. SPR can also be applied to challenging targets such as membrane receptors and enzymes. The high-level of immobilization of the protein target and its stability are key points for a relevant screening that can be optimized using oriented immobilized proteins and regenerable sensors. Furthermore, to decrease the rate of false negatives, a selectivity test may be performed in parallel on the main target bearing the binding site mutated or blocked with a low-off-rate ligand. Fragment-based drug design, integrated in a rational workflow led by SPR, will thus have a predominant role for the next wave of drug discovery which could be greatly enhanced by new improvements in SPR devices.

Primary and secondary fragmentation of crystal-bearing intermediate magma

NASA Astrophysics Data System (ADS)

Jones, Thomas J.; McNamara, Keri; Eychenne, Julia; Rust, Alison C.; Cashman, Katharine V.; Scheu, Bettina; Edwards, Robyn

2016-11-01

Crystal-rich intermediate magmas are subjected to both primary and secondary fragmentation processes, each of which may produce texturally distinct tephra. Of particular interest for volcanic hazards is the extent to which each process contributes ash to volcanic plumes. One way to address this question is by fragmenting pyroclasts under controlled conditions. We fragmented pumice samples from Soufriere Hills Volcano (SHV), Montserrat, by three methods: rapid decompression in a shock tube-like apparatus, impact by a falling piston, and milling in a ball mill. Grain size distributions of the products reveal that all three mechanisms produce fractal breakage patterns, and that the fractal dimension increases from a minimum of 2.1 for decompression fragmentation (primary fragmentation) to a maximum of 2.7 by repeated impact (secondary fragmentation). To assess the details of the fragmentation process, we quantified the shape, texture and components of constituent ash particles. Ash shape analysis shows that the axial ratio increases during milling and that particle convexity increases with repeated impacts. We also quantify the extent to which the matrix is separated from the crystals, which shows that secondary processes efficiently remove adhering matrix from crystals, particularly during milling (abrasion). Furthermore, measurements of crystal size distributions before (using x-ray computed tomography) and after (by componentry of individual grain size classes) decompression-driven fragmentation show not only that crystals influence particular size fractions across the total grain size distribution, but also that free crystals are smaller in the fragmented material than in the original pumice clast. Taken together, our results confirm previous work showing both the control of initial texture on the primary fragmentation process and the contributions of secondary processes to ash formation. Critically, however, our extension of previous analyses to characterisation

Dissecting fragment-based lead discovery at the von Hippel-Lindau protein:hypoxia inducible factor 1α protein-protein interface.

PubMed

Van Molle, Inge; Thomann, Andreas; Buckley, Dennis L; So, Ernest C; Lang, Steffen; Crews, Craig M; Ciulli, Alessio

2012-10-26

Fragment screening is widely used to identify attractive starting points for drug design. However, its potential and limitations to assess the tractability of often challenging protein:protein interfaces have been underexplored. Here, we address this question by means of a systematic deconstruction of lead-like inhibitors of the pVHL:HIF-1α interaction into their component fragments. Using biophysical techniques commonly employed for screening, we could only detect binding of fragments that violate the Rule of Three, are more complex than those typically screened against classical druggable targets, and occupy two adjacent binding subsites at the interface rather than just one. Analyses based on ligand and group lipophilicity efficiency of anchored fragments were applied to dissect the individual subsites and probe for binding hot spots. The implications of our findings for targeting protein interfaces by fragment-based approaches are discussed. Copyright © 2012 Elsevier Ltd. All rights reserved.

Development and Application of a Virtual Screening Protocol for the Identification of Multitarget Fragments.

PubMed

Bottegoni, Giovanni; Veronesi, Marina; Bisignano, Paola; Kacker, Puneet; Favia, Angelo D; Cavalli, Andrea

2016-06-20

In this study, we report on a virtual ligand screening protocol optimized to identify fragments endowed with activity at multiple targets. Thanks to this protocol, we were able to identify a fragment that displays activity in the low-micromolar range at both β-secretase 1 (BACE-1) and glycogen synthase kinase 3β (GSK-3β). These two structurally and physiologically unrelated enzymes likely contribute, through different pathways, to the onset of Alzheimer's disease (AD). Therefore, their simultaneous inhibition holds great potential in exerting a profound effect on AD. In perspective, the strategy outlined herein can be adapted to other target combinations. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

BcL-xL Conformational Changes upon Fragment Binding Revealed by NMR

PubMed Central

Aguirre, Clémentine; ten Brink, Tim; Walker, Olivier; Guillière, Florence; Davesne, Dany; Krimm, Isabelle

2013-01-01

Protein-protein interactions represent difficult but increasingly important targets for the design of therapeutic compounds able to interfere with biological processes. Recently, fragment-based strategies have been proposed as attractive approaches for the elaboration of protein-protein surface inhibitors from fragment-like molecules. One major challenge in targeting protein-protein interactions is related to the structural adaptation of the protein surface upon molecular recognition. Methods capable of identifying subtle conformational changes of proteins upon fragment binding are therefore required at the early steps of the drug design process. In this report we present a fast NMR method able to probe subtle conformational changes upon fragment binding. The approach relies on the comparison of experimental fragment-induced Chemical Shift Perturbation (CSP) of amine protons to CSP simulated for a set of docked fragment poses, considering the ring-current effect from fragment binding. We illustrate the method by the retrospective analysis of the complex between the anti-apoptotic Bcl-xL protein and the fragment 4′-fluoro-[1,1′-biphenyl]-4-carboxylic acid that was previously shown to bind one of the Bcl-xL hot spots. The CSP-based approach shows that the protein undergoes a subtle conformational rearrangement upon interaction, for residues located in helices 2, 3 and the very beginning of 5. Our observations are corroborated by residual dipolar coupling measurements performed on the free and fragment-bound forms of the Bcl-xL protein. These NMR-based results are in total agreement with previous molecular dynamic calculations that evidenced a high flexibility of Bcl-xL around the binding site. Here we show that CSP of protein amine protons are useful and reliable structural probes. Therefore, we propose to use CSP simulation to assess protein conformational changes upon ligand binding in the fragment-based drug design approach. PMID:23717610

From Protein Structure to Small-Molecules: Recent Advances and Applications to Fragment-Based Drug Discovery.

PubMed

Ferreira, Leonardo G; Andricopulo, Adriano D

2017-01-01

Fragment-based drug discovery (FBDD) is a broadly used strategy in structure-guided ligand design, whereby low-molecular weight hits move from lead-like to drug-like compounds. Over the past 15 years, an increasingly important role of the integration of these strategies into industrial and academic research platforms has been successfully established, allowing outstanding contributions to drug discovery. One important factor for the current prominence of FBDD is the better coverage of the chemical space provided by fragment-like libraries. The development of the field relies on two features: (i) the growing number of structurally characterized drug targets and (ii) the enormous chemical diversity available for experimental and virtual screenings. Indeed, fragment-based campaigns have contributed to address major challenges in lead optimization, such as the appropriate physicochemical profile of clinical candidates. This perspective paper outlines the usefulness and applications of FBDD approaches in medicinal chemistry and drug design. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Fragmentation of structural energetic materials: implications for performance

NASA Astrophysics Data System (ADS)

Aydelotte, B.; Braithwaite, C. H.; Thadhani, N. N.

2014-05-01

Fragmentation results for structural energetic materials based on intermetallic forming mixtures are reviewed and the implications of the fragment populations are discussed. Cold sprayed Ni+Al and explosively compacted mixtures of Ni+Al+W and Ni+Al+W+Zr powders were fabricated into ring shaped samples and explosively fragmented. Ring velocity was monitored and fragments were soft captured in order to study the fragmentation process. It was determined that the fragments produced by these structural energetic materials are much smaller than those typically produced by ductile metals such as steel or aluminum. This has implications for combustion processes that may occur subsequent to the fragmentation process.

Dual Fragment Impact of PBX Charges

NASA Astrophysics Data System (ADS)

Haskins, Peter; Briggs, Richard; Leeming, David; White, Nathan; Cheese, Philip; DE&S MoD UK Team; Ordnance Test Solutions Ltd Team

2017-06-01

Fragment impact can pose a significant hazard to many systems containing explosives or propellants. Testing for this threat is most commonly carried out using a single fragment. However, it can be argued that an initial fragment strike (or strikes) could sensitise the energetic material to subsequent impacts, which may then lead to a more violent reaction than would have been predicted based upon single fragment studies. To explore this potential hazard we have developed the capability to launch 2 fragments from the same gun at a range of velocities, and achieve impacts on an acceptor charge with good control over the spatial and temporal separation of the strikes. In this paper we will describe in detail the experimental techniques we have used, both to achieve the dual fragment launch and observe the acceptor charge response. In addition, we will describe the results obtained against PBX filled explosive targets; discuss the mechanisms controlling the target response and their significance for vulnerability assessment. Results of these tests have clearly indicated the potential for detonation upon the second strike, at velocities well below those needed for shock initiation by a single fragment.

Fragment-based virtual screening approach and molecular dynamics simulation studies for identification of BACE1 inhibitor leads.

PubMed

Manoharan, Prabu; Ghoshal, Nanda

2018-05-01

Traditional structure-based virtual screening method to identify drug-like small molecules for BACE1 is so far unsuccessful. Location of BACE1, poor Blood Brain Barrier permeability and P-glycoprotein (Pgp) susceptibility of the inhibitors make it even more difficult. Fragment-based drug design method is suitable for efficient optimization of initial hit molecules for target like BACE1. We have developed a fragment-based virtual screening approach to identify/optimize the fragment molecules as a starting point. This method combines the shape, electrostatic, and pharmacophoric features of known fragment molecules, bound to protein conjugate crystal structure, and aims to identify both chemically and energetically feasible small fragment ligands that bind to BACE1 active site. The two top-ranked fragment hits were subjected for a 53 ns MD simulation. Principle component analysis and free energy landscape analysis reveal that the new ligands show the characteristic features of established BACE1 inhibitors. The potent method employed in this study may serve for the development of potential lead molecules for BACE1-directed Alzheimer's disease therapeutics.

Giant Impacts on Earth-Like Worlds

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2016-05-01

examine the collisional histories of Earth-like planets that form. Their goal is to understand if our solar systems formation and evolution is typical or unique.How Common Are Giant Impacts?Histogram of the total number of giant impacts received by the 164 Earth-like worlds produced in the authors fragmentation-inclusive simulations. [Quintana et al. 2016]The authors find that including fragmentation does not affect the final number of planets that are formed in the simulation (an average of 34 in each system, consistent with our solar systems terrestrial planet count). But when fragmentation is included, fewer collisions end in merger which results in typical accretion timescales roughly doubling. So the effects of fragmentation influence the collisional history of the system and the length of time needed for the final system to form.Examining the 164 Earth-analogs produced in the fragmentation-inclusive simulations, Quintana and collaborators find that impacts large enough to completely strip a planets atmosphere are rare; fewer than 1% of the Earth-like worlds experienced this.But giant impacts that are able to strip ~50% of an Earth-analogs atmosphere roughly the energy of the giant impact thought to have formed our Moon are more common. Almost all of the authors Earth-analogs experienced at least 1 giant impact of this size in the 2-Gyr simulation, and the average Earth-like world experienced ~3 such impacts.These results suggest that our planets impact history with the Moon-forming impact likely being the last giant impact Earth experienced is fairly typical for Earth-like worlds. The outcomes also indicate that smaller impacts that are still potentially life-threatening are much more common than bulk atmospheric removal. Higher-resolution simulations could be used to examine such smaller impacts.CitationElisa V. Quintana et al 2016 ApJ 821 126. doi:10.3847/0004-637X/821/2/126

Exploring the temperature dependence of failure mechanisms in fragmenting metal cylinders

NASA Astrophysics Data System (ADS)

Jones, David; Chapman, David; Hazell, Paul; Bland, Simon; Eakins, Daniel

2011-06-01

We present current work to investigate the influence of temperature on the dynamic fragmentation of metals. Pre-heated/cooled cylinders of Ti-6Al-4V were subjected to rapid radial expansion up to and past the point of failure using a modified expanding insert method on a single stage gas gun. Additional experiments were performed using an electromagnetic drive system to produce uniform deformations on targets of differing dimensions (radius, wall thickness). Issues concerning the geometry of the experiments, methods of heating and cooling the sample and diagnostics are covered. Finally, the role of temperature on adiabatic shear banding and fragment distribution statistics is discussed.

Fragment-based screen against HIV protease.

PubMed

Perryman, Alexander L; Zhang, Qing; Soutter, Holly H; Rosenfeld, Robin; McRee, Duncan E; Olson, Arthur J; Elder, John E; Stout, C David

2010-03-01

We have employed a fragment-based screen against wild-type (NL4-3) HIV protease (PR) using the Active Sight fragment library and X-ray crystallography. The experiments reveal two new binding sites for small molecules. PR was co-crystallized with fragments, or crystals were soaked in fragment solutions, using five crystal forms, and 378 data sets were collected to 2.3-1.3 A resolution. Fragment binding induces a distinct conformation and specific crystal form of TL-3 inhibited PR during co-crystallization. One fragment, 2-methylcyclohexanol, binds in the 'exo site' adjacent to the Gly(16)Gly(17)Gln(18)loop where the amide of Gly(17)is a specific hydrogen bond donor, and hydrophobic contacts occur with the side chains of Lys(14)and Leu(63). Another fragment, indole-6-carboxylic acid, binds on the 'outside/top of the flap' via hydrophobic contacts with Trp(42), Pro(44), Met(46), and Lys(55), a hydrogen bond with Val(56), and a salt-bridge with Arg(57). 2-acetyl-benzothiophene also binds at this site. This study is the first fragment-based crystallographic screen against HIV PR, and the first time that fragments were screened against an inhibitor-bound drug target to search for compounds that both bind to novel sites and stabilize the inhibited conformation of the target.

Fragment-Based Screen against HIV Protease

PubMed Central

Perryman, A. L.; Zhang, Q.; Soutter, H. H.; Rosenfeld, R.; McRee, D. E.; Olson, A. J.; Elder, J. E.; Stout, C. D.

2009-01-01

We have employed a fragment-based screen against wild-type (NL4-3) HIV protease (PR) using the Active Sight fragment library and X-ray crystallography. The experiments reveal two new binding sites for small molecules. PR was co-crystallized with fragments, or crystals were soaked in fragment solutions, using five crystal forms, and 378 data sets were collected to 2.3-1.3 Å resolution. Fragment binding induces a distinct conformation and specific crystal form of TL-3 inhibited PR during co-crystallization. One fragment, 2-methylcyclohexanol, binds in the ‘exo site’ adjacent to the Gly16Gly17Gln18 loop where the amide of Gly17 is a specific hydrogen bond donor, and hydrophobic contacts occur with the side chains of Lys14 and Leu63. Another fragment, indole-6-carboxylic acid, binds on the ‘outside/top of the flap’ via hydrophobic contacts with Trp42, Pro44, Met46, and Lys55, a hydrogen bond with Val56, and a salt-bridge with Arg57. 2-acetyl-benzothiophene also binds at this site. This study is the first fragment-based crystallographic screen against HIV PR, and the first time that fragments were screened against an inhibitor-bound drug target to search for compounds that both bind to novel sites and stabilize the inhibited conformation of the target. PMID:20659109

Ubiquitin-Like Proteasome System Represents a Eukaryotic-Like Pathway for Targeted Proteolysis in Archaea

DOE PAGES

Fu, Xian; Liu, Rui; Sanchez, Iona; ...

2016-05-17

The molecular mechanisms of targeted proteolysis in archaea are poorly understood, yet they may have deep evolutionary roots shared with the ubiquitin-proteasome system of eukaryotic cells. Here, we demonstrate in archaea that TBP2, a TATA-binding protein (TBP) modified by ubiquitin-like isopeptide bonds, is phosphorylated and targeted for degradation by proteasomes. Rapid turnover of TBP2 required the functions of UbaA (the E1/MoeB/ThiF homolog of archaea), AAA ATPases (Cdc48/p97 and Rpt types), a type 2 JAB1/MPN/MOV34 metalloenzyme (JAMM/MPN+) homolog (JAMM2), and 20S proteasomes. The ubiquitin-like protein modifier small archaeal modifier protein 2 (SAMP2) stimulated the degradation of TBP2, but SAMP2 itself wasmore » not degraded. Analysis of the TBP2 fractions that were not modified by ubiquitin-like linkages revealed that TBP2 had multiple N termini, including Met1-Ser2, Ser2, and Met1-Ser2(p) [where (p) represents phosphorylation]. The evidence suggested that the Met1-Ser2(p) form accumulated in cells that were unable to degrade TBP2. We propose a model in archaea in which the attachment of ubiquitin-like tags can target proteins for degradation by proteasomes and be controlled by N-terminal degrons. In support of a proteolytic mechanism that is energy dependent and recycles the ubiquitin-like protein tags, we find that a network of AAA ATPases and a JAMM/MPN+ metalloprotease are required, in addition to 20S proteasomes, for controlled intracellular proteolysis. IMPORTANCEThis study advances the fundamental knowledge of signal-guided proteolysis in archaea and sheds light on components that are related to the ubiquitin-proteasome system of eukaryotes. In archaea, the ubiquitin-like proteasome system is found to require function of an E1/MoeB/ThiF homolog, a type 2 JAMM/MPN+ metalloprotease, and a network of AAA ATPases for the targeted destruction of proteins. We provide evidence that the attachment of the ubiquitin-like protein is controlled by an N

Single Chain Variable Fragments Produced in Escherichia coli against Heat-Labile and Heat-Stable Toxins from Enterotoxigenic E. coli.

PubMed

Ozaki, Christiane Y; Silveira, Caio R F; Andrade, Fernanda B; Nepomuceno, Roberto; Silva, Anderson; Munhoz, Danielle D; Yamamoto, Bruno B; Luz, Daniela; Abreu, Patrícia A E; Horton, Denise S P Q; Elias, Waldir P; Ramos, Oscar H P; Piazza, Roxane M F

2015-01-01

Diarrhea is a prevalent pathological condition frequently associated to the colonization of the small intestine by enterotoxigenic Escherichia coli (ETEC) strains, known to be endemic in developing countries. These strains can produce two enterotoxins associated with the manifestation of clinical symptoms that can be used to detect these pathogens. Although several detection tests have been developed, minimally equipped laboratories are still in need of simple and cost-effective methods. With the aim to contribute to the development of such diagnostic approaches, we describe here two mouse hybridoma-derived single chain fragment variable (scFv) that were produced in E. coli against enterotoxins of ETEC strains. Recombinant scFv were developed against ETEC heat-labile toxin (LT) and heat-stable toxin (ST), from previously isolated hybridoma clones. This work reports their design, construction, molecular and functional characterization against LT and ST toxins. Both antibody fragments were able to recognize the cell-interacting toxins by immunofluorescence, the purified toxins by ELISA and also LT-, ST- and LT/ST-producing ETEC strains. The developed recombinant scFvs against LT and ST constitute promising starting point for simple and cost-effective ETEC diagnosis.

Increasing Chemical Space Coverage by Combining Empirical and Computational Fragment Screens

PubMed Central

2015-01-01

Most libraries for fragment-based drug discovery are restricted to 1,000–10,000 compounds, but over 500,000 fragments are commercially available and potentially accessible by virtual screening. Whether this larger set would increase chemotype coverage, and whether a computational screen can pragmatically prioritize them, is debated. To investigate this question, a 1281-fragment library was screened by nuclear magnetic resonance (NMR) against AmpC β-lactamase, and hits were confirmed by surface plasmon resonance (SPR). Nine hits with novel chemotypes were confirmed biochemically with KI values from 0.2 to low mM. We also computationally docked 290,000 purchasable fragments with chemotypes unrepresented in the empirical library, finding 10 that had KI values from 0.03 to low mM. Though less novel than those discovered by NMR, the docking-derived fragments filled chemotype holes from the empirical library. Crystal structures of nine of the fragments in complex with AmpC β-lactamase revealed new binding sites and explained the relatively high affinity of the docking-derived fragments. The existence of chemotype holes is likely a general feature of fragment libraries, as calculation suggests that to represent the fragment substructures of even known biogenic molecules would demand a library of minimally over 32,000 fragments. Combining computational and empirical fragment screens enables the discovery of unexpected chemotypes, here by the NMR screen, while capturing chemotypes missing from the empirical library and tailored to the target, with little extra cost in resources. PMID:24807704

Fragmentation cross sections of medium-energy {sup 35}Cl, {sup 40}Ar, and {sup 48}Ti beams on elemental targets

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

Zeitlin, C.; Guetersloh, S.; Heilbronn, L.

Charge-changing and fragment production cross sections at 0 deg. have been obtained for interactions of 290, 400, and 650 MeV/nucleon {sup 40}Ar beams, 650 and 1000 MeV/nucleon {sup 35}Cl beams, and a 1000 MeV/nucleon {sup 48}Ti beam. Targets of C, CH{sub 2}, Al, Cu, Sn, and Pb were used. Using standard analysis methods, we obtained fragment cross sections for charges as low as 8 for Cl and Ar beams and as low as 10 for the Ti beam. Using data obtained with small-acceptance detectors, we report fragment production cross sections for charges as low as 5, corrected for acceptance usingmore » a simple model of fragment angular distributions. With the lower-charged fragment cross sections, we can compare the data to predictions from several models (including NUCFRG2, EPAX2, and PHITS) in a region largely unexplored in earlier work. As found in earlier work with other beams, NUCFRG2 and PHITS predictions agree reasonably well with the data for charge-changing cross sections, but these models do not accurately predict the fragment production cross sections. The cross sections for the lightest fragments demonstrate the inadequacy of several models in which the cross sections fall monotonically with the charge of the fragment. PHITS, despite its not agreeing particularly well with the fragment production cross sections on average, nonetheless qualitatively reproduces some significant features of the data that are missing from the other models.« less

Nail-like targets for laser plasma interaction experiments

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

Pasley, J; Wei, M; Shipton, E

2007-12-18

The interaction of ultra-high power picosecond laser pulses with solid targets is of interest both for benchmarking the results of hybrid particle in cell (PIC) codes and also for applications to re-entrant cone guided fast ignition. We describe the construction of novel targets in which copper/titanium wires are formed into 'nail-like' objects by a process of melting and micromachining, so that energy can be reliably coupled to a 24 {micro}m diameter wire. An extreme-ultraviolet image of the interaction of the Titan laser with such a target is shown.

Accurate Binding Free Energy Predictions in Fragment Optimization.

PubMed

Steinbrecher, Thomas B; Dahlgren, Markus; Cappel, Daniel; Lin, Teng; Wang, Lingle; Krilov, Goran; Abel, Robert; Friesner, Richard; Sherman, Woody

2015-11-23

Predicting protein-ligand binding free energies is a central aim of computational structure-based drug design (SBDD)--improved accuracy in binding free energy predictions could significantly reduce costs and accelerate project timelines in lead discovery and optimization. The recent development and validation of advanced free energy calculation methods represents a major step toward this goal. Accurately predicting the relative binding free energy changes of modifications to ligands is especially valuable in the field of fragment-based drug design, since fragment screens tend to deliver initial hits of low binding affinity that require multiple rounds of synthesis to gain the requisite potency for a project. In this study, we show that a free energy perturbation protocol, FEP+, which was previously validated on drug-like lead compounds, is suitable for the calculation of relative binding strengths of fragment-sized compounds as well. We study several pharmaceutically relevant targets with a total of more than 90 fragments and find that the FEP+ methodology, which uses explicit solvent molecular dynamics and physics-based scoring with no parameters adjusted, can accurately predict relative fragment binding affinities. The calculations afford R(2)-values on average greater than 0.5 compared to experimental data and RMS errors of ca. 1.1 kcal/mol overall, demonstrating significant improvements over the docking and MM-GBSA methods tested in this work and indicating that FEP+ has the requisite predictive power to impact fragment-based affinity optimization projects.

Fragment screening of cyclin G-associated kinase by weak affinity chromatography.

PubMed

Meiby, Elinor; Knapp, Stefan; Elkins, Jonathan M; Ohlson, Sten

2012-11-01

Fragment-based drug discovery (FBDD) has become a new strategy for drug discovery where lead compounds are evolved from small molecules. These fragments form low affinity interactions (dissociation constant (K(D)) = mM - μM) with protein targets, which require fragment screening methods of sufficient sensitivity. Weak affinity chromatography (WAC) is a promising new technology for fragment screening based on selective retention of fragments by a drug target. Kinases are a major pharmaceutical target, and FBDD has been successfully applied to several of these targets. In this work, we have demonstrated the potential to use WAC in combination with mass spectrometry (MS) detection for fragment screening of a kinase target-cyclin G-associated kinase (GAK). One hundred seventy fragments were selected for WAC screening by virtual screening of a commercial fragment library against the ATP-binding site of five different proteins. GAK protein was immobilized on a capillary HPLC column, and compound binding was characterized by frontal affinity chromatography. Compounds were screened in sets of 13 or 14, in combination with MS detection for enhanced throughput. Seventy-eight fragments (46 %) with K(D) < 200 μM were detected, including a few highly efficient GAK binders (K(D) of 2 μM; ligand efficiency = 0.51). Of special interest is that chiral screening by WAC may be possible, as two stereoisomeric fragments, which both contained one chiral center, demonstrated twin peaks. This ability, in combination with the robustness, sensitivity, and simplicity of WAC makes it a new method for fragment screening of considerable potential.

Screening a fragment cocktail library using ultrafiltration

PubMed Central

Shibata, Sayaka; Zhang, Zhongsheng; Korotkov, Konstantin V.; Delarosa, Jaclyn; Napuli, Alberto; Kelley, Angela M.; Mueller, Natasha; Ross, Jennifer; Zucker, Frank H.; Buckner, Frederick S.; Merritt, Ethan A.; Verlinde, Christophe L. M. J.; Van Voorhis, Wesley C.; Hol, Wim G. J.; Fan, Erkang

2011-01-01

Ultrafiltration provides a generic method to discover ligands for protein drug targets with millimolar to micromolar Kd, the typical range of fragment-based drug discovery. This method was tailored to a 96-well format, and cocktails of fragment-sized molecules, with molecular masses between 150 and 300 Da, were screened against medical structural genomics target proteins. The validity of the method was confirmed through competitive binding assays in the presence of ligands known to bind the target proteins. PMID:21750879

Long-term effects of fragmentation and fragment properties on bird species richness in Hawaiian forests

Treesearch

David J. Flaspohler; Christian P. Giardina; Gregory P. Asner; Patrick Hart; Jonathan Price; Cassie Ka’apu Lyons; Xeronimo Castaneda

2010-01-01

Forest fragmentation is a common disturbance affecting biological diversity, yet the impacts of fragmentation on many forest processes remain poorly understood. Forest restoration is likely to be more successful when it proceeds with an understanding of how native and exotic vertebrates utilize forest patches of different size. We used a system of forest fragments...

Magma Fragmentation

NASA Astrophysics Data System (ADS)

Gonnermann, Helge M.

2015-05-01

Magma fragmentation is the breakup of a continuous volume of molten rock into discrete pieces, called pyroclasts. Because magma contains bubbles of compressible magmatic volatiles, decompression of low-viscosity magma leads to rapid expansion. The magma is torn into fragments, as it is stretched into hydrodynamically unstable sheets and filaments. If the magma is highly viscous, resistance to bubble growth will instead lead to excess gas pressure and the magma will deform viscoelastically by fracturing like a glassy solid, resulting in the formation of a violently expanding gas-pyroclast mixture. In either case, fragmentation represents the conversion of potential energy into the surface energy of the newly created fragments and the kinetic energy of the expanding gas-pyroclast mixture. If magma comes into contact with external water, the conversion of thermal energy will vaporize water and quench magma at the melt-water interface, thus creating dynamic stresses that cause fragmentation and the release of kinetic energy. Lastly, shear deformation of highly viscous magma may cause brittle fractures and release seismic energy.

Lowered Insulin Signalling Ameliorates Age-Related Sleep Fragmentation in Drosophila

PubMed Central

Hendrich, Oliver; Hinze, Yvonne; Birras, Ulrike; Partridge, Linda

2014-01-01

Sleep fragmentation, particularly reduced and interrupted night sleep, impairs the quality of life of older people. Strikingly similar declines in sleep quality are seen during ageing in laboratory animals, including the fruit fly Drosophila. We investigated whether reduced activity of the nutrient- and stress-sensing insulin/insulin-like growth factor (IIS)/TOR signalling network, which ameliorates ageing in diverse organisms, could rescue the sleep fragmentation of ageing Drosophila. Lowered IIS/TOR network activity improved sleep quality, with increased night sleep and day activity and reduced sleep fragmentation. Reduced TOR activity, even when started for the first time late in life, improved sleep quality. The effects of reduced IIS/TOR network activity on day and night phenotypes were mediated through distinct mechanisms: Day activity was induced by adipokinetic hormone, dFOXO, and enhanced octopaminergic signalling. In contrast, night sleep duration and consolidation were dependent on reduced S6K and dopaminergic signalling. Our findings highlight the importance of different IIS/TOR components as potential therapeutic targets for pharmacological treatment of age-related sleep fragmentation in humans. PMID:24690889

Fragmentation of Structural Energetic Materials: Implications for Performance

NASA Astrophysics Data System (ADS)

Aydelotte, Brady; Braithwaite, Christopher; Thadhani, Naresh

2013-06-01

Fragmentation results for structural energetic materials based on intermetallic forming mixtures are reviewed and the implications of the fragment populations are discussed. Cold Sprayed Ni+Al and explosively compacted mixtures of Ni+Al+W and Ni+Al+W+Zr powders were fabricated into ring shaped samples and subjected to fragmentation tests. Ring velocity was monitored and fragments were soft captured in order to study the fragmentation process. It was determined that the fragments produced by these structural energetic materials are much smaller than those typically produced by ductile metals such as steel or aluminum. This has implications for combustion processes that may occur subsequent to the fragmentation process. ONR/MURI grant No. N00014-07-1-0740 Dr. Cliff Bedford PM.

Fragmentation of cosmic-string loops

NASA Technical Reports Server (NTRS)

York, Thomas

1989-01-01

The fragmentation of cosmic string loops is discussed, and the results of a simulation of this process are presented. The simulation can evolve any of a large class of loops essentially exactly, including allowing fragments that collide to join together. Such reconnection enhances the production of small fragments, but not drastically. With or without reconnections, the fragmentation process produces a collection of nonself-intersecting loops whose typical length is on the order of the persistence length of the initial loop.

A modular solid state detector for measuring high energy heavy ion fragmentation near the beam axis

NASA Technical Reports Server (NTRS)

Zeitlin, C. J.; Frankel, K. A.; Gong, W.; Heilbronn, L.; Lampo, E. J.; Leres, R.; Miller, J.; Schimmerling, W.

1994-01-01

A multi-element solid state detector has been designed to measure fluences of fragments produced near the beam axis by high energy heavy ion beams in thick targets. The detector is compact and modular, so as to be readily reconfigured according to the range of fragment charges and energies to be measured. Preamplifier gain settings and detector calibrations are adjustable remotely under computer control. We describe the central detector, its associated detectors and electronics, triggering scheme, data acquisition and particle identification techniques, illustrated by data taken with 600 MeV/u 56Fe beams and thick polyethylene targets at the LBL Bevalac. The applications of this work to space radiation protection are discussed.

Composite Overwrap Fragmentation Observations, Concerns, and Recommendations

NASA Technical Reports Server (NTRS)

Bangham, Mike; Hovater, Mary

2017-01-01

A series of test activities has raised some concerns about the generation of orbital debris caused by failures of composite overwrapped pressure vessels (COPVs). These tests have indicated that a large number of composite fragments can be produced by either pressure burst failures or by high-speed impacts. A review of prior high-speed tests with COPV indicates that other tests have produced large numbers of composite fragments. As was the case with the test referenced here, the tests tended to produce a large number of small composite fragments with relatively low velocities induced by the impact and or gas expansion.

Fragment library design: using cheminformatics and expert chemists to fill gaps in existing fragment libraries.

PubMed

Kutchukian, Peter S; So, Sung-Sau; Fischer, Christian; Waller, Chris L

2015-01-01

Fragment based screening (FBS) has emerged as a mainstream lead discovery strategy in academia, biotechnology start-ups, and large pharma. As a prerequisite of FBS, a structurally diverse library of fragments is desirable in order to identify chemical matter that will interact with the range of diverse target classes that are prosecuted in contemporary screening campaigns. In addition, it is also desirable to offer synthetically amenable starting points to increase the probability of a successful fragment evolution through medicinal chemistry. Herein we describe a method to identify biologically relevant chemical substructures that are missing from an existing fragment library (chemical gaps), and organize these chemical gaps hierarchically so that medicinal chemists can efficiently navigate the prioritized chemical space and subsequently select purchasable fragments for inclusion in an enhanced fragment library.

Fragmentation Patterns and Mechanisms of Singly and Doubly Protonated Peptoids Studied by Collision Induced Dissociation

NASA Astrophysics Data System (ADS)

Ren, Jianhua; Tian, Yuan; Hossain, Ekram; Connolly, Michael D.

2016-04-01

Peptoids are peptide-mimicking oligomers consisting of N-alkylated glycine units. The fragmentation patterns for six singly and doubly protonated model peptoids were studied via collision-induced dissociation tandem mass spectrometry. The experiments were carried out on a triple quadrupole mass spectrometer with an electrospray ionization source. Both singly and doubly protonated peptoids were found to fragment mainly at the backbone amide bonds to produce peptoid B-type N-terminal fragment ions and Y-type C-terminal fragment ions. However, the relative abundances of B- versus Y-ions were significantly different. The singly protonated peptoids fragmented by producing highly abundant Y-ions and lesser abundant B-ions. The Y-ion formation mechanism was studied through calculating the energetics of truncated peptoid fragment ions using density functional theory and by controlled experiments. The results indicated that Y-ions were likely formed by transferring a proton from the C-H bond of the N-terminal fragments to the secondary amine of the C-terminal fragments. This proton transfer is energetically favored, and is in accord with the observation of abundant Y-ions. The calculations also indicated that doubly protonated peptoids would fragment at an amide bond close to the N-terminus to yield a high abundance of low-mass B-ions and high-mass Y-ions. The results of this study provide further understanding of the mechanisms of peptoid fragmentation and, therefore, are a valuable guide for de novo sequencing of peptoid libraries synthesized via combinatorial chemistry.

Comparison of fragments created by low- and hyper-velocity impacts

NASA Astrophysics Data System (ADS)

Hanada, T.; Liou, J.-C.

This paper summarizes two new satellite impact experiments. The objective of the experiments was to investigate the outcome of low- and hyper-velocity impacts on two identical target satellites. The first experiment was performed at a low-velocity of 1.5 km/s using a 40-g aluminum alloy sphere. The second experiment was performed at a hyper-velocity of 4.4 km/s using a 4-g aluminum alloy sphere. The target satellites were 15 cm × 15 cm × 15 cm in size and 800 g in mass. The ratios of impact energy to target mass for the two experiments were approximately the same. The target satellites were completely fragmented in both experiments, although there were some differences in the characteristics of the fragments. The projectile of the low-velocity impact experiment was partially fragmented while the projectile of the hyper-velocity impact experiment was completely fragmented beyond recognition. To date, approximately 1500 fragments from each impact experiment have been collected for detailed analysis. Each piece has been weighed, measured, and analyzed based on the analytic method used in the NASA Standard Breakup Model (2000 revision). These fragments account for about 95% of the target mass for both impact experiments. Preliminary analysis results will be presented in this paper.

Producing radiometals in liquid targets: Proof of feasibility with {sup 94m}Tc

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

Hoehr, C.; Badesso, B.; Morley, T.

2012-12-19

{sup 94m}Tc was produced in a liquid target loaded with a molybdenum-salt solution. This novel technique allows for the irradiation of metals dissolved in a liquid solution, normally only available in metal powder or foil form. By using this approach, the existing liquid targets and transfer infrastructure of many PET cyclotrons can be used to produce radiometals, avoiding the need, expense and challenges of operating solid targets. Such an approach allows for rapid testing of new isotopes for proof of feasibility studies. Different concentrations of Mo solution and their effect on the target performance were tested. Sufficient quantities to allowmore » for preclinical studies were produced.« less

Evaluation and control of miRNA-like off-target repression for RNA interference.

PubMed

Seok, Heeyoung; Lee, Haejeong; Jang, Eun-Sook; Chi, Sung Wook

2018-03-01

RNA interference (RNAi) has been widely adopted to repress specific gene expression and is easily achieved by designing small interfering RNAs (siRNAs) with perfect sequence complementarity to the intended target mRNAs. Although siRNAs direct Argonaute (Ago), a core component of the RNA-induced silencing complex (RISC), to recognize and silence target mRNAs, they also inevitably function as microRNAs (miRNAs) and suppress hundreds of off-targets. Such miRNA-like off-target repression is potentially detrimental, resulting in unwanted toxicity and phenotypes. Despite early recognition of the severity of miRNA-like off-target repression, this effect has often been overlooked because of difficulties in recognizing and avoiding off-targets. However, recent advances in genome-wide methods and knowledge of Ago-miRNA target interactions have set the stage for properly evaluating and controlling miRNA-like off-target repression. Here, we describe the intrinsic problems of miRNA-like off-target effects caused by canonical and noncanonical interactions. We particularly focus on various genome-wide approaches and chemical modifications for the evaluation and prevention of off-target repression to facilitate the use of RNAi with secured specificity.

Bacteriocin-like inhibitor substances produced by Mexican strains of Bacillus thuringiensis.

PubMed

Barboza-Corona, J Eleazar; Vázquez-Acosta, Herminia; Bideshi, Dennis K; Salcedo-Hernández, Rubén

2007-02-01

Bacteriocins are antimicrobial peptides synthesized and secreted by bacteria and could potentially be used as natural food preservatives. Here, we report the production of bacteriocin-like inhibitor substances (Bt-BLIS) by five Mexican strains of Bacillus thuringiensis. Bacillus thuringiensis subsp. morrisoni (LBIT 269), B. thuringiensis subsp. kurstaki (LBIT 287), B. thuringiensis subsp kenyae (LBIT 404), B. thuringiensis subsp. entomocidus (LBIT 420) and B. thuringiensis subsp. tolworthi (LBIT 524) produced proteinaceous Bt-BLIS with high levels of activity against Bacillus cereus and other gram-positive bacteria. Although none was active against the gram-negative bacteria, Escherichia coli, Shigella species and Pseudomonas aeruginosa, the five Bt-BLIS demonstrated antimicrobial activity against Vibrio cholerae, the etiologic agent of cholera. Biochemical and biophysical studies demonstrated that the five Bt-BLIS could be categorized into two groups, those produced by LBIT 269 and 287 (Group A) and LBIT 404, 420, 524 (Group B), based on relative time of peptide synthesis, distinctive bacterial target specificity and stability in a wide range of temperatures and pH. Because of their stability and bactericidal activities against B. cereus and V. cholerae agents of emetic, diarrheal and lethal syndromes in humans, these Bt-BLIS could potentially be used as biodegradable preservatives in the food industry.

Targeting of a chlamydial protease impedes intracellular bacterial growth.

PubMed

Christian, Jan G; Heymann, Julia; Paschen, Stefan A; Vier, Juliane; Schauenburg, Linda; Rupp, Jan; Meyer, Thomas F; Häcker, Georg; Heuer, Dagmar

2011-09-01

Chlamydiae are obligate intracellular bacteria that propagate in a cytosolic vacuole. Recent work has shown that growth of Chlamydia induces the fragmentation of the Golgi apparatus (GA) into ministacks, which facilitates the acquisition of host lipids into the growing inclusion. GA fragmentation results from infection-associated cleavage of the integral GA protein, golgin-84. Golgin-84-cleavage, GA fragmentation and growth of Chlamydia trachomatis can be blocked by the peptide inhibitor WEHD-fmk. Here we identify the bacterial protease chlamydial protease-like activity factor (CPAF) as the factor mediating cleavage of golgin-84 and as the target of WEHD-fmk-inhibition. WEHD-fmk blocked cleavage of golgin-84 as well as cleavage of known CPAF targets during infection with C. trachomatis and C. pneumoniae. The same effect was seen when active CPAF was expressed in non-infected cells and in a cell-free system. Ectopic expression of active CPAF in non-infected cells was sufficient for GA fragmentation. GA fragmentation required the small GTPases Rab6 and Rab11 downstream of CPAF-activity. These results define CPAF as the first protein that is essential for replication of Chlamydia. We suggest that this role makes CPAF a potential anti-infective therapeutic target.

An experimental study of hydromagmatic fragmentation through energetic, non-explosive magma-water mixing

USGS Publications Warehouse

Mastin, L.G.; Spieler, O.; Downey, W.S.

2009-01-01

In this paper we report the first experimental investigation of non-explosive hydromagmatic fragmentation during energetic mixing with water. We mix magma and water by two methods: (1) pouring a basaltic melt between two converging water sprays; and (2) jetting basaltic melt at high pressure (3??MPa) through a nozzle into a tank of stagnant water. These experiments involved shear at relative velocities of ~ 5-16??m/s and vigorous mixing for less than a second, providing sufficient time for glassy rinds to grow but insufficient time for clot interiors to cool. In resulting fragments, we examined the gross morphology, which reflects fluid deformation during mixing, and surface textures, which reflect the growth and disruption of glassy rinds. We find major differences in both fragment morphology and surface texture between experiments. Water-spray experiments produced Pele's hair, thin bubble shards, melt droplets, and angular, fracture-bound droplet pieces. Melt-jet experiments produced mostly coarse (> 1??mm diameter), wavy fluidal fragments with broken ends. Fluidal surfaces of fragments produced by water-spray experiments were generally shiny under reflected light and, in microscopic examination, smooth down to micron scale, implying no disruption of glassy rinds, except for (a) rare flaking on Pele's hair that was bent prior to solidification; or (b) cracking and alligator-skin textures on segments of melt balls that had expanded before complete cooling. In contrast, textures of fluidal surfaces on fragments produced by melt-jet experiments are dull in reflected light and, in scanning electron images, exhibit ubiquitous discontinuous skins ("rinds") that are flaked, peeled, or smeared away in stripes. Adhering to these surfaces are flakes, blocks, and blobs of detached material microns to tens of microns in diameter. In the water-spray fragments, we interpret the scarcity of disrupted surface rinds to result from lack of bending after surfaces formed. In the

Advancement of magma fragmentation by inhomogeneous bubble distribution.

PubMed

Kameda, M; Ichihara, M; Maruyama, S; Kurokawa, N; Aoki, Y; Okumura, S; Uesugi, K

2017-12-01

Decompression times reported in previous studies suggest that thoroughly brittle fragmentation is unlikely in actual explosive volcanic eruptions. What occurs in practice is brittle-like fragmentation, which is defined as the solid-like fracture of a material whose bulk rheological properties are close to those of a fluid. Through laboratory experiments and numerical simulation, the link between the inhomogeneous structure of bubbles and the development of cracks that may lead to brittle-like fragmentation was clearly demonstrated here. A rapid decompression test was conducted to simulate the fragmentation of a specimen whose pore morphology was revealed by X-ray microtomography. The dynamic response during decompression was observed by high-speed photography. Large variation was observed in the responses of the specimens even among specimens with equal bulk rheological properties. The stress fields of the specimens under decompression computed by finite element analysis shows that the presence of satellite bubbles beneath a large bubble induced the stress concentration. On the basis of the obtained results, a new mechanism for brittle-like fragmentation is proposed. In the proposed scenario, the second nucleation of bubbles near the fragmentation surface is an essential process for the advancement of fragmentation in an upward magma flow in a volcanic conduit.

Producing the target seed: Seed collection, treatment, and storage

Treesearch

Robert P. Karrfalt

2011-01-01

The role of high quality seeds in producing target seedlings is reviewed. Basic seed handling and upgrading techniques are summarized. Current advances in seed science and technology as well as those on the horizon are discussed.

Meteorite Falls and the Fragmentation of Meteorites

NASA Technical Reports Server (NTRS)

Momeni, Daniel

2016-01-01

In order to understand the fragmentation of objects entering the atmosphere and why some produce more fragments than others, I have searched the Meteoritical Society database for meteorites greater than 20 kilograms that fell in the USA, China, and India. I also studied the video and film records of 21 fireballs that produced meteorites. A spreadsheet was prepared that noted smell, fireball, explosion, whistling, rumbling, the number of fragments, light, and impact sounds. Falls with large numbers of fragments were examined to look for common traits. These were: the Norton County aubrite, explosion and a flare greater than 100 fragments; the Forest City H5 chondrite explosion, a flare, a dust trail, 505 specimens; the Richardton H5 chondrite explosion and light, 71 specimens; the Juancheng H5 chondrite explosion, a rumbling, a flare, a dust trail,1000 specimens; the Tagish Lake C2 chondrite explosion, flare, dust trail, 500 specimens. I conclude that fragmentation is governed by the following: (1) Bigger meteors undergo more stress which results in more specimens; (2) Harder meteorites also require more force to break them up which will cause greater fragmentation; (3) Force and pressure are directly proportional during falls. General observations made were; (1) Meteorites produce fireballs sooner due to high friction; (2) Meteors tend to explode as well because of high stress; (3) Softer meteorites tend to cause dust trails; (4) Some falls produce light as they fall at high velocity. I am grateful to NASA Ames for this opportunity and Derek Sears, Katie Bryson, and Dan Ostrowski for discussions.

Mechanism-based Proteomic Screening Identifies Targets of Thioredoxin-like Proteins*

PubMed Central

Nakao, Lia S.; Everley, Robert A.; Marino, Stefano M.; Lo, Sze M.; de Souza, Luiz E.; Gygi, Steven P.; Gladyshev, Vadim N.

2015-01-01

Thioredoxin (Trx)-fold proteins are protagonists of numerous cellular pathways that are subject to thiol-based redox control. The best characterized regulator of thiols in proteins is Trx1 itself, which together with thioredoxin reductase 1 (TR1) and peroxiredoxins (Prxs) comprises a key redox regulatory system in mammalian cells. However, there are numerous other Trx-like proteins, whose functions and redox interactors are unknown. It is also unclear if the principles of Trx1-based redox control apply to these proteins. Here, we employed a proteomic strategy to four Trx-like proteins containing CXXC motifs, namely Trx1, Rdx12, Trx-like protein 1 (Txnl1) and nucleoredoxin 1 (Nrx1), whose cellular targets were trapped in vivo using mutant Trx-like proteins, under conditions of low endogenous expression of these proteins. Prxs were detected as key redox targets of Trx1, but this approach also supported the detection of TR1, which is the Trx1 reductant, as well as mitochondrial intermembrane proteins AIF and Mia40. In addition, glutathione peroxidase 4 was found to be a Rdx12 redox target. In contrast, no redox targets of Txnl1 and Nrx1 could be detected, suggesting that their CXXC motifs do not engage in mixed disulfides with cellular proteins. For some Trx-like proteins, the method allowed distinguishing redox and non-redox interactions. Parallel, comparative analyses of multiple thiol oxidoreductases revealed differences in the functions of their CXXC motifs, providing important insights into thiol-based redox control of cellular processes. PMID:25561728

Fragmentation of an aflatoxin-like gene cluster in a forest pathogen

USDA-ARS?s Scientific Manuscript database

Secondary metabolic pathway genes are typically clustered in fungi. An exception to this paradigm is seen for genes required for the production of dothistromin, an aflatoxin-like virulence factor produced by the pine needle pathogen Dothistroma septosporum. In contrast to the tight clustering of gen...

Towards a population synthesis model of self-gravitating disc fragmentation and tidal downsizing II: the effect of fragment-fragment interactions

NASA Astrophysics Data System (ADS)

Forgan, D. H.; Hall, C.; Meru, F.; Rice, W. K. M.

2018-03-01

It is likely that most protostellar systems undergo a brief phase where the protostellar disc is self-gravitating. If these discs are prone to fragmentation, then they are able to rapidly form objects that are initially of several Jupiter masses and larger. The fate of these disc fragments (and the fate of planetary bodies formed afterwards via core accretion) depends sensitively not only on the fragment's interaction with the disc, but also with its neighbouring fragments. We return to and revise our population synthesis model of self-gravitating disc fragmentation and tidal downsizing. Amongst other improvements, the model now directly incorporates fragment-fragment interactions while the disc is still present. We find that fragment-fragment scattering dominates the orbital evolution, even when we enforce rapid migration and inefficient gap formation. Compared to our previous model, we see a small increase in the number of terrestrial-type objects being formed, although their survival under tidal evolution is at best unclear. We also see evidence for disrupted fragments with evolved grain populations - this is circumstantial evidence for the formation of planetesimal belts, a phenomenon not seen in runs where fragment-fragment interactions are ignored. In spite of intense dynamical evolution, our population is dominated by massive giant planets and brown dwarfs at large semimajor axis, which direct imaging surveys should, but only rarely, detect. Finally, disc fragmentation is shown to be an efficient manufacturer of free-floating planetary mass objects, and the typical multiplicity of systems formed via gravitational instability will be low.

A fragmentation model of earthquake-like behavior in internet access activity

NASA Astrophysics Data System (ADS)

Paguirigan, Antonino A.; Angco, Marc Jordan G.; Bantang, Johnrob Y.

We present a fragmentation model that generates almost any inverse power-law size distribution, including dual-scaled versions, consistent with the underlying dynamics of systems with earthquake-like behavior. We apply the model to explain the dual-scaled power-law statistics observed in an Internet access dataset that covers more than 32 million requests. The non-Poissonian statistics of the requested data sizes m and the amount of time τ needed for complete processing are consistent with the Gutenberg-Richter-law. Inter-event times δt between subsequent requests are also shown to exhibit power-law distributions consistent with the generalized Omori law. Thus, the dataset is similar to the earthquake data except that two power-law regimes are observed. Using the proposed model, we are able to identify underlying dynamics responsible in generating the observed dual power-law distributions. The model is universal enough for its applicability to any physical and human dynamics that is limited by finite resources such as space, energy, time or opportunity.

Effect of isospin diffusion on the production of neutron-rich nuclei in multinucleon transfer reactions

NASA Astrophysics Data System (ADS)

Niu, Fei; Chen, Peng-Hui; Guo, Ya-Fei; Ma, Chun-Wang; Feng, Zhao-Qing

2018-03-01

The isospin dissipation dynamics in multinucleon transfer reactions has been investigated within the dinuclear system model. Production cross sections of neutron-rich isotopes around projectile-like and target-like fragments are estimated in collisions of Ni,6458+208Pb and 78.86,91Kr +198Pt near Coulomb barrier energies. The isospin diffusion in the nucleon transfer process is coupled to the dissipation of relative motion energy and angular momentum of colliding system. The available data of projectile-like fragments via multinucleon transfer reactions are nicely reproduced. It is found that the light projectile-like fragments are produced in the neutron-rich region because of the isospin equilibrium in two colliding nuclei. However, the heavy target-like fragments tend to be formed on the neutron-poor side above the β -stability line. The neutron-rich projectiles move the maximal yields of heavy nuclei to the neutron-rich domain and are available for producing the heavy exotic isotopes, in particular around the neutron shell closure of N =126 .

Solution NMR Spectroscopy in Target-Based Drug Discovery.

PubMed

Li, Yan; Kang, Congbao

2017-08-23

Solution NMR spectroscopy is a powerful tool to study protein structures and dynamics under physiological conditions. This technique is particularly useful in target-based drug discovery projects as it provides protein-ligand binding information in solution. Accumulated studies have shown that NMR will play more and more important roles in multiple steps of the drug discovery process. In a fragment-based drug discovery process, ligand-observed and protein-observed NMR spectroscopy can be applied to screen fragments with low binding affinities. The screened fragments can be further optimized into drug-like molecules. In combination with other biophysical techniques, NMR will guide structure-based drug discovery. In this review, we describe the possible roles of NMR spectroscopy in drug discovery. We also illustrate the challenges encountered in the drug discovery process. We include several examples demonstrating the roles of NMR in target-based drug discoveries such as hit identification, ranking ligand binding affinities, and mapping the ligand binding site. We also speculate the possible roles of NMR in target engagement based on recent processes in in-cell NMR spectroscopy.

Research on the photoelectric measuring method of warhead fragment velocity

NASA Astrophysics Data System (ADS)

Liu, Ji; Yu, Lixia; Zhang, Bin; Liu, Xiaoyan

2016-09-01

The velocity of warhead fragment is the key criteria to determine its mutilation efficiency. But owing to the small size, larger quantity, irregular shape, high speed, arbitrary direction, large dispersion of warhead fragment and adverse environment, the test of fragment velocity parameter is very difficult. The paper designed an optoelectronic system to measure the average velocity of warhead fragments accurately. The apparatus included two parallel laser screens spaced apart at a known fixed distance for providing time measurement between start and stop signals. The large effective screen area was composed of laser source, retro-reflector and large area photo-diode. Whenever a moving fragment interrupted two optical screens, the system would generate a target signal. Due to partial obscuration of the incident energy and the poor test condition of the explosion, fragment target signal is easily disturbed. Therefore, fragments signal processing technology has become a key technology of the system. The noise of signal was reduced by employing wavelet decomposition and reconstruction. The time of fragment passing though the target was obtained by adopting peak detection algorithm. Based on the method of search peak in different width scale and waveform trend by using optima wavelet, the problem of rolling waveform was solved. Lots of fragments experiments of the different types of the warheads were conducted. Experimental results show that: warhead fragments capture rate of system is better than 98%, which can give velocity of each fragment in the density of less than 20 pieces per m2.

The fragmentation of 510 MeV/nucleon iron-56 in polyethylene. I. Fragment fluence spectra

NASA Technical Reports Server (NTRS)

Zeitlin, C.; Miller, J.; Heilbronn, L.; Frankel, K.; Gong, W.; Schimmerling, W.

1996-01-01

The fragmentation of 510 MeV/nucleon iron ions in several thicknesses of polyethylene has been measured. Non-interacting primary beam particles and fragments have been identified and their LETs calculated by measuring ionization energy loss in a stack of silicon detectors. Fluences, normalized to the incident beam intensity and corrected for detector effects, are presented for each fragment charge and target. Histograms of fluence as a function of LET are also presented. Some implications of these data for measurements of the biological effects of heavy ions are discussed.

Polo-like kinase 1, a new therapeutic target in hepatocellular carcinoma

PubMed Central

Mok, Wei Chuen; Wasser, Shanthi; Tan, Theresa; Lim, Seng Gee

2012-01-01

AIM: To investigate the role of polo-like kinase 1 (PLK1) as a therapeutic target for hepatocellular carcinoma (HCC). METHODS: PLK1 gene expression was evaluated in HCC tissue and HCC cell lines. Gene knockdown with short-interfering RNA (siRNA) was used to study PLK1 gene and protein expression using real-time reverse transcription polymerase chain reaction (RT-PCR) and Western blotting, and cell proliferation using 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2(4-sulfophenyl)-2H-tetrazolium (MTS) and bromodeoxyuridine (BrdU) assays. Apoptosis was evaluated using the terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay, and caspase-inhibition assay. Huh-7 cells were transplanted into nude mice and co-cultured with PLK1 siRNA or control siRNA, and tumor progression was compared with controls. RESULTS: RT-PCR showed that PLK1 was overexpressed 12-fold in tumor samples compared with controls, and also was overexpressed in Huh-7 cells. siRNA against PLK1 showed a reduction in PLK1 gene and protein expression of up to 96% in Huh-7 cells, and a reduction in cell proliferation by 68% and 92% in MTS and BrdU cell proliferation assays, respectively. There was a 3-fold increase in apoptosis events, and TUNEL staining and caspase-3 assays suggested that this was caspase-independent. The pan-caspase inhibitor Z-VAD-FMK was unable to rescue the apoptotic cells. Immnofluorescence co-localized endonuclease-G to fragmented chromosomes, implicating it in apoptosis. Huh-7 cells transplanted subcutaneously into nude mice showed tumor regression in siPLK1-treated mice, but not in controls. CONCLUSION: Knockdown of PLK1 overexpression in HCC was shown to be a potential therapeutic target, leading to apoptosis through the endonuclease-G pathway. PMID:22826617

Using In Silico Fragmentation to Improve Routine Residue Screening in Complex Matrices.

PubMed

Kaufmann, Anton; Butcher, Patrick; Maden, Kathryn; Walker, Stephan; Widmer, Mirjam

2017-12-01

Targeted residue screening requires the use of reference substances in order to identify potential residues. This becomes a difficult issue when using multi-residue methods capable of analyzing several hundreds of analytes. Therefore, the capability of in silico fragmentation based on a structure database ("suspect screening") instead of physical reference substances for routine targeted residue screening was investigated. The detection of fragment ions that can be predicted or explained by in silico software was utilized to reduce the number of false positives. These "proof of principle" experiments were done with a tool that is integrated into a commercial MS vendor instrument operating software (UNIFI) as well as with a platform-independent MS tool (Mass Frontier). A total of 97 analytes belonging to different chemical families were separated by reversed phase liquid chromatography and detected in a data-independent acquisition (DIA) mode using ion mobility hyphenated with quadrupole time of flight mass spectrometry. The instrument was operated in the MS E mode with alternating low and high energy traces. The fragments observed from product ion spectra were investigated using a "chopping" bond disconnection algorithm and a rule-based algorithm. The bond disconnection algorithm clearly explained more analyte product ions and a greater percentage of the spectral abundance than the rule-based software (92 out of the 97 compounds produced ≥1 explainable fragment ions). On the other hand, tests with a complex blank matrix (bovine liver extract) indicated that the chopping algorithm reports significantly more false positive fragments than the rule based software. Graphical Abstract.

Using In Silico Fragmentation to Improve Routine Residue Screening in Complex Matrices

NASA Astrophysics Data System (ADS)

Kaufmann, Anton; Butcher, Patrick; Maden, Kathryn; Walker, Stephan; Widmer, Mirjam

2017-12-01

Targeted residue screening requires the use of reference substances in order to identify potential residues. This becomes a difficult issue when using multi-residue methods capable of analyzing several hundreds of analytes. Therefore, the capability of in silico fragmentation based on a structure database ("suspect screening") instead of physical reference substances for routine targeted residue screening was investigated. The detection of fragment ions that can be predicted or explained by in silico software was utilized to reduce the number of false positives. These "proof of principle" experiments were done with a tool that is integrated into a commercial MS vendor instrument operating software (UNIFI) as well as with a platform-independent MS tool (Mass Frontier). A total of 97 analytes belonging to different chemical families were separated by reversed phase liquid chromatography and detected in a data-independent acquisition (DIA) mode using ion mobility hyphenated with quadrupole time of flight mass spectrometry. The instrument was operated in the MSE mode with alternating low and high energy traces. The fragments observed from product ion spectra were investigated using a "chopping" bond disconnection algorithm and a rule-based algorithm. The bond disconnection algorithm clearly explained more analyte product ions and a greater percentage of the spectral abundance than the rule-based software (92 out of the 97 compounds produced ≥1 explainable fragment ions). On the other hand, tests with a complex blank matrix (bovine liver extract) indicated that the chopping algorithm reports significantly more false positive fragments than the rule based software. [Figure not available: see fulltext.

Quantum control of molecular fragmentation in strong laser fields

NASA Astrophysics Data System (ADS)

Zohrabi, Mohammad

Present advances in laser technology allow the production of ultrashort (<˜5 fs, approaching single cycle at 800 nm), intense tabletop laser pulses. At these high intensities laser-matter interactions cannot be described with perturbation theory since multiphoton processes are involved. This is in contrast to photodissociation by the absorption of a single photon, which is well described by perturbation theory. For example, at high intensities (<˜5x1013 W/cm2) the fragmentation of molecular hydrogen ions has been observed via the absorption of three or more photons. In another example, an intriguing dissociation mechanism has been observed where molecular hydrogen ions seem to fragment by apparently absorbing no photons. This is actually a two photon process, photoabsorption followed by stimulated emission, resulting in low energy fragments. We are interested in exploring these kinds of multiphoton processes. Our research group has studied the dynamics and control of fragmentation induced by strong laser fields in a variety of molecular targets. The main goal is to provide a basic understanding of fragmentation mechanisms and possible control schemes of benchmark systems such as H2+. This knowledge is further extended to more complex systems like the benchmark H3+ polyatomic and other molecules. In this dissertation, we report research based on two types of experiments. In the first part, we describe laser-induced fragmentation of molecular ion-beam targets. In the latter part, we discuss the formation of highly-excited neutral fragments from hydrogen molecules using ultrashort laser pulses. In carrying out these experiments, we have also extended experimental techniques beyond their previous capabilities. We have performed a few experiments to advance our understanding of laser-induced fragmentation of molecular-ion beams. For instance, we explored vibrationally resolved spectra of O2+ dissociation using various wavelengths. We observed a vibrational suppression

Mass spectrometry for fragment screening.

PubMed

Chan, Daniel Shiu-Hin; Whitehouse, Andrew J; Coyne, Anthony G; Abell, Chris

2017-11-08

Fragment-based approaches in chemical biology and drug discovery have been widely adopted worldwide in both academia and industry. Fragment hits tend to interact weakly with their targets, necessitating the use of sensitive biophysical techniques to detect their binding. Common fragment screening techniques include differential scanning fluorimetry (DSF) and ligand-observed NMR. Validation and characterization of hits is usually performed using a combination of protein-observed NMR, isothermal titration calorimetry (ITC) and X-ray crystallography. In this context, MS is a relatively underutilized technique in fragment screening for drug discovery. MS-based techniques have the advantage of high sensitivity, low sample consumption and being label-free. This review highlights recent examples of the emerging use of MS-based techniques in fragment screening. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Investigation of Source of Irritant Gas Produced by PATRIOT Missile System Air Conditioners

DTIC Science & Technology

1986-03-31

is the mass fragment CF3 . It is a common fragment of perfluorinated hydrocarbons, and is found to be present in most of the compounds detected by...used would allow detection of the target par3meters acrolein, aromatics, a broad range of organic compounds ,. formaldehyde, and hydrogen cyanide...organic compounds were observed. Thus, aromatic organic compounds were not produced by or from any of the four new units tested. 4 1CZ 3) With the

rRNA fragmentation induced by a yeast killer toxin.

PubMed

Kast, Alene; Klassen, Roland; Meinhardt, Friedhelm

2014-02-01

Virus like dsDNA elements (VLE) in yeast were previously shown to encode the killer toxins PaT and zymocin, which target distinct tRNA species via specific anticodon nuclease (ACNase) activities. Here, we characterize a third member of the VLE-encoded toxins, PiT from Pichia inositovora, and identify PiOrf4 as the cytotoxic subunit by conditional expression in Saccharomyces cerevisiae. In contrast to the tRNA targeting toxins, however, neither a change of the wobble uridine modification status by introduction of elp3 or trm9 mutations nor tRNA overexpression rescued from PiOrf4 toxicity. Consistent with a distinct RNA target, expression of PiOrf4 causes specific fragmentation of the 25S and 18S rRNA. A stable cleavage product comprising the first ∼ 130 nucleotides of the 18S rRNA was purified and characterized by linker ligation and subsequent reverse transcription; 3'-termini were mapped to nucleotide 131 and 132 of the 18S rRNA sequence, a region showing some similarity to the anticodon loop of tRNA(Glu)(UUC), the zymocin target. PiOrf4 residues Glu9 and His214, corresponding to catalytic sites Glu9 and His209 in the ACNase subunit of zymocin are essential for in vivo toxicity and rRNA fragmentation, raising the possibility of functionally conserved RNase modules in both proteins. © 2013 John Wiley & Sons Ltd.

Readability of HIV/AIDS educational materials: the role of the medium of communication, target audience, and producer characteristics.

PubMed

Wells, J A

1994-12-01

The reading difficulty of many HIV/AIDS brochures and pamphlets limits their effectiveness. This analysis addresses correlates of readability in 136 HIV/AIDS educational items. Readability is measured using the SMOG Index. The medium of communication is significantly related to readability: comic books and brochures are, on average, more readable than books and pamphlets (10.9 versus 11.9). The target audience also differentiates readability. Materials for HIV antibody test seekers, the general community, and sexually active adults have a more difficult reading grade, averaging 12.1, whereas materials for ethnic minorities average a more readable 9.2. The producer organization's type and location are unrelated to readability, but an AIDS-specific organizational focus correlates with better readability (grade 10.8 vs. 11.8). These findings remain significant in multivariate analysis. The results indicate that brochures and comics are more likely to be comprehended by low-literacy populations, that an understanding of the literacy of target audiences is needed to produce materials with appropriate reading levels, and that policies to influence producer organizations may result in the creation of more readable materials.

Fragmentation studies of relativistic iron ions using plastic nuclear track detectors.

PubMed

Scampoli, P; Durante, M; Grossi, G; Manti, L; Pugliese, M; Gialanella, G

2005-01-01

We measured fluence and fragmentation of high-energy (1 or 5 A GeV) 56Fe ions accelerated at the Alternating Gradient Synchrotron or at the NASA Space Radiation Laboratory (Brookhaven National Laboratory, NY, USA) using solid-state CR-39 nuclear track detectors. Different targets (polyethylene, PMMA, C, Al, Pb) were used to produce a large spectrum of charged fragments. CR-39 plastics were exposed both in front and behind the shielding block (thickness ranging from 5 to 30 g/cm2) at a normal incidence and low fluence. The radiation dose deposited by surviving Fe ions and charged fragments was measured behind the shield using an ionization chamber. The distribution of the measured track size was exploited to distinguish the primary 56Fe ions tracks from the lighter fragments. Measurements of projectile's fluence in front of the shield were used to determine the dose per incident particle behind the block. Simultaneous measurements of primary 56Fe ion tracks in front and behind the shield were used to evaluate the fraction of surviving iron projectiles and the total charge-changing fragmentation cross-section. These physical measurements will be used to characterize the beam used in parallel biological experiments. c2005 COSPAR. Published by Elsevier Ltd. All rights reserved.

Understanding the Physical Structure of the Comet Shoemaker-Levy 9 Fragments

NASA Astrophysics Data System (ADS)

Rettig, Terrence

2000-07-01

Images of the fragmented comet Shoemaker-Levy 9 {SL9} as it approached Jupiter in 1994 provided a unique opportunity to {1} probe the comae, {2} understand the structure of the 20 cometary objects, and {3} provide limits on the Jovian impact parameters. The primary cometary questions were: how were the fragments formed and what was their central structure? There still remains a diversity of opinion regarding the structure of the 21 comet-like fragments as well as the specifics of the disruption event itself. We have shown from Monte Carlo modeling of surface brightness profiles that SL9 fragments had unusual dust size distributions and outflow velocities. Further work of a preliminary nature showed some of the central reflecting area excesses derived from surface brightness profile fitting {w/psf} appeared distributed rather than centrally concentrated as would be expected for comet- like objects, some central excesses were negative and also, the excesses could vary with time. With an improved coma subtraction technique we propose to model each coma surface brightness profile, extract central reflecting areas or central brightness excesses for the non-star-contaminated WFPC-2 SL9, to determine the behavior and characteristics of the central excesses as the fragments approached Jupiter. A second phase of the proposal will be to use numerical techniques {in conjunction with D. Richardson} to investigate the various fragment models. This is a difficult modeling process that will allow us to model the structure and physical characteristics of the fragments and thus constrain parameters for the Jovian impact events. The results will be used to constrain the structure of the central fragment cores of SL9 and how the observed dust comae were produced. The results will provide evidence to discriminate between the parent nucleus models {i.e., were the fragments solid objects or swarms of particles?} and provide better constraints on the atmospheric impact models. The

A Recombinant Human Anti-Platelet scFv Antibody Produced in Pichia pastoris for Atheroma Targeting

PubMed Central

Vallet-Courbin, Amelie; Larivière, Mélusine; Hocquellet, Agnès; Hemadou, Audrey; Parimala, Sarjapura-Nagaraja; Laroche-Traineau, Jeanny; Santarelli, Xavier; Clofent-Sanchez, Gisèle; Jacobin-Valat, Marie-Josée; Noubhani, Abdelmajid

2017-01-01

Cells of the innate and adaptive immune system are key factors in the progression of atherosclerotic plaque, leading to plaque instability and rupture, potentially resulting in acute atherothrombotic events such as coronary artery disease, cerebrovascular disease and peripheral arterial disease. Here, we describe the cloning, expression, purification, and immunoreactivity assessment of a recombinant single-chain variable fragment (scFv) derived from a human anti-αIIbβ3 antibody (HuAb) selected to target atheromatous lesions for the presence of platelets. Indeed, platelets within atheroma plaques have been shown to play a role in inflammation, in platelet-leucocyte aggregates and in thrombi formation and might thus be considered relevant biomarkers of atherosclerotic progression. The DNA sequence that encodes the anti-αIIbβ3 TEG4 scFv previously obtained from a phage-display selection on activated platelets, was inserted into the eukaryote vector (pPICZαA) in fusion with a tag sequence encoding 2 cysteines useable for specific probes grafting experiments. The recombinant protein was expressed at high yields in Pichia pastoris (30 mg/L culture). The advantage of P. pastoris as an expression system is the production and secretion of recombinant proteins in the supernatant, ruling out the difficulties encountered when scFv are produced in the cytoplasm of bacteria (low yield, low solubility and reduced affinity). The improved conditions allowed for the recovery of highly purified and biologically active scFv fragments ready to be grafted in a site-directed way to nanoparticles for the imaging of atherosclerotic plaques involving inflammatory processes and thus at high risk of instability. PMID:28125612

In vivo characterization of the novel CD44v6-targeting Fab fragment AbD15179 for molecular imaging of squamous cell carcinoma: a dual-isotope study

PubMed Central

2014-01-01

Background Patients with squamous cell carcinoma in the head and neck region (HNSCC) offer a diagnostic challenge due to difficulties to detect small tumours and metastases. Imaging methods available are not sufficient, and radio-immunodiagnostics could increase specificity and sensitivity of diagnostics. The objective of this study was to evaluate, for the first time, the in vivo properties of the radiolabelled CD44v6-targeting fragment AbD15179 and to assess its utility as a targeting agent for radio-immunodiagnostics of CD44v6-expressing tumours. Methods The fully human CD44v6-targeting Fab fragment AbD15179 was labelled with 111In or 125I, as models for radionuclides suitable for imaging with SPECT or PET. Species specificity, antigen specificity and internalization properties were first assessed in vitro. In vivo specificity and biodistribution were then evaluated in tumour-bearing mice using a dual-tumour and dual-isotope setup. Results Both species-specific and antigen-specific binding of the conjugates were demonstrated in vitro, with no detectable internalization. The in vivo studies demonstrated specific tumour binding and favourable tumour targeting properties for both conjugates, albeit with higher tumour uptake, slower tumour dissociation, higher tumour-to-blood ratio and higher CD44v6 sensitivity for the 111In-labelled fragment. In contrast, the 125I-Fab demonstrated more favourable tumour-to-organ ratios for liver, spleen and kidneys. Conclusions We conclude that AbD15179 efficiently targets CD44v6-expressing squamous cell carcinoma xenografts, and particularly, the 111In-Fab displayed high and specific tumour uptake. CD44v6 emerges as a suitable target for radio-immunodiagnostics, and a fully human antibody fragment such as AbD15179 can enable further clinical imaging studies. PMID:24598405

Chameleon fragmentation

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

Brax, Philippe; Upadhye, Amol, E-mail: philippe.brax@cea.fr, E-mail: aupadhye@anl.gov

2014-02-01

A scalar field dark energy candidate could couple to ordinary matter and photons, enabling its detection in laboratory experiments. Here we study the quantum properties of the chameleon field, one such dark energy candidate, in an ''afterglow'' experiment designed to produce, trap, and detect chameleon particles. In particular, we investigate the possible fragmentation of a beam of chameleon particles into multiple particle states due to the highly non-linear interaction terms in the chameleon Lagrangian. Fragmentation could weaken the constraints of an afterglow experiment by reducing the energy of the regenerated photons, but this energy reduction also provides a unique signaturemore » which could be detected by a properly-designed experiment. We show that constraints from the CHASE experiment are essentially unaffected by fragmentation for φ{sup 4} and 1/φ potentials, but are weakened for steeper potentials, and we discuss possible future afterglow experiments.« less

Fragment Impact Toolkit (FIT)

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

Shevitz, Daniel Wolf; Key, Brian P.; Garcia, Daniel B.

2017-09-05

The Fragment Impact Toolkit (FIT) is a software package used for probabilistic consequence evaluation of fragmenting sources. The typical use case for FIT is to simulate an exploding shell and evaluate the consequence on nearby objects. FIT is written in the programming language Python and is designed as a collection of interacting software modules. Each module has a function that interacts with the other modules to produce desired results.

Velocity distribution of fragments of catastrophic impacts

NASA Technical Reports Server (NTRS)

Takagi, Yasuhiko; Kato, Manabu; Mizutani, Hitoshi

1992-01-01

Three dimensional velocities of fragments produced by laboratory impact experiments were measured for basalts and pyrophyllites. The velocity distribution of fragments obtained shows that the velocity range of the major fragments is rather narrow, at most within a factor of 3 and that no clear dependence of velocity on the fragment mass is observed. The NonDimensional Impact Stress (NDIS) defined by Mizutani et al. (1990) is found to be an appropriate scaling parameter to describe the overall fragment velocity as well as the antipodal velocity.

Concise Review: Emerging Drugs Targeting Epithelial Cancer Stem-Like Cells.

PubMed

Ahmed, Mehreen; Chaudhari, Kritika; Babaei-Jadidi, Roya; Dekker, Lodewijk V; Shams Nateri, Abdolrahman

2017-04-01

Increasing evidence suggests that cancer cell populations contain a small proportion of cells that display stem-like cell properties and which may be responsible for overall tumor maintenance. These cancer stem-like cells (CSCs) appear to have unique tumor-initiating ability and innate survival mechanisms that allow them to resist cancer therapies, consequently promoting relapses. Selective targeting of CSCs may provide therapeutic benefit and several recent reports have indicated this may be possible. In this article, we review drugs targeting CSCs, in selected epithelial cell-derived cancers. Stem Cells 2017;35:839-850. © 2017 AlphaMed Press.

The ways and means of fragment-based drug design.

PubMed

Doak, Bradley C; Norton, Raymond S; Scanlon, Martin J

2016-11-01

Fragment-based drug design (FBDD) has emerged as a mainstream approach for the rapid and efficient identification of building blocks that can be used to develop high-affinity ligands against protein targets. One of the strengths of FBDD is the relative ease and low cost of the primary screen to identify fragments that bind. However, the fragments that emerge from primary screens often have low affinities, with K D values in the high μM to mM range, and a significant challenge for FBDD is to develop the initial fragments into more potent ligands. Successful fragment elaboration often requires co-structures of the fragments bound to their target proteins, as well as a range of biophysical and biochemical assays to track potency and efficacy. These challenges have led to the development of specific chemical strategies for the elaboration of weakly-binding fragments into more potent "hits" and lead compounds. In this article we review different approaches that have been employed to meet these challenges and describe some of the strategies that have resulted in several fragment-derived compounds entering clinical trials. Copyright © 2016 Elsevier Inc. All rights reserved.

Microhydration Prevents Fragmentation of Uracil and Thymine by Low-Energy Electrons.

PubMed

Kočišek, J; Pysanenko, A; Fárník, M; Fedor, J

2016-09-01

When ionizing radiation passes biological matter, a large number of secondary electrons with very low energies (<3 eV) is produced. It is known that such electrons cause an efficient fragmentation of isolated nucleobases via dissociative electron attachment. We present an experimental study of the electron attachment to microhydrated nucleobases. Our novel approach allows significant control over the hydration of molecules studied in the molecular beam. We directly show for the first time that the presence of a few water molecules suppresses the dissociative channel and leads exclusively to formation of intact molecular and hydrated anions. The suppression of fragmentation is ascribed to caging-like effects and fast energy transfer to the solvent. This is in contrast with theoretical prediction that microhydration strongly enhances the fragmentation of nucleobases. The current observation impacts mechanisms of reductive DNA strand breaks proposed to date on the basis of gas-phase experiments.

MaRaCluster: A Fragment Rarity Metric for Clustering Fragment Spectra in Shotgun Proteomics.

PubMed

The, Matthew; Käll, Lukas

2016-03-04

Shotgun proteomics experiments generate large amounts of fragment spectra as primary data, normally with high redundancy between and within experiments. Here, we have devised a clustering technique to identify fragment spectra stemming from the same species of peptide. This is a powerful alternative method to traditional search engines for analyzing spectra, specifically useful for larger scale mass spectrometry studies. As an aid in this process, we propose a distance calculation relying on the rarity of experimental fragment peaks, following the intuition that peaks shared by only a few spectra offer more evidence than peaks shared by a large number of spectra. We used this distance calculation and a complete-linkage scheme to cluster data from a recent large-scale mass spectrometry-based study. The clusterings produced by our method have up to 40% more identified peptides for their consensus spectra compared to those produced by the previous state-of-the-art method. We see that our method would advance the construction of spectral libraries as well as serve as a tool for mining large sets of fragment spectra. The source code and Ubuntu binary packages are available at https://github.com/statisticalbiotechnology/maracluster (under an Apache 2.0 license).

Mineral-produced high-pressure striae and clay polish: Key evidence for nonballistic transport of ejecta from Ries crater

USGS Publications Warehouse

Chao, E.C.T.

1976-01-01

Recently discovered mineral-produced, deeply incised striae and mirror-like polish on broken surfaces of limestone fragments from the sedimentary ejecta of the Ries impact crater of southern Germany are described. The striae and polish were produced under high confining pressures during high-velocity nonballistic transport of the ejecta mass within the time span of the cratering event (measured in terms of seconds). The striae on these fragments were produced by scouring by small mineral grains embedded in the surrounding clay matrix, and the polish was formed under the same condition, by movements of relatively fragment-free clay against the fragment surfaces. The occurrence of these striae and polish is key evidence for estimating the distribution and determining the relative importance of nonballistic and ballistic transport of ejecta from the shallow Ries stony meteorite impact crater.

Fragmentation of Electrospray-produced Deprotonated Ions of Oligodeoxyribonucleotides Containing an Alkylated or Oxidized Thymidine

PubMed Central

Wang, Pengcheng; Williams, Renee T.; Guerrero, Candace R.; Ji, Debin; Wang, Yinsheng

2014-01-01

Alkylation and oxidation constitute major routes of DNA damage induced by endogenous and exogenous genotoxic agents. Understanding the biological consequences of DNA lesions often necessitates the availability of oligodeoxyribonucleotide (ODN) substrates harboring these lesions, and sensitive and robust methods for validating the identities of these ODNs. Tandem mass spectrometry is well suited for meeting these latter analytical needs. In the present study, we evaluated how the incorporation of an ethyl group to different positions (i.e., O2, N3 and O4) of thymine and the oxidation of its 5-methyl carbon impact collisionally activated dissociation (CAD) pathways of electrospray-produced deprotonated ions of ODNs harboring these thymine modifications. Unlike an unmodified thymine, which often manifests poor cleavage of the C3′-O3′ bond, the incorporation of an alkyl group to the O2 position and, to a much lesser extent, the O4 position, but not the N3 position of thymine, led to facile cleavage of the C3′-O3′ bond on the 3′ side of the modified thymine. Similar efficient chain cleavage was observed when thymine was oxidized to 5-formyluracil or 5-carboxyluracil, but not 5-hydroxymethyluracil. Additionally, with the support of computational modeling, we revealed that proton affinity and acidity of the modified nucleobases govern the fragmentation of ODNs containing the alkylated and oxidized thymidine derivatives, respectively. These results provided important insights into the effects of thymine modifications on ODN fragmentation. PMID:24664806

Experiences in fragment-based drug discovery.

PubMed

Murray, Christopher W; Verdonk, Marcel L; Rees, David C

2012-05-01

Fragment-based drug discovery (FBDD) has become established in both industry and academia as an alternative approach to high-throughput screening for the generation of chemical leads for drug targets. In FBDD, specialised detection methods are used to identify small chemical compounds (fragments) that bind to the drug target, and structural biology is usually employed to establish their binding mode and to facilitate their optimisation. In this article, we present three recent and successful case histories in FBDD. We then re-examine the key concepts and challenges of FBDD with particular emphasis on recent literature and our own experience from a substantial number of FBDD applications. Our opinion is that careful application of FBDD is living up to its promise of delivering high quality leads with good physical properties and that in future many drug molecules will be derived from fragment-based approaches. Copyright © 2012 Elsevier Ltd. All rights reserved.

Simulation of dependence of the cross section of deuterons beam fragmentation into cumulative pions and protons on the mass of the target nucleus

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

Litvinenko, A. G., E-mail: alitvin@jinr.ru; Litvinenko, E. I.

2015-03-15

We have studied the mechanisms influencing production of cumulative pions and protons in the fragmentation of the incident deuterons into cumulative pions and protons emitted at zero angle. We argue that the peripheral dependence on the atomic mass of the target nucleus, which was obtained in the experiments for medium and heavy nuclei, can be explained by scattering on target nucleons without introducing additional parameters.

Fragment-based protein-protein interaction antagonists of a viral dimeric protease

PubMed Central

Gable, Jonathan E.; Lee, Gregory M.; Acker, Timothy M.; Hulce, Kaitlin R.; Gonzalez, Eric R.; Schweigler, Patrick; Melkko, Samu; Farady, Christopher J.; Craik, Charles S.

2016-01-01

Fragment-based drug discovery has shown promise as an approach for challenging targets such as protein-protein interfaces. We developed and applied an activity-based fragment screen against dimeric Kaposi’s sarcoma-associated herpesvirus protease (KSHV Pr) using an optimized fluorogenic substrate. Dose response determination was performed as a confirmation screen and NMR spectroscopy was used to map fragment inhibitor binding to KSHV Pr. Kinetic assays demonstrated that several initial hits also inhibit human cytomegalovirus protease (HCMV Pr). Binding of these hits to HCMV Pr was also confirmed via NMR spectroscopy. Despite the use of a target-agnostic fragment library, more than 80% of confirmed hits disrupted dimerization and bound to a previously reported pocket at the dimer interface of KSHV Pr, not to the active site. One class of fragments, an aminothiazole scaffold, was further explored using commercially available analogs. These compounds demonstrated greater than 100-fold improvement of inhibition. This study illustrates the power of fragment-based screening for these challenging enzymatic targets and provides an example of the potential druggability of pockets at protein-protein interfaces. PMID:26822284

Recovery of uranium from an irradiated solid target after removal of molybdenum-99 produced from the irradiated target

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

Reilly, Sean Douglas; May, Iain; Copping, Roy

A process for minimizing waste and maximizing utilization of uranium involves recovering uranium from an irradiated solid target after separating the medical isotope product, molybdenum-99, produced from the irradiated target. The process includes irradiating a solid target comprising uranium to produce fission products comprising molybdenum-99, and thereafter dissolving the target and conditioning the solution to prepare an aqueous nitric acid solution containing irradiated uranium. The acidic solution is then contacted with a solid sorbent whereby molybdenum-99 remains adsorbed to the sorbent for subsequent recovery. The uranium passes through the sorbent. The concentrations of acid and uranium are then adjusted tomore » concentrations suitable for crystallization of uranyl nitrate hydrates. After inducing the crystallization, the uranyl nitrate hydrates are separated from a supernatant. The process results in the purification of uranyl nitrate hydrates from fission products and other contaminants. The uranium is therefore available for reuse, storage, or disposal.« less

A simplified model for the assessment of the impact probability of fragments.

PubMed

Gubinelli, Gianfilippo; Zanelli, Severino; Cozzani, Valerio

2004-12-31

A model was developed for the assessment of fragment impact probability on a target vessel, following the collapse and fragmentation of a primary vessel due to internal pressure. The model provides the probability of impact of a fragment with defined shape, mass and initial velocity on a target of a known shape and at a given position with respect to the source point. The model is based on the ballistic analysis of the fragment trajectory and on the determination of impact probabilities by the analysis of initial direction of fragment flight. The model was validated using available literature data.

Big dynorphin, a prodynorphin-derived peptide produces NMDA receptor-mediated effects on memory, anxiolytic-like and locomotor behavior in mice.

PubMed

Kuzmin, Alexander; Madjid, Nather; Terenius, Lars; Ogren, Sven Ove; Bakalkin, Georgy

2006-09-01

Effects of big dynorphin (Big Dyn), a prodynorphin-derived peptide consisting of dynorphin A (Dyn A) and dynorphin B (Dyn B) on memory function, anxiety, and locomotor activity were studied in mice and compared to those of Dyn A and Dyn B. All peptides administered i.c.v. increased step-through latency in the passive avoidance test with the maximum effective doses of 2.5, 0.005, and 0.7 nmol/animal, respectively. Effects of Big Dyn were inhibited by MK 801 (0.1 mg/kg), an NMDA ion-channel blocker whereas those of dynorphins A and B were blocked by the kappa-opioid antagonist nor-binaltorphimine (6 mg/kg). Big Dyn (2.5 nmol) enhanced locomotor activity in the open field test and induced anxiolytic-like behavior both effects blocked by MK 801. No changes in locomotor activity and no signs of anxiolytic-like behavior were produced by dynorphins A and B. Big Dyn (2.5 nmol) increased time spent in the open branches of the elevated plus maze apparatus with no changes in general locomotion. Whereas dynorphins A and B (i.c.v., 0.05 and 7 nmol/animal, respectively) produced analgesia in the hot-plate test Big Dyn did not. Thus, Big Dyn differs from its fragments dynorphins A and B in its unique pattern of memory enhancing, locomotor- and anxiolytic-like effects that are sensitive to the NMDA receptor blockade. The findings suggest that Big Dyn has its own function in the brain different from those of the prodynorphin-derived peptides acting through kappa-opioid receptors.

Charge-to-mass dispersion methods for abrasion-ablation fragmentation models

NASA Technical Reports Server (NTRS)

Townsend, L. W.; Norbury, J. W.

1985-01-01

Methods to describe the charge-to-mass dispersion distributions of projectile prefragments are presented and used to determine individual isotope cross-sections or various elements produced in the fragmentation of relativistic argon nuclei by carbon targets. Although slight improvements in predicted cross-sections are obtained for the quantum mechanical giant dipole resonance (GDR) distribution when compared qith the predictions of the geometric GDR model, the closest agreement between theory and experiment continues to be obtained with the simple hypergeometric distribution, which treats the nucleons in the nucleus as completely uncorrelated.

Target fragments in collisions of 1.8 GeV/nucleon Fe-56 nuclei with photoemulsion nuclei, and the cascade-evaporation model

NASA Technical Reports Server (NTRS)

Dudkin, V. E.; Kovalev, E. E.; Nefedov, N. A.; Antonchik, V. A.; Bogdanov, S. D.; Ostroumov, V. I.; Benton, E. V.; Crawford, H. J.

1995-01-01

Nuclear photographic emulsion is used to study the dependence of the characteristics of target-nucleus fragments on the masses and impact parameters of interacting nuclei. The data obtained are compared in all details with the calculation results made in terms of the Dubna version of the cascade-evaporation model (DCM).

Fab fragment labeled with ICG-derivative for detecting digestive tract cancer.

PubMed

Yano, Hiromi; Muguruma, Naoki; Ito, Susumu; Aoyagi, Eriko; Kimura, Tetsuo; Imoto, Yoshitaka; Cao, Jianxin; Inoue, Shohei; Sano, Shigeki; Nagao, Yoshimitsu; Kido, Hiroshi

2006-09-01

In previous studies, we generated infrared ray fluorescence-labeled monoclonal antibodies and developed an infrared ray fluorescence endoscope capable of detecting the monoclonal antibodies to establish a novel diagnostic technique for gastrointestinal cancer. Although the whole IgG molecule has commonly been used for preparation of labeled antibodies, labeled IgG displays insufficient sensitivity and specificity, probably resulting from non-specific binding of the Fc fragment to target cells or interference between fluorochromes on the identical labeled antibody, which might be caused by molecular structure. In this in vitro study, we characterized an Fc-free fluorescence-labeled Fab fragment, which was expected to yield more specific binding to target cells than the whole IgG molecule. An anti-mucin antibody and ICG-ATT, an ICG derivative, were used as the labeled antibody and labeling compound, respectively. Paraffin sections of excised gastric cancer tissues were subjected to staining. The labeled whole IgG molecule (ICG-ATT-labeled IgG) and the labeled Fab fragment (ICG-ATT-labeled Fab) were prepared according to a previous report, and the fluorescence properties, antibody activities, and features of fluorescence microscope images obtained from paraffin sections were compared. Both ICG-ATT-labeled Fab and ICG-ATT-labeled IgG were excited by a near infrared ray of 766nm, and maximum emission occurred at 804nm. Antibody activities of ICG-ATT-labeled Fab were shown to be similar to those of unlabeled anti-MUC1 antibody. The fluorescence intensity obtained from paraffin sections of excised gastric cancer tissues revealed a tendency to be greater with ICG-ATT-labeled Fab than with ICG-ATT-labeled IgG. The infrared ray fluorescence-labeled Fab fragment was likely to be more specific than the conventionally labeled antibodies. Fragmentation of antibodies is considered to contribute to improved sensitivity and specificity of labeled antibodies for detection of micro

Forward-backward multiplicity correlations of target fragments in nucleus-emulsion collisions at a few hundred MeV/u

NASA Astrophysics Data System (ADS)

Zhang, Dong-Hai; Chen, Yan-Ling; Wang, Guo-Rong; Li, Wang-Dong; Wang, Qing; Yao, Ji-Jie; Zhou, Jian-Guo; Li, Rong; Li, Jun-Sheng; Li, Hui-Ling

2015-01-01

The forward-backward multiplicity and correlations of a target evaporated fragment (black track particle) and target recoiled proton (grey track particle) emitted from 150 A MeV 4He, 290 A MeV 12C, 400 A MeV 12C, 400 A MeV 20Ne and 500 A MeV 56Fe induced different types of nuclear emulsion target interactions are investigated. It is found that the forward and backward averaged multiplicity of a grey, black and heavily ionized track particle increases with the increase of the target size. The averaged multiplicity of a forward black track particle, backward black track particle, and backward grey track particle do not depend on the projectile size and energy, but the averaged multiplicity of a forward grey track particle increases with an increase of projectile size and energy. The backward grey track particle multiplicity distribution follows an exponential decay law and the decay constant decreases with an increase of target size. The backward-forward multiplicity correlations follow linear law which is independent of the projectile size and energy, and the saturation effect is observed in some heavy target data sets.

Models of fragmentation with composite power laws

NASA Astrophysics Data System (ADS)

Tavassoli, Z.; Rodgers, G. J.

1999-06-01

Some models for binary fragmentation are introduced in which a time dependent transition size produces two regions of fragment sizes above and below the transition size. In the first model we assume a fixed rate of fragmentation for the largest fragment and two different rates of fragmentation in the two regions of sizes above and below the transition size. The model is solved exactly in the long time limit to reveal stable time-invariant solutions for the fragment size and mass distributions. These solutions exhibit composite power law behaviours; power laws with two different exponents for fragments in smaller and larger regions. A special case of the model with no fragmentation in the smaller size region is also examined. Another model is also introduced which have three regions of fragment sizes with different rates of fragmentation. The similarities between the stable distributions in our models and composite power law distributions from experimental work on shock fragmentation of long thin glass rods and thick clay plates are discussed.

Apparatus for producing cryogenic inertially driven fusion targets

DOEpatents

Miller, John R.

1981-01-01

A new technique for producing uniform layers of solid DT on microballoon surfaces. Local heating of the target, typically by means of a focused laser, within an isothermal freezing cell containing a low pressure cryogenic exchange gas such as helium, vaporizes the DT fuel contained within the microballoon. Removal of the laser heating source causes the DT gas to rapidly condense and freeze in a layer which exhibits a good degree of uniformity.

Robustness of optimal random searches in fragmented environments

NASA Astrophysics Data System (ADS)

Wosniack, M. E.; Santos, M. C.; Raposo, E. P.; Viswanathan, G. M.; da Luz, M. G. E.

2015-05-01

The random search problem is a challenging and interdisciplinary topic of research in statistical physics. Realistic searches usually take place in nonuniform heterogeneous distributions of targets, e.g., patchy environments and fragmented habitats in ecological systems. Here we present a comprehensive numerical study of search efficiency in arbitrarily fragmented landscapes with unlimited visits to targets that can only be found within patches. We assume a random walker selecting uniformly distributed turning angles and step lengths from an inverse power-law tailed distribution with exponent μ . Our main finding is that for a large class of fragmented environments the optimal strategy corresponds approximately to the same value μopt≈2 . Moreover, this exponent is indistinguishable from the well-known exact optimal value μopt=2 for the low-density limit of homogeneously distributed revisitable targets. Surprisingly, the best search strategies do not depend (or depend only weakly) on the specific details of the fragmentation. Finally, we discuss the mechanisms behind this observed robustness and comment on the relevance of our results to both the random search theory in general, as well as specifically to the foraging problem in the biological context.

Micro-Satellite Impact Tests to Investigate Multi-Layer Insulation Fragments

NASA Technical Reports Server (NTRS)

Liou, J.C.; Murakami, Junko; Hanaha, Toshiya

2009-01-01

This paper summarizes two satellite impact experiments completed in 2008. The objective of the experiments is to investigate the physical properties of satellite fragments, including those originated from Multi-Layer Insulation (MLI) and solar panels. The ultimate goal is to use the results to improve the NASA Standard Breakup Model. The targets were two cubic micro-satellites, 20 cm by 20 cm by 20 cm in size, and approximately 1,500 g in mass. The main structure of each micro-satellite was composed of five layers; the top and bottom layers and three internal layers parallel to the top and bottom layers, plus four side panels. The top layer was equipped with solar cells that was mounted to an aluminum honeycomb sandwich panel with CFRP face sheets. The four side panels and the bottom layer are all covered with MLI. The two satellite impact experiments were conducted using the two-stage light gas gun at the Kyushu Institute of Technology in Kitakyusyu, Japan. For the first experiment (labeled Shot F), the satellite was oriented in such a way that the solar panel was facing the incoming projectile, a 39.3 g aluminum alloy solid sphere. For the second experiment (labeled Shot R), the satellite was oriented so that the solar panel was on the opposite side of the impact surface. The projectile used in the second shot was a 39.2 g aluminum alloy solid sphere. The impact speeds of Shot F and Shot R were 1.74 km/s and 1.78 km/s, respectively. The ratio of the impact kinetic energy to satellite mass for the two experiments was about 40 J/g. Both target satellites were completely fragmented, although there were noticeable differences in the characteristics of the fragments. Approximately 1,800 fragments were collected from Shot F but only 1,000 fragments were collected from Shot R. This difference primarily comes from the number of needle-like CFRP and MLI fragments. The difference in CFRP pieces depends on how the CFRP panels were fragmented. Regarding the MLI pieces, a

TINS, target immobilized NMR screening: an efficient and sensitive method for ligand discovery.

PubMed

Vanwetswinkel, Sophie; Heetebrij, Robert J; van Duynhoven, John; Hollander, Johan G; Filippov, Dmitri V; Hajduk, Philip J; Siegal, Gregg

2005-02-01

We propose a ligand screening method, called TINS (target immobilized NMR screening), which reduces the amount of target required for the fragment-based approach to drug discovery. Binding is detected by comparing 1D NMR spectra of compound mixtures in the presence of a target immobilized on a solid support to a control sample. The method has been validated by the detection of a variety of ligands for protein and nucleic acid targets (K(D) from 60 to 5000 muM). The ligand binding capacity of a protein was undiminished after 2000 different compounds had been applied, indicating the potential to apply the assay for screening typical fragment libraries. TINS can be used in competition mode, allowing rapid characterization of the ligand binding site. TINS may allow screening of targets that are difficult to produce or that are insoluble, such as membrane proteins.

Experimental determination of particle range and dose distribution in thick targets through fragmentation reactions of stable heavy ions.

PubMed

Inaniwa, Taku; Kohno, Toshiyuki; Tomitani, Takehiro; Urakabe, Eriko; Sato, Shinji; Kanazawa, Mitsutaka; Kanai, Tatsuaki

2006-09-07

In radiation therapy with highly energetic heavy ions, the conformal irradiation of a tumour can be achieved by using their advantageous features such as the good dose localization and the high relative biological effectiveness around their mean range. For effective utilization of such properties, it is necessary to evaluate the range of incident ions and the deposited dose distribution in a patient's body. Several methods have been proposed to derive such physical quantities; one of them uses positron emitters generated through projectile fragmentation reactions of incident ions with target nuclei. We have proposed the application of the maximum likelihood estimation (MLE) method to a detected annihilation gamma-ray distribution for determination of the range of incident ions in a target and we have demonstrated the effectiveness of the method with computer simulations. In this paper, a water, a polyethylene and a polymethyl methacrylate target were each irradiated with stable (12)C, (14)N, (16)O and (20)Ne beams. Except for a few combinations of incident beams and targets, the MLE method could determine the range of incident ions R(MLE) with a difference between R(MLE) and the experimental range of less than 2.0 mm under the circumstance that the measurement of annihilation gamma rays was started just after the irradiation of 61.4 s and lasted for 500 s. In the process of evaluating the range of incident ions with the MLE method, we must calculate many physical quantities such as the fluence and the energy of both primary ions and fragments as a function of depth in a target. Consequently, by using them we can obtain the dose distribution. Thus, when the mean range of incident ions is determined with the MLE method, the annihilation gamma-ray distribution and the deposited dose distribution can be derived simultaneously. The derived dose distributions in water for the mono-energetic heavy-ion beams of four species were compared with those measured with an

Characterization of OXA-48-like carbapenemase producers in Canada, 2011-14.

PubMed

Mataseje, Laura F; Boyd, David A; Fuller, Jeffrey; Haldane, David; Hoang, Linda; Lefebvre, Brigitte; Melano, Roberto G; Poutanen, Susan; Van Caeseele, Paul; Mulvey, Michael R

2017-12-18

Since the first identification of the OXA-48 carbapenemase in 2001, Enterobacteriaceae harbouring OXA-48-like enzymes have been reported globally. Here, we applied WGS to characterize the molecular epidemiology of these bacterial isolates. Enterobacteriaceae non-susceptible to carbapenems isolated from patients between 2011 and 2014 were voluntarily submitted to the Canadian National Microbiology Laboratory where they were screened for carbapenemase genes. WGS was conducted on OXA-48-like producers using the Illumina MiSeq platform. WGS data were used for single nucleotide variant (SNV) analysis, MLST analysis, detection of resistance genes and partial plasmid characterization. Susceptibilities were determined using Vitek2 and Etest. Patient data provided from sites were reviewed. Sixty-seven non-duplicated cases were identified among Escherichia coli (n = 21) and Klebsiella pneumoniae (n = 46). Recent international travel was observed in 40.4% of cases. OXA-181 (52.2%) and OXA-48 (31.3%) were the most common variants, one E. coli OXA-48 producer was found to harbour the acquired colistin resistance gene mcr-1. The dominant STs were ST38 and ST410 in E. coli and ST14 in K. pneumoniae. Three common plasmid types were observed among isolates: IncL/M associated with OXA-48 producers, and ColKP3 and IncX3 associated with OXA-181/232 producers. Enterobacteriaceae with OXA-48-like carbapenemases are emerging in Canada. This study highlights the complexity of OXA-48-types identified in Canada owing to travel and the successful clones and plasmids harbouring the OXA-48-like enzyme. © Her Majesty the Queen in Right of Canada 2017. Reproduced with the permission of the Minister of Health.

A theoretical and mass spectrometry study of the fragmentation of mycosporine-like amino acids

NASA Astrophysics Data System (ADS)

Cardozo, Karina H. M.; Vessecchi, Ricardo; Carvalho, Valdemir M.; Pinto, Ernani; Gates, Paul J.; Colepicolo, Pio; Galembeck, Sérgio E.; Lopes, Norberto P.

2008-06-01

In the present study, the mycosporine-like amino acids (MAAs) were isolated from the marine red alga Gracilaria tenuistipitata and analysed by high-resolution accurate-mass sequential mass spectrometry (MSn). In addition to the proposed fragmentation mechanism based on the MSn analysis, it is clearly demonstrated that the elimination of mass 15 is a radical processes taking place at the methoxyl substituent of the double bond. This characteristic loss of a methyl radical was studied by theoretical calculations and the homolytic cleavage of the OC bond is suggested to be dependent on the bond weakening. The protonation site of the MAAs was indicated by analysis of the Fukui functions and the relative Gibbs energies of the several possible protonated forms.

Development of a potent and selective FLT3 kinase inhibitor by systematic expansion of a non-selective fragment-screening hit.

PubMed

Nakano, Hirofumi; Hasegawa, Tsukasa; Imamura, Riyo; Saito, Nae; Kojima, Hirotatsu; Okabe, Takayoshi; Nagano, Tetsuo

2016-05-01

A non-selective inhibitor (1) of FMS-like tyrosine kinase-3 (FLT3) was identified by fragment screening and systematically modified to afford a potent and selective inhibitor 26. We confirmed that 26 inhibited the growth of FLT-3-activated human acute myeloid leukemia cell line MV4-11. Our design strategy enabled rapid development of a novel type of FLT3 inhibitor from the hit fragment in the absence of target-structural information. Copyright © 2016 Elsevier Ltd. All rights reserved.

Fragment-based hit discovery and structure-based optimization of aminotriazoloquinazolines as novel Hsp90 inhibitors.

PubMed

Casale, Elena; Amboldi, Nadia; Brasca, Maria Gabriella; Caronni, Dannica; Colombo, Nicoletta; Dalvit, Claudio; Felder, Eduard R; Fogliatto, Gianpaolo; Galvani, Arturo; Isacchi, Antonella; Polucci, Paolo; Riceputi, Laura; Sola, Francesco; Visco, Carlo; Zuccotto, Fabio; Casuscelli, Francesco

2014-08-01

In the last decade the heat shock protein 90 (Hsp90) has emerged as a major therapeutic target and many efforts have been dedicated to the discovery of Hsp90 inhibitors as new potent anticancer agents. Here we report the identification of a novel class of Hsp90 inhibitors by means of a biophysical FAXS-NMR based screening of a library of fragments. The use of X-ray structure information combined with modeling studies enabled the fragment evolution of the initial triazoloquinazoline hit to a class of compounds with nanomolar potency and drug-like properties suited for further lead optimization. Copyright © 2014 Elsevier Ltd. All rights reserved.

Research with Radioactive Targets

NASA Astrophysics Data System (ADS)

Ahle, Larry

2004-10-01

Obtaining precise information about neutron capture cross-sections for s-process branch points is a key goal of nuclear astrophysics. Since these nuclei are unstable and neutron targets do not exist, performing these measurements require a facility that can produce the nuclei of interest at a sufficient rate to allow formation of a meaningful target (at least 1015 atoms). The Rare Isotope Accelerator (RIA) promises such rates, often enabling collection of greater than 1016 atoms after only of few days of production running. By properly designing both the ISOL and fragmentation lines, these collections will often be possible to obtained parasitically to other radioactive ion beam production. But given a target, performing the neutron capture cross-section measurement also presents its own challenges. In many cases, activation measurements are feasible, providing one obtains a target of sufficient purity. But for many branch point nuclei, the capture product is stable or long enough lived that no radiation signature is available for detection. Measurements for these nuclei will require a BaF2 array like DANCE at Los Alamos National Laboratory, which uses gamma calorimetry to detect neutron capture events. Plans and issues associated with isotope harvesting will be discussed, as well as challenges associated with performing theses measurements. Current plans for doing DANCE type measurements at RIA will also be discussed. This work was performed under the auspices of the U.S. Department of Energy by the University of California, Lawrence Livermore National Laboratory under contract No. W-7405-Eng-48.

Collapse and Fragmentation of Molecular Cloud Cores. VII. Magnetic Fields and Multiple Protostar Formation

NASA Astrophysics Data System (ADS)

Boss, Alan P.

2002-04-01

Recent observations of star-forming regions suggest that binary and multiple young stars are the rule rather than the exception and implicate fragmentation as the likely mechanism for their formation. Most numerical hydrodynamic calculations of fragmentation have neglected the possibly deleterious effects of magnetic fields, despite ample evidence for the importance of magnetic support of precollapse clouds. We present here the first numerical hydrodynamic survey of the collapse and fragmentation of initially magnetically supported clouds that takes into account several magnetic field effects in an approximate manner. The models are calculated with a three-dimensional, finite differences code that solves the equations of hydrodynamics, gravitation, and radiative transfer in the Eddington and diffusion approximations. Magnetic field effects are included through two simple approximations: magnetic pressure is added to the gas pressure, and magnetic tension is approximated by gravity dilution once collapse is well underway. Ambipolar diffusion of the magnetic field leading to cloud collapse is treated approximately as well. Models are calculated for a variety of initial cloud density profiles, shapes, and rotation rates. We find that in spite of the inclusion of magnetic field effects, dense cloud cores are capable of fragmenting into binary and multiple protostar systems. Initially prolate clouds tend to fragment into binary protostars, while initially oblate clouds tend to fragment into multiple protostar systems containing a small number (of the order of 4) of fragments. The latter are likely to be subject to rapid orbital evolution, with close encounters possibly leading to the ejection of fragments. Contrary to expectation, magnetic tension effects appear to enhance fragmentation, allowing lower mass fragments to form than would otherwise be possible, because magnetic tension helps to prevent a central density singularity from forming and producing a dominant

SHOP: a method for structure-based fragment and scaffold hopping.

PubMed

Fontaine, Fabien; Cross, Simon; Plasencia, Guillem; Pastor, Manuel; Zamora, Ismael

2009-03-01

A new method for fragment and scaffold replacement is presented that generates new families of compounds with biological activity, using GRID molecular interaction fields (MIFs) and the crystal structure of the targets. In contrast to virtual screening strategies, this methodology aims only to replace a fragment of the original molecule, maintaining the other structural elements that are known or suspected to have a critical role in ligand binding. First, we report a validation of the method, recovering up to 95% of the original fragments searched among the top-five proposed solutions, using 164 fragment queries from 11 diverse targets. Second, six key customizable parameters are investigated, concluding that filtering the receptor MIF using the co-crystallized ligand atom type has the greatest impact on the ranking of the proposed solutions. Finally, 11 examples using more realistic scenarios have been performed; diverse chemotypes are returned, including some that are similar to compounds that are known to bind to similar targets.

Preparation and evaluation of nanoparticles loading plasmid DNAs inserted with siRNA fragments targeting c-Myc gene.

PubMed

Ma, Tao; Jiang, Jin-Ling; Liu, Ying; Ye, Zheng-Bao; Zhang, Jun

2014-09-01

c-Myc plays a key role in glioma cancer stem cell maintenance. A drug delivery system, nanoparticles loading plasmid DNAs inserted with siRNA fragments targeting c-Myc gene (NPs-c-Myc-siRNA-pDNAs), for the treatment of glioma, has not previously been reported. NPs-c-Myc-siRNA-pDNAs were prepared and evaluated in vitro. Three kinds of c-Myc-siRNA fragments were separately synthesized and linked with empty siRNA expression vectors in the mole ratio of 3:1 by T4 DNA ligase. The linked products were then separately transfected into Escherichia coli. DH5α followed by extraction with Endofree plasmid Mega kit (Qiagen, Hilden, Germany) obtained c-Myc-siRNA-pDNAs. Finally, the recombinant c-Myc-siRNA3-pDNAs, generating the highest transfection efficiency and the greatest apoptotic ability, were chosen for encapsulation into NPs by the double-emulsion solvent-evaporation procedure, followed by stability, transfection efficiency, as well as qualitative and quantitative apoptosis evaluation. NPs-c-Myc-siRNA3-pDNAs were obtained with spherical shape in uniform size below 150 nm, with the zeta potential about -18 mV, the encapsulation efficiency and loading capacity as 76.3 ± 5.4% and 1.91 ± 0.06%, respectively. The stability results showed that c-Myc-siRNA3-pDNAs remained structurally and functionally stable after encapsulated into NPs, and NPs could prevent the loaded c-Myc-siRNA3-pDNAs from DNase degradation. The transfection efficiency of NPs-c-Myc-siRNA3-pDNAs was proven to be positive. Furthermore, NPs-c-Myc-siRNA3-pDNAs produced significant apoptosis with the apoptotic rate at 24.77 ± 5.39% and early apoptosis cells observed. Methoxy-poly-(ethylene-glycol)-poly-(lactide-co-glycolide) nanoparticles (MPEG-PLGA-NPs) are potential delivery carriers for c-Myc-siRNA3-pDNAs.

Collagen like peptide bioconjugates for targeted drug delivery applications

NASA Astrophysics Data System (ADS)

Luo, Tianzhi

the coil/globule conformational transition of the PDEGMEMA building block above its LCST with stabilization of the nanostructures by the hydrophilic CLP. To the best of our knowledge, this is the first report on such assembled nanostructures from collagen-like peptide containing copolymers. Due to the strong propensity for CLPs to bind to natural collagen via strand invasion processes, these nanosized vesicles may be used as drug carriers for targeted delivery. In addition to synthetic polymers, the collagen like peptide is then conjugated with a thermoresponsive elastin-like peptide (ELP). The resulting ELP-CLP diblock conjugates show a remarkable reduction in the inverse transition temperature of the ELP domain, attributed to the anchoring effect of the CLP triple helix. The lower transition temperature of the conjugate enables facile formation of well-defined vesicles at physiological temperature and the unexpected resolubilization of the vesicles at elevated temperatures upon unfolding of the CLP domain. Given the ability of CLPs to modify collagens, this work provides not only a simple and versatile avenue for controlling the inverse transition behavior of elastin-like peptides, but also suggest future opportunities for these thermoresponsive nanostructures in biologically relevant environments. In the last section, the potential of using the ELP-CLP nanoparticles as drug delivery vehicles for targeting collagen containing matrices is evaluated. A sustained release of clinically relevant amount of encapsulated modelled drug is achieved within three weeks, followed by a thermally controlled burst release. As expected, the ELP-CLP nanoparticles show strong retention on collagen substrate, via specific binding through collagen triple helix hybridization. Additionally, cell viability and proliferation studies using fibroblasts and chondrocytes suggest the nanoparticles are non-cytotoxic. Additionally, almost no TNF-alpha expression from macrophages is observed

Fragment-Based Protein-Protein Interaction Antagonists of a Viral Dimeric Protease.

PubMed

Gable, Jonathan E; Lee, Gregory M; Acker, Timothy M; Hulce, Kaitlin R; Gonzalez, Eric R; Schweigler, Patrick; Melkko, Samu; Farady, Christopher J; Craik, Charles S

2016-04-19

Fragment-based drug discovery has shown promise as an approach for challenging targets such as protein-protein interfaces. We developed and applied an activity-based fragment screen against dimeric Kaposi's sarcoma-associated herpesvirus protease (KSHV Pr) using an optimized fluorogenic substrate. Dose-response determination was performed as a confirmation screen, and NMR spectroscopy was used to map fragment inhibitor binding to KSHV Pr. Kinetic assays demonstrated that several initial hits also inhibit human cytomegalovirus protease (HCMV Pr). Binding of these hits to HCMV Pr was also confirmed by NMR spectroscopy. Despite the use of a target-agnostic fragment library, more than 80 % of confirmed hits disrupted dimerization and bound to a previously reported pocket at the dimer interface of KSHV Pr, not to the active site. One class of fragments, an aminothiazole scaffold, was further explored using commercially available analogues. These compounds demonstrated greater than 100-fold improvement of inhibition. This study illustrates the power of fragment-based screening for these challenging enzymatic targets and provides an example of the potential druggability of pockets at protein-protein interfaces. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Method for producing fluorinated diamond-like carbon films

DOEpatents

Hakovirta, Marko J.; Nastasi, Michael A.; Lee, Deok-Hyung; He, Xiao-Ming

2003-06-03

Fluorinated, diamond-like carbon (F-DLC) films are produced by a pulsed, glow-discharge plasma immersion ion processing procedure. The pulsed, glow-discharge plasma was generated at a pressure of 1 Pa from an acetylene (C.sub.2 H.sub.2) and hexafluoroethane (C.sub.2 F.sub.6) gas mixture, and the fluorinated, diamond-like carbon films were deposited on silicon <100>substrates. The film hardness and wear resistance were found to be strongly dependent on the fluorine content incorporated into the coatings. The hardness of the F-DLC films was found to decrease considerably when the fluorine content in the coatings reached about 20%. The contact angle of water on the F-DLC coatings was found to increase with increasing film fluorine content and to saturate at a level characteristic of polytetrafluoroethylene.

Incorporation of the statistical multi-fragmentation model in PHITS and its application for simulation of fragmentation by heavy ions and protons

NASA Astrophysics Data System (ADS)

Ogawa, Tatsuhiko; Sato, Tatsuhiko; Hashimoto, Shintaro; Niita, Koji

2014-06-01

The fragmentation reactions of relativistic-energy nucleus-nucleus and proton-nucleus collisions were simulated using the Statistical Multi-fragmentation Model (SMM) incorporated with the Particle and Heavy Ion Transport code System (PHITS). The comparisons of calculated cross-sections with literature data showed that PHITS-SMM predicts the fragmentation cross-sections of heavy nuclei up to two orders of magnitude more accurately than PHITS for heavy-ion-induced reactions. For proton-induced reactions, noticeable improvements are observed for interactions of the heavy target with protons at an energy greater than 1 GeV. Therefore, consideration for multi-fragmentation reactions is necessary for the accurate simulation of energetic fragmentation reactions of heavy nuclei.

Design of Potent and Druglike Nonphenolic Inhibitors for Catechol O-Methyltransferase Derived from a Fragment Screening Approach Targeting the S-Adenosyl-l-methionine Pocket.

PubMed

Lerner, Christian; Jakob-Roetne, Roland; Buettelmann, Bernd; Ehler, Andreas; Rudolph, Markus; Rodríguez Sarmiento, Rosa María

2016-11-23

A fragment screening approach designed to target specifically the S-adenosyl-l-methionine pocket of catechol O-methyl transferase allowed the identification of structurally related fragments of high ligand efficiency and with activity on the described orthogonal assays. By use of a reliable enzymatic assay together with X-ray crystallography as guidance, a series of fragment modifications revealed an SAR and, after several expansions, potent lead compounds could be obtained. For the first time nonphenolic and small low nanomolar potent, SAM competitive COMT inhibitors are reported. These compounds represent a novel series of potent COMT inhibitors that might be further optimized to new drugs useful for the treatment of Parkinson's disease, as adjuncts in levodopa based therapy, or for the treatment of schizophrenia.

Generation of high-affinity, internalizing anti-FGFR2 single-chain variable antibody fragment fused with Fc for targeting gastrointestinal cancers.

PubMed

Borek, Aleksandra; Sokolowska-Wedzina, Aleksandra; Chodaczek, Grzegorz; Otlewski, Jacek

2018-01-01

Fibroblast growth factor receptors (FGFRs) are promising targets for antibody-based cancer therapies, as their substantial overexpression has been found in various tumor cells. Aberrant activation of FGF receptor 2 (FGFR2) signaling through overexpression of FGFR2 and/or its ligands, mutations, or receptor amplification has been reported in multiple cancer types, including gastric, colorectal, endometrial, ovarian, breast and lung cancer. In this paper, we describe application of the phage display technology to produce a panel of high affinity single chain variable antibody fragments (scFvs) against the extracellular ligand-binding domain of FGFR2 (ECD_FGFR2). The binders were selected from the human single chain variable fragment scFv phage display libraries Tomlinson I + J and showed high specificity and binding affinity towards human FGFR2 with nanomolar KD values. To improve the affinity of the best binder selected, scFvF7, we reformatted it to a bivalent diabody format, or fused it with the Fc region (scFvF7-Fc). The scFvF7-Fc antibody construct presented the highest affinity for FGFR2, with a KD of 0.76 nM, and was selectively internalized into cancer cells overexpressing FGFR2, Snu-16 and NCI-H716. Finally, we prepared a conjugate of scFvF7-Fc with the cytotoxic drug monomethyl-auristatin E (MMAE) and evaluated its cytotoxicity. The conjugate delivered MMAE selectively to FGFR2-positive tumor cells. These results indicate that scFvF7-Fc-vcMMAE is a highly potent molecule for the treatment of cancers with FGFR2 overexpression.

Late-time particle emission from laser-produced graphite plasma

NASA Astrophysics Data System (ADS)

Harilal, S. S.; Hassanein, A.; Polek, M.

2011-09-01

We report a late-time "fireworks-like" particle emission from laser-produced graphite plasma during its evolution. Plasmas were produced using graphite targets excited with 1064 nm Nd: yttrium aluminum garnet (YAG) laser in vacuum. The time evolution of graphite plasma was investigated using fast gated imaging and visible emission spectroscopy. The emission dynamics of plasma is rapidly changing with time and the delayed firework-like emission from the graphite target followed a black-body curve. Our studies indicated that such firework-like emission is strongly depended on target material properties and explained due to material spallation caused by overheating the trapped gases through thermal diffusion along the layer structures of graphite.

Functional and proteomic comparison of different techniques to produce equine anti-tetanus immunoglobulin F(ab')2 fragments.

PubMed

Zhang, Xue-Jun; Li, Hai-Ling; Deng, Da-Yi; Ji, Chong; Yao, Xiao-Dong; Liu, Jia-Xin

2018-05-29

Tetanus is still a major cause of human deaths in several developing countries. In particular, the neonatal form remains a significant public health problem. According to the World Health Organization, administration of tetanus toxoid is recommended for neonatal tetanus patients. Furthermore, tetanus antitoxin or anti-tetanus immunoglobulin (Ig) are used for mild case or intensive care. This paper discusses a novel purification technique for improving equine anti-tetanus Ig production. First, equine plasma dealt with two steps salting out with ammonium sulfate; second, ultrafiltration concentration liquid purified by one successive protein G based affinity chromatography steps; finally, the purified F(ab')2 fragments was characterized using biochemical and proteomic methods and shown to be pure and homogeneous. Compared with the original technique product, specific activity increased by 80% (about 90,000 IU/g) and recovery of F(ab')2 is approximately equal 75%. Furthermore, Proteomic profiling of total technique process is demonstrated by nano-HPLC-MS and bioinformatics analysis. New technique to produce equine anti-tetanus immunoglobulin F(ab')2 fragments from crude plasma in high quality and yield. And it also could be used for industrial amplification. Copyright © 2018 Elsevier B.V. All rights reserved.

Peptide Fragmentation Induced by Radicals at Atmospheric Pressure

PubMed Central

Vilkov, Andrey N.; Laiko, Victor V.; Doroshenko, Vladimir M.

2009-01-01

A novel ion dissociation technique, which is capable of providing an efficient fragmentation of peptides at essentially atmospheric pressure conditions, is developed. The fragmentation patterns observed often contain c-type fragments that are specific to ECD/ETD, along with the y-/b- fragments that are specific to CAD. In the presented experimental setup, ion fragmentation takes place within a flow reactor located in the atmospheric pressure region between the ion source and the mass spectrometer. According to a proposed mechanism, the fragmentation results from the interaction of ESI-generated analyte ions with the gas-phase radical species produced by a corona discharge source. PMID:19034885

Assessing the lipophilicity of fragments and early hits

NASA Astrophysics Data System (ADS)

Mortenson, Paul N.; Murray, Christopher W.

2011-07-01

A key challenge in many drug discovery programs is to accurately assess the potential value of screening hits. This is particularly true in fragment-based drug design (FBDD), where the hits often bind relatively weakly, but are correspondingly small. Ligand efficiency (LE) considers both the potency and the size of the molecule, and enables us to estimate whether or not an initial hit is likely to be optimisable to a potent, druglike lead. While size is a key property that needs to be controlled in a small molecule drug, there are a number of additional properties that should also be considered. Lipophilicity is amongst the most important of these additional properties, and here we present a new efficiency index (LLEAT) that combines lipophilicity, size and potency. The index is intuitively defined, and has been designed to have the same target value and dynamic range as LE, making it easily interpretable by medicinal chemists. Monitoring both LE and LLEAT should help both in the selection of more promising fragment hits, and controlling molecular weight and lipophilicity during optimisation.

Role of mTOR, Bad, and Survivin in RasGAP Fragment N-Mediated Cell Protection

PubMed Central

Yang, Jiang-Yan; Widmann, Christian

2013-01-01

Partial cleavage of p120 RasGAP by caspase-3 in stressed cells generates an N-terminal fragment, called fragment N, which activates an anti-apoptotic Akt-dependent survival response. Akt regulates several effectors but which of these mediate fragment N-dependent cell protection has not been defined yet. Here we have investigated the role of mTORC1, Bad, and survivin in the capacity of fragment N to protect cells from apoptosis. Neither rapamycin, an inhibitor of mTORC1, nor silencing of raptor, a subunit of the mTORC1 complex, altered the ability of fragment N from inhibiting cisplatin- and Fas ligand-induced death. Cells lacking Bad, despite displaying a stronger resistance to apoptosis, were still protected by fragment N against cisplatin-induced death. Fragment N was also able to protect cells from Fas ligand-induced death in conditions where Bad plays no role in apoptosis regulation. Fragment N expression in cells did neither modulate survivin mRNA nor its protein expression. Moreover, the expression of cytoplasmic survivin, known to exert anti-apoptotic actions in cells, still occurred in UV-B-irradiated epidermis of mouse expressing a caspase-3-resistant RasGAP mutant that cannot produce fragment N. Additionally, survivin function in cell cycle progression was not affected by fragment N. These results indicate that, taken individually, mTOR, Bad, or Survivin are not required for fragment N to protect cells from cell death. We conclude that downstream targets of Akt other than mTORC1, Bad, or survivin mediate fragment N-induced protection or that several Akt effectors can compensate for each other to induce the pro-survival fragment N-dependent response. PMID:23826368

Fragment-based discovery of a potent NAMPT inhibitor.

PubMed

Korepanova, Alla; Longenecker, Kenton L; Pratt, Steve D; Panchal, Sanjay C; Clark, Richard F; Lake, Marc; Gopalakrishnan, Sujatha M; Raich, Diana; Sun, Chaohong; Petros, Andrew M

2017-12-12

NAMPT expression is elevated in many cancers, making this protein a potential target for anticancer therapy. We have carried out both NMR based and TR-FRET based fragment screens against human NAMPT and identified six novel binders with a range of potencies. Co-crystal structures were obtained for two of the fragments bound to NAMPT while for the other four fragments force-field driven docking was employed to generate a bound pose. Based on structural insights arising from comparison of the bound fragment poses to that of bound FK866 we were able to synthetically elaborate one of the fragments into a potent NAMPT inhibitor. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nuclear fragmentation of GCR-like ions: comparisons between data and PHITS

NASA Astrophysics Data System (ADS)

Zeitlin, Cary; Guetersloh, Stephen; Heilbronn, Lawrence; Miller, Jack; Sihver, Lembit; Mancusi, Davide; Fukumura, Aki; Iwata, Yoshi; Murakami, Takeshi

We present a summary of results from recent work in which we have compared nuclear fragmentation cross section data to predictions of the PHITS Monte Carlo simulation. The studies used beams of 12 C, 35 Cl, 40 Ar, 48 Ti, and 56 Fe at energies ranging from 290 MeV/nucleon to 1000 MeV/nucleon. Some of the data were obtained at the Brookhaven National Laboratory, others at the National Institute of Radiological Sciences in Japan. These energies and ion species are representative of the heavy ion component of the Galactic Cosmic Rays (GCR), which contribute significantly to the dose and dose equivalent that will be received by astronauts on deep-space missions. A critical need for NASA is the ability to accurately model the transport of GCR heavy ions through matter, including spacecraft walls, equipment racks, and other shielding materials, as well as through tissue. Nuclear interaction cross sections are of primary importance in the GCR transport problem. These interactions generally cause the incoming ion to break up (fragment) into one or more lighter ions, which continue approximately along the initial trajectory and with approximately the same velocity the incoming ion had prior to the interaction. Since the radiation dose delivered by a particle is proportional to the square of the quantity (charge/velocity), i.e., to (Z/β)2 , fragmentation reduces the dose (and, typically, dose equivalent) delivered by incident ions. The other mechanism by which dose can be reduced is ionization energy loss, which can lead to some particles stopping in the shielding. This is the conventional notion of shielding, but it is not applicable to human spaceflight, since the particles in the GCR tend to be highly energetic and because shielding must be relatively thin in order to keep overall mass as low as possible, keeping launch costs within reason. To support these goals, our group has systematically measured a large number of nuclear cross sections, intended to be used as either

Validation of Geant4 fragmentation for Heavy Ion Therapy

NASA Astrophysics Data System (ADS)

Bolst, David; Cirrone, Giuseppe A. P.; Cuttone, Giacomo; Folger, Gunter; Incerti, Sebastien; Ivanchenko, Vladimir; Koi, Tatsumi; Mancusi, Davide; Pandola, Luciano; Romano, Francesco; Rosenfeld, Anatoly B.; Guatelli, Susanna

2017-10-01

12C ion therapy has had growing interest in recent years for its excellent dose conformity. However at therapeutic energies, which can be as high as 400 MeV/u, carbon ions produce secondary fragments. For an incident 400 MeV/u 12C ion beam, ∼ 70 % of the beam will undergo fragmentation before the Bragg Peak. The dosimetric and radiobiological impact of these fragments must be accurately characterised, as it can result in increasing the risk of secondary cancer for the patient as well as altering the relative biological effectiveness. This work investigates the accuracy of three different nuclear fragmentation models available in the Monte Carlo Toolkit Geant4, the Binary Intranuclear Cascade (BIC), the Quantum Molecular Dynamics (QMD) and the Liege Intranuclear Cascade (INCL++). The models were benchmarked against experimental data for a pristine 400 MeV/u 12C beam incident upon a water phantom, including fragment yield, angular and energy distribution. For fragment yields the three alternative models agreed between ∼ 5 and ∼ 35 % with experimental measurements, the QMD using the "Frag" option gave the best agreement for lighter fragments but had reduced agreement for larger fragments. For angular distributions INCL++ was seen to provide the best agreement among the models for all elements with the exception of Hydrogen, while BIC and QMD was seen to produce broader distributions compared to experiment. BIC and QMD performed similar to one another for kinetic energy distributions while INCL++ suffered from producing lower energy distributions compared to the other models and experiment.

Validation of Geant4 fragmentation for Heavy Ion Therapy

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

Bolst, David; Cirrone, Giuseppe A. P.; Cuttone, Giacomo

12C ion therapy has had growing interest in recent years for its excellent dose conformity. However at therapeutic energies, which can be as high as 400 MeV/u, carbon ions produce secondary fragments. For an incident 400 MeV/u 12C ion beam, ~70% of the beam will undergo fragmentation before the Bragg Peak. The dosimetric and radiobiological impact of these fragments must be accurately characterised, as it can result in increasing the risk of secondary cancer for the patient as well as altering the relative biological effectiveness. Here, this work investigates the accuracy of three different nuclear fragmentation models available in themore » Monte Carlo Toolkit Geant4, the Binary Intranuclear Cascade (BIC), the Quantum Molecular Dynamics (QMD) and the Liege Intranuclear Cascade (INCL++). The models were benchmarked against experimental data for a pristine 400 MeV/u 12C beam incident upon a water phantom, including fragment yield, angular and energy distribution. For fragment yields the three alternative models agreed between ~5 and ~35% with experimental measurements, the QMD using the “Frag” option gave the best agreement for lighter fragments but had reduced agreement for larger fragments. For angular distributions INCL++ was seen to provide the best agreement among the models for all elements with the exception of Hydrogen, while BIC and QMD was seen to produce broader distributions compared to experiment. BIC and QMD performed similar to one another for kinetic energy distributions while INCL++ suffered from producing lower energy distributions compared to the other models and experiment.« less

Validation of Geant4 fragmentation for Heavy Ion Therapy

DOE PAGES

Bolst, David; Cirrone, Giuseppe A. P.; Cuttone, Giacomo; ...

2017-07-12

12C ion therapy has had growing interest in recent years for its excellent dose conformity. However at therapeutic energies, which can be as high as 400 MeV/u, carbon ions produce secondary fragments. For an incident 400 MeV/u 12C ion beam, ~70% of the beam will undergo fragmentation before the Bragg Peak. The dosimetric and radiobiological impact of these fragments must be accurately characterised, as it can result in increasing the risk of secondary cancer for the patient as well as altering the relative biological effectiveness. Here, this work investigates the accuracy of three different nuclear fragmentation models available in themore » Monte Carlo Toolkit Geant4, the Binary Intranuclear Cascade (BIC), the Quantum Molecular Dynamics (QMD) and the Liege Intranuclear Cascade (INCL++). The models were benchmarked against experimental data for a pristine 400 MeV/u 12C beam incident upon a water phantom, including fragment yield, angular and energy distribution. For fragment yields the three alternative models agreed between ~5 and ~35% with experimental measurements, the QMD using the “Frag” option gave the best agreement for lighter fragments but had reduced agreement for larger fragments. For angular distributions INCL++ was seen to provide the best agreement among the models for all elements with the exception of Hydrogen, while BIC and QMD was seen to produce broader distributions compared to experiment. BIC and QMD performed similar to one another for kinetic energy distributions while INCL++ suffered from producing lower energy distributions compared to the other models and experiment.« less

Fragment-Based Whole Cell Screen Delivers Hits against M. tuberculosis and Non-tuberculous Mycobacteria.

PubMed

Moreira, Wilfried; Lim, Jia Jie; Yeo, Si Ying; Ramanujulu, Pondy M; Dymock, Brian W; Dick, Thomas

2016-01-01

Reactive multi-target 'fragment drugs' represent critical components of current tuberculosis regimens. These compounds, such as pyrazinamide, are old synthetic antimycobacterials that are activated inside Mycobacterium tuberculosis bacilli and are smaller than the usual drug-like, single-target molecules. Based on the success of small 'dirty' drugs in the chemotherapy of tuberculosis, we suggested previously that fragment-based whole cell screens should be introduced in our current antimycobacterial drug discovery efforts. Here, we carried out such a screen and characterized bactericidal activity, selectivity and spectrum of hits we obtained. A library of 1725 fragments was tested at a single concentration for growth inhibitory activity against M. bovis BCG as screening strain and 38 of 116 primary hits were confirmed in dose response analyses to be active against virulent M. tuberculosis. Bacterial kill experiments showed that most hits displayed bactericidal activity at their minimal inhibitory concentration. Cytotoxicity assays established that a large proportion of hits displayed a favorable selectivity index for mammalian cells. Importantly, one third of M. tuberculosis active fragments were also active against M. abscessus and M. avium, two emerging non-tuberculous mycobacterial (NTM) pathogens, opening the opportunity to develop broad spectrum antimycobacterials. Activity determination against Gram positive (Staphylococcus aureus) and Gram negative (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa) bacteria, as well as fungi (Candida albicans, Cryptococcus neoformans) showed only a small overlap indicating a generally narrow spectrum of these novel antimicrobial hits for mycobacteria. In conclusion, we carried out the first fragment-based whole cell screen against bacteria and identified a substantial number of hits with excellent physicochemical properties and dual activity against M. tuberculosis and NTM pathogens

Determination of Impact Parameters in Aligned Breakup of Projectile-like Fragments in $$^{197}$$Au + $$^{197}$$Au Collisions at 23$A$MeV

DOE PAGES

Cap, T.; Siwek-Wilczyńska, K.; Wilczynski, J.; ...

2016-03-01

Symmetric and asymmetric aligned breakup of projectile-like fragments inmore » $$^{197}$$Au + $$^{197}$$Au collisions at 23$A$,MeV was studied. Independently of the asymmetry, the reaction yields have been found peaked at a common, very narrow range of impact parameters.« less

AAVS1-Targeted Plasmid Integration in AAV Producer Cell Lines.

PubMed

Luo, Yuxia; Frederick, Amy; Martin, John M; Scaria, Abraham; Cheng, Seng H; Armentano, Donna; Wadsworth, Samuel C; Vincent, Karen A

2017-06-01

Adeno-associated virus (AAV) producer cell lines are created via transfection of HeLaS3 cells with a single plasmid containing three components (the vector sequence, the AAV rep and cap genes, and a selectable marker gene). As this plasmid contains both the cis (Rep binding sites) and trans (Rep protein encoded by the rep gene) elements required for site-specific integration, it was predicted that plasmid integration might occur within the AAVS1 locus on human chromosome 19 (chr19). The objective of this study was to investigate whether integration in AAVS1 might be correlated with vector yield. Plasmid integration sites within several independent cell lines were assessed via Southern, fluorescence in situ hybridization (FISH) and PCR analyses. In the Southern analyses, the presence of fragments detected by both rep- and AAVS1-specific probes suggested that for several mid- and high-producing lines, plasmid DNA had integrated into the AAVS1 locus. Analysis with puroR and AAVS1-specific probes suggested that integration in AAVS1 was a more widespread phenomenon. High-producing AAV2-secreted alkaline phosphatase (SEAP) lines (masterwell 82 [MW82] and MW278) were evaluated via FISH using probes specific for the plasmid, AAVS1, and a chr19 marker. FISH analysis detected two plasmid integration sites in MW278 (neither in AAVS1), while a total of three sites were identified in MW82 (two in AAVS1). An inverse PCR assay confirmed integration within AAVS1 for several mid- and high-producing lines. In summary, the FISH, Southern, and PCR data provide evidence of site-specific integration of the plasmid within AAVS1 in several AAV producer cell lines. The data also suggest that integration in AAVS1 is a general phenomenon that is not necessarily restricted to high producers. The results also suggest that plasmid integration within the AAVS1 locus is not an absolute requirement for a high vector yield.

Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes.

PubMed

Yin, Xingyu; Scalia, Alexander; Leroy, Ludmila; Cuttitta, Christina M; Polizzo, Gina M; Ericson, Daniel L; Roessler, Christian G; Campos, Olven; Ma, Millie Y; Agarwal, Rakhi; Jackimowicz, Rick; Allaire, Marc; Orville, Allen M; Sweet, Robert M; Soares, Alexei S

2014-05-01

Acoustic droplet ejection (ADE) is a powerful technology that supports crystallographic applications such as growing, improving and manipulating protein crystals. A fragment-screening strategy is described that uses ADE to co-crystallize proteins with fragment libraries directly on MiTeGen MicroMeshes. Co-crystallization trials can be prepared rapidly and economically. The high speed of specimen preparation and the low consumption of fragment and protein allow the use of individual rather than pooled fragments. The Echo 550 liquid-handling instrument (Labcyte Inc., Sunnyvale, California, USA) generates droplets with accurate trajectories, which allows multiple co-crystallization experiments to be discretely positioned on a single data-collection micromesh. This accuracy also allows all components to be transferred through small apertures. Consequently, the crystallization tray is in equilibrium with the reservoir before, during and after the transfer of protein, precipitant and fragment to the micromesh on which crystallization will occur. This strict control of the specimen environment means that the crystallography experiments remain identical as the working volumes are decreased from the few microlitres level to the few nanolitres level. Using this system, lysozyme, thermolysin, trypsin and stachydrine demethylase crystals were co-crystallized with a small 33-compound mini-library to search for fragment hits. This technology pushes towards a much faster, more automated and more flexible strategy for structure-based drug discovery using as little as 2.5 nl of each major component.

Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes

PubMed Central

Yin, Xingyu; Scalia, Alexander; Leroy, Ludmila; Cuttitta, Christina M.; Polizzo, Gina M.; Ericson, Daniel L.; Roessler, Christian G.; Campos, Olven; Ma, Millie Y.; Agarwal, Rakhi; Jackimowicz, Rick; Allaire, Marc; Orville, Allen M.; Sweet, Robert M.; Soares, Alexei S.

2014-01-01

Acoustic droplet ejection (ADE) is a powerful technology that supports crystallographic applications such as growing, improving and manipulating protein crystals. A fragment-screening strategy is described that uses ADE to co-crystallize proteins with fragment libraries directly on MiTeGen MicroMeshes. Co-crystallization trials can be prepared rapidly and economically. The high speed of specimen preparation and the low consumption of fragment and protein allow the use of individual rather than pooled fragments. The Echo 550 liquid-handling instrument (Labcyte Inc., Sunnyvale, California, USA) generates droplets with accurate trajectories, which allows multiple co-crystallization experiments to be discretely positioned on a single data-collection micromesh. This accuracy also allows all components to be transferred through small apertures. Consequently, the crystallization tray is in equilibrium with the reservoir before, during and after the transfer of protein, precipitant and fragment to the micromesh on which crystallization will occur. This strict control of the specimen environment means that the crystallography experiments remain identical as the working volumes are decreased from the few microlitres level to the few nanolitres level. Using this system, lysozyme, thermolysin, trypsin and stachydrine demethylase crystals were co-crystallized with a small 33-compound mini-library to search for fragment hits. This technology pushes towards a much faster, more automated and more flexible strategy for structure-based drug discovery using as little as 2.5 nl of each major component. PMID:24816088

Forest fragmentation in the Pacific Northwest: quantification and correlations

Treesearch

Brett J. Butler; Jennifer J. Swenson; Ralph J. Alig

2004-01-01

A forest fragmentation index was produced for western Oregon and western Washington that combined measures of forested area, percentage edge, and interspersion. While natural, human land-cover, and human land-use processes contribute to forest fragmentation in the region, the drivers of these processes are categorically different. Here we examine forest fragmentation...

Damage of target edges in brush-like geometry in the course of ELM-like plasma pulses in QSPA Kh-50

NASA Astrophysics Data System (ADS)

Makhlaj, V. A.; Garkusha, I. E.; Aksenov, N. N.; Bazylev, B.; Byrka, O. V.; Chebotarev, V. V.; Landman, I.; Herashchenko, S. S.; Staltsov, V. V.

2015-08-01

Castellated edges of macro-brush armour elements of ITER divertor can be a source of molten/solid dust particles which are injected into the plasma. The targets that combined in brush-like geometry have been irradiated under different inclination angles in QSPA Kh-50. The cubic brushes element has typical size of 1 cm. The titanium was used to investigate dynamics of mountains' formation. The onset of dust particles ejection from the exposed castellated targets has been studied. Formation of resolidified bridges through the gaps of brush-like targets due to the melt motion is studied in dynamics. With following plasma impacts such resolidified bridges became additional source of dust.

Fragmentation of relativistic nuclei in peripheral interactions in nuclear track emulsion

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

Artemenkov, D. A., E-mail: artemenkov@lhe.jinr.ru; Bradnova, V.; Chernyavsky, M. M.

2008-09-15

The technique of nuclear track emulsions is used to explore the fragmentation of light relativistic nuclei down to the most peripheral interactions: nuclear 'white' stars. A complete pattern of the relativistic dissociation of a 8B nucleus with target fragment accompaniment is presented. Relativistic dissociation {sup 9}Be {yields} 2{alpha} is explored using significant statistics, and a relative contribution of {sup 8}Be decays from 0+ and 2+ states is established. Target fragment accompaniments are shown for relativistic fragmentation {sup 14}N {yields} 3He +H and {sup 22}Ne {yields} 5He. The leading role of the electromagnetic dissociation on heavy nuclei with respect to breakupsmore » on target protons is demonstrated in all these cases. It is possible to conclude that the peripheral dissociation of relativistic nuclei in nuclear track emulsion is a unique tool to study many-body systems composed of the lightest nuclei and nucleons in the energy scale relevant for nuclear astrophysics.« less

First experimental results of a cryogenic stopping cell with short-lived, heavy uranium fragments produced at 1000 MeV/u

NASA Astrophysics Data System (ADS)

Purushothaman, S.; Reiter, M. P.; Haettner, E.; Dendooven, P.; Dickel, T.; Geissel, H.; Ebert, J.; Jesch, C.; Plass, W. R.; Ranjan, M.; Weick, H.; Amjad, F.; Ayet, S.; Diwisch, M.; Estrade, A.; Farinon, F.; Greiner, F.; Kalantar-Nayestanaki, N.; Knöbel, R.; Kurcewicz, J.; Lang, J.; Moore, I. D.; Mukha, I.; Nociforo, C.; Petrick, M.; Pfützner, M.; Pietri, S.; Prochazka, A.; Rink, A.-K.; Rinta-Antila, S.; Scheidenberger, C.; Takechi, M.; Tanaka, Y. K.; Winfield, J. S.; Yavor, M. I.

2013-11-01

A cryogenic stopping cell (CSC) has been commissioned with 238U projectile fragments produced at 1000 MeV/u. The spatial isotopic separation in flight was performed with the FRS applying a monoenergetic degrader. For the first time, a stopping cell was operated with exotic nuclei at cryogenic temperatures (70 to 100 K). A helium stopping gas density of up to 0.05\\ \\text{mg/cm}^3 was used, about two times higher than reached before for a stopping cell with RF ion repelling structures. An overall efficiency of up to 15%, a combined ion survival and extraction efficiency of about 50%, and extraction times of 24 ms were achieved for heavy α-decaying uranium fragments. Mass spectrometry with a multiple-reflection time-of-flight mass spectrometer has demonstrated the excellent cleanliness of the CSC. This setup has opened a new field for the spectroscopy of short-lived nuclei.

Studies on cryogenic Xe capillary jet target for laser-produced plasma EUV-light source

NASA Astrophysics Data System (ADS)

Inoue, T.; Nica, P. E.; Kaku, K.; Shimoura, A.; Amano, S.; Miyamoto, S.; Mochizuki, T.

2006-03-01

In this paper, characterizations of a cryogenic Xe capillary jet target for a laser-produced plasma extreme ultraviolet (EUV) light source are reported. The capillary jet target is a candidate of fast-supplying targets for mitigating debris generation and target consumption in a vacuum chamber without reducing the EUV conversion efficiency. Xe capillary jets (jet velocity ~ 0.4 m/s) were generated in vacuum by using annular nozzles chilled to ~ 170 K at a Xe backing pressure of ~ 0.7 MPa. Forming mechanisms of the capillary jet targets were studied by using numerical calculations. Furthermore, laser-produced plasma EUV generation was performed by irradiating a Nd:YAG laser (1064 nm, ~ 0.5 J, 10 ns, 120 μmφ, ~ 4×10 11 W/cm2) on a Xe capillary jet target (outer / inner diameter = 100 / 70 μmφ). The angular distribution of EUV generation was approximately uniform around the Xe capillary jet target, and the peak kinetic energy of the fast-ions was evaluated to be ~ 2 keV.

Nuclear reactor target assemblies, nuclear reactor configurations, and methods for producing isotopes, modifying materials within target material, and/or characterizing material within a target material

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

Toth, James J.; Wall, Donald; Wittman, Richard S.

Target assemblies are provided that can include a uranium-comprising annulus. The assemblies can include target material consisting essentially of non-uranium material within the volume of the annulus. Reactors are disclosed that can include one or more discrete zones configured to receive target material. At least one uranium-comprising annulus can be within one or more of the zones. Methods for producing isotopes within target material are also disclosed, with the methods including providing neutrons to target material within a uranium-comprising annulus. Methods for modifying materials within target material are disclosed as well as are methods for characterizing material within a targetmore » material.« less

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.

Status of Reconstruction of Fragmented Diamond-on-Silicon Collector From Genesis Spacecraft Solar Wind Concentrator

NASA Technical Reports Server (NTRS)

Rodriquez, Melissa C.; Calaway, M. C.; McNamara, K. M.; Hittle, J. D.

2009-01-01

In addition to passive solar wind collector surfaces, the Genesis Discovery Mission science canister had on board an electrostatic concave mirror for concentrating the solar wind ions, known as the concentrator . The 30-mm-radius collector focal point (the target) was comprised of 4 quadrants: two of single crystal SiC, one of polycrystalline 13C diamond and one of diamond-like-carbon (DLC) on a silicon substrate. [DLC-on-silicon is also sometimes referenced as Diamond-on-silicon, DOS.] Three of target quadrants survived the hard landing intact, but the DLC-on-silicon quadrant fractured into numerous pieces (Fig. 1). This abstract reports the status of identifying the DLC target fragments and reconstructing their original orientation.

Expression of Human Immunodeficiency Virus Type 1 Neutralizing Antibody Fragments Using Human Vaginal Lactobacillus.

PubMed

Marcobal, Angela; Liu, Xiaowen; Zhang, Wenlei; Dimitrov, Antony S; Jia, Letong; Lee, Peter P; Fouts, Timothy R; Parks, Thomas P; Lagenaur, Laurel A

Eradication of human immunodeficiency virus type 1 (HIV-1) by vaccination with epitopes that produce broadly neutralizing antibodies is the ultimate goal for HIV prevention. However, generating appropriate immune responses has proven difficult. Expression of broadly neutralizing antibodies by vaginal colonizing lactobacilli provides an approach to passively target these antibodies to the mucosa. We tested the feasibility of expressing single-chain and single-domain antibodies (dAbs) in Lactobacillus to be used as a topical microbicide/live biotherapeutic. Lactobacilli provide an excellent platform to express anti-HIV proteins. Broadly neutralizing antibodies have been identified against epitopes on the HIV-1 envelope and have been made into active antibody fragments. We tested single-chain variable fragment m9 and dAb-m36 and its derivative m36.4 as prototype antibodies. We cloned and expressed the antibody fragments m9, m36, and m36.4 in Lactobacillus jensenii-1153 and tested the expression levels and functionality. We made a recombinant L. jensenii 1153-1128 that expresses dAb-m36.4. All antibody fragments m9, m36, and m36.4 were expressed by lactobacilli. However, we noted the smaller m36/m36.4 were expressed to higher levels, ≥3 μg/ml. All L. jensenii-expressed antibody fragments bound to gp120/CD4 complex; Lactobacillus-produced m36.4 inhibited HIV-1 BaL in a neutralization assay. Using a TZM-bl assay, we characterized the breadth of neutralization of the m36.4. Delivery of dAbs by Lactobacillus could provide passive transfer of these antibodies to the mucosa and longevity at the site of HIV-1 transmission.

Identification of verotoxin type 2 variant B subunit genes in Escherichia coli by the polymerase chain reaction and restriction fragment length polymorphism analysis.

PubMed Central

Tyler, S D; Johnson, W M; Lior, H; Wang, G; Rozee, K R

1991-01-01

A set of synthetic oligonucleotide primers was designed for use in a polymerase chain reaction protocol to specifically detect the B subunit genes in vtx2ha and vtx2hb, which code for the production of the VT2 (Shiga-like toxin II) variant cytotoxins VT2v-a and VT2v-b, respectively. An additional set of primers amplified a fragment common to the B subunits of the VT2 and the VT2 variant genes. Subsequent restriction endonuclease digestion of this amplicon permitted prediction of specific VT2 and variant genotypes on the basis of predetermined restriction fragment length polymorphisms. Genotypes of 21 VT2-producing strains of Escherichia coli were determined using this polymerase chain reaction-restriction fragment length polymorphism procedure. Four strains contained B subunit target sequences only for VT2 genes, 9 strains contained sequences only for VT2v-a genes, and 3 strains contained sequences only for VT2v-b. For genes in combination, one strain contained B subunit genes for both VT2 and VT2v-a and two strains contained B subunit genes for VT2 and VT2v-b. Two strains of E. coli O91:H21 contained both VT2v-a and VT2v-b B subunit genes. The VT2 reference strain of E. coli, E32511, was found to contain the targeted sequences from both VT2 and VT2v-a genes, whereas the recombinant E. coli, pEB1, possessed only that of the VT2 gene. The specific activities of extracellular VT2 determined in HeLa cells ranged from 0.3 to 41.7 TCD50 per microgram of protein in strains carrying the VT2 gene target and from 0 to 50.0 TCD50 per microgram of protein in strains carrying only the VT2 variant target (TCD50 is the tissue culture dose by which 50% of the cells were affected), suggesting that phenotypic expression does not correlate with genotype. Images PMID:1679436

Laser-produced plasma EUV source using a colloidal microjet target containing tin dioxide nanoparticles

NASA Astrophysics Data System (ADS)

Higashiguchi, Takeshi; Dojyo, Naoto; Sasaki, Wataru; Kubodera, Shoichi

2006-10-01

We realized a low-debris laser-produced plasma extreme ultraviolet (EUV) source by use of a colloidal microjet target, which contained low-concentration (6 wt%) tin-dioxide nanoparticles. An Nd:YAG laser was used to produce a plasma at the intensity on the order of 10^11 W/cm^2. The use of low concentration nanoparticles in a microjet target with a diameter of 50 μm regulated the neutral debris emission from a target, which was monitored by a silicon witness plate placed 30 cm apart from the source in a vacuum chamber. No XPS signals of tin and/or oxygen atoms were observed on the plate after ten thousand laser exposures. The low concentration nature of the target was compensated and the conversion efficiency (CE) was improved by introducing double pulses of two Nd:YAG lasers operated at 532 and 1064 nm as a result of controlling the micro-plasma characteristics. The EUV CE reached its maximum of 1.2% at the delay time of approximately 100 ns with the main laser intensiy of 2 x10^11 W/cm^2. The CE value was comparable to that of a tin bulk target, which, however, produced a significant amount of neutral debris.

Creation of a Novel Class of Potent and Selective MutT Homologue 1 (MTH1) Inhibitors Using Fragment-Based Screening and Structure-Based Drug Design.

PubMed

Rahm, Fredrik; Viklund, Jenny; Trésaugues, Lionel; Ellermann, Manuel; Giese, Anja; Ericsson, Ulrika; Forsblom, Rickard; Ginman, Tobias; Günther, Judith; Hallberg, Kenth; Lindström, Johan; Persson, Lars Boukharta; Silvander, Camilla; Talagas, Antoine; Díaz-Sáez, Laura; Fedorov, Oleg; Huber, Kilian V M; Panagakou, Ioanna; Siejka, Paulina; Gorjánácz, Mátyás; Bauser, Marcus; Andersson, Martin

2018-03-22

Recent literature has both suggested and questioned MTH1 as a novel cancer target. BAY-707 was just published as a target validation small molecule probe for assessing the effects of pharmacological inhibition of MTH1 on tumor cell survival, both in vitro and in vivo. (1) In this report, we describe the medicinal chemistry program creating BAY-707, where fragment-based methods were used to develop a series of highly potent and selective MTH1 inhibitors. Using structure-based drug design and rational medicinal chemistry approaches, the potency was increased over 10,000 times from the fragment starting point while maintaining high ligand efficiency and drug-like properties.

DNA fragment sizing and sorting by laser-induced fluorescence

DOEpatents

Hammond, Mark L.; Jett, James H.; Keller, Richard A.; Marrone, Babetta L.; Martin, John C.

1996-01-01

A method is provided for sizing DNA fragments using high speed detection systems, such as flow cytometry to determine unique characteristics of DNA pieces from a sample. In one characterization the DNA piece is fragmented at preselected sites to produce a plurality of DNA fragments. The DNA piece or the resulting DNA fragments are treated with a dye effective to stain stoichiometrically the DNA piece or the DNA fragments. The fluorescence from the dye in the stained fragments is then examined to generate an output functionally related to the number of nucleotides in each one of the DNA fragments. In one embodiment, the intensity of the fluorescence emissions from each fragment is linearly related to the fragment length. The distribution of DNA fragment sizes forms a characterization of the DNA piece for use in forensic and research applications.

Method of preparing and applying single stranded DNA probes to double stranded target DNAs in situ

DOEpatents

Gray, Joe W.; Pinkel, Daniel

1991-01-01

A method is provided for producing single stranded non-self-complementary nucleic acid probes, and for treating target DNA for use therewith. Probe is constructed by treating DNA with a restriction enzyme and an exonuclease to form template/primers for a DNA polymerase. The digested strand is resynthesized in the presence of labeled nucleoside triphosphate precursor. Labeled single stranded fragments are separated from the resynthesized fragments to form the probe. Target DNA is treated with the same restriction enzyme used to construct the probe, and is treated with an exonuclease before application of the probe. The method significantly increases the efficiency and specificity of hybridization mixtures by increasing effective probe concentration by eliminating self-hybridization between both probe and target DNAs, and by reducing the amount of target DNA available for mismatched hybridizations.

Millisecond laser ablation of molybdenum target in reactive gas toward MoS2 fullerene-like nanoparticles with thermally stable photoresponse.

PubMed

Song, Shu-Tao; Cui, Lan; Yang, Jing; Du, Xi-Wen

2015-01-28

As a promising material for photoelectrical application, MoS2 has attracted extensive attention on its facile synthesis and unique properties. Herein, we explored a novel strategy of laser ablation to synthesize MoS2 fullerene-like nanoparticles (FL-NPs) with stable photoresponse under high temperature. Specifically, we employed a millisecond pulsed laser to ablate the molybdenum target in dimethyl trisulfide gas, and as a result, the molybdenum nanodroplets were ejected from the target and interacted with the highly reactive ambient gas to produce MoS2 FL-NPs. In contrast, the laser ablation in liquid could only produce core-shell nanoparticles. The crucial factors for controlling final nanostructures were found to be laser intensity, cooling rate, and gas reactivity. Finally, the MoS2 FL-NPs were assembled into a simple photoresponse device which exhibited excellent thermal stability, indicating their great potentialities for high-temperature photoelectrical applications.

Composition and methods of preparation of target material for producing radionuclides

DOEpatents

Seropeghin, Yurii D; Zhuikov, Boris L

2013-05-28

A composition suitable for use as a target containing antimony to be irradiated by accelerated charged particles (e.g., by protons to produce tin-117m) comprises an intermetallic compound of antimony and titanium which is synthesized at high-temperature, for example, in an arc furnace. The formed material is powdered and melted in an induction furnace, or heated at high gas pressure in gas static camera. The obtained product has a density, temperature stability, and heat conductivity sufficient to provide an appropriate target material.

Fragmentation of interstellar clouds and star formation

NASA Technical Reports Server (NTRS)

Silk, J.

1982-01-01

The principal issues are addressed: the fragmentation of molecular clouds into units of stellar mass and the impact of star formation on molecular clouds. The observational evidence for fragmentation is summarized, and the gravitational instability described of a uniform spherical cloud collapsing from rest. The implications are considered of a finite pressure for the minimum fragment mass that is attainable in opacity-limited fragmentation. The role of magnetic fields is discussed in resolving the angular momentum problem and in making the collapse anisotropic, with notable consequences for fragmentation theory. Interactions between fragments are described, with emphasis on the effect of protostellar winds on the ambient cloud matter and on inhibiting further star formation. Such interactions are likely to have profound consequences for regulating the rate of star formation and on the energetics and dynamics of molecular clouds.

From small to powerful: the fragments universe and its "chem-appeal".

PubMed

Sancineto, Luca; Massari, Serena; Iraci, Nunzio; Tabarrini, Oriana

2013-01-01

While increasing expertise in molecular biology and proteomics is markedly speeding up the target elucidation process, various strategies have been proposed that improve the chances of identifying active molecules. Among them, the Fragment Based Drug Design (FBDD) is surely worth noting. The FBDD entails the screening of a small number of low molecular weight compounds in the hopes of finding even low affine but high ligand efficient fragments that have high probability to became drug candidates. Since 1996, when the first paper on FBDD was reported, the potentialities of this strategy became progressively more apparent as testified by the growing number of publications. Many drug discovery projects started with the identification of fragments which after the optimization gave many molecules close to the approval and one marketed drug Vemurafenib, approved in 2011. A preamble that highlights the advantages of dealing with simple and "very small" molecules over conventional drug-like compounds will be herein given prior to discussing the canonical FBDD stages, from fragment library design, to the different screening methods concluding with the various optimization strategies, in an attempt to illustrate the whole FBDD workflow while discussing the most recent and successful applications. While this review is a tribute to the success achieved by the researchers in this field, it is particularly addressed to scientists who want to become aware of the versatility and potentiality of FBDD.

A comparison of DNA fragmentation methods - Applications for the biochip technology.

PubMed

Sapojnikova, Nelly; Asatiani, Nino; Kartvelishvili, Tamar; Asanishvili, Lali; Zinkevich, Vitaly; Bogdarina, Irina; Mitchell, Julian; Al-Humam, Abdulmohsen

2017-08-20

The efficiency of hybridization signal detection in a biochip is affected by the method used for test DNA preparation, such as fragmentation, amplification and fluorescent labelling. DNA fragmentation is the commonest methods used and it is recognised as a critical step in biochip analysis. Currently methods used for DNA fragmentation are based either on sonication or on the enzymatic digestion. In this study, we compared the effect of different types of enzymatic DNA fragmentations, using DNase I to generate ssDNA breaks, NEBNext dsDNA fragmentase and SaqAI restrictase, on DNA labelling. DNA from different Desulfovibrio species was used as a substrate for these enzymes. Of the methods used, DNA fragmented by NEBNext dsDNA Fragmentase digestion was subsequently labelled with the greatest efficiency. As a result of this, the use of this enzyme to fragment target DNA increases the sensitivity of biochip-based detection significantly, and this is an important consideration when determining the presence of targeted DNA in ecological and medical samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Increasing on-target cleavage efficiency for CRISPR/Cas9-induced large fragment deletion in Myxococcus xanthus.

PubMed

Yang, Ying-Jie; Wang, Ye; Li, Zhi-Feng; Gong, Ya; Zhang, Peng; Hu, Wen-Chao; Sheng, Duo-Hong; Li, Yue-Zhong

2017-08-16

The CRISPR/Cas9 system is a powerful tool for genome editing, in which the sgRNA binds and guides the Cas9 protein for the sequence-specific cleavage. The protocol is employable in different organisms, but is often limited by cell damage due to the endonuclease activity of the introduced Cas9 and the potential off-target DNA cleavage from incorrect guide by the 20 nt spacer. In this study, after resolving some critical limits, we have established an efficient CRISPR/Cas9 system for the deletion of large genome fragments related to the biosynthesis of secondary metabolites in Myxococcus xanthus cells. We revealed that the high expression of a codon-optimized cas9 gene in M. xanthus was cytotoxic, and developed a temporally high expression strategy to reduce the cell damage from high expressions of Cas9. We optimized the deletion protocol by using the tRNA-sgRNA-tRNA chimeric structure to ensure correct sgRNA sequence. We found that, in addition to the position-dependent nucleotide preference, the free energy of a 20 nt spacer was a key factor for the deletion efficiency. By using the developed protocol, we achieved the CRISPR/Cas9-induced deletion of large biosynthetic gene clusters for secondary metabolites in M. xanthus DK1622 and its epothilone-producing mutant. The findings and the proposals described in this paper were suggested to be workable in other organisms, for example, other Gram negative bacteria with high GC content.

Fragment-based approaches to anti-HIV drug discovery: state of the art and future opportunities.

PubMed

Huang, Boshi; Kang, Dongwei; Zhan, Peng; Liu, Xinyong

2015-12-01

The search for additional drugs to treat HIV infection is a continuing effort due to the emergence and spread of HIV strains resistant to nearly all current drugs. The recent literature reveals that fragment-based drug design/discovery (FBDD) has become an effective alternative to conventional high-throughput screening strategies for drug discovery. In this critical review, the authors describe the state of the art in FBDD strategies for the discovery of anti-HIV drug-like compounds. The article focuses on fragment screening techniques, direct fragment-based design and early hit-to-lead progress. Rapid progress in biophysical detection and in silico techniques has greatly aided the application of FBDD to discover candidate agents directed at a variety of anti-HIV targets. Growing evidence suggests that structural insights on key proteins in the HIV life cycle can be applied in the early phase of drug discovery campaigns, providing valuable information on the binding modes and efficiently prompting fragment hit-to-lead progression. The combination of structural insights with improved methodologies for FBDD, including the privileged fragment-based reconstruction approach, fragment hybridization based on crystallographic overlays, fragment growth exploiting dynamic combinatorial chemistry, and high-speed fragment assembly via diversity-oriented synthesis followed by in situ screening, offers the possibility of more efficient and rapid discovery of novel drugs for HIV-1 prevention or treatment. Though the use of FBDD in anti-HIV drug discovery is still in its infancy, it is anticipated that anti-HIV agents developed via fragment-based strategies will be introduced into the clinic in the future.

Inhibition of tumor angiogenesis and tumor growth by the DSL domain of human Delta-like 1 targeted to vascular endothelial cells.

PubMed

Zhao, Xing-Cheng; Dou, Guo-Rui; Wang, Li; Liang, Liang; Tian, Deng-Mei; Cao, Xiu-Li; Qin, Hong-Yan; Wang, Chun-Mei; Zhang, Ping; Han, Hua

2013-07-01

The growth of solid tumors depends on neovascularization. Several therapies targeting tumor angiogenesis have been developed. However, poor response in some tumors and emerging resistance necessitate further investigations of new drug targets. Notch signal pathway plays a pivotal role in vascular development and tumor angiogenesis. Either blockade or forced activation of this pathway can inhibit angiogenesis. As blocking Notch pathway results in the formation of vascular neoplasm, activation of Notch pathway to prevent tumor angiogenesis might be an alternative choice. However, an in vivo deliverable reagent with highly efficient Notch-activating capacity has not been developed. Here, we generated a polypeptide, hD1R, which consists of the Delta-Serrate-Lag-2 fragment of the human Notch ligand Delta-like 1 and an arginine-glycine-aspartate (RGD) motif targeting endothelial cells (ECs). We showed that hD1R could bind to ECs specifically through its RGD motif and effectively triggered Notch signaling in ECs. We demonstrated both in vitro and in vivo that hD1R inhibited angiogenic sprouting and EC proliferation. In tumor-bearing mice, the injection of hD1R effectively repressed tumor growth, most likely through increasing tumor hypoxia and tissue necrosis. The amount and width of vessels reduced remarkably in tumors of mice treated with hD1R. Moreover, vessels in tumors of mice treated with hD1R recruited more NG2(+) perivascular cells and were better perfused. Combined application of hD1R and chemotherapy with cisplatin and teniposide revealed that these two treatments had additive antitumor effects. Our study provided a new strategy for antiangiogenic tumor therapy.

Cytosolic expression of functional Fab fragments in Escherichia coli using a novel combination of dual SUMO expression cassette and EnBase® cultivation mode.

PubMed

Rezaie, F; Davami, F; Mansouri, K; Agha Amiri, S; Fazel, R; Mahdian, R; Davoudi, N; Enayati, S; Azizi, M; Khalaj, V

2017-05-08

The Escherichia coli expression system is highly effective in producing recombinant proteins. However, there are some limitations in this system, especially in obtaining correctly folded forms of some complex proteins such as Fab fragments. To improve the solubility and folding quality of Fab fragments, we have examined the effect of simultaneous application of a SUMO fusion tag, EnBase ® cultivation mode and a redox mutant strain in the E. coli expression system. A bicistronic gene construct was designed to express an antivascular endothelial growth factor (VEGF) Fab fragment as a model system. The construct contained a dual SUMO fusion gene fragment to encode SUMO-tagged heavy and light chains. While the expression of the construct in batch cultures of BL21 or SHuffle ® transformants produced insoluble and unfolded products, the induction of the transformants in EnBase ® medium resulted in soluble and correctly folded Fab fragment, reaching as high as 19% of the total protein in shuffle strain. The functional assays indicated that the biological activity of the target Fab is similar to the commercial anti-VEGF, Lucentis ® . This study demonstrated that the combination of SUMO fusion technology, EnBase ® cultivation system and recruiting a redox mutant of E. coli can efficiently enhance the solubility and productivity of recombinant Fab fragments. The presented strategy provides not only a novel method to produce soluble and active form of an anti-VEGF Fab but also may use in the efficient production of other antibody fragments. © 2017 The Society for Applied Microbiology.

Dynamic Failure and Fragmentation of a Hot-Pressed Boron Carbide

NASA Astrophysics Data System (ADS)

Sano, Tomoko; Vargas-Gonzalez, Lionel; LaSalvia, Jerry; Hogan, James David

2017-12-01

This study investigates the failure and fragmentation of a hot-pressed boron carbide during high rate impact experiments. Four impact experiments are performed using a composite-backed target configuration at similar velocities, where two of the impact experiments resulted in complete target penetration and two resulted in partial penetration. This paper seeks to evaluate and understand the dynamic behavior of the ceramic that led to either the complete or partial penetration cases, focusing on: (1) surface and internal failure features of fragments using optical, scanning electron, and transmission electron microscopy, and (2) fragment size analysis using state-of-the-art particle-sizing technology that informs about the consequences of failure. Detailed characterization of the mechanical properties and the microstructure is also performed. Results indicate that transgranular fracture was the primary mode of failure in this boron carbide material, and no stress-induced amorphization features were observed. Analysis of the fragment sizes for the partial and completely penetrated experiments revealed a possible correlation between larger fragment sizes and impact performance. The results will add insight into designing improved advanced ceramics for impact protection applications.

Ecosystem extent and fragmentation

USGS Publications Warehouse

Sayre, Roger; Hansen, Matt

2017-01-01

One of the candidate essential biodiversity variable (EBV) groups described in the seminal paper by Pereira et al. (2014) concerns Ecosystem Structure. This EBV group is distinguished from another EBV group which encompasses aspects of Ecosystem Function. While the Ecosystem Function EBV treats ecosystem processes like nutrient cycling, primary production, trophic interactions, etc., the Ecosystem Structure EBV relates to the set of biophysical properties of ecosystems that create biophysical environmental context, confer biophysical structure, and occur geographically. The Ecosystem Extent and Fragmentation EBV is one of the EBVs in the Ecosystem Structure EBV group.Ecosystems are understood to exist at multiple scales, from very large areas (macro-ecosystems) like the Arctic tundra, for example, to something as small as a tree in an Amazonian rain forest. As such, ecosystems occupy space and therefore can be mapped across any geography of interest, whether that area of interest be a site, a nation, a region, a continent, or the planet. One of the most obvious and seemingly straightforward EBVs is Ecosystem Extent and Fragmentation. Ecosystem extent refers to the location and geographic distribution of ecosystems across landscapes or in the oceans, while ecosystem fragmentation refers to the spatial pattern and connectivity of ecosystem occurrences on the landscape.

Bioinspired Pollen-Like Hierarchical Surface for Efficient Recognition of Target Cancer Cells.

PubMed

Wang, Wenshuo; Yang, Gao; Cui, Haijun; Meng, Jingxin; Wang, Shutao; Jiang, Lei

2017-08-01

The efficient recognition and isolation of rare cancer cells holds great promise for cancer diagnosis and prognosis. In nature, pollens exploit spiky structures to realize recognition and adhesion to stigma. Herein, a bioinspired pollen-like hierarchical surface is developed by replicating the assembly of pollen grains, and efficient and specific recognition to target cancer cells is achieved. The pollen-like surface is fabricated by combining filtering-assisted assembly and soft lithography-based replication of pollen grains of wild chrysanthemum. After modification with a capture agent specific to cancer cells, the pollen-like surface enables the capture of target cancer cells with high efficiency and specificity. In addition, the pollen-like surface not only assures high viability of captured cells but also performs well in cell mixture system and at low cell density. This study represents a good example of constructing cell recognition biointerfaces inspired by pollen-stigma adhesion. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A note on the self-similar solutions to the spontaneous fragmentation equation

NASA Astrophysics Data System (ADS)

Breschi, Giancarlo; Fontelos, Marco A.

2017-05-01

We provide a method to compute self-similar solutions for various fragmentation equations and use it to compute their asymptotic behaviours. Our procedure is applied to specific cases: (i) the case of mitosis, where fragmentation results into two identical fragments, (ii) fragmentation limited to the formation of sufficiently large fragments, and (iii) processes with fragmentation kernel presenting a power-like behaviour.

Fragment assignment in the cloud with eXpress-D

PubMed Central

2013-01-01

Background Probabilistic assignment of ambiguously mapped fragments produced by high-throughput sequencing experiments has been demonstrated to greatly improve accuracy in the analysis of RNA-Seq and ChIP-Seq, and is an essential step in many other sequence census experiments. A maximum likelihood method using the expectation-maximization (EM) algorithm for optimization is commonly used to solve this problem. However, batch EM-based approaches do not scale well with the size of sequencing datasets, which have been increasing dramatically over the past few years. Thus, current approaches to fragment assignment rely on heuristics or approximations for tractability. Results We present an implementation of a distributed EM solution to the fragment assignment problem using Spark, a data analytics framework that can scale by leveraging compute clusters within datacenters–“the cloud”. We demonstrate that our implementation easily scales to billions of sequenced fragments, while providing the exact maximum likelihood assignment of ambiguous fragments. The accuracy of the method is shown to be an improvement over the most widely used tools available and can be run in a constant amount of time when cluster resources are scaled linearly with the amount of input data. Conclusions The cloud offers one solution for the difficulties faced in the analysis of massive high-thoughput sequencing data, which continue to grow rapidly. Researchers in bioinformatics must follow developments in distributed systems–such as new frameworks like Spark–for ways to port existing methods to the cloud and help them scale to the datasets of the future. Our software, eXpress-D, is freely available at: http://github.com/adarob/express-d. PMID:24314033

The causes and ecological correlates of head scale asymmetry and fragmentation in a tropical snake.

PubMed

Brown, Gregory P; Madsen, Thomas; Dubey, Sylvain; Shine, Rick

2017-09-12

The challenge of identifying the proximate causes and ecological consequences of phenotypic variation can be facilitated by studying traits that are usually but not always bilaterally symmetrical; deviations from symmetry likely reflect disrupted embryogenesis. Based on a 19-year mark-recapture study of >1300 slatey-grey snakes (Stegonotus cucullatus) in tropical Australia, and incubation of >700 eggs, we document developmental and ecological correlates of two morphological traits: asymmetry and fragmentation of head scales. Asymmetry was directional (more scales on the left side) and was higher in individuals with lower heterozygosity, but was not heritable. In contrast, fragmentation was heritable and was higher in females than males. Both scale asymmetry and fragmentation were increased by rapid embryogenesis but were not affected by hydric conditions during incubation. Snakes with asymmetry and fragmentation exhibited slightly lower survival and increased (sex-specific) movements, and females with more scale fragmentation produced smaller eggs. Counterintuitively, snakes with more asymmetry had higher growth rates (possibly reflecting trade-offs with other traits), and snakes with more fragmentation had fewer parasites (possibly due to lower feeding rates). Our data paint an unusually detailed picture of the complex genetic and environmental factors that, by disrupting early embryonic development, generate variations in morphology that have detectable correlations with ecological performance.

Development of a homogeneous immunoassay system using protein A fusion fragmented Renilla luciferase.

PubMed

Mie, Masayasu; Thuy, Ngo Phan Bich; Kobatake, Eiry

2012-03-07

A homogeneous immunoassay system was developed using fragmented Renilla luciferase (Rluc). The B domain of protein A was fused to two Rluc fragments. When complexes between an antibody and fragmented Rluc fusion proteins bind to target molecules, the Rluc fragments come into close proximity and the luminescence activity of fragmented Rluc is restored by complementation. As proof-of-principle, this fragmented Rluc system was used to detect E. coli homogeneously using an anti-E. coli antibody.

A graph-based approach to construct target-focused libraries for virtual screening.

PubMed

Naderi, Misagh; Alvin, Chris; Ding, Yun; Mukhopadhyay, Supratik; Brylinski, Michal

2016-01-01

Due to exorbitant costs of high-throughput screening, many drug discovery projects commonly employ inexpensive virtual screening to support experimental efforts. However, the vast majority of compounds in widely used screening libraries, such as the ZINC database, will have a very low probability to exhibit the desired bioactivity for a given protein. Although combinatorial chemistry methods can be used to augment existing compound libraries with novel drug-like compounds, the broad chemical space is often too large to be explored. Consequently, the trend in library design has shifted to produce screening collections specifically tailored to modulate the function of a particular target or a protein family. Assuming that organic compounds are composed of sets of rigid fragments connected by flexible linkers, a molecule can be decomposed into its building blocks tracking their atomic connectivity. On this account, we developed eSynth, an exhaustive graph-based search algorithm to computationally synthesize new compounds by reconnecting these building blocks following their connectivity patterns. We conducted a series of benchmarking calculations against the Directory of Useful Decoys, Enhanced database. First, in a self-benchmarking test, the correctness of the algorithm is validated with the objective to recover a molecule from its building blocks. Encouragingly, eSynth can efficiently rebuild more than 80 % of active molecules from their fragment components. Next, the capability to discover novel scaffolds is assessed in a cross-benchmarking test, where eSynth successfully reconstructed 40 % of the target molecules using fragments extracted from chemically distinct compounds. Despite an enormous chemical space to be explored, eSynth is computationally efficient; half of the molecules are rebuilt in less than a second, whereas 90 % take only about a minute to be generated. eSynth can successfully reconstruct chemically feasible molecules from molecular fragments

Adaptation to fragmentation: evolutionary dynamics driven by human influences.

PubMed

Cheptou, Pierre-Olivier; Hargreaves, Anna L; Bonte, Dries; Jacquemyn, Hans

2017-01-19

Fragmentation-the process by which habitats are transformed into smaller patches isolated from each other-has been identified as a major threat for biodiversity. Fragmentation has well-established demographic and population genetic consequences, eroding genetic diversity and hindering gene flow among patches. However, fragmentation should also select on life history, both predictably through increased isolation, demographic stochasticity and edge effects, and more idiosyncratically via altered biotic interactions. While species have adapted to natural fragmentation, adaptation to anthropogenic fragmentation has received little attention. In this review, we address how and whether organisms might adapt to anthropogenic fragmentation. Drawing on selected case studies and evolutionary ecology models, we show that anthropogenic fragmentation can generate selection on traits at both the patch and landscape scale, and affect the adaptive potential of populations. We suggest that dispersal traits are likely to experience especially strong selection, as dispersal both enables migration among patches and increases the risk of landing in the inhospitable matrix surrounding them. We highlight that suites of associated traits are likely to evolve together. Importantly, we show that adaptation will not necessarily rescue populations from the negative effects of fragmentation, and may even exacerbate them, endangering the entire metapopulation.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'. © 2016 The Author(s).

NMR screening in fragment-based drug design: a practical guide.

PubMed

Kim, Hai-Young; Wyss, Daniel F

2015-01-01

Fragment-based drug design (FBDD) comprises both fragment-based screening (FBS) to find hits and elaboration of these hits to lead compounds. Typical fragment hits have lower molecular weight (<300-350 Da) and lower initial potency but higher ligand efficiency when compared to those from high-throughput screening. NMR spectroscopy has been widely used for FBDD since it identifies and localizes the binding site of weakly interacting hits on the target protein. Here we describe ligand-based NMR methods for hit identification from fragment libraries and for functional cross-validation of primary hits.

Detection of Listeria monocytogenes with short peptide fragments from class IIa bacteriocins as recognition elements.

PubMed

Azmi, Sarfuddin; Jiang, Keren; Stiles, Michael; Thundat, Thomas; Kaur, Kamaljit

2015-03-09

We employed a direct peptide-bacteria binding assay to screen peptide fragments for high and specific binding to Listeria monocytogenes. Peptides were screened from a peptide array library synthesized on cellulose membrane. Twenty four peptide fragments (each a 14-mer) were derived from three potent anti-listerial peptides, Leucocin A, Pediocin PA1, and Curvacin A, that belong to class IIa bacteriocins. Fragment Leu10 (GEAFSAGVHRLANG), derived from the C-terminal region of Leucocin A, displayed the highest binding among all of the library fragments toward several pathogenic Gram-positive bacteria, including L. monocytogenes, Enterococcus faecalis, and Staphylococcus aureus. The specific binding of Leu10 to L. monocytogenes was further validated using microcantilever (MCL) experiments. Microcantilevers coated with gold were functionalized with peptides by chemical conjugation using a cysteamine linker to yield a peptide density of ∼4.8×10(-3) μmol/cm2 for different peptide fragments. Leu10 (14-mer) functionalized MCL was able to detect Listeria with same sensitivity as that of Leucocin A (37-mer) functionalized MCL, validating the use of short peptide fragments in bacterial detection platforms. Fragment Leu10 folded into a helical conformation in solution, like that of native Leucocin A, suggesting that both Leu10 and Leucocin A may employ a similar mechanism for binding target bacteria. The results show that peptide-conjugated microcantilevers can function as highly sensitive platforms for Listeria detection and hold potential to be developed as biosensors for pathogenic bacteria.

Development of a high-power neutron-producing lithium target for boron neutron capture therapy

NASA Astrophysics Data System (ADS)

Brown, Adam V.; Scott, Malcolm C.

2000-12-01

A neutron producing lithium target for a novel, accelerator based cancer treatment requires the removal of up to 6kW of heat produced by 1-2mA beam of 2.3-3.0MeV protons. This paper presents the results form computer simulations which show that, using submerged jet cooling, a solid lithium target can be maintained up to 1.6mA, and a liquid target up to 2.6mA, assuming a 3.0MeV proton beam. The predictions from the simulations are verified through the use of an experimental heat transfer test-rig and the result form a number of metallurgical studies made to select a compatible substrate material for the lithium are reported.

Detection of N2O-producing fungi in environment using nitrite reductase gene (nirK)-targeting primers.

PubMed

Chen, Huaihai; Yu, Fangbo; Shi, Wei

2016-12-01

Fungal denitrification has been increasingly investigated, but its community ecology is poorly understood due to the lack of culture-independent tools. In this work, four pairs of nirK-targeting primers were designed and evaluated for primer specificity and efficiency using thirty N 2 O-producing fungal cultures and an agricultural soil. All primers amplified nirK from fungi and soil, but their efficiency and specificity were different. A primer set, FnirK_F3/R2 amplified ∼80 % of tested fungi, including Aspergillus, Fusarium, Penicillium, and Trichoderma, as compared to ∼40-70 % for other three primers. The nirK fragments of fungal and soil DNA amplified by FnirK_F3/R2 were phylogenetically related to denitrifying fungi in the orders Eurotiales, Hypocreales, and Sordariales; and clone sequences were also distributed in the clusters of Chaetomium, Metarhizium, and Myceliophthora that were uncultured from soil in our previous work. This proved the wide-range capability of primers for amplifying diverse denitrifying fungi from environment. However, our primers and recently-developed other primers amplified bacterial nirK from soil and this co-amplification of fungal and bacterial nirK was theoretically discussed. The FnirK_F3/R2 was further compared with published primers; results from clone libraries demonstrated that FnirK_F3/R2 was more specifically targeted on fungi and had broader taxonomical coverage than some others. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Fragment-based design of kinase inhibitors: a practical guide.

PubMed

Erickson, Jon A

2015-01-01

Fragment-based drug design has become an important strategy for drug design and development over the last decade. It has been used with particular success in the development of kinase inhibitors, which are one of the most widely explored classes of drug targets today. The application of fragment-based methods to discovering and optimizing kinase inhibitors can be a complicated and daunting task; however, a general process has emerged that has been highly fruitful. Here a practical outline of the fragment process used in kinase inhibitor design and development is laid out with specific examples. A guide to the overall process from initial discovery through fragment screening, including the difficulties in detection, to the computational methods available for use in optimization of the discovered fragments is reported.

Method of preparing and applying single stranded DNA probes to double stranded target DNAs in situ

DOEpatents

Gray, J.W.; Pinkel, D.

1991-07-02

A method is provided for producing single stranded non-self-complementary nucleic acid probes, and for treating target DNA for use therewith. The probe is constructed by treating DNA with a restriction enzyme and an exonuclease to form template/primers for a DNA polymerase. The digested strand is resynthesized in the presence of labeled nucleoside triphosphate precursor. Labeled single stranded fragments are separated from the resynthesized fragments to form the probe. Target DNA is treated with the same restriction enzyme used to construct the probe, and is treated with an exonuclease before application of the probe. The method significantly increases the efficiency and specificity of hybridization mixtures by increasing effective probe concentration by eliminating self-hybridization between both probe and target DNAs, and by reducing the amount of target DNA available for mismatched hybridizations. No Drawings

Design of a multi-purpose fragment screening library using molecular complexity and orthogonal diversity metrics

NASA Astrophysics Data System (ADS)

Lau, Wan F.; Withka, Jane M.; Hepworth, David; Magee, Thomas V.; Du, Yuhua J.; Bakken, Gregory A.; Miller, Michael D.; Hendsch, Zachary S.; Thanabal, Venkataraman; Kolodziej, Steve A.; Xing, Li; Hu, Qiyue; Narasimhan, Lakshmi S.; Love, Robert; Charlton, Maura E.; Hughes, Samantha; van Hoorn, Willem P.; Mills, James E.

2011-07-01

Fragment Based Drug Discovery (FBDD) continues to advance as an efficient and alternative screening paradigm for the identification and optimization of novel chemical matter. To enable FBDD across a wide range of pharmaceutical targets, a fragment screening library is required to be chemically diverse and synthetically expandable to enable critical decision making for chemical follow-up and assessing new target druggability. In this manuscript, the Pfizer fragment library design strategy which utilized multiple and orthogonal metrics to incorporate structure, pharmacophore and pharmacological space diversity is described. Appropriate measures of molecular complexity were also employed to maximize the probability of detection of fragment hits using a variety of biophysical and biochemical screening methods. In addition, structural integrity, purity, solubility, fragment and analog availability as well as cost were important considerations in the selection process. Preliminary analysis of primary screening results for 13 targets using NMR Saturation Transfer Difference (STD) indicates the identification of uM-mM hits and the uniqueness of hits at weak binding affinities for these targets.

Design of a multi-purpose fragment screening library using molecular complexity and orthogonal diversity metrics.

PubMed

Lau, Wan F; Withka, Jane M; Hepworth, David; Magee, Thomas V; Du, Yuhua J; Bakken, Gregory A; Miller, Michael D; Hendsch, Zachary S; Thanabal, Venkataraman; Kolodziej, Steve A; Xing, Li; Hu, Qiyue; Narasimhan, Lakshmi S; Love, Robert; Charlton, Maura E; Hughes, Samantha; van Hoorn, Willem P; Mills, James E

2011-07-01

Fragment Based Drug Discovery (FBDD) continues to advance as an efficient and alternative screening paradigm for the identification and optimization of novel chemical matter. To enable FBDD across a wide range of pharmaceutical targets, a fragment screening library is required to be chemically diverse and synthetically expandable to enable critical decision making for chemical follow-up and assessing new target druggability. In this manuscript, the Pfizer fragment library design strategy which utilized multiple and orthogonal metrics to incorporate structure, pharmacophore and pharmacological space diversity is described. Appropriate measures of molecular complexity were also employed to maximize the probability of detection of fragment hits using a variety of biophysical and biochemical screening methods. In addition, structural integrity, purity, solubility, fragment and analog availability as well as cost were important considerations in the selection process. Preliminary analysis of primary screening results for 13 targets using NMR Saturation Transfer Difference (STD) indicates the identification of uM-mM hits and the uniqueness of hits at weak binding affinities for these targets.

Fragment-based screening by protein crystallography: successes and pitfalls.

PubMed

Chilingaryan, Zorik; Yin, Zhou; Oakley, Aaron J

2012-10-08

Fragment-based drug discovery (FBDD) concerns the screening of low-molecular weight compounds against macromolecular targets of clinical relevance. These compounds act as starting points for the development of drugs. FBDD has evolved and grown in popularity over the past 15 years. In this paper, the rationale and technology behind the use of X-ray crystallography in fragment based screening (FBS) will be described, including fragment library design and use of synchrotron radiation and robotics for high-throughput X-ray data collection. Some recent uses of crystallography in FBS will be described in detail, including interrogation of the drug targets β-secretase, phenylethanolamine N-methyltransferase, phosphodiesterase 4A and Hsp90. These examples provide illustrations of projects where crystallography is straightforward or difficult, and where other screening methods can help overcome the limitations of crystallography necessitated by diffraction quality.

Fragment-Based Screening by Protein Crystallography: Successes and Pitfalls

PubMed Central

Chilingaryan, Zorik; Yin, Zhou; Oakley, Aaron J.

2012-01-01

Fragment-based drug discovery (FBDD) concerns the screening of low-molecular weight compounds against macromolecular targets of clinical relevance. These compounds act as starting points for the development of drugs. FBDD has evolved and grown in popularity over the past 15 years. In this paper, the rationale and technology behind the use of X-ray crystallography in fragment based screening (FBS) will be described, including fragment library design and use of synchrotron radiation and robotics for high-throughput X-ray data collection. Some recent uses of crystallography in FBS will be described in detail, including interrogation of the drug targets β-secretase, phenylethanolamine N-methyltransferase, phosphodiesterase 4A and Hsp90. These examples provide illustrations of projects where crystallography is straightforward or difficult, and where other screening methods can help overcome the limitations of crystallography necessitated by diffraction quality. PMID:23202926

The Complex Stratigraphy of the Highland Crust in the Serenitatis Region of the Moon Inferred from Mineral Fragment Chemistry

NASA Technical Reports Server (NTRS)

Ryder, Graham; Norman, Marc D.; Taylor, G. Jeffrey

1997-01-01

Large impact basins are natural drill holes into the Moon, and their ejecta carries unique information about the rock types and stratigraphy of the lunar crust. We have conducted an electron microprobe study of mineral fragments in the poikilitic melt breccias collected from the Taurus Mountains at the Apollo 17 landing site. These breccias are virtually unanimously agreed to be impact melt produced in the Serenitatis impact event. They contain lithic fragments and much more abundant mineral fragments of crustal origin. We have made precise microprobe analyses of minor element abundances in fragments of olivine, pyroxene, and plagioclase to provide new information on the possible source rocks and the crustal stratigraphy in the Serenitatis region. These data were also intended to elucidate the nature of the cryptic geochemical component in breccias such as these with low-K Fra Mauro basalt compositions. We chose the finest-grained (i.e., most rapidly quenched) breccias for study, to avoid reacted and partly assimilated fragments as much as possible. Most of the mineral fragments appear to have been derived from rocks that would fall into the pristine igneous Mg-suite as represented by lithic fragments in the Apollo collection, or reasonable extensions of it. Gabbroic rocks were more abundant in the target stratigraphy than is apparent from the Apollo sample collection. Some pyroxene and plagiociase, but probably not much olivine, could be derived from feldspathic granulites, which are metamorphosed polymict breccias. Some mineral fragments are from previously unknown rocks. These include highly magnesian olivines (up to Fo(sub 94)), possibly volcanic in origin, that exacerbate the difficulty in explaining highly magnesian rocks in the lunar crust. It appears that some part of the lunar interior has an mg*(= 100 x Mg/(Mg/Fe) atomic) greater than the conventional bulk Moon value of 80-84. Other volcanic rocks, including mare basalts, and rapidly- cooled impact melt

Biosensor-based small molecule fragment screening with biolayer interferometry

NASA Astrophysics Data System (ADS)

Wartchow, Charles A.; Podlaski, Frank; Li, Shirley; Rowan, Karen; Zhang, Xiaolei; Mark, David; Huang, Kuo-Sen

2011-07-01

Biosensor-based fragment screening is a valuable tool in the drug discovery process. This method is advantageous over many biochemical methods because primary hits can be distinguished from non-specific or non-ideal interactions by examining binding profiles and responses, resulting in reduced false-positive rates. Biolayer interferometry (BLI), a technique that measures changes in an interference pattern generated from visible light reflected from an optical layer and a biolayer containing proteins of interest, is a relatively new method for monitoring small molecule interactions. The BLI format is based on a disposable sensor that is immersed in 96-well or 384-well plates. BLI has been validated for small molecule detection and fragment screening with model systems and well-characterized targets where affinity constants and binding profiles are generally similar to those obtained with surface plasmon resonsance (SPR). Screens with challenging targets involved in protein-protein interactions including BCL-2, JNK1, and eIF4E were performed with a fragment library of 6,500 compounds, and hit rates were compared for these targets. For eIF4E, a protein containing a PPI site and a nucleotide binding site, results from a BLI fragment screen were compared to results obtained in biochemical HTS screens. Overlapping hits were observed for the PPI site, and hits unique to the BLI screen were identified. Hit assessments with SPR and BLI are described.

Fragmentation of mercury compounds under ultraviolet light irradiation

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

Kokkonen, E.; Hautala, L.; Jänkälä, K.

2015-08-21

Ultraviolet light induced photofragmentation of mercury compounds is studied experimentally with electron energy resolved photoelectron-photoion coincidence techniques and theoretically with computational quantum chemical methods. A high resolution photoelectron spectrum using synchrotron radiation is presented. Fragmentation of the molecule is studied subsequent to ionization to the atomic-mercury-like d orbitals. State dependent fragmentation behaviour is presented and specific reactions for dissociation pathways are given. The fragmentation is found to differ distinctly in similar orbitals of different mercury compounds.

FIRST experiment: Fragmentation of Ions Relevant for Space and Therapy

NASA Astrophysics Data System (ADS)

Agodi, C.; Abou-Haidar, Z.; Alvarez, M. A. G.; Aumann, T.; Balestra, F.; Battistoni, G.; Bocci, A.; Bohlen, T. T.; Bondì, M.; Boudard, A.; Brunetti, A.; Carpinelli, M.; Cappuzzello, F.; Cavallaro, M.; Carbone, D.; Cirrone, G. A. P.; Cortes-Giraldo, M. A.; Cuttone, G.; De Napoli, M.; Durante, M.; Fernandez-Garcia, J. P.; Finck, C.; Foti, A.; Gallardo, M. I.; Golosio, B.; Iarocci, E.; Iazzi, F.; Ickert, G.; Introzzi, R.; Juliani, D.; Krimmer, J.; Kurz, N.; Labalme, M.; Lavagno, A.; Leifels, Y.; Le Fevre, A.; Leray, S.; Marchetto, F.; Monaco, V.; Morone, M. C.; Nicolosi, D.; Oliva, P.; Paoloni, A.; Patera, V.; Piersanti, L.; Pleskac, R.; Quesada, J. M.; Randazzo, N.; Romano, F.; Rossi, D.; Rosso, V.; Rousseau, M.; Sacchi, R.; Sala, P.; Sarti, A.; Scheidenberger, C.; Schuy, C.; Sciubba, A.; Sfienti, C.; Simon, H.; Sipala, V.; Spiriti, E.; Stuttge, L.; Tropea, S.; Younis, H.

2013-03-01

Nuclear fragmentation processes are relevant in different fields of basic research and applied physics and are of particular interest for tumor therapy and for space radiation protection applications. The FIRST (Fragmentation of Ions Relevant for Space and Therapy) experiment at SIS accelerator of GSI laboratory in Darmstadt, has been designed for the measurement of different ions fragmentation cross sections at different energies between 100 and 1000 MeV/nucleon. The experiment is performed by an international collaboration made of institutions from Germany, France, Italy and Spain. The experimental apparatus is partly based on an already existing setup made of the ALADIN magnet, the MUSIC IV TPC, the LAND2 neutron detector and the TOFWALL scintillator TOF system, integrated with newly designed detectors in the interaction Region (IR) around the carbon removable target: a scintillator Start Counter, a Beam Monitor drift chamber, a silicon Vertex Detector and a Proton Tagger for detection of light fragments emitted at large angles (KENTROS). The scientific program of the FIRST experiment started on summer 2011 with the study of the 400 MeV/nucleon 12C beam fragmentation on thin (8mm) carbon target.

Methods and apparatus for producing cryogenic inertially driven fusion targets

DOEpatents

Miller, John R.

1981-01-01

A new technique for producing uniform layers of solid DT on microballoon surfaces. Local heating of the target, typically by means of a focused laser, within an isothermal freezing cell containing a low pressure cryogenic exchange gas such as helium, vaporizes the DT fuel. Removal of the laser heating source causes the DT gas to rapidly condense and freeze in a layer which exhibits a good degree of uniformity.

Fragment-based drug discovery using rational design.

PubMed

Jhoti, H

2007-01-01

Fragment-based drug discovery (FBDD) is established as an alternative approach to high-throughput screening for generating novel small molecule drug candidates. In FBDD, relatively small libraries of low molecular weight compounds (or fragments) are screened using sensitive biophysical techniques to detect their binding to the target protein. A lower absolute affinity of binding is expected from fragments, compared to much higher molecular weight hits detected by high-throughput screening, due to their reduced size and complexity. Through the use of iterative cycles of medicinal chemistry, ideally guided by three-dimensional structural data, it is often then relatively straightforward to optimize these weak binding fragment hits into potent and selective lead compounds. As with most other lead discovery methods there are two key components of FBDD; the detection technology and the compound library. In this review I outline the two main approaches used for detecting the binding of low affinity fragments and also some of the key principles that are used to generate a fragment library. In addition, I describe an example of how FBDD has led to the generation of a drug candidate that is now being tested in clinical trials for the treatment of cancer.

Kinematics of current region fragmentation in semi-inclusive deeply inelastic scattering

DOE PAGES

Boglione, M.; Collins, J.; Gamberg, L.; ...

2017-01-16

Different kinematical regions of semi-inclusive deeply inelastic scattering (SIDIS) processes correspond to different underlying partonic pictures, and it is important to understand the transition between them. We find criteria in semi-inclusive deeply inelastic scattering (SIDIS) for identifying the current fragmentation region — the kinematical region where a factorization picture with fragmentation functions is appropriate, especially for studies of transverse-momentum-dependent (TMD) functions. This region is distinguished from the central (soft) and target fragmentation regions. The basis of our argument is in the errors in approximations used in deriving factorization. As compared with previous work, we show that it is essential tomore » take account of the transverse momentum of the detected hadron, and we find a much more restricted range for genuine current fragmentation. As a result, we show that it is important to develop an extended factorization formulation to treat hadronization in the central region, as well as the current and target fragmentation regions, and to obtain a unified formalism spanning all rapidities for the detected hadron.« less

Fragmentation of alpha-Radical Cations of Arginine-Containing Peptides

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

Laskin, Julia; Yang, Zhibo; Ng, Dominic C.

2010-04-01

Fragmentation pathways of peptide radical cations, M+, with well-defined initial location of the radical site were explored using collision-induced dissociation (CID) experiments. Peptide radical cations were produced by gas-phase fragmentation of CoIII(salen)-peptide complexes [salen = N,N´-ethylenebis (salicylideneaminato)]. Subsequent hydrogen abstraction from the -carbon of the side chain followed by Ca-C bond cleavage results in the loss of a neutral side chain and formation of an a-radical cation with the radical site localized on the a-carbon of the backbone. Similar CID spectra dominated by radical-driven dissociation products were obtained for a number of a-radicals when the basic arginine side chain wasmore » present in the sequence. In contrast, proton-driven fragmentation dominates CID spectra of a-radicals produced via the loss of the arginine side chain. Our results suggest that in most cases radical migration precedes fragmentation of large peptide radical cations.« less

Uterine progesterone signaling is a target for metformin therapy in PCOS-like rats.

PubMed

Hu, Min; Zhang, Yuehui; Feng, Jiaxing; Xu, Xue; Zhang, Jiao; Zhao, Wei; Guo, Xiaozhu; Li, Juan; Vestin, Edvin; Cui, Peng; Li, Xin; Wu, Xiao-Ke; Brännström, Mats; Shao, Linus R; Billig, Håkan

2018-05-01

Impaired progesterone (P4) signaling is linked to endometrial dysfunction and infertility in women with polycystic ovary syndrome (PCOS). Here, we report for the first time that elevated expression of progesterone receptor (PGR) isoforms A and B parallels increased estrogen receptor (ER) expression in PCOS-like rat uteri. The aberrant PGR-targeted gene expression in PCOS-like rats before and after implantation overlaps with dysregulated expression of Fkbp52 and Ncoa2 , two genes that contribute to the development of uterine P4 resistance. In vivo and in vitro studies of the effects of metformin on the regulation of the uterine P4 signaling pathway under PCOS conditions showed that metformin directly inhibits the expression of PGR and ER along with the regulation of several genes that are targeted dependently or independently of PGR-mediated uterine implantation. Functionally, metformin treatment corrected the abnormal expression of cell-specific PGR and ER and some PGR-target genes in PCOS-like rats with implantation. Additionally, we documented how metformin contributes to the regulation of the PGR-associated MAPK/ERK/p38 signaling pathway in the PCOS-like rat uterus. Our data provide novel insights into how metformin therapy regulates uterine P4 signaling molecules under PCOS conditions. © 2018 Society for Endocrinology.

Characterization of airborne ice-nucleation-active bacteria and bacterial fragments

NASA Astrophysics Data System (ADS)

Šantl-Temkiv, Tina; Sahyoun, Maher; Finster, Kai; Hartmann, Susan; Augustin-Bauditz, Stefanie; Stratmann, Frank; Wex, Heike; Clauss, Tina; Nielsen, Niels Woetmann; Sørensen, Jens Havskov; Korsholm, Ulrik Smith; Wick, Lukas Y.; Karlson, Ulrich Gosewinkel

2015-05-01

Some bacteria have the unique capacity of synthesising ice-nucleation-active (INA) proteins and exposing them at their outer membrane surface. As INA bacteria enter the atmosphere, they may impact the formation of clouds and precipitation. We studied members of airborne bacterial communities for their capacity to catalyse ice formation and we report on the excretion of INA proteins by airborne Pseudomonas sp. We also observed for the first time that INA biological fragments <220 nm were present in precipitation samples (199 and 482 INA fragments per L of precipitation), which confirms the presence of submicron INA biological fragments in the atmosphere. During 14 precipitation events, strains affiliated with the genus Pseudomonas, which are known to carry ina genes, were dominant. A screening for INA properties revealed that ∼12% of the cultivable bacteria caused ice formation at ≤-7 °C. They had likely been emitted to the atmosphere from terrestrial surfaces, e.g. by convective transport. We tested the ability of isolated INA strains to produce outer membrane vesicles and found that two isolates could do so. However, only very few INA vesicles were released per INA cell. Thus, the source of the submicron INA proteinaceous particles that we detected in the atmosphere remains to be elucidated.

Tank fragmentation test

NASA Technical Reports Server (NTRS)

Daye, C. J.; Cooksey, D.; Walters, R. J.; Auble, A. E.

1973-01-01

A photographic study of a simulated tank fragmentation test was made. Sixteen disks and four spheres were ejected from a test article mounted in a vertical orientation 110 ft above a target installed on the test chamber floor. The test was performed at a chamber pressure of 25 microns. Velocities at impingement on the target ranged from 88 to 120 ft/sec; corresponding ejection velocities at the exit plane of the ejector assembly ranged from 29 to 87 ft/sec. Tumble axes of the disks were expected to be all in the north-south direction; the majority of those measured were, while some were skewed from this direction, the maximum observed being 90 deg. A typical measured tumble rate was 2.4 turns/sec. The dispersion pattern measured on the target was reasonably regular, and measured approximately 16 ft east-to-west by 11 ft north-to-south.

A fragment-based approach applied to a highly flexible target: Insights and challenges towards the inhibition of HSP70 isoforms

NASA Astrophysics Data System (ADS)

Jones, Alan M.; Westwood, Isaac M.; Osborne, James D.; Matthews, Thomas P.; Cheeseman, Matthew D.; Rowlands, Martin G.; Jeganathan, Fiona; Burke, Rosemary; Lee, Diane; Kadi, Nadia; Liu, Manjuan; Richards, Meirion; McAndrew, Craig; Yahya, Norhakim; Dobson, Sarah E.; Jones, Keith; Workman, Paul; Collins, Ian; van Montfort, Rob L. M.

2016-10-01

The heat shock protein 70s (HSP70s) are molecular chaperones implicated in many cancers and of significant interest as targets for novel cancer therapies. Several HSP70 inhibitors have been reported, but because the majority have poor physicochemical properties and for many the exact mode of action is poorly understood, more detailed mechanistic and structural insight into ligand-binding to HSP70s is urgently needed. Here we describe the first comprehensive fragment-based inhibitor exploration of an HSP70 enzyme, which yielded an amino-quinazoline fragment that was elaborated to a novel ATP binding site ligand with different physicochemical properties to known adenosine-based HSP70 inhibitors. Crystal structures of amino-quinazoline ligands bound to the different conformational states of the HSP70 nucleotide binding domain highlighted the challenges of a fragment-based approach when applied to this particular flexible enzyme class with an ATP-binding site that changes shape and size during its catalytic cycle. In these studies we showed that Ser275 is a key residue in the selective binding of ATP. Additionally, the structural data revealed a potential functional role for the ATP ribose moiety in priming the protein for the formation of the ATP-bound pre-hydrolysis complex by influencing the conformation of one of the phosphate binding loops.

Fungal Fragments as Indoor Air Biocontaminants

PubMed Central

Górny, Rafał L.; Reponen, Tiina; Willeke, Klaus; Schmechel, Detlef; Robine, Enric; Boissier, Marjorie; Grinshpun, Sergey A.

2002-01-01

The aerosolization process of fungal propagules of three species (Aspergillus versicolor, Penicillium melinii, and Cladosporium cladosporioides) was studied by using a newly designed and constructed aerosolization chamber. We discovered that fungal fragments are aerosolized simultaneously with spores from contaminated agar and ceiling tile surfaces. Concentration measurements with an optical particle counter showed that the fragments are released in higher numbers (up to 320 times) than the spores. The release of fungal propagules varied depending on the fungal species, the air velocity above the contaminated surface, and the texture and vibration of the contaminated material. In contrast to spores, the release of fragments from smooth surfaces was not affected by air velocity, indicating a different release mechanism. Correlation analysis showed that the number of released fragments cannot be predicted on the basis of the number of spores. Enzyme-linked immunosorbent assays with monoclonal antibodies produced against Aspergillus and Penicillium fungal species showed that fragments and spores share common antigens, which not only confirmed the fungal origin of the fragments but also established their potential biological relevance. The considerable immunological reactivity, the high number, and the small particle size of the fungal fragments may contribute to human health effects that have been detected in buildings with mold problems but had no scientific explanation until now. This study suggests that future fungal spore investigations in buildings with mold problems should include the quantitation of fungal fragments. PMID:12089037

Fragment screening for drug leads by weak affinity chromatography (WAC-MS).

PubMed

Ohlson, Sten; Duong-Thi, Minh-Dao

2018-02-23

Fragment-based drug discovery is an important tool for design of small molecule hit-to-lead compounds against various biological targets. Several approved drugs have been derived from an initial fragment screen and many such candidates are in various stages of clinical trials. Finding fragment hits, that are suitable for optimisation by medicinal chemists, is still a challenge as the binding between the small fragment and its target is weak in the range of mM to µM of K d and irrelevant non-specific interactions are abundant in this area of transient interactions. Fortunately, there are methods that can study weak interactions quite efficiently of which NMR, surface plasmon resonance (SPR) and X-ray crystallography are the most prominent. Now, a new technology based on zonal affinity chromatography, weak affinity chromatography (WAC), has been introduced which has remedied many of the problems with other technologies. By combining WAC with mass spectrometry (WAC-MS), it is a powerful tool to identify binders quantitatively in terms of affinity and kinetics either from fragment libraries or from complex mixtures of biological extracts. As WAC-MS can be multiplexed by analysing mixtures of fragments (20-100 fragments) in one sample, this approach yields high throughput, where a whole library of e.g. >2000 fragments can be analysed quantitatively within a day. WAC-MS is easy to perform, where the robustness and quality of HPLC is fully utilized. This review will highlight the rationale behind the application of WAC-MS for fragment screening in drug discovery. Copyright © 2018 Elsevier Inc. All rights reserved.

Total reaction cross sections and neutron-removal cross sections of neutron-rich light nuclei measured by the COMBAS fragment-separator

NASA Astrophysics Data System (ADS)

Hue, B. M.; Isataev, T.; Erdemchimeg, B.; Artukh, A. G.; Aznabaev, D.; Davaa, S.; Klygin, S. A.; Kononenko, G. A.; Khuukhenkhuu, G.; Kuterbekov, K.; Lukyanov, S. M.; Mikhailova, T. I.; Maslov, V. A.; Mendibaev, K.; Sereda, Yu M.; Penionzhkevich, Yu E.; Vorontsov, A. N.

2017-12-01

Preliminary results of measurements of the total reaction cross sections σR and neutron removal cross section σ-xn for weakly bound 6He, 8Li, 9Be and 10Be nuclei at energy range (20-35) A MeV with 28Si target is presented. The secondary beams of light nuclei were produced by bombardment of the 22Ne (35 A MeV) primary beam on Be target and separated by COMBAS fragment-separator. In dispersive focal plane a horizontal slit defined the momentum acceptance as 1% and a wedge degrader of 200 μm Al was installed. The Bρ of the second section of the fragment-separator was adjusted for measurements in energy range (20-35) A MeV. Two-neutron removal cross sections for 6He and 10Be and one -neutron removal cross sections 8Li and 9Be were measured.

Cloning, expression and characterisation of an HtrA-like serine protease produced in vivo by Mycobacterium leprae.

PubMed

Ribeiro-Guimarães, Michelle Lopes; Marengo, Eliana Blini; Tempone, Antonio Jorge; Amaral, Julio Jablonski; Klitzke, Clécio F; Silveira, Erika K Xavier da; Portaro, Fernanda Calheta Vieira; Pessolani, Maria Cristina Vidal

2009-12-01

Members of the high temperature requirement A (HtrA) family of chaperone proteases have been shown to play a role in bacterial pathogenesis. In a recent report, we demonstrated that the gene ML0176, which codes for a predicted HtrA-like protease, a gene conserved in other species of mycobacteria, is transcribed by Mycobacterium leprae in human leprosy lesions. In the present study, the recombinant ML0176 protein was produced and its enzymatic properties investigated. M. lepraerecombinant ML0176 was able to hydrolyse a variety of synthetic and natural peptides. Similar to other HtrA proteins, this enzyme displayed maximum proteolytic activity at temperatures above 40 degrees C and was completely inactivated by aprotinin, a protease inhibitor with high selectivity for serine proteases. Finally, analysis of M. leprae ML0176 specificity suggested a broader cleavage preference than that of previously described HtrAs homologues. In summary, we have identified an HtrA-like protease in M. lepraethat may constitute a potential new target for the development of novel prophylactic and/or therapeutic strategies against mycobacterial infections.

Discrimination between landmine and mine-like targets using wavelets and spectral analysis

NASA Astrophysics Data System (ADS)

Mohana, Mahmoud A.; Abbas, Abbas M.; Gomaa, Mohamed L.; Ebrahim, Shereen M.

2013-06-01

Landmine is an explosive apparatus hidden in or on the ground, which blows up when a person or vehicle passes over it. Egypt is one of the countries suffering due to the unexploded ordnance (UXO). Around 2 million UXO are present in the Egyptian soil especially at Al-Alameen province, north of the western desert. Detection of buried landmines is a problem of military and humanitarian importance. Ground penetrating radar (GPR) is a powerful and non-destructive geophysical approach with a wide range of advantages in the field of landmine inspection. In the present paper, we apply different simulation models with Vivaldi antenna and mine-like targets by using the CST Microwave studio program. The field work is carried out by using a GPR device of model SIR 2000 from GSSI (Geophysical Survey Systems Incorporation) connected to 900 MHz antenna where the targets were buried in sand soil. Depending on the fact that the receiving powers (reflected, refracted and scattered) from the different materials are different, we study the spectral power densities for the received power from the different targets. The techniques used in this study are: direct fast Fourier transform, short time Fourier transform (spectrogram), wavelets transform and denoising techniques. Our results ought to be considered as finger prints for different scanned targets during this work. So we can discriminate between landmines and mine-like targets.

Charged Particle Identification for Prefragmentation Studies

NASA Astrophysics Data System (ADS)

Hu, Jonathan; MoNA Collaboration

2017-09-01

Projectile fragmentation refers to high energy (>50 MeV/u) heavy ion beams on production targets to generate intermediate mass and target fragments at facilities like the NSCL, FRIB, GSI, GANIL and RIKEN. The resulting secondary beams can then be isolated by fragment separators like the NCSL's A1900 and that secondary beam then used on reaction targets for a variety of experiments. Predictions of beam intensities for experiment planning depend on models and data. The MoNA Collaboration performed an experiment at the NSCL in which a 48Ca primary beam was used with a 9Be target to produce a 32Mg secondary beam with energy 86 MeV/u that was incident on a second target of 9Be. By characterizing the energy distributions of final fragments of neon, sodium, and fluorine in coincidence with neutrons created both by prefragmentation processes and reaction mechanisms, we are able to extract information about prefragmentation dynamics. The identification of charged fragments is a multi-step process crucial to this analysis. This work is supported by the National Science Foundation under Grant No. PHY-1613429.

Stable expression and purification of a functional processed Fab' fragment from a single nascent polypeptide in CHO cells expressing the mCAT-1 retroviral receptor.

PubMed

Camper, Nicolas; Byrne, Teresa; Burden, Roberta E; Lowry, Jenny; Gray, Breena; Johnston, James A; Migaud, Marie E; Olwill, Shane A; Buick, Richard J; Scott, Christopher J

2011-09-30

Monoclonal antibodies and derivative formats such as Fab' fragments are used in a broad range of therapeutic, diagnostic and research applications. New systems and methodologies that can improve the production of these proteins are consequently of much interest. Here we present a novel approach for the rapid production of processed Fab' fragments in a CHO cell line that has been engineered to express the mouse cationic amino acid transporter receptor 1 (mCAT-1). This facilitated the introduction of the target antibody gene through retroviral transfection, rapidly producing stable expression. Using this system, we designed a single retroviral vector construct for the expression of a target Fab' fragment as a single polypeptide with a furin cleavage site and a FMDV 2A self-cleaving peptide introduced to bridge the light and truncated heavy chain regions. The introduction of these cleavage motifs ensured equimolar expression and processing of the heavy and light domains as exemplified by the production of an active chimeric Fab' fragment against the Fas receptor, routinely expressed in 1-2mg/L yield in spinner-flask cell cultures. These results demonstrate that this method could have application in the facile production of bioactive Fab' fragments. Copyright © 2011 Elsevier B.V. All rights reserved.

Conserved stem fragment from H3 influenza hemagglutinin elicits cross-clade neutralizing antibodies through stalk-targeted blocking of conformational change during membrane fusion.

PubMed

Gong, Xin; Yin, He; Shi, Yuhua; Guan, Shanshan; He, Xiaoqiu; Yang, Lan; Yu, Yongjiao; Kuai, Ziyu; Jiang, Chunlai; Kong, Wei; Wang, Song; Shan, Yaming

2016-04-01

Currently available influenza vaccines typically fail to elicit/boost broadly neutralizing antibodies due to the mutability of virus sequences and conformational changes during protective immunity, thereby limiting their efficacy. This problem needs to be addressed by further understanding the mechanisms of neutralization and finding the desired neutralizing site during membrane fusion. This study specifically focused on viruses of the H3N2 subtype, which have persisted as a principal source of influenza-related morbidity and mortality in humans since the 1968 influenza pandemic. Through sequence alignment and epitope prediction, a series of highly conserved stem fragments (spanning 47 years) were found and coupled to the Keyhole Limpet Hemocyanin (KLH) protein. By application of a combinatorial display library and crystal structure modeling, a stem fragment immunogen, located at the turning point of the HA neck undergoing conformational change during membrane fusion with both B- and T-cell epitopes, was identified. After synthesis of the optimal stem fragment using a multiple antigen peptide (MAP) system, strong humoral immune responses and cross-clade neutralizing activities against strains from the H3 subtype of group 2 influenza viruses after animal immunizations were observed. By detection of nuclear protein immunofluorescence with acid bypass treatment, antisera raised against MAP4 immunogens of the stem fragment showed the potential to inhibit the conformational change of HA in stem-targeted virus neutralization. The identification of this conserved stem fragment provides great potential for exploitation of this site of vulnerability in therapeutic and vaccine design. Copyright © 2016 European Federation of Immunological Societies. Published by Elsevier B.V. All rights reserved.

Proton induced target fragmentation studies on solid state nuclear track detectors using Carbon radiators

NASA Astrophysics Data System (ADS)

Szabó, J.; Pálfalvi, J. K.; Strádi, A.; Bilski, P.; Swakoń, J.; Stolarczyk, L.

2018-04-01

One of the limiting factors of an astronaut's career is the dose received from space radiation. High energy protons, being the main components of the complex radiation field present on a spacecraft, give a significant contribution to the dose. To investigate the behavior of solid state nuclear track detectors (SSNTDs) if they are irradiated by such particles, SSNTD stacks containing carbon blocks were exposed to high energy proton beams (70, 100, 150 and 230 MeV) at the Proteus cyclotron, IFJ PAN -Krakow. The incident protons cannot be detected directly; however, tracks of secondary particles, recoils and fragments of the constituent atoms of the detector material and of the carbon radiator are formed. It was found that as the proton energy increases, the number of tracks induced in the PADC material by secondary particles decreases. From the measured geometrical parameters of the tracks the linear energy transfer (LET) spectrum and the dosimetric quantities were determined, applying appropriate calibration. In the LET spectra the LET range of the most important secondary particles could be identified and their abundance showed differences in the spectra if the detectors were short or long etched. The LET spectra obtained on the SSNTDs irradiated by protons were compared to LET spectra of detectors flown on the International Space Station (ISS): they were quite similar, resulting in a quality factor difference of only 5%. Thermoluminescent detectors (TLDs) were applied in each case to measure the dose from primary protons and other lower LET particles present in space. Comparing and analyzing the results of the TLD and SSNTD measurements, it was obtained that proton induced target fragments contributed to the total absorbed dose in 3.2% and to the dose equivalent in 14.2% in this particular space experiment.

Low-energy mass-selected ion beam production of fragments produced from hexamethyldisilane for SiC film formation

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

Yoshimura, Satoru, E-mail: yosimura@ppl.eng.osaka-u.ac.jp; Sugimoto, Satoshi; Kiuchi, Masato

2016-03-14

We have proposed an experimental methodology which makes it possible to deposit silicon carbide (SiC) films on Si substrates with a low-energy mass-selected ion beam system using hexamethyldisilane (HMD) as a gas source. In this study, one of the fragment ions produced from HMD, SiCH{sub 4}{sup +}, was mass-selected. The ion energy was approximately 100 eV. Then, the SiCH{sub 4}{sup +} ions were irradiated to a Si(100) substrate. When the temperature of the Si substrate was set at 800 °C during the ion irradiation, the X-ray diffraction and Raman spectroscopy of the substrate following the completion of ion irradiation experiment demonstrated themore » occurrence of 3C-SiC deposition.« less

Characteristic fragment size distributions in dynamic fragmentation

NASA Astrophysics Data System (ADS)

Zhou, Fenghua; Molinari, Jean-François; Ramesh, K. T.

2006-06-01

The one-dimensional fragmentation of a dynamically expanding ring (Mott's problem) is studied numerically to obtain the fragment signatures under different strain rates. An empirical formula is proposed to calculate an average fragment size. Rayleigh distribution is found to describe the statistical properties of the fragment populations.

Endogenous proteolytic cleavage of disease-associated prion protein to produce C2 fragments is strongly cell- and tissue-dependent.

PubMed

Dron, Michel; Moudjou, Mohammed; Chapuis, Jérôme; Salamat, Muhammad Khalid Farooq; Bernard, Julie; Cronier, Sabrina; Langevin, Christelle; Laude, Hubert

2010-04-02

The abnormally folded form of the prion protein (PrP(Sc)) accumulating in nervous and lymphoid tissues of prion-infected individuals can be naturally cleaved to generate a N-terminal-truncated fragment called C2. Information about the identity of the cellular proteases involved in this process and its possible role in prion biology has remained limited and controversial. We investigated PrP(Sc) N-terminal trimming in different cell lines and primary cultured nerve cells, and in the brain and spleen tissue from transgenic mice infected by ovine and mouse prions. We found the following: (i) the full-length to C2 ratio varies considerably depending on the infected cell or tissue. Thus, in primary neurons and brain tissue, PrP(Sc) accumulated predominantly as untrimmed species, whereas efficient trimming occurred in Rov and MovS cells, and in spleen tissue. (ii) Although C2 is generally considered to be the counterpart of the PrP(Sc) proteinase K-resistant core, the N termini of the fragments cleaved in vivo and in vitro can actually differ, as evidenced by a different reactivity toward the Pc248 anti-octarepeat antibody. (iii) In lysosome-impaired cells, the ratio of full-length versus C2 species dramatically increased, yet efficient prion propagation could occur. Moreover, cathepsin but not calpain inhibitors markedly inhibited C2 formation, and in vitro cleavage by cathepsins B and L produced PrP(Sc) fragments lacking the Pc248 epitope, strongly arguing for the primary involvement of acidic hydrolases of the endolysosomal compartment. These findings have implications on the molecular analysis of PrP(Sc) and cell pathogenesis of prion infection.

Endogenous Proteolytic Cleavage of Disease-associated Prion Protein to Produce C2 Fragments Is Strongly Cell- and Tissue-dependent*

PubMed Central

Dron, Michel; Moudjou, Mohammed; Chapuis, Jérôme; Salamat, Muhammad Khalid Farooq; Bernard, Julie; Cronier, Sabrina; Langevin, Christelle; Laude, Hubert

2010-01-01

The abnormally folded form of the prion protein (PrPSc) accumulating in nervous and lymphoid tissues of prion-infected individuals can be naturally cleaved to generate a N-terminal-truncated fragment called C2. Information about the identity of the cellular proteases involved in this process and its possible role in prion biology has remained limited and controversial. We investigated PrPSc N-terminal trimming in different cell lines and primary cultured nerve cells, and in the brain and spleen tissue from transgenic mice infected by ovine and mouse prions. We found the following: (i) the full-length to C2 ratio varies considerably depending on the infected cell or tissue. Thus, in primary neurons and brain tissue, PrPSc accumulated predominantly as untrimmed species, whereas efficient trimming occurred in Rov and MovS cells, and in spleen tissue. (ii) Although C2 is generally considered to be the counterpart of the PrPSc proteinase K-resistant core, the N termini of the fragments cleaved in vivo and in vitro can actually differ, as evidenced by a different reactivity toward the Pc248 anti-octarepeat antibody. (iii) In lysosome-impaired cells, the ratio of full-length versus C2 species dramatically increased, yet efficient prion propagation could occur. Moreover, cathepsin but not calpain inhibitors markedly inhibited C2 formation, and in vitro cleavage by cathepsins B and L produced PrPSc fragments lacking the Pc248 epitope, strongly arguing for the primary involvement of acidic hydrolases of the endolysosomal compartment. These findings have implications on the molecular analysis of PrPSc and cell pathogenesis of prion infection. PMID:20154089

The discovery of cholera - like enterotoxins produced by Escherichia coli causing secretory diarrhoea in humans

PubMed Central

Sack, R. Bradley

2011-01-01

Non-vibrio cholera has been recognized as a clinical entity for as long as cholera was known to be caused by Vibrio cholerae. Until 1968, the aetiologic agent of this syndrome was not known. Following a series of studies in patients with non-vibrio cholera it was found that these patients had large concentrations of Escherichia coli in the small bowel and stools which produced cholera toxin-like enterotoxins, and had fluid and electrolyte transport abnormalities in the small bowel similar to patients with documented cholera. Furthermore, these patients developed antibodies to the cholera-like enterotoxin. Later studies showed that these strains, when fed to volunteers produced a cholera-like disease and that two enterotoxins were found to be produced by these organisms: a heat-labile enterotoxin (LT) which is nearly identical to cholera toxin, and a heat-stable enterotoxin (ST), a small molecular weight polypeptide. E. coli that produced one or both of these enterotoxins were designated enterotoxigenic E. coli (ETEC). ETEC are now known not only to cause a severe cholera-like illness, but to be the most common bacterial cause of acute diarrhoea in children in the developing world, and to be the most common cause of travellers’ diarrhoea in persons who visit the developing world. PMID:21415491

An analysis of the wounding factors of four different shapes of fragments.

PubMed

Ma, Y Y; Feng, T S; Fu, R X; Li, M

1988-01-01

The wounding characteristics to a biological target of four typical shapes of fragments (square, triangular, cylindrical, and spherical) with masses of less than 1 gram and velocities between 460 and 1,500 m/s are studied in this paper. The following conclusions about the effects of the wounding factors, such as energy transfer, velocity, mass, and shape of fragment are presented: 1) For given target characteristics, the important wounding factors of fragments are impact velocity, mass, and shape, and of these velocity is the most important. 2) Besides direct effects, the fragment velocity has great influence on far-reaching, indirect wounding effects. When velocity increases, it not only increases the size of direct wound, but also the rate of indirect bone fracture. 3) The rate of energy transfer is affected by fragment shape, and it is also a decreasing function of mass. 4) Under the same conditions there are differences in wounding effectiveness among the four fragment shapes, the triangular with a comparatively high wounding effectiveness, followed by the square, cylindrical, and spherical. The types of wound channels are also different, the cylindrical and spherical making a "through" type, the square and triangular making a "blind-tube" type.

A Ligand-observed Mass Spectrometry Approach Integrated into the Fragment Based Lead Discovery Pipeline

PubMed Central

Chen, Xin; Qin, Shanshan; Chen, Shuai; Li, Jinlong; Li, Lixin; Wang, Zhongling; Wang, Quan; Lin, Jianping; Yang, Cheng; Shui, Wenqing

2015-01-01

In fragment-based lead discovery (FBLD), a cascade combining multiple orthogonal technologies is required for reliable detection and characterization of fragment binding to the target. Given the limitations of the mainstream screening techniques, we presented a ligand-observed mass spectrometry approach to expand the toolkits and increase the flexibility of building a FBLD pipeline especially for tough targets. In this study, this approach was integrated into a FBLD program targeting the HCV RNA polymerase NS5B. Our ligand-observed mass spectrometry analysis resulted in the discovery of 10 hits from a 384-member fragment library through two independent screens of complex cocktails and a follow-up validation assay. Moreover, this MS-based approach enabled quantitative measurement of weak binding affinities of fragments which was in general consistent with SPR analysis. Five out of the ten hits were then successfully translated to X-ray structures of fragment-bound complexes to lay a foundation for structure-based inhibitor design. With distinctive strengths in terms of high capacity and speed, minimal method development, easy sample preparation, low material consumption and quantitative capability, this MS-based assay is anticipated to be a valuable addition to the repertoire of current fragment screening techniques. PMID:25666181

Production of spin-polarized radioactive ion beams via projectile fragmentation reaction

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

Kameda, D.; Ueno, H.; Yoshimi, A.

2008-02-06

Spin-polarized radioactive ion beams are produced in the projectile fragmentation reaction induced by intermediate-energy heavy ion beams. The degree of spin polarization shows characteristic dependence on the outgoing momentum of the projectile fragment in the magnitude around 1{approx}10%. The qualitative behavior is well described by the kinematical model of the fragmentation process. Recently, we have successfully produced spin-polarized beams of aluminum isotopes in the mass A{approx}30 region via the fragmentation of 95 MeV/u {sup 40}Ar projectiles. The magnetic moments of {sup 30}Al and {sup 32}Al and the electric quadrupole moments of {sup 31}Al and {sup 32}Al have been measured usingmore » the {beta}-NMR technique with the polarized RI beams of the Al isotopes.« less

Native and exotic plants of fragments of sagebrush steppe produced by geomorphic processes versus land use

USGS Publications Warehouse

Huntly, N.; Bangert, R.; Hanser, S.E.

2011-01-01

Habitat fragmentation and invasion by exotic species are regarded as major threats to the biodiversity of many ecosystems. We surveyed the plant communities of two types of remnant sagebrush-steppe fragments from nearby areas on the Snake River Plain of southeastern Idaho, USA. One type resulted from land use (conversion to dryland agriculture; hereafter AG Islands) and the other from geomorphic processes (Holocene volcanism; hereafter kipukas). We assessed two predictions for the variation in native plant species richness of these fragments, using structural equation models (SEM). First, we predicted that the species richness of native plants would follow the MacArthur-Wilson (M-W) hypothesis of island biogeography, as often is expected for the communities of habitat fragments. Second, we predicted a negative relationship between native and exotic plants, as would be expected if exotic plants are decreasing the diversity of native plants. Finally, we assessed whether exotic species were more strongly associated with the fragments embedded in the agricultural landscape, as would be expected if agriculture had facilitated the introduction and naturalization of non-native species, and whether the communities of the two types of fragments were distinct. Species richness of native plants was not strongly correlated with M-W characteristics for either the AG Islands or the **kipukas. The AG Islands had more species and higher cover of exotics than the kipukas, and exotic plants were good predictors of native plant species richness. Our results support the hypothesis that proximity to agriculture can increase the diversity and abundance of exotic plants in native habitat. In combination with other information, the results also suggest that agriculture and exotic species have caused loss of native diversity and reorganization of the sagebrush-steppe plant community. ?? 2011 Springer Science+Business Media B.V.

High-intensity laser-accelerated ion beam produced from cryogenic micro-jet target

DOE PAGES

Gauthier, M.; Kim, J. B.; Curry, C. B.; ...

2016-08-24

Here, we report on the successful operation of a newly developed cryogenic jet target at high intensity laser-irradiation. Using the frequency-doubled Titan short pulse laser system at Jupiter Laser Facility, Lawrence Livermore National Laboratory, we demonstrate the generation of a pure proton beam a with maximum energy of 2 MeV. Furthermore, we record a quasi-monoenergetic peak at 1.1 MeV in the proton spectrum emitted in the laser forward direction suggesting an alternative acceleration mechanism. Using a solid-density mixed hydrogen-deuterium target, we are also able to produce pure proton-deuteron ion beams. With its high purity, limited size, near-critical density, and high-repetitionmore » rate capability, this target is promising for future applications.« less

High-intensity laser-accelerated ion beam produced from cryogenic micro-jet target

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

Gauthier, M., E-mail: maxence.gauthier@stanford.edu; Kim, J. B.; Curry, C. B.

2016-11-15

We report on the successful operation of a newly developed cryogenic jet target at high intensity laser-irradiation. Using the frequency-doubled Titan short pulse laser system at Jupiter Laser Facility, Lawrence Livermore National Laboratory, we demonstrate the generation of a pure proton beam a with maximum energy of 2 MeV. Furthermore, we record a quasi-monoenergetic peak at 1.1 MeV in the proton spectrum emitted in the laser forward direction suggesting an alternative acceleration mechanism. Using a solid-density mixed hydrogen-deuterium target, we are also able to produce pure proton-deuteron ion beams. With its high purity, limited size, near-critical density, and high-repetition ratemore » capability, this target is promising for future applications.« less

Ketamine produces antidepressant-like effects through phosphorylation-dependent nuclear export of histone deacetylase 5 (HDAC5) in rats

PubMed Central

Choi, Miyeon; Lee, Seung Hoon; Wang, Sung Eun; Ko, Seung Yeon; Song, Mihee; Choi, June-Seek; Duman, Ronald S.; Son, Hyeon

2015-01-01

Ketamine produces rapid antidepressant-like effects in animal assays for depression, although the molecular mechanisms underlying these behavioral actions remain incomplete. Here, we demonstrate that ketamine rapidly stimulates histone deacetylase 5 (HDAC5) phosphorylation and nuclear export in rat hippocampal neurons through calcium/calmodulin kinase II- and protein kinase D-dependent pathways. Consequently, ketamine enhanced the transcriptional activity of myocyte enhancer factor 2 (MEF2), which leads to regulation of MEF2 target genes. Transfection of a HDAC5 phosphorylation-defective mutant (Ser259/Ser498 replaced by Ala259/Ala498, HDAC5-S/A), resulted in resistance to ketamine-induced nuclear export, suppression of ketamine-mediated MEF2 transcriptional activity, and decreased expression of MEF2 target genes. Behaviorally, viral-mediated hippocampal knockdown of HDAC5 blocked or occluded the antidepressant effects of ketamine both in unstressed and stressed animals. Taken together, our results reveal a novel role of HDAC5 in the actions of ketamine and suggest that HDAC5 could be a potential mechanism contributing to the therapeutic actions of ketamine. PMID:26647181

Self-proton/ion radiography of laser-produced proton/ion beam from thin foil targets

NASA Astrophysics Data System (ADS)

Paudel, Y.; Renard-Le Galloudec, N.; Nicolai, Ph.; d'Humieres, E.; Ya. Faenov, A.; Kantsyrev, V. L.; Safronova, A. S.; Shrestha, I.; Osborne, G. C.; Shlyaptseva, V. V.; Sentoku, Y.

2012-12-01

Protons and multicharged ions generated from high-intensity laser interactions with thin foil targets have been studied with a 100 TW laser system. Protons/ions with energies up to 10 MeV are accelerated either from the front or the rear surface of the target material. We have observed for the first time that the protons/ions accelerated from the front surface of the target, in a direction opposite to the laser propagation direction, are turned around and pulled back to the rear surface, in the laser propagation direction. This proton/ion beam is able to create a self-radiograph of the target and glass stalk holding the target itself recorded through the radiochromic film stack. This unique result indicates strong long-living (ns time scale) magnetic fields present in the laser-produced plasma, which are extremely important in energy transport during the intense laser irradiation. The magnetic field from laser main pulse expands rapidly in the preformed plasma to rotate the laser produced protons. Radiation hydrodynamic simulations and ray tracing found that the magnetic field created by the amplified spontaneous emission prepulse is not sufficient to explain the particle trajectories, but the additional field created by the main pulse interaction estimated from particle-in-cell simulation is able to change the particle trajectories.

Recombinant immunotoxins and retargeted killer cells: employing engineered antibody fragments for tumor-specific targeting of cytotoxic effectors.

PubMed

Wels, Winfried; Biburger, Markus; Müller, Tina; Dälken, Benjamin; Giesübel, Ulrike; Tonn, Torsten; Uherek, Christoph

2004-03-01

Over the past years, monoclonal antibodies have attracted enormous interest as targeted therapeutics, and a number of such reagents are in clinical use. However, responses could not be achieved in all patients with tumors expressing high levels of the respective target antigens, suggesting that other factors such as limited recruitment of endogenous immune effector mechanisms can also influence treatment outcome. This justifies the search for alternative, potentially more effective reagents. Antibody-toxins and cytolytic effector cells genetically modified to carry antibody-based receptors on the surface, represent such tailor-made targeting vehicles with the potential of improved tumor localization and enhanced efficacy. In this way, advances in recombinant antibody technology have made it possible to circumvent problems inherent in chemical coupling of antibodies and toxins, and have allowed construction via gene fusion of recombinant molecules which combine antibody-mediated recognition of tumor cells with specific delivery of potent protein toxins of bacterial or plant origin. Likewise, recombinant antibody fragments provide the basis for the construction of chimeric antigen receptors that, upon expression in cytotoxic T lymphocytes (CTLs) or natural killer (NK) cells, link antibody-mediated recognition of tumor antigens with these effector cells' potent cytolytic activities, thereby making them promising cellular therapeutics for adoptive cancer therapy. Here, general principles for the derivation of cytotoxic proteins and effector cells with antibody-dependent tumor specificity are summarized, and current strategies to employ these molecules and cells for directed cancer therapy are discussed, focusing mainly on the tumor-associated antigens epidermal growth factor receptor (EGFR) and the closely related ErbB2 (HER2) as targets.

Fragment based drug discovery: practical implementation based on ¹⁹F NMR spectroscopy.

PubMed

Jordan, John B; Poppe, Leszek; Xia, Xiaoyang; Cheng, Alan C; Sun, Yax; Michelsen, Klaus; Eastwood, Heather; Schnier, Paul D; Nixey, Thomas; Zhong, Wenge

2012-01-26

Fragment based drug discovery (FBDD) is a widely used tool for discovering novel therapeutics. NMR is a powerful means for implementing FBDD, and several approaches have been proposed utilizing (1)H-(15)N heteronuclear single quantum coherence (HSQC) as well as one-dimensional (1)H and (19)F NMR to screen compound mixtures against a target of interest. While proton-based NMR methods of fragment screening (FBS) have been well documented and are widely used, the use of (19)F detection in FBS has been only recently introduced (Vulpetti et al. J. Am. Chem. Soc.2009, 131 (36), 12949-12959) with the aim of targeting "fluorophilic" sites in proteins. Here, we demonstrate a more general use of (19)F NMR-based fragment screening in several areas: as a key tool for rapid and sensitive detection of fragment hits, as a method for the rapid development of structure-activity relationship (SAR) on the hit-to-lead path using in-house libraries and/or commercially available compounds, and as a quick and efficient means of assessing target druggability.

Effects of Word and Fragment Writing during L2 Vocabulary Learning

ERIC Educational Resources Information Center

Barcroft, Joe

2007-01-01

This study examined how writing (copying) target words and word fragments affects intentional second language (L2) vocabulary learning. English-speaking first-semester learners of Spanish attempted to learn 24 Spanish nouns via word-picture repetition in three conditions: (1) word writing, (2) fragment writing, and (3) no writing. After the…

When low-warmth targets are liked: the roles of competence, gender, and relative status.

PubMed

Lin, Wen-Ying; Wang, Jenn-Wu; Lin, Hung-Yu; Lin, Hui-Tzu; Johnson, Blair T

2011-01-01

Previous research has shown that people use warmth and competence as basic dimensions to evaluate others and to interpret their behavior, but little research has examined the conditions under which low-warmth targets are liked. A series of 3 experiments involving 4 vignettes showed, in general, that low-warmth targets were better liked when they exhibited higher competence and that high-status persons displayed greater tolerance toward the low-warmth person of low status. Exceptions to these patterns were predicted and found as a function of the type of organizational context in which evaluations were made: groups that place priority on individual goals over common goals and groups that are performance oriented rather than relationship oriented. Target gender interacted with competence and relative status.

A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community

PubMed Central

2013-01-01

Background Butyrate, which is produced by the human microbiome, is essential for a well-functioning colon. Bacteria that produce butyrate are phylogenetically diverse, which hinders their accurate detection based on conventional phylogenetic markers. As a result, reliable information on this important bacterial group is often lacking in microbiome research. Results In this study we describe a gene-targeted approach for 454 pyrotag sequencing and quantitative polymerase chain reaction for the final genes in the two primary bacterial butyrate synthesis pathways, butyryl-CoA:acetate CoA-transferase (but) and butyrate kinase (buk). We monitored the establishment and early succession of butyrate-producing communities in four patients with ulcerative colitis who underwent a colectomy with ileal pouch anal anastomosis and compared it with three control samples from healthy colons. All patients established an abundant butyrate-producing community (approximately 5% to 26% of the total community) in the pouch within the 2-month study, but patterns were distinctive among individuals. Only one patient harbored a community profile similar to the healthy controls, in which there was a predominance of but genes that are similar to reference genes from Acidaminococcus sp., Eubacterium sp., Faecalibacterium prausnitzii and Roseburia sp., and an almost complete absence of buk genes. Two patients were greatly enriched in buk genes similar to those of Clostridium butyricum and C. perfringens, whereas a fourth patient displayed abundant communities containing both genes. Most butyrate producers identified in previous studies were detected and the general patterns of taxa found were supported by 16S rRNA gene pyrotag analysis, but the gene-targeted approach provided more detail about the potential butyrate-producing members of the community. Conclusions The presented approach provides quantitative and genotypic insights into butyrate-producing communities and facilitates a more specific

Identifying Interactions that Determine Fragment Binding at Protein Hotspots.

PubMed

Radoux, Chris J; Olsson, Tjelvar S G; Pitt, Will R; Groom, Colin R; Blundell, Tom L

2016-05-12

Locating a ligand-binding site is an important first step in structure-guided drug discovery, but current methods do little to suggest which interactions within a pocket are the most important for binding. Here we illustrate a method that samples atomic hotspots with simple molecular probes to produce fragment hotspot maps. These maps specifically highlight fragment-binding sites and their corresponding pharmacophores. For ligand-bound structures, they provide an intuitive visual guide within the binding site, directing medicinal chemists where to grow the molecule and alerting them to suboptimal interactions within the original hit. The fragment hotspot map calculation is validated using experimental binding positions of 21 fragments and subsequent lead molecules. The ligands are found in high scoring areas of the fragment hotspot maps, with fragment atoms having a median percentage rank of 97%. Protein kinase B and pantothenate synthetase are examined in detail. In each case, the fragment hotspot maps are able to rationalize a Free-Wilson analysis of SAR data from a fragment-based drug design project.

Fragment Length of Circulating Tumor DNA

PubMed Central

Underhill, Hunter R.; Kitzman, Jacob O.; Hellwig, Sabine; Welker, Noah C.; Daza, Riza; Gligorich, Keith M.; Rostomily, Robert C.; Shendure, Jay

2016-01-01

Malignant tumors shed DNA into the circulation. The transient half-life of circulating tumor DNA (ctDNA) may afford the opportunity to diagnose, monitor recurrence, and evaluate response to therapy solely through a non-invasive blood draw. However, detecting ctDNA against the normally occurring background of cell-free DNA derived from healthy cells has proven challenging, particularly in non-metastatic solid tumors. In this study, distinct differences in fragment length size between ctDNAs and normal cell-free DNA are defined. Human ctDNA in rat plasma derived from human glioblastoma multiforme stem-like cells in the rat brain and human hepatocellular carcinoma in the rat flank were found to have a shorter principal fragment length than the background rat cell-free DNA (134–144 bp vs. 167 bp, respectively). Subsequently, a similar shift in the fragment length of ctDNA in humans with melanoma and lung cancer was identified compared to healthy controls. Comparison of fragment lengths from cell-free DNA between a melanoma patient and healthy controls found that the BRAF V600E mutant allele occurred more commonly at a shorter fragment length than the fragment length of the wild-type allele (132–145 bp vs. 165 bp, respectively). Moreover, size-selecting for shorter cell-free DNA fragment lengths substantially increased the EGFR T790M mutant allele frequency in human lung cancer. These findings provide compelling evidence that experimental or bioinformatic isolation of a specific subset of fragment lengths from cell-free DNA may improve detection of ctDNA. PMID:27428049

Fragment Length of Circulating Tumor DNA.

PubMed

Underhill, Hunter R; Kitzman, Jacob O; Hellwig, Sabine; Welker, Noah C; Daza, Riza; Baker, Daniel N; Gligorich, Keith M; Rostomily, Robert C; Bronner, Mary P; Shendure, Jay

2016-07-01

Malignant tumors shed DNA into the circulation. The transient half-life of circulating tumor DNA (ctDNA) may afford the opportunity to diagnose, monitor recurrence, and evaluate response to therapy solely through a non-invasive blood draw. However, detecting ctDNA against the normally occurring background of cell-free DNA derived from healthy cells has proven challenging, particularly in non-metastatic solid tumors. In this study, distinct differences in fragment length size between ctDNAs and normal cell-free DNA are defined. Human ctDNA in rat plasma derived from human glioblastoma multiforme stem-like cells in the rat brain and human hepatocellular carcinoma in the rat flank were found to have a shorter principal fragment length than the background rat cell-free DNA (134-144 bp vs. 167 bp, respectively). Subsequently, a similar shift in the fragment length of ctDNA in humans with melanoma and lung cancer was identified compared to healthy controls. Comparison of fragment lengths from cell-free DNA between a melanoma patient and healthy controls found that the BRAF V600E mutant allele occurred more commonly at a shorter fragment length than the fragment length of the wild-type allele (132-145 bp vs. 165 bp, respectively). Moreover, size-selecting for shorter cell-free DNA fragment lengths substantially increased the EGFR T790M mutant allele frequency in human lung cancer. These findings provide compelling evidence that experimental or bioinformatic isolation of a specific subset of fragment lengths from cell-free DNA may improve detection of ctDNA.

Combining targeted drugs to overcome and prevent resistance of solid cancers with some stem-like cell features

PubMed Central

Koivunen, Peppi; Koivunen, Jussi P.

2014-01-01

Treatment resistance significantly inhibits the efficiency of targeted cancer therapies in drug-sensitive genotypes. In the current work, we studied mechanisms for rapidly occurring, adaptive resistance in targeted therapy-sensitive lung, breast, and melanoma cancer cell lines. The results show that in ALK translocated lung cancer lines H3122 and H2228, cells with cancer stem-like cell features characterized by high expression of cancer stem cell markers and/or in vivo tumorigenesis can mediate adaptive resistance to oncogene ablative therapy. When pharmacological ablation of ALK oncogene was accompanied with PI3K inhibitor or salinomycin therapy, cancer stem-like cell features were reversed which was accompanied with decreased colony formation. Furthermore, co-targeting was able to block the formation of acquired resistance in H3122 line. The results suggest that cells with cancer stem-like cell features can mediate adaptive resistance to targeted therapies. Since these cells follow the stochastic model, concurrent therapy with an oncogene ablating agent and a stem-like cell-targeting drug is needed for maximal therapeutic efficiency. PMID:25238228

Characterization of Hypervelocity Metal Fragments for Explosive Initiation

NASA Astrophysics Data System (ADS)

Yeager, John; Bowden, Patrick; Guildenbecher, Daniel; Olles, Joseph

2017-06-01

The off-normal detonation behavior of two plastic-bonded explosive (PBX) formulations was studied using explosively-driven aluminum fragments moving at hypersonic velocity. Witness plate materials, including copper and polycarbonate, were used to characterize the distribution of particles, finding that the aluminum did not fragment homogeneously but rather with larger particles in a ring surrounding finer particles. Digital holography experiments were conducted to measure three-dimensional shape and size of the fastest-moving fragments, which ranged between 100 and 700 microns and traveled between 2 and 3.5 km/s. Crucially, these experiments showed variability in the fragmentation in terms of the number of fragments at the leading edge of the fragment field, indicating that both single and multiple shock impacts could be imparted to the target material. Lower density PBX 9407 (RDX-based) was initiable at up to 4.5 inches, while higher density PBX 9501 (HMX-based) was only initiable at up to 0.25 inches. This type of data is critical for safety experiments and hydrocode simulations to quantify shock-to-detonation transition mechanisms and the associated risk-margins for these materials.

Deletion of a target gene in Indica rice via CRISPR/Cas9.

PubMed

Wang, Ying; Geng, Lizhao; Yuan, Menglong; Wei, Juan; Jin, Chen; Li, Min; Yu, Kun; Zhang, Ya; Jin, Huaibing; Wang, Eric; Chai, Zhijian; Fu, Xiangdong; Li, Xianggan

2017-08-01

Using CRISPR/Cas9, we successfully deleted large fragments of the yield-related gene DENSE AND ERECT PANICLE1 in Indica rice at relatively high frequency and generated gain-of-function dep1 mutants. CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 is a rapidly developing technology used to produce gene-specific modifications in both mammalian and plant systems. Most CRISPR-induced modifications in plants reported to date have been small insertions or deletions. Few large target gene deletions have thus far been reported, especially for Indica rice. In this study, we designed multiple CRISPR sgRNAs and successfully deleted DNA fragments in the gene DENSE AND ERECT PANICLE1 (DEP1) in the elite Indica rice line IR58025B. We achieved deletion frequencies of up to 21% for a 430 bp target and 9% for a 10 kb target among T0 events. Constructs with four sgRNAs did not generate higher full-length deletion frequencies than constructs with two sgRNAs. The multiple mutagenesis frequency reached 93% for four targets, and the homozygous mutation frequency reached 21% at the T0 stage. Important yield-related trait characteristics, such as dense and erect panicles and reduced plant height, were observed in dep1 homozygous T0 mutant plants produced by CRISPR/Cas9. Therefore, we successfully obtained deletions in DEP1 in the Indica background using the CRISPR/Cas9 editing tool at relatively high frequency.

Electromagnetic Dissociation Cross Sections for High LET Fragments

NASA Technical Reports Server (NTRS)

Norbury, John

2016-01-01

Nuclear interaction cross sections are used in space radiation transport codes to calculate the probability of fragment emission in high energy nucleus-nucleus collisions. Strong interactions usually dominate in these collisions, but electromagnetic (EM) interactions can also sometimes be important. Strong interactions typically occur when the projectile nucleus hits a target nucleus, with a small impact parameter. For impact parameters larger than the sum of the nuclear radii, EM reactions dominate and the process is called electromagnetic dissociation (EMD) if one of the nuclei undergo fragmentation. Previous models of EMD have been used to calculate single proton (p) production, single neutron (n) production or light ion production, where a light ion is defined as an isotope of hydrogen (H) or helium (He), such as a deuteron (2H), a triton (3H), a helion (3He) or an alpha particle (4He). A new model is described which can also account for multiple nucleon production, such as 2p, 2n, 1p1n, 2p1n, 2p2n, etc. in addition to light ion production. Such processes are important to include for the following reasons. Consider, for example, the EMD reaction 56Fe + Al --> 52Cr + X + Al, for a 56Fe projectile impacting Al, which produces the high linear energy transfer (LET) fragment 52Cr. In this reaction, the most probable particles representing X are either 2p2n or 4He. Therefore, production of the high LET fragment 52Cr, must include the multiple nucleon production of 2p2n in addition to the light ion production of 4He. Previous models, such as the NUCFRG3 model, could only account for the 4He production process in this reaction and could not account for 2p2n. The new EMD model presented in this work accounts for both the light ion and multiple nucleon processes, and is therefore able to correctly account for the production of high LET products such as 52Cr. The model will be described and calculations will be presented that show the importance of light ion and multiple

Formation of wide binaries by turbulent fragmentation

NASA Astrophysics Data System (ADS)

Lee, Jeong-Eun; Lee, Seokho; Dunham, Michael M.; Tatematsu, Ken'ichi; Choi, Minho; Bergin, Edwin A.; Evans, Neal J.

2017-08-01

Understanding the formation of wide-binary systems of very low-mass stars (M ≤ 0.1 solar masses, M⊙) is challenging 1,2,3 . The most obvious route is through widely separated low-mass collapsing fragments produced by turbulent fragmentation of a molecular core4,5. However, close binaries or multiples from disk fragmentation can also evolve to wide binaries over a few initial crossing times of the stellar cluster through tidal evolution6. Finding an isolated low-mass wide-binary system in the earliest stage of formation, before tidal evolution could occur, would prove that turbulent fragmentation is a viable mechanism for (very) low-mass wide binaries. Here we report high-resolution ALMA observations of a known wide-separation protostellar binary, showing that each component has a circumstellar disk. The system is too young7 to have evolved from a close binary, and the disk axes are misaligned, providing strong support for the turbulent fragmentation model. Masses of both stars are derived from the Keplerian rotation of the disks; both are very low-mass stars.

Jet transverse fragmentation momentum from h-h correlations in pp and p-Pb collisions

NASA Astrophysics Data System (ADS)

Viinikainen, J.; Alice Collaboration

2017-08-01

QCD color coherence phenomena, like angular ordering, can be studied by looking at jet fragmentation. As the jet is fragmenting, it is expected to go through two different phases. First, there is QCD branching that is calculable in perturbative QCD. Next, the produced partons hadronize in a non-perturbative way later in a hadronization process. The jet fragmentation can be studied using the method of two particle correlations. A useful observable is the jet transverse fragmentation momentum jT, which describes the angular width of the jet. In this contribution, a differential study will be presented in which separate jT components for branching and hadronization will be distinguished from the data measured by the ALICE experiment. The pTt dependence of the hadronization component √{ 〈jT2 〉 } is found to be rather flat, which is consistent with universal hadronization assumption. However, the branching component shows slightly rising trend in pTt. The √{ s } = 7 TeV pp and √{sNN } = 5.02 TeV p-Pb data give the same results within error bars, suggesting that this observable is not affected by cold nuclear matter effects in p-Pb collisions. The measured data will also be compared to the results obtained from PYTHIA8 simulations.

Fragment screening by SPR and advanced application to GPCRs.

PubMed

Shepherd, Claire A; Hopkins, Andrew L; Navratilova, Iva

2014-01-01

Surface plasmon resonance (SPR) is one of the primary biophysical methods for the screening of low molecular weight 'fragment' libraries, due to its low protein consumption and 'label-free' methodology. SPR biosensor interaction analysis is employed to both screen and confirm the binding of compounds in fragment screening experiments, as it provides accurate information on the affinity and kinetics of molecular interactions. The most advanced application of the use of SPR for fragment screening is against membrane protein drug targets, such G-protein coupled receptors (GPCRs). Biophysical GPCR assays using SPR have been validated with pharmacological measurements approximate to cell-based methods, yet provide the advantage of biophysical methods in their ability to measure the weak affinities of low molecular weight fragments. A number of SPR fragment screens against GPCRs have now been disclosed in the literature. SPR fragment screening is proving versatile to screen both thermostabilised GPCRs and solubilised wild type receptors. In this chapter, we discuss the state-of-the-art in GPCR fragment screening by SPR and the technical considerations in performing such experiments. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Target of Rapamycin (TOR)-like 1 Kinase Is Involved in the Control of Polyphosphate Levels and Acidocalcisome Maintenance in Trypanosoma brucei*

PubMed Central

de Jesus, Teresa Cristina Leandro; Tonelli, Renata Rosito; Nardelli, Sheila C.; da Silva Augusto, Leonardo; Motta, Maria Cristina M.; Girard-Dias, Wendell; Miranda, Kildare; Ulrich, Paul; Jimenez, Veronica; Barquilla, Antonio; Navarro, Miguel; Docampo, Roberto; Schenkman, Sergio

2010-01-01

Target of rapamycin (TOR) kinases are highly conserved protein kinases that integrate signals from nutrients and growth factors to coordinate cell growth and cell cycle progression. It has been previously described that two TOR kinases control cell growth in the protozoan parasite Trypanosoma brucei, the causative agent of African trypanosomiasis. Here we studied an unusual TOR-like protein named TbTOR-like 1 containing a PDZ domain and found exclusively in kinetoplastids. TbTOR-like 1 localizes to unique cytosolic granules. After hyperosmotic stress, the localization of the protein shifts to the cell periphery, different from other organelle markers. Ablation of TbTOR-like 1 causes a progressive inhibition of cell proliferation, producing parasites accumulating in the S/G2 phase of the cell cycle. TbTOR-like 1 knocked down cells have an increased area occupied by acidic vacuoles, known as acidocalcisomes, and are enriched in polyphosphate and pyrophosphate. These results suggest that TbTOR-like 1 might be involved in the control of acidocalcisome and polyphosphate metabolism in T. brucei. PMID:20495004

Effective progression of nuclear magnetic resonance-detected fragment hits.

PubMed

Eaton, Hugh L; Wyss, Daniel F

2011-01-01

Fragment-based drug discovery (FBDD) has become increasingly popular over the last decade as an alternate lead generation tool to HTS approaches. Several compounds have now progressed into the clinic which originated from a fragment-based approach, demonstrating the utility of this emerging field. While fragment hit identification has become much more routine and may involve different screening approaches, the efficient progression of fragment hits into quality lead series may still present a major bottleneck for the broadly successful application of FBDD. In our laboratory, we have extensive experience in fragment-based NMR screening (SbN) and the subsequent iterative progression of fragment hits using structure-assisted chemistry. To maximize impact, we have applied this approach strategically to early- and high-priority targets, and those struggling for leads. Its application has yielded a clinical candidate for BACE1 and lead series in about one third of the SbN/FBDD projects. In this chapter, we will give an overview of our strategy and focus our discussion on NMR-based FBDD approaches. Copyright © 2011 Elsevier Inc. All rights reserved.

Magmatic and fragmentation controls on volcanic ash surface chemistry

NASA Astrophysics Data System (ADS)

Ayris, Paul M.; Diplas, Spyros; Damby, David E.; Hornby, Adrian J.; Cimarelli, Corrado; Delmelle, Pierre; Scheu, Bettina; Dingwell, Donald B.

2016-04-01

The chemical effects of silicate ash ejected by explosive volcanic eruptions on environmental systems are fundamentally mediated by ash particle surfaces. Ash surfaces are a composite product of magmatic properties and fragmentation mechanisms, as well as in-plume and atmospheric alteration processes acting upon those surfaces during and after the eruption. Recent attention has focused on the capacity of alteration processes to shape ash surfaces; most notably, several studies have utilised X-ray photoelectron spectroscopy (XPS), a technique probing the elemental composition and coordination state of atoms within the top 10 nm of ash surfaces, to identify patterns of elemental depletions and enrichments relative to bulk ash chemical composition. Under the presumption of surface and bulk equivalence, any disparities have been previously attributed to surface alteration processes, but the ubiquity of some depletions (e.g., Ca, Fe) across multiple ash studies, irrespective of eruptive origin, could suggest these to be features of the surface produced at the instant of magma fragmentation. To investigate this possibility further, we conducted rapid decompression experiments at different pressure conditions and at ambient and magmatic temperature on porous andesitic rocks. These experiments produced fragmented ash material untouched by secondary alteration, which were compared to particles produced by crushing of large clasts from the same experiments. We investigated a restricted size fraction (63-90 μm) from both fragmented and crushed materials, determining bulk chemistry and mineralogy via XRF, SEM-BSE and EPMA, and investigated the chemical composition of the ash surface by XPS. Analyses suggest that fragmentation under experimental conditions partitioned a greater fraction of plagioclase-rich particles into the selected size fraction, relative to particles produced by crushing. Trends in surface chemical composition in fragmented and crushed particles mirror that

Spotlight on the microbes that produce heat shock protein 90-targeting antibiotics.

PubMed

Piper, Peter W; Millson, Stefan H

2012-12-12

Heat shock protein 90 (Hsp90) is a promising cancer drug target as a molecular chaperone critical for stabilization and activation of several of the oncoproteins that drive cancer progression. Its actions depend upon its essential ATPase, an activity fortuitously inhibited with a very high degree of selectivity by natural antibiotics: notably the actinomycete-derived benzoquinone ansamycins (e.g. geldanamycin) and certain fungal-derived resorcyclic acid lactones (e.g. radicicol). The molecular interactions made by these antibiotics when bound within the ADP/ATP-binding site of Hsp90 have served as templates for the development of several synthetic Hsp90 inhibitor drugs. Much attention now focuses on the clinical trials of these drugs. However, because microbes have evolved antibiotics to target Hsp90, it is probable that they often exploit Hsp90 inhibition when interacting with each other and with plants. Fungi known to produce Hsp90 inhibitors include mycoparasitic, as well as plant-pathogenic, endophytic and mycorrhizal species. The Hsp90 chaperone may, therefore, be a prominent target in establishing a number of mycoparasitic (interfungal), fungal pathogen-plant and symbiotic fungus-plant relationships. Furthermore the Hsp90 family proteins of the microbes that produce Hsp90 inhibitor antibiotics are able to reveal how drug resistance can arise by amino acid changes in the highly conserved ADP/ATP-binding site of Hsp90.

Fragment Based Strategies for Discovery of Novel HIV-1 Reverse Transcriptase and Integrase Inhibitors.

PubMed

Latham, Catherine F; La, Jennifer; Tinetti, Ricky N; Chalmers, David K; Tachedjian, Gilda

2016-01-01

Human immunodeficiency virus (HIV) remains a global health problem. While combined antiretroviral therapy has been successful in controlling the virus in patients, HIV can develop resistance to drugs used for treatment, rendering available drugs less effective and limiting treatment options. Initiatives to find novel drugs for HIV treatment are ongoing, although traditional drug design approaches often focus on known binding sites for inhibition of established drug targets like reverse transcriptase and integrase. These approaches tend towards generating more inhibitors in the same drug classes already used in the clinic. Lack of diversity in antiretroviral drug classes can result in limited treatment options, as cross-resistance can emerge to a whole drug class in patients treated with only one drug from that class. A fresh approach in the search for new HIV-1 drugs is fragment-based drug discovery (FBDD), a validated strategy for drug discovery based on using smaller libraries of low molecular weight molecules (<300 Da) screened using primarily biophysical assays. FBDD is aimed at not only finding novel drug scaffolds, but also probing the target protein to find new, often allosteric, inhibitory binding sites. Several fragment-based strategies have been successful in identifying novel inhibitory sites or scaffolds for two proven drug targets for HIV-1, reverse transcriptase and integrase. While any FBDD-generated HIV-1 drugs have yet to enter the clinic, recent FBDD initiatives against these two well-characterised HIV-1 targets have reinvigorated antiretroviral drug discovery and the search for novel classes of HIV-1 drugs.

Rheological changes induced by clast fragmentation in debris flows

NASA Astrophysics Data System (ADS)

Caballero, Lizeth; Sarocchi, Damiano; Soto, Enrique; Borselli, Lorenzo

2014-09-01

On the basis of rotating drum analogue experiments, we describe a fragmentation process acting within debris flows during transport and its influence on rheologic behavior. Our hypothesis is based on a detailed textural analysis including granulometry, clast morphology, and rheologic properties of the fluid matrix. Results of the experiments point out that breakage of certain granulometric classes produces fine particles like fine sand and silt. The population growth of fine clasts with time leads to an increase in yield strength and viscosity that progressively modifies the rheologic behavior. From a textural point of view, this is reflected in a bimodal granulometric distribution. Up to now this characteristic has been explained as the effect of bulking and/or sedimentation processes during transport. Our experimental results show that the type of fragmentation depends on particle size and is the consequence of strong clast-clast interaction and clast-fluid interactions. Coarse particles develop small fractures which cause the loss of sharp edges and asperities. Medium-sized particles develop through-going fractures that cause them to break apart. The latter process explains why intermediate granulometric classes progressively diminish with time in debris flows. Analogue experiments enable us to study the efficacy of clast fragmentation in modifying the textural character and flow behavior of debris flows without the influence of external factors such as erosion and sedimentation. The obtained results constitute the base of a new approach for modeling debris flow dynamics.

Advances in fragment-based drug discovery platforms.

PubMed

Orita, Masaya; Warizaya, Masaichi; Amano, Yasushi; Ohno, Kazuki; Niimi, Tatsuya

2009-11-01

Fragment-based drug discovery (FBDD) has been established as a powerful alternative and complement to traditional high-throughput screening techniques for identifying drug leads. At present, this technique is widely used among academic groups as well as small biotech and large pharmaceutical companies. In recent years, > 10 new compounds developed with FBDD have entered clinical development, and more and more attention in the drug discovery field is being focused on this technique. Under the FBDD approach, a fragment library of relatively small compounds (molecular mass = 100 - 300 Da) is screened by various methods and the identified fragment hits which normally weakly bind to the target are used as starting points to generate more potent drug leads. Because FBDD is still a relatively new drug discovery technology, further developments and optimizations in screening platforms and fragment exploitation can be expected. This review summarizes recent advances in FBDD platforms and discusses the factors important for the successful application of this technique. Under the FBDD approach, both identifying the starting fragment hit to be developed and generating the drug lead from that starting fragment hit are important. Integration of various techniques, such as computational technology, X-ray crystallography, NMR, surface plasmon resonance, isothermal titration calorimetry, mass spectrometry and high-concentration screening, must be applied in a situation-appropriate manner.

Isomer Information from Ion Mobility Separation of High-Mannose Glycan Fragments.

PubMed

Harvey, David J; Seabright, Gemma E; Vasiljevic, Snezana; Crispin, Max; Struwe, Weston B

2018-05-01

Extracted arrival time distributions of negative ion CID-derived fragments produced prior to traveling-wave ion mobility separation were evaluated for their ability to provide structural information on N-linked glycans. Fragmentation of high-mannose glycans released from several glycoproteins, including those from viral sources, provided over 50 fragments, many of which gave unique collisional cross-sections and provided additional information used to assign structural isomers. For example, cross-ring fragments arising from cleavage of the reducing terminal GlcNAc residue on Man 8 GlcNAc 2 isomers have unique collision cross-sections enabling isomers to be differentiated in mixtures. Specific fragment collision cross-sections enabled identification of glycans, the antennae of which terminated in the antigenic α-galactose residue, and ions defining the composition of the 6-antenna of several of the glycans were also found to have different cross-sections from isomeric ions produced in the same spectra. Potential mechanisms for the formation of the various ions are discussed and the estimated collisional cross-sections are tabulated. Graphical Abstract ᅟ.

Isomer Information from Ion Mobility Separation of High-Mannose Glycan Fragments

NASA Astrophysics Data System (ADS)

Harvey, David J.; Seabright, Gemma E.; Vasiljevic, Snezana; Crispin, Max; Struwe, Weston B.

2018-05-01

Extracted arrival time distributions of negative ion CID-derived fragments produced prior to traveling-wave ion mobility separation were evaluated for their ability to provide structural information on N-linked glycans. Fragmentation of high-mannose glycans released from several glycoproteins, including those from viral sources, provided over 50 fragments, many of which gave unique collisional cross-sections and provided additional information used to assign structural isomers. For example, cross-ring fragments arising from cleavage of the reducing terminal GlcNAc residue on Man8GlcNAc2 isomers have unique collision cross-sections enabling isomers to be differentiated in mixtures. Specific fragment collision cross-sections enabled identification of glycans, the antennae of which terminated in the antigenic α-galactose residue, and ions defining the composition of the 6-antenna of several of the glycans were also found to have different cross-sections from isomeric ions produced in the same spectra. Potential mechanisms for the formation of the various ions are discussed and the estimated collisional cross-sections are tabulated. [Figure not available: see fulltext.

A new approach for manufacturing and processing targets to produce 99mTc with cyclotrons

NASA Astrophysics Data System (ADS)

Matei, L.; McRae, G.; Galea, R.; Niculae, D.; Craciun, L.; Leonte, R.; Surette, G.; Langille, S.; Louis, C. St.; Gelbart, W.; Abeysekera, B.; Johnson, R. R.

2017-06-01

The most important radioisotope for nuclear medicine is 99mTc. After the supply crisis of 99Mo starting in 2008, the availability of 99mTc became a worldwide concern. Alternative methods for producing the medical imaging isotope 99mTc are actively being developed around the world. The reaction 100Mo(p, 2n)99mTc provides a direct route that can be incorporated into routine production in nuclear medicine centers that possess medical cyclotrons for production of other isotopes, such as those used for Positron Emission Tomography. This paper describes a new approach for manufacturing targets for the (p, 2n) nuclear reaction on 100Mo and the foundation for the subsequent commercial separation and purification of the 99mTc produced. Two designs of targets are presented. The targets used to produce 99mTc are subject to a number of operational constraints.They must withstand the temperatures generated by the irradiation, accommodate temperature gradients from cooling system of the target, must be resilient and must be easily post-processed to separate the 99mTc. After irradiation, the separation of Tc from Mo was carried out using an innovative two-step approach. The process described in this paper can be automated with modules that easily fit in standard production hot cells found in nuclear medicine facilities.

Isotopic fission-fragment distributions of 238U, 239Np, 240Pu, 244Cm, and 250Cf produced through inelastic scattering, transfer, and fusion reactions in inverse kinematics

NASA Astrophysics Data System (ADS)

Ramos, D.; Caamaño, M.; Farget, F.; Rodríguez-Tajes, C.; Audouin, L.; Benlliure, J.; Casarejos, E.; Clement, E.; Cortina, D.; Delaune, O.; Derkx, X.; Dijon, A.; Doré, D.; Fernández-Domínguez, B.; de France, G.; Heinz, A.; Jacquot, B.; Navin, A.; Paradela, C.; Rejmund, M.; Roger, T.; Salsac, M.-D.; Schmitt, C.

2018-05-01

Transfer- and fusion-induced fission in inverse kinematics has proved to be a powerful tool to investigate nuclear fission, widening information on the fission fragments and access to unstable fissioning systems with respect to other experimental approaches. An experimental campaign is being carried out at GANIL with this technique since 2008. In these experiments, a beam of 238U, accelerated to 6.1 MeV/u, impinges on a 12C target. Fissioning systems from U to Cf are populated through inelastic scattering, transfer, and fusion reactions, with excitation energies that range from a few MeV up to 46 MeV. The use of inverse kinematics, the SPIDER telescope, and the VAMOS spectrometer allow the characterization of the fissioning system in terms of mass, nuclear charge, and excitation energy, and the isotopic identification of the full fragment distribution. This work reports on new data from the second experiment of the campaign on fission-fragment yields of the heavy actinides 238U, 239Np, 240Pu, 244Cm, and 250Cf, which are of interest from both fundamental and application points of view.

Fullerene-like organization of HIV gag-protein shell in virus-like particles produced by recombinant baculovirus.

PubMed

Nermut, M V; Hockley, D J; Jowett, J B; Jones, I M; Garreau, M; Thomas, D

1994-01-01

Virus-like particles produced by a recombinant baculovirus containing the HIV gag gene were examined by negative staining after delipidization. This technique demonstrated that the gag-protein shell consisted of radially arranged short rods which formed a network of ring-like structures. Similar structures were observed at the plasma membrane of infected cells which had been opened by wet-cleaving. Occasionally five or six subunits were observed forming a ring. These findings suggest that the gag-encoded precursor (pr55) is a rod-like molecule about 34 A in diameter and 85 A in length. A protein cylinder of such dimensions would have a molecular weight of 56K. The center-to-center distance of two neighboring rings formed by the rods was 66 +/- 8 A (N = 200) by direct measurements and 65 A as obtained from averaged images. This morphology and these dimensions indicate that the virus-like particles contain the gag precursor in the form of a near-spherical "fullerene-like" icosahedral shell. Our data indicate that the triangulation number of the rings equals 63. However, since one rod of pr55 is shared by two rings, the number of copies of the precursor will be 1890 as opposed to 2522 if the molecules were closely packed. The particle diameter of 102 nm deduced from the proposed model was close to the diameter obtained from thin sections of low-temperature-embedded specimens (103-108 nm).

Clinical and molecular insights into adenoid cystic carcinoma: Neural crest‐like stemness as a target

PubMed Central

Panaccione, Alexander; Chang, Michael T.; Ivanov, Sergey V.

2016-01-01

Objectives This review surveys trialed therapies and molecular defects in adenoid cystic carcinoma (ACC), with an emphasis on neural crest‐like stemness characteristics of newly discovered cancer stem cells (CSCs) and therapies that may target these CSCs. Data Sources Articles available on Pubmed or OVID MEDLINE databases and unpublished data. Review Methods Systematic review of articles pertaining to ACC and neural crest‐like stem cells. Results Adenoid cystic carcinoma of the salivary gland is a slowly growing but relentless cancer that is prone to nerve invasion and metastases. A lack of understanding of molecular etiology and absence of targetable drivers has limited therapy for patients with ACC to surgery and radiation. Currently, no curative treatments are available for patients with metastatic disease, which highlights the need for effective new therapies. Research in this area has been inhibited by the lack of validated cell lines and a paucity of clinically useful markers. The ACC research environment has recently improved, thanks to the introduction of novel tools, technologies, approaches, and models. Improved understanding of ACC suggests that neural crest‐like stemness is a major target in this rare tumor. New cell culture techniques and patient‐derived xenografts provide tools for preclinical testing. Conclusion Preclinical research has not identified effective targets in ACC, as confirmed by the large number of failed clinical trials. New molecular data suggest that drivers of neural crest‐like stemness may be required for maintenance of ACC; as such, CSCs are a target for therapy of ACC. PMID:28894804

The importance of hydration thermodynamics in fragment-to-lead optimization.

PubMed

Ichihara, Osamu; Shimada, Yuzo; Yoshidome, Daisuke

2014-12-01

Using a computational approach to assess changes in solvation thermodynamics upon ligand binding, we investigated the effects of water molecules on the binding energetics of over 20 fragment hits and their corresponding optimized lead compounds. Binding activity and X-ray crystallographic data of published fragment-to-lead optimization studies from various therapeutically relevant targets were studied. The analysis reveals a distinct difference between the thermodynamic profile of water molecules displaced by fragment hits and those displaced by the corresponding optimized lead compounds. Specifically, fragment hits tend to displace water molecules with notably unfavorable excess entropies-configurationally constrained water molecules-relative to those displaced by the newly added moieties of the lead compound during the course of fragment-to-lead optimization. Herein we describe the details of this analysis with the goal of providing practical guidelines for exploiting thermodynamic signatures of binding site water molecules in the context of fragment-to-lead optimization. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development of a Double Allylboration Reagent Targeting 1,5-syn-(E)-Diols: Application to the Synthesis of the C(23)-C(40) Fragment of Tetrafibricin

PubMed Central

Nuhant, Philippe; Kister, Jeremy; Lira, Ricardo; Sorg, Achim; Roush, William R.

2011-01-01

Interest in the synthesis of the C(23)-C(40) fragment 2 of tetrafibricin prompted us to develop a new method for the synthesis of 1,5-syn-(E)-diols. Toward this end, the kinetically controlled hydroboration of allenes 6, 33, ent-39, 42 and 45 with the Soderquist borane 25R were studied. Tetrabutylammonium allenyltrifluoroborate 45 gave superior results and was utilized in a double allylboration sequence with two different aldehydes to provide the targeted 1,5-syn-(E)-diols in generally high yields (72–98%), and with high enantioselectivity (>95% e.e.), diastereoselectivity (d.r. >20:1), and (E)/(Z) selectivity (>20:1). This new method was applied to the synthesis of the C(23)-C(40) fragment 2 of tetrafibricin. PMID:21857752

Computational Fragment-Based Drug Design: Current Trends, Strategies, and Applications.

PubMed

Bian, Yuemin; Xie, Xiang-Qun Sean

2018-04-09

Fragment-based drug design (FBDD) has become an effective methodology for drug development for decades. Successful applications of this strategy brought both opportunities and challenges to the field of Pharmaceutical Science. Recent progress in the computational fragment-based drug design provide an additional approach for future research in a time- and labor-efficient manner. Combining multiple in silico methodologies, computational FBDD possesses flexibilities on fragment library selection, protein model generation, and fragments/compounds docking mode prediction. These characteristics provide computational FBDD superiority in designing novel and potential compounds for a certain target. The purpose of this review is to discuss the latest advances, ranging from commonly used strategies to novel concepts and technologies in computational fragment-based drug design. Particularly, in this review, specifications and advantages are compared between experimental and computational FBDD, and additionally, limitations and future prospective are discussed and emphasized.

Dihydrodaidzein-producing Clostridium-like intestinal bacterium, strain TM-40, affects in vitro metabolism of daidzein by fecal microbiota of human male equol producer and non-producers.

PubMed

Tamura, Motoi; Hori, Sachiko; Nakagawa, Hiroyuki

2011-01-01

Much attention has been focused on the biological effects of equol, a metabolite of daidzein produced by intestinal microbiota. However, little is known about the role of isoflavone metabolizing bacteria in the intestinal microbiota. Recently, we isolated a dihydrodaidzein (DHD)-producing Clostridium-like bacterium, strain TM-40, from human feces. We investigated the effects of strain TM-40 on in vitro daidzein metabolism by human fecal microbiota from a male equol producer and two male equol non-producers. In the fecal suspension from the male equol non-producer and DHD producer, DHD was detected in the in vitro fecal incubation of daidzein after addition of TM-40. The DHD concentration increased as the concentration of strain TM-40 increased. In the fecal suspension from the equol producer, the fecal equol production was increased by the addition of strain TM-40. The occupation ratios of Bifidobacterium and Lactobacillales were higher in the equol non-producers than in the equol producer. Adding isoflavone-metabolizing bacteria to the fecal microbiota should facilitate the estimation of the metabolism of isoflavonoids by fecal microbiota. Studies on the interactions among equol-producing microbiota and DHD-producing bacteria might lead to clarification of some of the mechanisms regulating the production of equol by fecal microbiota.

Dihydrodaidzein-producing Clostridium-like intestinal bacterium, strain TM-40, affects in vitro metabolism of daidzein by fecal microbiota of human male equol producer and non-producers

PubMed Central

TAMURA, Motoi; HORI, Sachiko; NAKAGAWA, Hiroyuki

2011-01-01

Much attention has been focused on the biological effects of equol, a metabolite of daidzein produced by intestinal microbiota. However, little is known about the role of isoflavone metabolizing bacteria in the intestinal microbiota. Recently, we isolated a dihydrodaidzein (DHD)-producing Clostridium-like bacterium, strain TM-40, from human feces. We investigated the effects of strain TM-40 on in vitro daidzein metabolism by human fecal microbiota from a male equol producer and two male equol non-producers. In the fecal suspension from the male equol non-producer and DHD producer, DHD was detected in the in vitro fecal incubation of daidzein after addition of TM-40. The DHD concentration increased as the concentration of strain TM-40 increased. In the fecal suspension from the equol producer, the fecal equol production was increased by the addition of strain TM-40. The occupation ratios of Bifidobacterium and Lactobacillales were higher in the equol non-producers than in the equol producer. Adding isoflavone-metabolizing bacteria to the fecal microbiota should facilitate the estimation of the metabolism of isoflavonoids by fecal microbiota. Studies on the interactions among equol-producing microbiota and DHD-producing bacteria might lead to clarification of some of the mechanisms regulating the production of equol by fecal microbiota. PMID:25045313

Towards novel therapeutics for HIV through fragment-based screening and drug design.

PubMed

Tiefendbrunn, Theresa; Stout, C David

2014-01-01

Fragment-based drug discovery has been applied with varying levels of success to a number of proteins involved in the HIV (Human Immunodeficiency Virus) life cycle. Fragment-based approaches have led to the discovery of novel binding sites within protease, reverse transcriptase, integrase, and gp41. Novel compounds that bind to known pockets within CCR5 have also been identified via fragment screening, and a fragment-based approach to target the TAR-Tat interaction was explored. In the context of HIV-1 reverse transcriptase (RT), fragment-based approaches have yielded fragment hits with mid-μM activity in an in vitro activity assay, as well as fragment hits that are active against drug-resistant variants of RT. Fragment-based drug discovery is a powerful method to elucidate novel binding sites within proteins, and the method has had significant success in the context of HIV proteins.

Cloning of a CACTA transposon-like insertion in intron I of tomato invertase Lin5 gene and identification of transposase-like sequences of Solanaceae species.

PubMed

Proels, Reinhard K; Roitsch, Thomas

2006-03-01

Very few CACTA transposon-like sequences have been described in Solanaceae species. Sequence information has been restricted to partial transposase (TPase)-like fragments, and no target gene of CACTA-like transposon insertion has been described in tomato to date. In this manuscript, we report on a CACTA transposon-like insertion in intron I of tomato (Lycopersicon esculentum) invertase gene Lin5 and TPase-like sequences of several Solanaceae species. Consensus primers deduced from the TPase region of the tomato CACTA transposon-like element allowed the amplification of similar sequences from various Solanaceae species of different subfamilies including Solaneae (Solanum tuberosum), Cestreae (Nicotiana tabacum) and Datureae (Datura stramonium). This demonstrates the ubiquitous presence of CACTA-like elements in Solanaceae genomes. The obtained partial sequences are highly conserved, and allow further detection and detailed analysis of CACTA-like transposons throughout Solanaceae species. CACTA-like transposon sequences make possible the evaluation of their use for genome analysis, functional studies of genes and the evolutionary relationships between plant species.

Characterization of hypervelocity metal fragments for explosive initiation

NASA Astrophysics Data System (ADS)

Yeager, John D.; Bowden, Patrick R.; Guildenbecher, Daniel R.; Olles, Joseph D.

2017-07-01

The fragment impact response of two plastic-bonded explosive (PBX) formulations was studied using explosively driven aluminum fragments. A generic aluminum-capped detonator generated sub-mm aluminum particles moving at hypersonic velocities. The ability of these fragments to initiate reaction or otherwise damage two PBX materials was assessed using go/no-go experiments at standoff distances of up to 160 mm. Lower density PBX 9407 (RDX-based) was initiable at up to 115 mm, while higher density PBX 9501 (HMX-based) was only initiable at up to 6 mm. Several techniques were used to characterize the size, distribution, and velocity of the particles. Witness plate materials, including copper and polycarbonate, and backlit high speed video were used to characterize the distribution of particles, finding that the aluminum cap did not fragment homogeneously but rather with larger particles in a ring surrounding finer particles. Finally, precise digital holography experiments were conducted to measure the three-dimensional shape and size of the fastest-moving fragments, which ranged between 100 and 700 μm and traveled between 2.2 and 3.2 km/s. Crucially, these experiments showed variability in the fragmentation in terms of the number of fragments at the leading edge of the fragment field, indicating that both single and multiple shock impacts could be imparted to the target material. These types of data are critical for safety experiments and hydrocode simulations to quantify shock-to-detonation transition mechanisms and the associated risk-margins for these materials.

On the fragmentation boundary in magnetized self-gravitating discs

NASA Astrophysics Data System (ADS)

Forgan, Duncan; Price, Daniel J.; Bonnell, Ian

2017-04-01

We investigate the role of magnetic fields in the fragmentation of self-gravitating discs using 3D global ideal magnetohydrodynamic simulations performed with the PHANTOM smoothed particle hydrodynamics code. For initially toroidal fields, we find two regimes. In the first, where the cooling time is greater than five times the dynamical time, magnetic fields reduce spiral density wave amplitudes, which in turn suppresses fragmentation. This is the case even if the magnetic pressure is only a 10th of the thermal pressure. The second regime occurs when the cooling time is sufficiently short that magnetic fields cannot halt fragmentation. We find that magnetized discs produce more massive fragments, due to both the additional pressure exerted by the magnetic field and the additional angular momentum transport induced by Maxwell stresses. The fragments are confined to a narrower range of initial semimajor axes than those in unmagnetized discs. The orbital eccentricity and inclination distributions of unmagnetized and magnetized disc fragments are similar. Our results suggest that the fragmentation boundary could be at cooling times a factor of 2 lower than predicted by purely hydrodynamical models.

Quality and cost assessment of a recombinant antibody fragment produced from mammalian, yeast and prokaryotic host cells: A case study prior to pharmaceutical development.

PubMed

Lebozec, Kristell; Jandrot-Perrus, Martine; Avenard, Gilles; Favre-Bulle, Olivier; Billiald, Philippe

2018-09-25

Monoclonal antibody fragments (Fab) are a promising class of therapeutic agents. Fabs are aglycosylated proteins and so many expression platforms have been developed including prokaryotic, yeast and mammalian cells. However, these platforms are not equivalent in terms of cell line development and culture time, product quality and possibly cost of production that greatly influence the success of a drug candidate's pharmaceutical development. This study is an assessment of the humanized Fab fragment ACT017 produced from two microorganisms (Escherichia coli and Pichia pastoris) and one mammalian cell host (CHO). Following low scale production and Protein L-affinity purification under generic conditions, physico-chemical and functional quality assessments were carried out prior to economic analysis of industrial scale production using a specialized software (Biosolve, Biopharm Services, UK). Results show higher titer production when using E. coli but associated with high heterogeneity of the protein content recovered in the supernatant. We also observed glycoforms of the Fab produced from P. pastoris, while Fab secreted from CHO was the most homogeneous despite a much longer culture time and slightly higher estimated cost of goods. This study may help inform future pharmaceutical development of this class of therapeutic proteins. Copyright © 2018 Elsevier B.V. All rights reserved.

A molecular fragment cheminformatics roadmap for mesoscopic simulation.

PubMed

Truszkowski, Andreas; Daniel, Mirco; Kuhn, Hubert; Neumann, Stefan; Steinbeck, Christoph; Zielesny, Achim; Epple, Matthias

2014-12-01

Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even larger molecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix (array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformatics approach tackles these problems and provides solutions for a considerably enhanced accessibility. This study aims at outlining a complete cheminformatics roadmap that frames a mesoscopic Molecular Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application. The molecular fragment cheminformatics roadmap consists of four consecutive building blocks: An adequate fragment structure representation (1), defined operations on these fragment structures (2), the description of compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of a whole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like line notation (denoted f SMILES) with connected molecular fragments to represent a molecular structure. The f SMILES notation and the following concepts and methods for building blocks 2-4 are outlined with examples and practical usage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existing open-source cheminformatics software. Mesoscopic simulation techniques like MFD may be considerably alleviated and broadened for practical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and

Fragment-based drug design and identification of HJC0123, a novel orally bioavailable STAT3 inhibitor for cancer therapy

PubMed Central

Chen, Haijun; Yang, Zhengduo; Ding, Chunyong; Chu, Lili; Zhang, Yusong; Terry, Kristin; Liu, Huiling; Shen, Qiang; Zhou, Jia

2013-01-01

Fragment-based drug design (FBDD) is a promising approach for the generation of lead molecules with enhanced activity and especially drug-like properties against therapeutic targets. Herein, we report the fragment-based drug design, systematic chemical synthesis and pharmacological evaluation of novel scaffolds as potent anticancer agents by utilizing six privileged fragments from known STAT3 inhibitors. Several new molecules such as compounds 5, 12, and 19 that may act as advanced chemical leads have been identified. The most potent compound 5 (HJC0123) has demonstrated to inhibit STAT3 promoter activity, downregulate phosphorylation of STAT3, increase the expression of cleaved caspase-3, inhibit cell cycle progression and promote apoptosis in breast and pancreatic cancer cells with low micromolar to nanomolar IC50 values. Furthermore, compound 5 significantly suppressed estrogen receptor (ER)-negative breast cancer MDA-MB-231 xenograft tumor growth in vivo (p.o.), indicating its great potential as an efficacious and orally bioavailable drug candidate for human cancer therapy. PMID:23416191

Fragment generation, survival, and attachment of Dictyota spp. at Conch Reef in the Florida Keys, USA

NASA Astrophysics Data System (ADS)

Herren, L. W.; Walters, L. J.; Beach, K. S.

2006-05-01

During the past decade, the relative abundance of the brown macroalgae Dictyota spp. has been high in the Florida Keys. Recent studies have shown that members of this genus successfully reproduce via vegetative fragmentation. To investigate the importance of fragmentation on the reef community, this study examined: (1) the degree of epiphytism on benthic organisms, (2) the rate of fragment production through fish foraging activities, (3) the likelihood of fragment entanglement, and (4) the fragment attachment and success rate. It was found that reef fish contributed substantially to the fragment pool; furthermore, most fish-produced fragments produced rhizoids and attached to sand grains within 24 h in the field. Fragments of Dictyota spp. most commonly became entangled around and then attached themselves to the green alga Halimeda tuna, and other Dictyota spp. These results suggest that vegetative fragmentation of Dictyota spp. plays an important role in the changing community structure on the Florida Keys reef tract.

BEAM ON TARGET MODEL Produces All Gamma Ray Burst Phenomena Including Afterglow

NASA Astrophysics Data System (ADS)

Greyber, H.

2000-12-01

While one must applaud the splendid research by L. Piro et al and L. Amati et al reported in SCIENCE recently, one must question, as M. Rees and S. Woolsey have done, their conclusion that a ``supranova model" is the only explanation for these new X-ray observations. In fact L. Piro was quoted as saying, ``Our data helps rule out the scenario where two neutron stars or black holes collide. We think GRBs result from something similar to a supernova explosion, but much more powerful." A relatively unknown physical model for GRBs, Greyber's Beam On Target model (BOT), dating back to the first CGRO observations, can plausibly explain the iron emission lines observed for GRB991216, and also the mass of the dense medium within a light-day of the GRB being roughly equivalent to at least one-tenth solar mass, as well as the initial shedding of material followed by the GRB event. When a galaxy forms under gravitational collapse in the presence of a primordial magnetic field, Mestel and Strittmatter demonstrated that, for finite Ohmic diffusion, a growing equatorial current loop is formed. Even if this stable ``Storage Ring" has only 10exp-9 of the total energy released during a typical galaxy's formation, the relativistic beam can possess 10exp58 ergs. The GRB ``fireball" occurs when a target star races across the powerful beam, blowing off target material as a hot, rapidly expanding plasma cloud, simulating an explosion. Since currents in space are known to be sometimes filamentary, sharp millisecond spikes can be expected in some GRBs. Proton and alpha particle nuclear reactions produce a gamma ray beam. Beam particles impinging on denser cloud material create an electromagnetic shower, producing X-ray, optical and radio radiation. Since the Storage Ring has an intense magnetic field around it, synchrotron radiation is expected. The beam, striking a highly evolved massive target star, produces the iron emission lines. H. D. Greyber, in ``After the Dark Ages:When Galaxies

Thermally targeted delivery of chemotherapeutics and anti-cancer peptides by elastin-like polypeptide.

PubMed

Raucher, Drazen; Massodi, Iqbal; Bidwell, Gene L

2008-03-01

Current chemotherapy treatment of solid tumors is limited due to a lack of specific delivery of the drugs to the tumor, leading to systemic toxicity. Therefore, it is necessary to develop targeted cancer therapies and tumor-targeted drug carriers. The authors review the development of elastin-like polypeptide (ELP) as a potential carrier for thermally targeted delivery of therapeutics. The authors searched Medline for articles concerning the application of ELP as a drug delivery vector for small molecule drugs and therapeutic peptides. ELP has been demonstrated to be a promising thermally targeted carrier. Further examination of the in vivo biodistribution and efficacy will provide the necessary data to advance ELP technology toward the ultimate goal of human therapeutics.

Evolutions in fragment-based drug design: the deconstruction–reconstruction approach

PubMed Central

Chen, Haijun; Zhou, Xiaobin; Wang, Ailan; Zheng, Yunquan; Gao, Yu; Zhou, Jia

2014-01-01

Recent advances in the understanding of molecular recognition and protein–ligand interactions have facilitated rapid development of potent and selective ligands for therapeutically relevant targets. Over the past two decades, a variety of useful approaches and emerging techniques have been developed to promote the identification and optimization of leads that have high potential for generating new therapeutic agents. Intriguingly, the innovation of a fragment-based drug design (FBDD) approach has enabled rapid and efficient progress in drug discovery. In this critical review, we focus on the construction of fragment libraries and the advantages and disadvantages of various fragment-based screening (FBS) for constructing such libraries. We also highlight the deconstruction–reconstruction strategy by utilizing privileged fragments of reported ligands. PMID:25263697

Current perspectives in fragment-based lead discovery (FBLD)

PubMed Central

Lamoree, Bas; Hubbard, Roderick E.

2017-01-01

It is over 20 years since the first fragment-based discovery projects were disclosed. The methods are now mature for most ‘conventional’ targets in drug discovery such as enzymes (kinases and proteases) but there has also been growing success on more challenging targets, such as disruption of protein–protein interactions. The main application is to identify tractable chemical startpoints that non-covalently modulate the activity of a biological molecule. In this essay, we overview current practice in the methods and discuss how they have had an impact in lead discovery – generating a large number of fragment-derived compounds that are in clinical trials and two medicines treating patients. In addition, we discuss some of the more recent applications of the methods in chemical biology – providing chemical tools to investigate biological molecules, mechanisms and systems. PMID:29118093

A simple and robust approach to immobilization of antibody fragments.

PubMed

Ikonomova, Svetlana P; He, Ziming; Karlsson, Amy J

2016-08-01

Antibody fragments, such as the single-chain variable fragment (scFv), have much potential in research and diagnostics because of their antigen-binding ability similar to a full-sized antibody and their ease of production in microorganisms. Some applications of antibody fragments require immobilization on a surface, and we have established a simple immobilization method that is based on the biotin-streptavidin interaction and does not require a separate purification step. We genetically fused two biotinylation tags-the biotin carboxyl carrier protein (BCCP) or the AviTag minimal sequence-to six different scFvs (scFv13R4, scFvD10, scFv26-10, scFv3, scFv5, and scFv12) for site-specific biotinylation in vivo by endogenous biotin ligases produced by Escherichia coli. The biotinylated scFvs were immobilized onto streptavidin-coated plates directly from cell lysates, and immobilization was detected through enzyme-linked immunosorbent assays. All scFvs fusions were successfully immobilized, and scFvs biotinylated via the BCCP tag tended to immobilize better than those biotinylated via the AviTag, even when biotinylation efficiency was improved with the biotin ligase BirA. The ability of immobilized scFvs to bind antigens was confirmed using scFv13R4 and scFvD10 with their respective targets β-galactosidase and bacteriophage lambda head protein D (gpD). The immobilized scFv13R4 bound to β-galactosidase at the same level for both biotinylation tags when the surface was saturated with the scFv, and immobilized scFvs retained their functionality for at least 100days after immobilization. The simplicity and robustness of our method make it a promising approach for future applications that require antibody fragment immobilization. Copyright © 2016 Elsevier B.V. All rights reserved.

A heteromeric Texas coral snake toxin targets acid-sensing ion channels to produce pain.

PubMed

Bohlen, Christopher J; Chesler, Alexander T; Sharif-Naeini, Reza; Medzihradszky, Katalin F; Zhou, Sharleen; King, David; Sánchez, Elda E; Burlingame, Alma L; Basbaum, Allan I; Julius, David

2011-11-16

Natural products that elicit discomfort or pain represent invaluable tools for probing molecular mechanisms underlying pain sensation. Plant-derived irritants have predominated in this regard, but animal venoms have also evolved to avert predators by targeting neurons and receptors whose activation produces noxious sensations. As such, venoms provide a rich and varied source of small molecule and protein pharmacophores that can be exploited to characterize and manipulate key components of the pain-signalling pathway. With this in mind, here we perform an unbiased in vitro screen to identify snake venoms capable of activating somatosensory neurons. Venom from the Texas coral snake (Micrurus tener tener), whose bite produces intense and unremitting pain, excites a large cohort of sensory neurons. The purified active species (MitTx) consists of a heteromeric complex between Kunitz- and phospholipase-A2-like proteins that together function as a potent, persistent and selective agonist for acid-sensing ion channels (ASICs), showing equal or greater efficacy compared with acidic pH. MitTx is highly selective for the ASIC1 subtype at neutral pH; under more acidic conditions (pH < 6.5), MitTx massively potentiates (>100-fold) proton-evoked activation of ASIC2a channels. These observations raise the possibility that ASIC channels function as coincidence detectors for extracellular protons and other, as yet unidentified, endogenous factors. Purified MitTx elicits robust pain-related behaviour in mice by activation of ASIC1 channels on capsaicin-sensitive nerve fibres. These findings reveal a mechanism whereby snake venoms produce pain, and highlight an unexpected contribution of ASIC1 channels to nociception. © 2011 Macmillan Publishers Limited. All rights reserved

Speed genome editing by transient CRISPR/Cas9 targeting and large DNA fragment deletion.

PubMed

Luo, Jing; Lu, Liaoxun; Gu, Yanrong; Huang, Rong; Gui, Lin; Li, Saichao; Qi, Xinhui; Zheng, Wenping; Chao, Tianzhu; Zheng, Qianqian; Liang, Yinming; Zhang, Lichen

2018-06-07

Genetic engineering of cell lines and model organisms has been facilitated enormously by the CRISPR/Cas9 system. However, in cell lines it remains labor intensive and time consuming to obtain desirable mutant clones due to the difficulties in isolating the mutated clones and sophisticated genotyping. In this study, we have validated fluorescent protein reporter aided cell sorting which enables the isolation of maximal diversity in mutant cells. We further applied two spectrally distinct fluorescent proteins DsRed2 and ECFP as reporters for independent CRISPR/Cas9 mediated targeting, which allows for one-cell-one-well sorting of the mutant cells. Because of ultra-high efficiency of the CRISPR/Cas9 system with dual reporters and large DNA fragment deletion resulting from independent loci cleavage, monoclonal mutant cells could be easily identified by conventional PCR. In the speed genome editing method presented here, sophisticated genotyping methods are not necessary to identify loss of function mutations after CRISPR/Cas9 genome editing, and desirable loss of function mutant clones could be obtained in less than one month following transfection. Copyright © 2018 Elsevier B.V. All rights reserved.

Subduction controls the distribution and fragmentation of Earth’s tectonic plates.

PubMed

Mallard, Claire; Coltice, Nicolas; Seton, Maria; Müller, R Dietmar; Tackley, Paul J

2016-07-07

The theory of plate tectonics describes how the surface of Earth is split into an organized jigsaw of seven large plates of similar sizes and a population of smaller plates whose areas follow a fractal distribution. The reconstruction of global tectonics during the past 200 million years suggests that this layout is probably a long-term feature of Earth, but the forces governing it are unknown. Previous studies, primarily based on the statistical properties of plate distributions, were unable to resolve how the size of the plates is determined by the properties of the lithosphere and the underlying mantle convection. Here we demonstrate that the plate layout of Earth is produced by a dynamic feedback between mantle convection and the strength of the lithosphere. Using three-dimensional spherical models of mantle convection that self-consistently produce the plate size–frequency distribution observed for Earth, we show that subduction geometry drives the tectonic fragmentation that generates plates. The spacing between the slabs controls the layout of large plates, and the stresses caused by the bending of trenches break plates into smaller fragments. Our results explain why the fast evolution in small back-arc plates reflects the marked changes in plate motions during times of major reorganizations. Our study opens the way to using convection simulations with plate-like behaviour to unravel how global tectonics and mantle convection are dynamically connected.

Virtual fragment preparation for computational fragment-based drug design.

PubMed

Ludington, Jennifer L

2015-01-01

Fragment-based drug design (FBDD) has become an important component of the drug discovery process. The use of fragments can accelerate both the search for a hit molecule and the development of that hit into a lead molecule for clinical testing. In addition to experimental methodologies for FBDD such as NMR and X-ray Crystallography screens, computational techniques are playing an increasingly important role. The success of the computational simulations is due in large part to how the database of virtual fragments is prepared. In order to prepare the fragments appropriately it is necessary to understand how FBDD differs from other approaches and the issues inherent in building up molecules from smaller fragment pieces. The ultimate goal of these calculations is to link two or more simulated fragments into a molecule that has an experimental binding affinity consistent with the additive predicted binding affinities of the virtual fragments. Computationally predicting binding affinities is a complex process, with many opportunities for introducing error. Therefore, care should be taken with the fragment preparation procedure to avoid introducing additional inaccuracies.This chapter is focused on the preparation process used to create a virtual fragment database. Several key issues of fragment preparation which affect the accuracy of binding affinity predictions are discussed. The first issue is the selection of the two-dimensional atomic structure of the virtual fragment. Although the particular usage of the fragment can affect this choice (i.e., whether the fragment will be used for calibration, binding site characterization, hit identification, or lead optimization), general factors such as synthetic accessibility, size, and flexibility are major considerations in selecting the 2D structure. Other aspects of preparing the virtual fragments for simulation are the generation of three-dimensional conformations and the assignment of the associated atomic point charges.

Confounding factors in the detection of species responses to habitat fragmentation.

PubMed

Ewers, Robert M; Didham, Raphael K

2006-02-01

Habitat loss has pervasive and disruptive impacts on biodiversity in habitat remnants. The magnitude of the ecological impacts of habitat loss can be exacerbated by the spatial arrangement -- or fragmentation -- of remaining habitat. Fragmentation per se is a landscape-level phenomenon in which species that survive in habitat remnants are confronted with a modified environment of reduced area, increased isolation and novel ecological boundaries. The implications of this for individual organisms are many and varied, because species with differing life history strategies are differentially affected by habitat fragmentation. Here, we review the extensive literature on species responses to habitat fragmentation, and detail the numerous ways in which confounding factors have either masked the detection, or prevented the manifestation, of predicted fragmentation effects. Large numbers of empirical studies continue to document changes in species richness with decreasing habitat area, with positive, negative and no relationships regularly reported. The debate surrounding such widely contrasting results is beginning to be resolved by findings that the expected positive species-area relationship can be masked by matrix-derived spatial subsidies of resources to fragment-dwelling species and by the invasion of matrix-dwelling species into habitat edges. Significant advances have been made recently in our understanding of how species interactions are altered at habitat edges as a result of these changes. Interestingly, changes in biotic and abiotic parameters at edges also make ecological processes more variable than in habitat interiors. Individuals are more likely to encounter habitat edges in fragments with convoluted shapes, leading to increased turnover and variability in population size than in fragments that are compact in shape. Habitat isolation in both space and time disrupts species distribution patterns, with consequent effects on metapopulation dynamics and the

Fragmentation of protoplanetary discs around M-dwarfs

NASA Astrophysics Data System (ADS)

Backus, Isaac; Quinn, Thomas

2016-12-01

We investigate the conditions required for planet formation via gravitational instability (GI) and protoplanetary disc (PPD) fragmentation around M-dwarfs. Using a suite of 64 SPH simulations with 106 particles, the parameter space of disc mass, temperature, and radius is explored, bracketing reasonable values based on theory and observation. Our model consists of an equilibrium, gaseous, and locally isothermal disc orbiting a central star of mass M* = M⊙/3. Discs with a minimum Toomre Q of Qmin ≲ 0.9 will fragment and form gravitationally bound clumps. Some previous literature has found Qmin < 1.3-1.5 to be sufficient for fragmentation. Increasing disc height tends to stabilize discs, and when incorporated into Q as Qeff ∝ Q(H/R)α for α = 0.18 is sufficient to predict fragmentation. Some discrepancies in the literature regarding Qcrit may be due to different methods of generating initial conditions (ICs). A series of 15 simulations demonstrates that perturbing ICs slightly out of equilibrium can cause discs to fragment for higher Q. Our method for generating ICs is presented in detail. We argue that GI likely plays a role in PPDs around M-dwarfs and that disc fragmentation at large radii is a plausible outcome for these discs.

Beam On Target (BOT) Produces Gamma Ray Burst (GRB) Fireballs and Afterglows

NASA Astrophysics Data System (ADS)

Greyber, H. D.

1997-12-01

Unlike the myriads of ad hoc models that have been offered to explain GRB, the BOT process is simply the very common process used worldwide in accelerator laboratories to produce gamma rays. The Strong Magnetic Field (SMF) model postulates an extremely intense, highly relativistic current ring formed during the original gravitational collapse of a distant galaxy when the plasma cloud was permeated by a primordial magnetic field. GRB occur when solid matter (asteroid, white dwarf, neutron star, planet) falls rapidly through the Storage Ring beam producing a very strongly collimated electromagnetic shower, and a huge amount of matter from the target, in the form of a giant, hot, expanding plasma cloud, or ``Fireball,'' is blown off. BOT satisfies all the ``severe constraints imposed on the source of this burst --'' concluded by the CGRO team (Sommer et al, Astrophys. J. 422 L63 (1994)) for the huge intense burst GRB930131, whereas neutron star merger models are ``difficult to reconcile.'' BOT expects the lowest energy gamma photons to arrive very slightly later than higher energy photons due to the time for the shower to penetrate the target. The millisecond spikes in bursts are due to the slender filaments of current that make up the Storage Ring beam. Delayed photons can be explained by a broken target ``rock.'' See H. Greyber in the book ``Compton Gamma Ray Observatory,'' AIP Conf. Proc. 280, 569 (1993).

Laser Subdivision of the Genesis Concentrator Target Sample 60000

NASA Technical Reports Server (NTRS)

Lauer, Howard V., Jr.; Burkett, P. J.; Rodriquez, M. C.; Nakamura-Messenger, K.; Clemett, S. J.; Gonzales, C. P.; Allton, J. H.; McNamara, K. M.; See, T. H.

2013-01-01

The Genesis Allocation Committee received a request for 1 square centimeter of the diamond-like-carbon (DLC) concentrator target for the analysis of solar wind nitrogen isotopes. The target consists of a single crystal float zone (FZ) silicon substrate having a thickness on the order of 550 micrometers with a 1.5-3.0 micrometer-thick coating of DLC on the exposed surface. The solar wind is implanted shallowly in the front side DLC. The original target was a circular quadrant with a radius of 3.1 cm; however, the piece did not survive intact when the spacecraft suffered an anomalous landing upon returning to Earth on September 8, 2004. An estimated 75% of the DLC target was recovered in at least 18 fragments. The largest fragment, Genesis sample 60000, has been designated for this allocation and is the first sample to be subdivided using our laser scribing system Laser subdivision has associated risks including thermal diffusion of the implant if heating occurs and unintended breakage during cleavage. A careful detailed study and considerable subdividing practice using non-flight FZ diamond on silicon, DOS, wafers has considerably reduced the risk of unplanned breakage during the cleaving process. In addition, backside scribing reduces the risk of possible thermal excursions affecting the implanted solar wind, implanted shallowly in the front side DLC.

Inhibiting nucleation of amyloid structure in a huntingtin fragment by targeting α-helix rich oligomeric intermediates

PubMed Central

Mishra, Rakesh; Jayaraman, Murali; Roland, Bartholomew P.; Landrum, Elizabeth; Fullam, Timothy; Kodali, Ravindra; Thakur, Ashwani K.; Arduini, Irene; Wetzel, Ronald

2011-01-01

Although oligomeric intermediates are transiently formed in almost all known amyloid assembly reactions, their mechanistic roles are poorly understood. Recently we demonstrated a critical role for the 17 amino acid N-terminal segment (httNT) of huntingtin (htt) in oligomer-mediated amyloid assembly of htt N-terminal fragments. In this mechanism, the httNT segment forms the α-helix rich core of the oligomers, leaving most or all of each polyglutamine (polyQ) segment disordered and solvent-exposed. Nucleation of amyloid structure occurs within this local high concentration of disordered polyQ. Here we demonstrate the kinetic importance of httNT self-assembly by describing inhibitory httNT-containing peptides that appear to work by targeting nucleation within the oligomer fraction. These molecules inhibit amyloid nucleation by forming mixed oligomers with the httNT domains of polyQ-containing htt N-terminal fragments. In one class of inhibitor, nucleation is passively suppressed due to the reduced local concentration of polyQ within the mixed oligomer. In the other class, nucleation is actively suppressed by a proline-rich polyQ segment covalently attached to httNT. Studies with D-amino acid and scrambled sequence versions of httNT suggest that inhibition activity is strongly linked to the propensity of inhibitory peptides to make amphipathic α-helices. HttNT derivatives with C-terminal cell penetrating peptide segments, also exhibit excellent inhibitory activity. The httNT-based peptides described here, especially those with protease-resistant D-amino acids and/or with cell penetrating sequences, may prove useful as lead therapeutics for inhibiting nucleation of amyloid formation in Huntington’s disease. PMID:22178478

Complex fragmentation and silicification structures in fault zones: quartz crystallization and repeated fragmentation in the Rusey fault zone (Cornwall/UK)

NASA Astrophysics Data System (ADS)

Yilmaz, Tim I.; Blenkinsop, Tom; Duschl, Florian; Kruhl, Jörn H.

2015-04-01

Silicified fault rocks typically show structures resulting from various stages of fragmentation and quartz crystallization. Both processes interact episodically and result in complex structures on various scales, which require a wide spectrum of analysis tools. Based on field and microstructural data, the spatial-temporal connection between deformation, quartz crystallization and fluid and material flow along the Rusey fault zone was investigated. The fault can be examined in detail in three dimensions on the north Cornwall coast, UK. It occurs within Carboniferous sandstones, siltstones, mudstones and slates of the Culm basin, and is likely to have had a long history. The fault rocks described here formed during the younger events, possibly due to Tertiary strike-slip reactivation. Frequent fragmentation, flow and crystallization events and their interaction led to various generations of complex-structured quartz units, among them quartz-mantled and partly silicified wall-rock fragments, microcrystalline quartz masses of different compositions and structures, and quartz vein patterns of various ages. Lobate boundaries of quartz masses indicate viscous flow. Fragments are separated by quartz infill, which contains cm-sized open pores, in which quartz crystals have pyramidal terminations. Based on frequent occurrence of feathery textures and the infill geometry, quartz crystallization from chalcedony appears likely, and an origin from silica gel is discussed. Fragmentation structures are generally fractal. This allows differentiation between various processes, such as corrosive wear, wear abrasion and hydraulic brecciation. Material transport along the brittle shear zone, and displacement of the wall-rocks, were at least partly governed by flow of mobile fluid-quartz-particle suspensions. The complex meso- to microstructures were generated by repeated processes of fragmentation, quartz precipitation and grain growth. In general, the brittle Rusey fault zone

RNase-Resistant Virus-Like Particles Containing Long Chimeric RNA Sequences Produced by Two-Plasmid Coexpression System▿

PubMed Central

Wei, Yuxiang; Yang, Changmei; Wei, Baojun; Huang, Jie; Wang, Lunan; Meng, Shuang; Zhang, Rui; Li, Jinming

2008-01-01

RNase-resistant, noninfectious virus-like particles containing exogenous RNA sequences (armored RNA) are good candidates as RNA controls and standards in RNA virus detection. However, the length of RNA packaged in the virus-like particles with high efficiency is usually less than 500 bases. In this study, we describe a method for producing armored L-RNA. Armored L-RNA is a complex of MS2 bacteriophage coat protein and RNA produced in Escherichia coli by the induction of a two-plasmid coexpression system in which the coat protein and maturase are expressed from one plasmid and the target RNA sequence with modified MS2 stem-loop (pac site) is transcribed from another plasmid. A 3V armored L-RNA of 2,248 bases containing six gene fragments—hepatitis C virus, severe acute respiratory syndrome coronavirus (SARS-CoV1, SARS-CoV2, and SARS-CoV3), avian influenza virus matrix gene (M300), and H5N1 avian influenza virus (HA300)—was successfully expressed by the two-plasmid coexpression system and was demonstrated to have all of the characteristics of armored RNA. We evaluated the 3V armored L-RNA as a calibrator for multiple virus assays. We used the WHO International Standard for HCV RNA (NIBSC 96/790) to calibrate the chimeric armored L-RNA, which was diluted by 10-fold serial dilutions to obtain samples containing 106 to 102 copies. In conclusion, the approach we used for armored L-RNA preparation is practical and could reduce the labor and cost of quality control in multiplex RNA virus assays. Furthermore, we can assign the chimeric armored RNA with an international unit for quantitative detection. PMID:18305135

Does the range of IMF affect rise and fall trend in fragmentation?

NASA Astrophysics Data System (ADS)

Sharma, Sakshi; Kumar, Rohit; Puri, Rajeev K.

2018-05-01

We study the rise and fall behavior in the multiplicity of intermediate mass fragments produced in the asymmetric reactions of 36S+ 198Pt using isospin-dependent quantum molecular dynamics model. We use different definitions of intermediate mass fragments according to various experimental studies. We find that the use of one or the other definition of intermediate mass fragments does not alter results significantly.

Structural basis of mammalian glycan targeting by Vibrio cholerae cytolysin and biofilm proteins

PubMed Central

De, Swastik; Kaus, Katherine; Sinclair, Shada

2018-01-01

Vibrio cholerae is an aquatic gram-negative microbe responsible for cholera, a pandemic disease causing life-threatening diarrheal outbreaks in populations with limited access to health care. Like most pathogenic bacteria, V. cholerae secretes virulence factors to assist colonization of human hosts, several of which bind carbohydrate receptors found on cell-surfaces. Understanding how pathogenic virulence proteins specifically target host cells is important for the development of treatment strategies to fight bacterial infections. Vibrio cholerae cytolysin (VCC) is a secreted pore-forming toxin with a carboxy-terminal β-prism domain that targets complex N-glycans found on mammalian cell-surface proteins. To investigate glycan selectivity, we studied the VCC β-prism domain and two additional β-prism domains found within the V. cholerae biofilm matrix protein RbmC. We show that the two RbmC β-prism domains target a similar repertoire of complex N-glycan receptors as VCC and find through binding and modeling studies that a branched pentasaccharide core (GlcNAc2-Man3) represents the likely footprint interacting with these domains. To understand the structural basis of V. cholerae β-prism selectivity, we solved high-resolution crystal structures of fragments of the pentasaccharide core bound to one RbmC β-prism domain and conducted mutagenesis experiments on the VCC toxin. Our results highlight a common strategy for cell-targeting utilized by both toxin and biofilm matrix proteins in Vibrio cholerae and provide a structural framework for understanding the specificity for individual receptors. Our results suggest that a common strategy for disrupting carbohydrate interactions could affect multiple virulence factors produced by V. cholerae, as well as similar β-prism domains found in other vibrio pathogens. PMID:29432487

A fragment of alpha-actinin promotes monocyte/macrophage maturation in vitro.

PubMed

Luikart, S; Wahl, D; Hinkel, T; Masri, M; Oegema, T

1999-02-01

Conditioned media (CM) from cultures of HL-60 myeloid leukemia cells grown on extracellular bone marrow matrix contains a factor that induces macrophage-like maturation of HL-60 cells. This factor was purified from the CM of HL-60 cells grown on bone marrow stroma by ammonium sulfate precipitation, then sequential chromatography on DEAE, affi-gel blue affinity, gel exclusion, and wheat germ affinity columns, followed by C-4 reverse phase HPLC, and SDS-PAGE. The maturation promoting activity of the CM was identified in a single 31 kD protein. Amino acid sequence analysis of four internal tryptic peptides of this protein confirmed significant homology with amino acid residues 48-60, 138-147, 215-220, and 221-236 of human cytoskeletal alpha-actinin. An immunoaffinity purified rabbit polyclonal anti-chicken alpha-actinin inhibited the activity of HL-60 conditioned media. A 27 kD amino-terminal fragment of alpha-actinin produced by thermolysin digestion of chicken gizzard alpha-actinin, but not intact alpha-actinin, had maturation promoting activity on several cell types, including blood monocytes, as measured by lysozyme secretion and tartrate-resistant acid phosphatase staining. We conclude that an extracellular alpha-actinin fragment can promote monocyte/macrophage maturation. This represents the first example of a fragment of a cytoskeletal component, which may be released during tissue remodeling and repair, playing a role in phagocyte maturation.

Construction of an agglutination tool: recombinant Fab fragments biotinylated in vitro.

PubMed

Czerwinski, Marcin; Krop-Watorek, Anna; Wasniowska, Kazimiera; Smolarek, Dorota; Spitalnik, Steven L

2009-11-30

The pComb3H vector system is used for constructing and panning recombinant antibody libraries. It allows for expression of monovalent Fab fragments, either on the surface of M13 phage, or in the form of soluble proteins secreted into the periplasmic space of bacteria. We constructed a modified pComb3H vector containing cDNA encoding for a 23-amino acid fragment of the Escherichia coli biotin carboxy carrier protein (BCCP), which is an acceptor sequence for biotinylation. The vector was used to express the Fab fragment recognizing human glycophorin A. The purified Fab fragment containing this biotin acceptor sequence was effectively biotinylated in vitro using biotin ligase (BirA). The specificity and avidity of the biotinylated Fab fragments were similar to the previously produced, unmodified Fab fragments. An avidin-alkaline phosphatase conjugate was used to detect the recombinant Fab fragments, instead of secondary antibody. In addition, when biotinylated Fab fragments were mixed with avidin, red blood cells were directly agglutinated.

Micro-cone targets for producing high energy and low divergence particle beams

DOEpatents

Le Galloudec, Nathalie

2013-09-10

The present invention relates to micro-cone targets for producing high energy and low divergence particle beams. In one embodiment, the micro-cone target includes a substantially cone-shaped body including an outer surface, an inner surface, a generally flat and round, open-ended base, and a tip defining an apex. The cone-shaped body tapers along its length from the generally flat and round, open-ended base to the tip defining the apex. In addition, the outer surface and the inner surface connect the base to the tip, and the tip curves inwardly to define an outer surface that is concave, which is bounded by a rim formed at a juncture where the outer surface meets the tip.

Characterization of hypervelocity metal fragments for explosive initiation

DOE PAGES

Yeager, John D.; Bowden, Patrick R.; Guildenbecher, Daniel R.; ...

2017-07-17

The fragment impact response of two plastic-bonded explosive (PBX) formulations was studied using explosively driven aluminum fragments. A generic aluminum-capped detonator generated sub-mm aluminum particles moving at hypersonic velocities. The ability of these fragments to initiate reaction or otherwise damage two PBX materials was assessed using go/no-go experiments at standoff distances of up to 160 mm. Lower density PBX 9407 (RDX-based) was initiable at up to 115 mm, while higher density PBX 9501 (HMX-based) was only initiable at up to 6 mm. Several techniques were used to characterize the size, distribution, and velocity of the particles. Witness plate materials, includingmore » copper and polycarbonate, and backlit high speed video were used to characterize the distribution of particles, finding that the aluminum cap did not fragment homogeneously but rather with larger particles in a ring surrounding finer particles. Finally, precise digital holography experiments were conducted to measure the three-dimensional shape and size of the fastest-moving fragments, which ranged between 100 and 700 μm and traveled between 2.2 and 3.2 km/s. Crucially, these experiments showed variability in the fragmentation in terms of the number of fragments at the leading edge of the fragment field, indicating that both single and multiple shock impacts could be imparted to the target material. As a result, these types of data are critical for safety experiments and hydrocode simulations to quantify shock-to-detonation transition mechanisms and the associated risk-margins for these materials.« less