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Sample records for active zone molecule

  1. Physical activation of molecules

    A brief review of processes of physical activation of molecules on the basis of phenomena of electronic and vibrational excitation, electron polarization is presented. Consideration is given to activation by electron impact, photo-, magneto- and mechanoactivation, as well as to radiation activation, proceeding under the effect of high-power radiations (102-107 eV). The character of disturbance of molecules, participating in chemical reactions, under the effect of different types of ionizing radiation (α-particles, electrons, γ-quanta etc.) is discussed

  2. Presynaptic active zone density during development and synaptic plasticity.

    Gwenaëlle L Clarke

    2012-02-01

    Full Text Available Neural circuits transmit information through synapses, and the efficiency of synaptic transmission is closely related to the density of presynaptic active zones, where synaptic vesicles are released. The goal of this review is to highlight recent insights into the molecular mechanisms that control the number of active zones per presynaptic terminal (active zone density during developmental and stimulus-dependent changes in synaptic efficacy. At the neuromuscular junctions (NMJs, the active zone density is preserved across species, remains constant during development, and is the same between synapses with different activities. However, the NMJ active zones are not always stable, as exemplified by the change in active zone density during acute experimental manipulation or as a result of aging. Therefore, a mechanism must exist to maintain its density. In the central nervous system (CNS, active zones have restricted maximal size, exist in multiple numbers in larger presynaptic terminals, and maintain a constant density during development. These findings suggest that active zone density in the CNS is also controlled. However, in contrast to the NMJ, active zone density in the CNS can also be increased, as observed in hippocampal synapses in response to synaptic plasticity. Although the numbers of known active zone proteins and protein interactions have increased, less is known about the mechanism that controls the number or spacing of active zones. The following molecules are known to control active zone density and will be discussed herein: extracellular matrix laminins and voltage-dependent calcium channels, amyloid precursor proteins, the small GTPase Rab3, an endocytosis mechanism including synaptojanin, cytoskeleton protein spectrins and β-adducin, and a presynaptic web including spectrins. The molecular mechanisms that organize the active zone density are just beginning to be elucidated.

  3. Serpentine in active subduction zones

    Reynard, Bruno

    2013-09-01

    Serpentinization is a key phenomenon for understanding the geodynamics of subduction zones in the 10-200 km depth range. Serpentines are a major water carrier, and their rheological properties have a strong influence on deformation partitioning and seismicity at depths. I review experimental investigations that have been conducted on serpentines, with emphasis on the large body of data acquired over the past decade. Determinations of physical properties at the pressure and temperature conditions of subductions allow interpreting geophysical data in active subduction in terms of mineralogy and petrology, and to link the presence of serpentinites with deformation and fluid circulation. The fluid budget can be partially constrained from geophysical data. Elasticity data provide a quantitative basis for mapping serpentinization in the mantle wedge and slab from seismic tomography. Anisotropy suggests the existence of thin serpentinite channels above the plate interface, that account for mechanical decoupling inferred from down-dip limit of the seismogenic zone and heat flow. Strain-rate dependent rheology of antigorite serpentine is consistent with stable deformation of this thin layer or channel over timescales ranging from those of the seismic cycle to those of thermal equilibration and exhumation of high-pressure rocks, and with the geological record of subduction-related deformation. Circulation of serpentinizing fluids depends on the permeability structure, and is imaged by electrical conductivity tomography. It could be controlled by fracturing in the undeformed cold nose of the mantle wedge, and by plastic deformation along the plate interface. Fluid migration mechanisms are similar to those inferred from petrological and geochemical data on exhumed serpentinites. Estimation of the fluid budget associated with serpentine formation will rely on numerical simulations for which coupling of kinetics of hydration and dehydration at scales ranging from grain size up

  4. Chemical activation of molecules during coordination

    Activation processes of N2, O2, NO molecules in transition metal complexes and electron reconstructions of coordination sphere of compounds, related with it, were considered on tha basis of single-parameter approximation of vibronic activation theory. A special attention is paid to CO molecule activation in carbonyl complexes of transition metals (V, Nb, Mo, W, Tc, Re, Ru and others) and lanthanides. The effect of metal oxidation degree, the nature of metal and ligand, complex structure on chemical activation processes is analyzed

  5. Raman Optical Activity Spectra for Large Molecules through Molecules-in-Molecules Fragment-Based Approach.

    Jovan Jose, K V; Raghavachari, Krishnan

    2016-02-01

    We present an efficient method for the calculation of the Raman optical activity (ROA) spectra for large molecules through the molecules-in-molecules (MIM) fragment-based method. The relevant higher energy derivatives from smaller fragments are used to build the property tensors of the parent molecule to enable the extension of the MIM method for evaluating ROA spectra (MIM-ROA). Two factors were found to be particularly important in yielding accurate results. First, the link-atom tensor components are projected back onto the corresponding host and supporting atoms through the Jacobian projection method, yielding a mathematically rigorous method. Second, the long-range interactions between fragments are taken into account by using a less computationally expensive lower level of theory. The performance of the MIM-ROA model is calibrated on the enantiomeric pairs of 10 carbohydrate benchmark molecules, with strong intramolecular interactions. The vibrational frequencies and ROA intensities are accurately reproduced relative to the full, unfragmented, results for these systems. In addition, the MIM-ROA method is employed to predict the ROA spectra of d-maltose, α-D-cyclodextrin, and cryptophane-A, yielding spectra in excellent agreement with experiment. The accuracy and performance of the benchmark systems validate the MIM-ROA model for exploring ROA spectra of large molecules. PMID:26760444

  6. Uranium-mediated activation of small molecules.

    Arnold, Polly L

    2011-08-28

    Molecular complexes of uranium are capable of activating a range of industrially and economically important small molecules such as CO, CO(2), and N(2); new and often unexpected reactions provide insight into an element that needs to be well-understood if future clean-energy solutions are to involve nuclear power. PMID:21614341

  7. Synaptic Vesicle Proteins and Active Zone Plasticity

    Kittel, Robert J.; Heckmann, Manfred

    2016-01-01

    Neurotransmitter is released from synaptic vesicles at the highly specialized presynaptic active zone (AZ). The complex molecular architecture of AZs mediates the speed, precision and plasticity of synaptic transmission. Importantly, structural and functional properties of AZs vary significantly, even for a given connection. Thus, there appear to be distinct AZ states, which fundamentally influence neuronal communication by controlling the positioning and release of synaptic vesicles. Vice versa, recent evidence has revealed that synaptic vesicle components also modulate organizational states of the AZ. The protein-rich cytomatrix at the active zone (CAZ) provides a structural platform for molecular interactions guiding vesicle exocytosis. Studies in Drosophila have now demonstrated that the vesicle proteins Synaptotagmin-1 (Syt1) and Rab3 also regulate glutamate release by shaping differentiation of the CAZ ultrastructure. We review these unexpected findings and discuss mechanistic interpretations of the reciprocal relationship between synaptic vesicles and AZ states, which has heretofore received little attention.

  8. Novel approaches for single molecule activation and detection

    Benfenati, Fabio; Torre, Vincent

    2014-01-01

    How can we obtain tools able to process and exchange information at the molecular scale In order to do this, it is necessary to activate and detect single molecules under controlled conditions. This book focuses on the generation of biologically-inspired molecular devices. These devices are based on the developments of new photonic tools able to activate and stimulate single molecule machines. Additionally, new light sensitive molecules can be selectively activated by photonic tools. These technological innovations will provide a way to control activation of single light-sensitive molecules, a

  9. Active zone stability:insights from fly neuromuscular junction

    Xiaolin Tian; Chunlai Wu

    2015-01-01

    The presynaptic active zone is a dynamic structure that orchestrates regulated release of neurotrans-mitters. Developmental and aging processes, and changes in neuronal network activity can all modulate the number, size and composition of active zone and thereby synaptic efifcacy. However, very little is known about the mechanism that controls the structural stability of active zone. By study-ing a model synapse, theDrosophila neuromuscular junction, our recent work shed light on how two scaffolding proteins at the active zone regulate active zone stability by promoting a localized dephos-phorylation event at the nerve terminal. Here we discuss the major insights from our ifndings and their implications for future research.

  10. A Potent Activator of Melanogenesis Identified from Small Molecule Screening

    McNaughton, Brian R.; Gareiss, Peter C.; Jacobs, Stacey E.; Fricke, Alex F.; Scott, Glynis A.; Miller, Benjamin L.

    2009-01-01

    Small molecules that increase the cellular level of melanin can be used to study melanogenesis, and have therapeutic potential for melanin-related diseases such as albinism. We describe the identification of a potent activator of melanogenesis from a targeted combinatorial library. Treating melanocytes with our most active molecule results in a 1.8-fold increase in melanin, and an increase in tyrosinase-catalyzed oxidation of L-tyrosine, a key step in melanin biosynthesis.

  11. Exploration of the spontaneous fluctuating activity of single enzyme molecules

    Schwabe, A.; Maarleveld, T.R.; Bruggeman, F.J.

    2013-01-01

    Single enzyme molecules display inevitable, stochastic fluctuations in their catalytic activity. In metabolism, for instance, the stochastic activity of individual enzymes is averaged out due to their high copy numbers per single cell. However, many processes inside cells rely on single enzyme activ

  12. Leishmanicidal activity of plants from the Peruvian traditional pharmacopeia and molecules of synthesis; study structure-activity relationship.

    Estevez, Yannick

    2009-01-01

    New world Leishmaniasis are parasitosis with heavy socio-economic consequences. Nowadays the commercially available treatments require parenteral administrations and are not affordable for the concerned populations. The search for new active molecules is thus urgently needed. To contribute to the research effort of therapeutic alternative, we were interested in traditional pharmacopeia of populations living in endemic zone (two ethnic groups of Peruvian Amazonia: the Chayahuita and the Yanesh...

  13. Exploration of the spontaneous fluctuating activity of single enzyme molecules

    Schwabe, Anne; Maarleveld, Timo; Bruggeman, Frank

    2013-01-01

    Single enzyme molecules display inevitable, stochastic fluctuations in their catalytic activity. In metabolism, for instance, the stochastic activity of individual enzymes is averaged out due to their high copy numbers per single cell. However, many processes inside cells rely on single enzyme activity, such as transcription, replication, translation, and histone modifications. Here we introduce the main theoretical concepts of stochastic single-enzyme activity starting from the Michaelis–Men...

  14. Identification of small molecule activators of BMP signaling.

    Karen Vrijens

    Full Text Available Bone Morphogenetic Proteins (BMPs are morphogens that play a major role in regulating development and homeostasis. Although BMPs are used for the treatment of bone and kidney disorders, their clinical use is limited due to the supra-physiological doses required for therapeutic efficacy causing severe side effects. Because recombinant BMPs are expensive to produce, small molecule activators of BMP signaling would be a cost-effective alternative with the added benefit of being potentially more easily deliverable. Here, we report our efforts to identify small molecule activators of BMP signaling. We have developed a cell-based assay to monitor BMP signaling by stably transfecting a BMP-responsive human cervical carcinoma cell line (C33A with a reporter construct in which the expression of luciferase is driven by a multimerized BMP-responsive element from the Id1 promoter. A BMP-responsive clone C33A-2D2 was used to screen a bioactive library containing ∼5,600 small molecules. We identified four small molecules of the family of flavonoids all of which induced luciferase activity in a dose-dependent manner and ventralized zebrafish embryos. Two of the identified compounds induced Smad1, 5 phosphorylation (P-Smad, Id1 and Id2 expression in a dose-dependent manner demonstrating that our assays identified small molecule activators of BMP signaling.

  15. Functionalization of hydroxyl terminated polybutadiene with biologically active fluorescent molecule

    R Murali Sankar; Subhadeep Saha; K Seeni Meera; Tushar Jana

    2009-10-01

    A biologically active molecule, 2-chloro-4,6-bis(dimethylamino)-1,3,5-triazine (CBDT), has been covalently attached at the terminal carbon atoms of the hydroxyl terminated polybutadiene (HTPB) backbone. The modification of HTPB backbone by CBDT molecule does not affect the unique physico-chemical properties such as fluidity, hydroxyl value and microstructure of the parent HTPB. The formation of hydrogen bonding between the terminal hydroxyl groups and the nitrogen atoms of triazine moiety is the driving force for the terminal attachment chemistry. The functionalized HTPB (HTPB–CBDT) shows a strong fluorescence emission at 385 nm.

  16. Triggered tremors beneath the seismogenic zone of an active fault zone, Kyushu, Japan

    Miyazaki, Masahiro; Matsumoto, Satoshi; Shimizu, Hiroshi

    2015-11-01

    Non-volcanic tremors were induced by the surface waves of the 2012 Sumatra earthquake around the Hinagu fault zone in Kyushu, Japan. We inferred from dense seismic observation data that the hypocenters of these tremors were located beneath the seismogenic zone of the Hinagu fault. Focal mechanisms of the tremors were estimated using S-wave polarization angles. The estimated focal mechanisms show similarities to those of shallow earthquakes in this region. In addition, one of the nodal planes of the focal mechanisms is almost parallel to the strike direction of the Hinagu fault. These observations suggest that the tremors were triggered at the deeper extension of the active fault zone under stress conditions similar to those in the shallower seismogenic region. A low-velocity anomaly beneath the hypocentral area of the tremors might be related to the tremor activity.

  17. Quantitative analysis on tectonic deformation of active rupture zones

    JIANG Zai-sen; NIU An-fu; WANG Min; LI Kai-wu; FANG Ying; ZHANG Xi; ZHANG Xiao-liang

    2005-01-01

    Based on the regional GPS data of high spatial resolution, we present a method of quantitative analysis on the tectonic deformation of active rupture zones in order to predict the location of forthcoming major earthquakes. Firstly we divide the main fault area into certain deformation units, then derive the geometric deformation and relative dislocation parameters of each unit and finally estimate quantitatively the slip and strain rates in each segment of the rupture zone. Furthermore, by comparing the consistency of deformation in all segments of the whole rupture zone, we can determine the possible anomalous segments as well as their properties and amplitudes. In analyzing the eastern boundaries of Sichuan-Yunnan block with the GPS velocity data for the period of 1991~2001, we have discovered that the Mianning-Ningnan-Dongchuan segment on the Zemuhe-Xiaojiang fault zone is relatively locked and the left-lateral shear strain rate here is higher.

  18. Small molecules reveal an alternative mechanism of Bax activation.

    Brahmbhatt, Hetal; Uehling, David; Al-Awar, Rima; Leber, Brian; Andrews, David

    2016-04-15

    The pro-apoptotic protein Bax commits a cell to death by permeabilizing the mitochondrial outer membrane (MOM). To obtain small-molecule probes for elucidating the molecular mechanism(s) of Bax activation, we screened for compounds that induced Bax-mediated liposome permeabilization. We identified five structurally different small molecules that promoted both Bax targeting to and oligomerization at membranes. All five compounds initiated Bax oligomerization in the absence of membranes by a mechanism unlike Bax activation by Bcl-2 homology 3 domain (BH3) proteins. Some of the compounds induced Bax/Bak-dependent apoptosis in cells. Activation of Bax by the most active compound was poorly inhibited by the anti-apoptotic protein Bcl-XL and requires a cysteine residue at position 126 of Bax that is not required for activation by BH3 proteins. Our results reveal a novel pathway for Bax activation independent of pro-apoptotic BH3 proteins that may have important implications for the regulation of Bax activity in cells. PMID:26916338

  19. Structure and Structure-activity Relationship of Functional Organic Molecules

    2011-01-01

    @@ Research theme The group is made up of junior scientists from the State Key Laboratory of Elemento-organic Chemistry, Nankai University.The scientists focus their studis on the structure and structure-activity relationship of functional organic molecules not only because it has been the basis of their research, but also because the functional study of organic compounds is now a major scientific issue for organic chemists around the world.

  20. Where Does Metonymy Stop? Senses, Facets, and Active Zones

    Paradis, Carita

    2004-01-01

    The purpose of this article is to propose a constrained lexical semantic definition of referential metonymy within a model of meaning as ontology and construal. Due to their various types of lexical-referential pairings, 3 types of construals that are frequently referred to as metonymy in the cognitive literature are distinguished as metonymization, facetization, and zone activation. Metonymization involves the use of a lexical item to evoke the sense of something that is not conventionally l...

  1. Super-resolution microscopy of the synaptic active zone

    Markus Sauer; Kittel, Robert J.

    2015-01-01

    Brain function relies on accurate information transfer at chemical synapses. At the presynaptic active zone (AZ) a variety of specialised proteins are assembled to complex architectures, which set the basis for speed, precision and plasticity of synaptic transmission. Calcium (Ca2+) channels are pivotal for the initiation of excitation-secretion coupling and, correspondingly, capture a central position at the AZ. Combining quantitative functional studies with modelling approaches has prov...

  2. Inhibition of Nek2 by Small Molecules Affects Proteasome Activity

    Lingyao Meng

    2014-01-01

    Full Text Available Background. Nek2 is a serine/threonine kinase localized to the centrosome. It promotes cell cycle progression from G2 to M by inducing centrosome separation. Recent studies have shown that high Nek2 expression is correlated with drug resistance in multiple myeloma patients. Materials and Methods. To investigate the role of Nek2 in bortezomib resistance, we ectopically overexpressed Nek2 in several cancer cell lines, including multiple myeloma lines. Small-molecule inhibitors of Nek2 were discovered using an in-house library of compounds. We tested the inhibitors on proteasome and cell cycle activity in several cell lines. Results. Proteasome activity was elevated in Nek2-overexpressing cell lines. The Nek2 inhibitors inhibited proteasome activity in these cancer cell lines. Treatment with these inhibitors resulted in inhibition of proteasome-mediated degradation of several cell cycle regulators in HeLa cells, leaving them arrested in G2/M. Combining these Nek2 inhibitors with bortezomib increased the efficacy of bortezomib in decreasing proteasome activity in vitro. Treatment with these novel Nek2 inhibitors successfully mitigated drug resistance in bortezomib-resistant multiple myeloma. Conclusion. Nek2 plays a central role in proteasome-mediated cell cycle regulation and in conferring resistance to bortezomib in cancer cells. Taken together, our results introduce Nek2 as a therapeutic target in bortezomib-resistant multiple myeloma.

  3. Bilirubin: an endogenous molecule with antiviral activity in vitro.

    CesareMancuso

    2012-03-01

    Full Text Available Bilirubin-IX-alpha (BR is the final product of heme metabolism through the heme oxygenase/biliverdin reductase (HO/BVR system. Previous papers reported on the microbicidal effects of the HO by-products biliverdin-IX-alpha, carbon monoxide and iron, through either direct or indirect mechanisms. In this paper the evidence of a virucidal effect of BR against human herpes simplex virus type 1 (HSV-1 and the enterovirus EV71 was provided. Bilirubin-IX-alpha, at concentrations 1-10 µM, close to those found in blood and tissues, significantly reduced HSV-1 and EV71 replication in Hep-2 and Vero cell lines, respectively. Bilirubin-IX-alpha inhibited viral infection of Hep-2 and Vero cells when given 2 hours before, concomitantly and 2 hours after viral infection. Furthermore, BR retained its antiviral activity even complexed with a saturating concentration of human serum-albumin. Moreover, 10 µM BR increased the formation of nitric oxide and the phosphorylation of JNK in Vero and Hep-2 cell lines, respectively, thus implying a role of these two pathways in the mechanism of antiviral activity of the bile pigment. In conclusion, these results support the antiviral effect of BR against HSV-1 and enterovirus in vitro, and put the basis for further basic and clinical studies to understand the real role of BR as an endogenous antiviral molecule.

  4. Geophysical equipment meant for complex studies in geodynamic active zones

    The main purpose of the geophysical equipment is to investigate the electromagnetic (EM) and electric phenomena induced by the crustal and subcrustal processes, especially by the natural and anthropic hazard (seismic active and landslides zones, land collapses in the mining areas with salt dissolution etc.). The equipment's applicability includes electromagnetic (10 kHz to 4096 sec (0.2x10-3 Hz)) and DC observations having the following major objectives: (1) to investigate the shallow and deep structures in order to develop the adequate geodynamic models, (2) to draw up the EM tomographs at different levels to point out the active fault, the geometry of the relic slab in seismo-active zones, caverns with salt dissolution in mining areas, landslide's surfaces, etc., (3) to establish optimum placement and geoelectric pattern (type of geological structure and its strike direction, the standard deviation of the detectable parameters in non-seismic conditions), so that a regular monitoring of some EM parameters be accomplished, simultaneously with seismic events, with the aim to reveal the earthquakes' precursory parameters. (authors)

  5. 50 CFR Table 8 to Part 679 - Harvest Zone Codes for Use With Vessel Activity Reports

    2010-10-01

    ... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Harvest Zone Codes for Use With Vessel... ECONOMIC ZONE OFF ALASKA Pt. 679, Table 8 Table 8 to Part 679—Harvest Zone Codes for Use With Vessel Activity Reports Harvest Zone Description A1 BSAI EEZ off Alaska A2 GOA EEZ off Alaska B State waters...

  6. Manipulating lipid bilayer material properties using biologically active amphipathic molecules

    Ashrafuzzaman, Md [Department of Physiology and Biophysics, Weill Medical College of University of Cornell, New York, NY 10021 (United States); Lampson, M A [Department of Physiology and Biophysics, Weill Medical College of University of Cornell, New York, NY 10021 (United States); Greathouse, D V [Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701 (United States); II, R E Koeppe [Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701 (United States); Andersen, O S [Department of Physiology and Biophysics, Weill Medical College of University of Cornell, New York, NY 10021 (United States)

    2006-07-19

    Lipid bilayers are elastic bodies with properties that can be manipulated/controlled by the adsorption of amphipathic molecules. The resulting changes in bilayer elasticity have been shown to regulate integral membrane protein function. To further understand the amphiphile-induced modulation of bilayer material properties (thickness, intrinsic monolayer curvature and elastic moduli), we examined how an enantiomeric pair of viral anti-fusion peptides (AFPs)-Z-Gly-D-Phe and Z-Gly-Phe, where Z denotes a benzyloxycarbonyl group, as well as Z-Phe-Tyr and Z-D-Phe-Phe-Gly-alters the function of enantiomeric pairs of gramicidin channels of different lengths in planar bilayers. For both short and long channels, the channel lifetimes and appearance frequencies increase as linear functions of the aqueous AFP concentration, with no apparent effect on the single-channel conductance. These changes in channel function do not depend on the chirality of the channels or the AFPs. At pH 7.0, the relative changes in channel lifetimes do not vary when the channel length is varied, indicating that these compounds exert their effects primarily by causing a positive-going change in the intrinsic monolayer curvature. At pH 4.0, the AFPs are more potent than at pH 7.0 and have greater effects on the shorter channels, indicating that these compounds now change the bilayer elastic moduli. When AFPs of different anti-fusion potencies are compared, the rank order of the anti-fusion activity and the channel-modifying activity is similar, but the relative changes in anti-fusion potency are larger than the changes in channel-modifying activity. We conclude that gramicidin channels are useful as molecular force transducers to probe the influence of small amphiphiles upon lipid bilayer material properties.

  7. Friction mediated by redox-active supramolecular connector molecules.

    Bozna, B L; Blass, J; Albrecht, M; Hausen, F; Wenz, G; Bennewitz, R

    2015-10-01

    We report on a friction study at the nanometer scale using atomic force microscopy under electrochemical control. Friction arises from the interaction between two surfaces functionalized with cyclodextrin molecules. The interaction is mediated by connector molecules with (ferrocenylmethyl)ammonium end groups forming supramolecular complexes with the cyclodextrin molecules. With ferrocene connector molecules in solution, the friction increases by a factor of up to 12 compared to control experiments without connector molecules. The electrochemical oxidation of ferrocene to ferrocenium causes a decrease in friction owing to the lower stability of ferrocenium-cyclodextrin complex. Upon switching between oxidative and reduction potentials, a change in friction by a factor of 1.2-1.8 is observed. Isothermal titration calorimetry reveals fast dissociation and rebinding kinetics and thus an equilibrium regime for the friction experiments. PMID:26367352

  8. Activated leukocyte cell adhesion molecule in breast cancer: prognostic indicator

    Activated leukocyte cell adhesion molecule (ALCAM) (CD166) is an immunoglobulin molecule that has been implicated in cell migration. The present study examined the expression of ALCAM in human breast cancer and assessed its prognostic value. The immunohistochemical distribution and location of ALCAM was assessed in normal breast tissue and carcinoma. The levels of ALCAM transcripts in frozen tissue (normal breast, n = 32; breast cancer, n = 120) were determined using real-time quantitative PCR. The results were then analyzed in relation to clinical data including the tumor type, the grade, the nodal involvement, distant metastases, the tumor, node, metastasis (TNM) stage, the Nottingham Prognostic Index (NPI), and survival over a 6-year follow-up period. Immunohistochemical staining on tissue sections in ducts/acini in normal breast and in breast carcinoma was ALCAM-positive. Differences in the number of ALCAM transcripts were found in different types of breast cancer. The level of ALCAM transcripts was lower (P = 0.05) in tumors from patients who had metastases to regional lymph nodes compared with those patients without, in higher grade tumors compared with Grade 1 tumors (P < 0.01), and in TNM Stage 3 tumors compared with TNM Stage 1 tumors (P < 0.01). Tumors from patients with poor prognosis (with NPI > 5.4) had significantly lower levels (P = 0.014) of ALCAM transcripts compared with patients with good prognosis (with NPI < 3.4), and tumors from patients with local recurrence had significantly lower levels than those patients without local recurrence or metastases (P = 0.04). Notably, tumors from patients who died of breast cancer had significantly lower levels of ALCAM transcripts (P = 0.0041) than those with primary tumors but no metastatic disease or local recurrence. Patients with low levels of ALCAM transcripts had significantly (P = 0.009) more incidents (metastasis, recurrence, death) compared with patients with primary breast tumors with high levels of

  9. How to Make an Active Zone: Unexpected Universal Functional Redundancy between RIMs and RIM-BPs.

    Acuna, Claudio; Liu, Xinran; Südhof, Thomas C

    2016-08-17

    RIMs and RIM-binding proteins (RBPs) are evolutionary conserved multidomain proteins of presynaptic active zones that are known to recruit Ca(2+) channels; in addition, RIMs perform well-recognized functions in tethering and priming synaptic vesicles for exocytosis. However, deletions of RIMs or RBPs in mice cause only partial impairments in various active zone functions and have no effect on active zone structure, as visualized by electron micrographs, suggesting that their contribution to active zone functions is limited. Here, we show in synapses of the calyx of Held in vivo and hippocampal neurons in culture that combined, but not individual, deletions of RIMs and RBPs eliminate tethering and priming of synaptic vesicles, deplete presynaptic Ca(2+) channels, and ablate active zone complexes, as analyzed by electron microscopy of chemically fixed synapses. Thus, RBPs perform unexpectedly broad roles at the active zone that together with those of RIMs are essential for all active zone functions. PMID:27537484

  10. Understanding Enzyme Activity Using Single Molecule Tracking (Poster)

    Liu, Y.-S.; Zeng, Y.; Luo, Y.; Xu, Q.; Himmel, M.; Smith S.; Wei, H.; Ding, S.-Y.

    2009-06-01

    This poster describes single-molecule tracking and total internal reflection fluorescence microscopy. It discusses whether the carbohydrate-binding module (CBM) moves on cellulose, how the CBM binds to cellulose, and the mechanism of cellulosome assembly.

  11. Nano-sensing of the orientation of fluorescing molecules with active coated nano-particles

    Arslanagic, Samel; Ziolkowski, Richard W.

    2015-01-01

    The potential of using active coated nano-particles to determine the orientation of fluorescing molecules is reported. By treating each fluorescing molecule as an electric Hertzian dipole, single and multiple fluorescing molecules emitting coherently and incoherently in various orientations are...

  12. Small molecules with antiviral activity against the Ebola virus

    Nadia Litterman; Christopher Lipinski; Sean Ekins

    2015-01-01

    The recent outbreak of the Ebola virus in West Africa has highlighted the clear shortage of broad-spectrum antiviral drugs for emerging viruses. There are numerous FDA approved drugs and other small molecules described in the literature that could be further evaluated for their potential as antiviral compounds. These molecules are in addition to the few new antivirals that have been tested in Ebola patients but were not originally developed against the Ebola virus, and may play an important r...

  13. 77 FR 26737 - Foreign-Trade Zone 235-Lakewood, NJ: Notification of Proposed Production Activity; Cosmetic...

    2012-05-07

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE Foreign-Trade Zones Board Foreign-Trade Zone 235--Lakewood, NJ: Notification of Proposed Production Activity; Cosmetic Essence Innovations, LLC (Fragrance Bottling); Holmdel, NJ Cosmetic Essence...

  14. The relations between seismically active and electrically conductive zones

    A. I. Ruzajkin

    1997-06-01

    Full Text Available The higher electrical conductivity of rocks in the middle and lower parts of the Earth's crust is generally related to the presence of fluids in rocks. The metamorphic processes of dehydration contribute to release of fluids, above all, water; these processes are also responsible for an increase in rock porosity and fracturing. These processes influence the stressed-strained state of the medium under specific conditions. A probable mechanism of earthquake source formation on the contact of blocks with different rates of dehydration and, consequently, different electrical conductivity is discussed. The spatial positions of electrically conductive and seismically active zones are correlated and definite relations between them are found with special reference to the vast area of the Northern Tien Shan within Kirgizstan and some other regions. The greatest concentration of earthquake sources is observed mainly near the contacts between blocks with contrastingly different electrical conductivity values and on sites with a sharp drop in conductive-layer depths.

  15. Super-resolution microscopy of the synaptic active zone

    Markus Sauer

    2015-01-01

    Full Text Available Brain function relies on accurate information transfer at chemical synapses. At the presynaptic active zone (AZ a variety of specialised proteins are assembled to complex architectures, which set the basis for speed, precision and plasticity of synaptic transmission. Calcium (Ca2+ channels are pivotal for the initiation of excitation-secretion coupling and, correspondingly, capture a central position at the AZ. Combining quantitative functional studies with modelling approaches has provided predictions of channel properties, numbers and even positions on the nanometre scale. However, elucidating the nanoscopic organisation of the surrounding protein network requires direct ultrastructural access. Without this information, knowledge of molecular synaptic structure-function relationships remains incomplete. Recently, super-resolution microscopy techniques have begun to enter the neurosciences. These approaches combine high spatial resolution with the molecular specificity of fluorescence microscopy. Here, we discuss how super-resolution microscopy can be used to obtain information on the organisation of AZ proteins.

  16. Novel Molecular Non-Volatile Memory: Application of Redox-Active Molecules

    Hao Zhu; Qiliang Li

    2015-01-01

    This review briefly describes the development of molecular electronics in the application of non-volatile memory. Molecules, especially redox-active molecules, have become interesting due to their intrinsic redox behavior, which provides an excellent basis for low-power, high-density and high-reliability non-volatile memory applications. Recently, solid-state non-volatile memory devices based on redox-active molecules have been reported, exhibiting fast speed, low operation voltage, excellent...

  17. Small molecules with antiviral activity against the Ebola virus.

    Litterman, Nadia; Lipinski, Christopher; Ekins, Sean

    2015-01-01

    The recent outbreak of the Ebola virus in West Africa has highlighted the clear shortage of broad-spectrum antiviral drugs for emerging viruses. There are numerous FDA approved drugs and other small molecules described in the literature that could be further evaluated for their potential as antiviral compounds. These molecules are in addition to the few new antivirals that have been tested in Ebola patients but were not originally developed against the Ebola virus, and may play an important role as we await an effective vaccine. The balance between using FDA approved drugs versus novel antivirals with minimal safety and no efficacy data in humans should be considered. We have evaluated 55 molecules from the perspective of an experienced medicinal chemist as well as using simple molecular properties and have highlighted 16 compounds that have desirable qualities as well as those that may be less desirable. In addition we propose that a collaborative database for sharing such published and novel information on small molecules is needed for the research community studying the Ebola virus. PMID:25713700

  18. Seismically active fracture zones in the continental wedge above the Andean subduction zone in the Arica Elbow region

    Vaněk, Jiří; Hanuš, Václav; Slancová, Alice; Špičák, Aleš

    2007-01-01

    Roč. 9, č. 1-4 (2007), s. 39-57. ISSN 0163-3171 R&D Projects: GA ČR GA205/95/0264; GA AV ČR IAA3012805 Grant ostatní: UNESCO(FR) IGCP project No. 345 Institutional research plan: CEZ:AV0Z30120515 Source of funding: V - iné verejné zdroje Keywords : continental lithosphere * Wadati-Benioff zone * seismically active zones Subject RIV: DC - Siesmology, Volcanology, Earth Structure

  19. Contemporary approaches to studying and mapping of active water exchange zone of ground water

    Moraru, C. Ye

    2016-03-01

    The article deals with a zone of ground water active exchange. New principles of the zone study and mapping under the platform hydrogeological condition are discussed. The assessment and distribution techniques are suggested for the active water exchange zone under the condition of hydrogeological parameterization uncertainty. The efficiency and significance of the suggested techniques are proved using the example of ground water in the southwest of Black Sea artesian basin.

  20. A Proposition for Geodetic Recording of Active Fault Zones

    Ladislav Placer

    2007-12-01

    Full Text Available Establishing recent displacements along faults is an important and delicate task. Larger faults are accompanied by broader fault zones that require a specificapproachtogeodeticmeasurements of fault block displacements. The vector of fault block displacements, or resultant, is a vector sum of differential displacements within the fault zone. For the purposes of recording the displacements we propose the stabilization of a geodetic network of points positioned in fault blocks outside the fault zone, whereby the displacements would be manifested in the deformation of the network. The resultant displacement vector can then be derived from the latter deformation, and from that, the dip and strike of the fault zone as well as the extent of the displacement.

  1. A Proposition for Geodetic Recording of Active Fault Zones

    Ladislav Placer; Božo Koler

    2007-01-01

    Establishing recent displacements along faults is an important and delicate task. Larger faults are accompanied by broader fault zones that require a specific approach to geodetic measurements of fault block displacements. The vector of fault block displacements, or resultant, is a vector sum of differential displacements within the fault zone. For the purposes of recording the displacements we propose the stabilization of a geodetic network of points positioned in fault blocks...

  2. Dynamics of water molecules in the active-site cavity of human cytochromes P450

    Rydberg, Patrik; Rod, Thomas Holm; Olsen, Lars;

    2007-01-01

    We have studied the dynamics of water molecules in six crystal structures of four human cytochromes P450, 2A6, 2C8, 2C9, and 3A4, with molecular dynamics simulations. In the crystal structures, only a few water molecules are seen and the reported sizes of the active-site cavity vary a lot. In the...

  3. Adhesion molecules levels in blood correlate with MRI activity and clinical activity in multiple sclerosis

    Research into pathogenesis of multiple sclerosis (MS) has prompted efforts to identify immunological markers associated with disease activity. Adhesion molecules ICAM-1 and VCAM-1 are associated with inflammatory mediated blood-brain barrier (BBB) dysfunction. In this study investigates the correlation between blood level of circulating ICAM-1 and VCAM-1 and magnetic resonance imaging (MRI) activity in different clinical phases of patients with MS. We show that RRMS and SPMS patients in clinically active phase with Gd-enhancing lesions in CNS had higher blood levels of cICAM-1 and cVCAM-1 compared these parameters levers of RRMS patients in remission stage. These results suggest that cICAM-1 and cVCAM-1 is a sensitive indicator of disease activity associated with BBB inflammatory dysfunction. Elevated blood level of cICAM-1 more strongly correlated with clinical activity and BBB damage, than cVCAM-1 and that could be used as biological marker of disease activity. Circulating VCAM-1 as an early indicator of BBB disturbance, may also serve as marker of beneficial activity in relapses phase of MS course. (authors)

  4. High quality, small molecule-activity datasets for kinase research.

    Sharma, Rajan; Schürer, Stephan C; Muskal, Steven M

    2016-01-01

    Kinases regulate cell growth, movement, and death. Deregulated kinase activity is a frequent cause of disease. The therapeutic potential of kinase inhibitors has led to large amounts of published structure activity relationship (SAR) data. Bioactivity databases such as the Kinase Knowledgebase (KKB), WOMBAT, GOSTAR, and ChEMBL provide researchers with quantitative data characterizing the activity of compounds across many biological assays. The KKB, for example, contains over 1.8M kinase structure-activity data points reported in peer-reviewed journals and patents. In the spirit of fostering methods development and validation worldwide, we have extracted and have made available from the KKB 258K structure activity data points and 76K associated unique chemical structures across eight kinase targets. These data are freely available for download within this data note. PMID:27429748

  5. Activated leukocyte cell adhesion molecule and prognosis in acute ischemic stroke

    Smedbakken, Linda; Jensen, Jesper K; Hallén, Jonas;

    2011-01-01

    Biomarkers predicting mortality and functional outcome in stroke may be clinically helpful in identification of patients likely to benefit from intervention. Activated leukocyte cell adhesion molecule (ALCAM) is upregulated during neuroinflammation; we investigated whether ALCAM concentrations ar...

  6. Atmospheric Aerosols: Cloud Condensation Nucleus Activity of Selected Organic Molecules

    Rosenorn, T.; Henning, S.; Hartz, K. H.; Kiss, G.; Pandis, S.; Bilde, M.

    2005-12-01

    Gas/particle partitioning of vapors in the atmosphere plays a major role in both climate through micro meteorology and in the physical and chemical processes of a single particle. This work has focused on the cloud droplet activation of a number of pure and mixed compounds. The means used to investigate these processes have been the University of Copenhagen cloud condensation nucleus counter setup and the Carnegie Mellon University CCNC setup. The importance of correct water activity modeling has been addressed and it has been pointed out that the molecular mass is an important parameter to consider when choosing model compounds for cloud activation models. It was shown that both traditional Kohler theory and Kohler theory modified to account for limited solubility reproduce measurements of soluble compounds well. For less soluble compounds it is necessary to use Kohler theory modified to account for limited solubility. It was also shown that this works for mixtures of compounds containing both inorganic salts and dicarboxylic acids. It has also been shown that particle phase and humidity history is important for activation behavior of particles consisting of two slightly soluble organic substances (succinic and adipic acid) and a soluble salt (NaCl). Model parameters for terpene oxidation product cloud activation have been derived. These are based on two sets of average parameters covering monoterpene oxidation products and sesquiterpene oxidation products. All parameters except the solubility were estimated and an effective solubility was calculated as the fitting parameter. The average solubility of the model compound found for mono terpene oxidation products is similar to those of sodium chloride and ammonium sulfate; however the higher molecular weight leads to a slightly higher activation diameter at fixed supersaturation. On a molar basis the monoterpene oxidation products show a 1.5 times higher effective solubility than the sesquiterpene oxidation products.

  7. Interaction of metallic clusters with biologically active curcumin molecules

    Gupta, Sanjeev K.; He, Haiying; Liu, Chunhui; Dutta, Ranu; Pandey, Ravindra

    2015-09-01

    We have investigated the interaction of subnano metallic Gd and Au clusters with curcumin, an important biomolecule having pharmacological activity. Gd clusters show different site preference to curcumin and much stronger interaction strength, in support of the successful synthesis of highly stable curcumin-coated Gd nanoparticles as reported recently. It can be attributed to significant charge transfer from the Gd cluster to curcumin together with a relatively strong hybridization of the Gd df-orbitals with curcumin p-orbitals. These results suggest that Gd nanoparticles can effectively be used as delivery carriers for curcumin at the cellular level for therapy and medical imaging applications.

  8. Ozone: A Multifaceted Molecule with Unexpected Therapeutic Activity.

    Zanardi, I; Borrelli, E; Valacchi, G; Travagli, V; Bocci, V

    2016-01-01

    A comprehensive outline for understanding and recommending the therapeutic use of ozone in combination with established therapy in diseases characterized by a chronic oxidative stress is currently available. The view of the absolute ozone toxicity is incorrect, because it has been based either on lung or on studies performed in artificial environments that do not correspond to the real antioxidant capacity of body compartments. In fact, ozone exerts either a potent toxic activity or it can stimulate biological responses of vital importance, analogously to gases with prospective therapeutic value such as NO, CO, H2S, H2, as well as O2 itself. Such a crucial difference has increasingly become evident during the last decade. The purpose of this review is to explain the aspects still poorly understood, highlighting the divergent activity of ozone on the various biological districts. It will be clarified that such a dual effect does not depend only upon the final gas concentration, but also on the particular biological system where ozone acts. The real significance of ozone as adjuvant therapeutic treatment concerns severe chronic pathologies among which are cardiovascular diseases, chronic obstructive pulmonary diseases, multiple sclerosis, and the dry form of age-related macular degeneration. It is time for a full insertion of ozone therapy within pharmaceutical sciences, responding to all the requirements of quality, efficacy and safety, rather than as either an alternative or an esoteric approach. PMID:26687830

  9. Root Zone Microbial Populations, Urease Activities, and Purification Efficiency for a Constructed Wetland

    LIANG Wei; WU Zhen-Bin; ZHAN Fa-Cui; DENG Jia-Qi

    2004-01-01

    In order to investigate the effects of microorganisms and their urease activities in macrophytic root zones on pollutant removal, four small-scale plots (SSPs) of vertical/reverse-vertical flow wetlands were set up to determine: a) the relationship between the abundance of microorganisms in the root zones and water purification efficiency; and b) the relationship between urease activities in the root zones and pollutant removal in a constructed wetland system. Total numbers of the microbial population (bacteria, fungi, and actinomyces) along with urease activities in the macrophytic root zones were determined. In addition, the relationships between microbial populations and urease activities as well as the wastewater purification efficiencies of total phosphorus (TP), total Kjeldahl nitrogen (TKN), biochemical oxygen demand in 5 days (BOD5), and chemical oxygen demand (COD) were also analyzed. The results showed that there was a highly significant positive correlation (r = 0.9772, P < 0.01) between the number of bacteria in the root zones and BOD5 removal efficiency and a significant negative correlation (r = -0.9092, P < 0.05) between the number of fungi and the removal efficiency of TKN. Meanwhile, there was a significant positive correlation (r -- 0.8830, P < 0.05) between urease activities in the root zones and the removal efficiency of TKN. Thus, during wastewater treatment in a constructed wetland system,microorganism and urease activities in the root zones were very important factors.

  10. Auroral Electrojet Index Designed to Provide a Global Measure, Hourly Intervals, of Auroral Zone Magnetic Activity

    National Oceanic and Atmospheric Administration, Department of Commerce — The Auroral Electrojet (AE) index is designed to provide a global quantitative measure of auroral zone magnetic activity produced by enhanced ionospheric currents...

  11. Group Problem Solving as a Zone of Proximal Development activity

    Brewe, Eric

    2006-12-01

    Vygotsky described learning as a process, intertwined with development, which is strongly influenced by social interactions with others that are at differing developmental stages.i These interactions create a Zone of Proximal Development for each member of the interaction. Vygotsky’s notion of social constructivism is not only a theory of learning, but also of development. While teaching introductory physics in an interactive format, I have found manifestations of Vygotsky’s theory in my classroom. The source of evidence is a paired problem solution. A standard mechanics problem was solved by students in two classes as a homework assignment. Students handed in the homework and then solved the same problem in small groups. The solutions to both the group and individual problem were assessed by multiple reviewers. In many cases the group score was the same as the highest individual score in the group, but in some cases, the group score was higher than any individual score. For this poster, I will analyze the individual and group scores and focus on three groups solutions and video that provide evidence of learning through membership in a Zone of Proximal Development. Endnotes i L. Vygotsky -Mind and society: The development of higher mental processes. Cambridge, MA: Harvard University Press. (1978).

  12. Geomorphic Indices in the Assessment of Tectonic Activity in Forearc of the Active Mexican Subduction Zone

    Gaidzik, K.; Ramirez-Herrera, M. T.

    2015-12-01

    Rapid development of GIS techniques and constant advancement of digital elevation models significantly improved the accuracy of extraction of information on active tectonics from landscape features. Numerous attempts were made to quantitatively evaluate recent tectonic activity using GIS and DEMs, and a set of geomorphic indices (GI), however these studies focused mainly on sub-basins or small-scale areal units. In forearc regions where crustal deformation is usually large-scale and do not concentrate only along one specific fault, an assessment of the complete basin is more accurate. We present here the first attempt to implement thirteen GI in the assessment of active tectonics of a forearc region of an active convergent margin using the entire river basins. The GIs were divided into groups: BTAI - basin geomorphic indices (reflecting areal erosion vs. tectonics) and STAI - stream geomorphic indices (reflecting vertical erosion vs. tectonics). We calculated selected indices for 9 large (> 450 km2) drainage basins. Then we categorized the obtained results of each index into three classes of relative tectonic activity: 1 - high, 2 - moderate, and 3 - low. Finally we averaged these classes for each basin to determine the tectonic activity level (TAI). The analysis for the case study area, the Guerrero sector at the Mexican subduction zone, revealed high tectonic activity in this area, particularly in its central and, to a lesser degree, eastern part. This pattern agrees with and is supported by interpretation of satellite images and DEM, and field observations. The results proved that the proposed approach indeed allows identification and recognition of areas witnessing recent tectonic deformation. Moreover, our results indicated that, even though no large earthquake has been recorded in this sector for more than 100 years, the area is highly active and may represent a seismic hazard for the region.

  13. Brazing zone structure at active brazing of alumina ceramics

    2005-01-01

    @@ Nowadays one of the most effective methods of joining of oxide ceramics with other elements of construction is active brazing based on using of active metals (Ti, Zr), which increase reactivity of brazing alloy relative to ceramic element of a joining.

  14. Investigating organic molecules responsible of auxin-like activity of humic acid fraction extracted from vermicompost.

    Scaglia, Barbara; Nunes, Ramom Rachide; Rezende, Maria Olímpia Oliveira; Tambone, Fulvia; Adani, Fabrizio

    2016-08-15

    This work studied the auxin-like activity of humic acids (HA) obtained from vermicomposts produced using leather wastes plus cattle dung at different maturation stages (fresh, stable and mature). Bioassays were performed by testing HA concentrations in the range of 100-6000mgcarbonL(-1). (13)C CPMAS-NMR and GC-MS instrumental methods were used to assess the effect of biological processes and starting organic mixtures on HA composition. Not all HAs showed IAA-like activity and in general, IAA-like activity increased with the length of the vermicomposting process. The presence of leather wastes was not necessary to produce the auxin-like activity of HA, since HA extracted from a mix of cattle manure and sawdust, where no leather waste was added, showed IAA-like activity as well. CPMAS (13)CNMR revealed that HAs were similar independently of the mix used and that the humification process involved the increasing concentration of pre-existing alkali soluble fractions in the biomass. GC/MS allowed the identification of the molecules involved in IAA-like effects: carboxylic acids and amino acids. The concentration of active molecules, rather than their simple presence in HA, determined the bio-stimulating effect, and a good linear regression between auxin-like activity and active stimulating molecules concentration was found (R(2)=-0.85; p<0.01, n=6). PMID:27100009

  15. Single-active-electron potentials for molecules in intense laser fields

    Abu-Samha, Mahmoud; Madsen, Lars Bojer

    2010-01-01

    Single-active-electron potentials are computed for selected molecules, and molecular wave functions with the correct asymptotic behavior are produced. Asymptotic expansion coefficients are extracted from the wave functions and used to compute alignment-dependent ionization yields from molecular...

  16. Activated leukocyte cell adhesion molecule expression predicts lymph node metastasis in oral squamous cell carcinoma.

    Brand, M. van den; Takes, R.P.; Blokpoel-deRuyter, M.; Slootweg, P.J.; Kempen, L.C.L.T. van

    2010-01-01

    Lymphatic metastasis of oral squamous cell carcinoma (SCC) is important for prognosis and clinical decision making concerning the treatment of the neck but may be difficult to detect. Activated leukocyte cell adhesion molecule (ALCAM), has been shown to correlate with prognosis or tumor grade in dif

  17. Harnessing microbial metabolic exchange for the discovery of biologically active molecules

    Liu, Wei-Ting

    2012-01-01

    Microbial metabolic exchange mediates microbial interactions and plays key roles in regulating biology and has shaped modern healthcare, agriculture and other commercial processes. In this thesis, cutting edge mass spectrometry techniques, new genome mining approaches, and innovative bioinformatics tools were coupled and developed into investigating microbial metabolic exchange and led to the identification and characterization of biological active molecules that may have therapeutic values. ...

  18. Database searching for compounds with similar biological activity using short binary bit string representations of molecules.

    Xue, L; Godden, J W; Bajorath, J

    1999-01-01

    In an effort to identify biologically active molecules in compound databases, we have investigated similarity searching using short binary bit strings with a maximum of 54 bit positions. These "minifingerprints" (MFPs) were designed to account for the presence or absence of structural fragments and/or aromatic character, flexibility, and hydrogen-bonding capacity of molecules. MFP design was based on an analysis of distributions of molecular descriptors and structural fragments in two large compound collections. The performance of different MFPs and a reference fingerprint was tested by systematic "one-against-all" similarity searches of molecules in a database containing 364 compounds with different biological activities. For each fingerprint, the most effective similarity cutoff value was determined. An MFP accounting for only 32 structural fragments showed less than 2% false positive similarity matches and correctly assigned on average approximately 40% of the compounds with the same biological activity to a query molecule. Inclusion of three numerical two-dimensional (2D) molecular descriptors increased the performance by 15%. This MFP performed better than a complex 2D fingerprint. At a similarity cutoff value of 0.85, the 2D fingerprint totally eliminated false positives but recognized less than 10% of the compounds within the same activity class. PMID:10529986

  19. Single-molecule imaging of DNA polymerase I (Klenow fragment) activity by atomic force microscopy

    Chao, J.; Zhang, P.; Wang, Q.; Wu, N.; Zhang, F.; Hu, J.; Fan, C. H.; Li, B.

    2016-03-01

    We report a DNA origami-facilitated single-molecule platform that exploits atomic force microscopy to study DNA replication. We imaged several functional activities of the Klenow fragment of E. coli DNA polymerase I (KF) including binding, moving, and dissociation from the template DNA. Upon completion of these actions, a double-stranded DNA molecule was formed. Furthermore, the direction of KF activities was captured and then confirmed by shifting the KF binding sites on the template DNA.We report a DNA origami-facilitated single-molecule platform that exploits atomic force microscopy to study DNA replication. We imaged several functional activities of the Klenow fragment of E. coli DNA polymerase I (KF) including binding, moving, and dissociation from the template DNA. Upon completion of these actions, a double-stranded DNA molecule was formed. Furthermore, the direction of KF activities was captured and then confirmed by shifting the KF binding sites on the template DNA. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06544e

  20. Optically active push-pull molecules intercalated into layered phosphates and phosphonates

    Zima, Vítězslav; Melánová, Klára; Svoboda, Jan; Beneš, L.; Bureš, F.

    Praha: Ústav fyzikální chemie Jaroslava Heyrovského AV ČR,v.v.i, 2015. OP1. [Workshop on Layered Materials . 15.09.2015-19.09.2015, Třešť] Institutional support: RVO:61389013 Keywords : phosphate * phosphonate * optically active molecules Subject RIV: CA - Inorganic Chemistry

  1. Machine learning models identify molecules active against the Ebola virus in vitro.

    Ekins, Sean; Freundlich, Joel S; Clark, Alex M; Anantpadma, Manu; Davey, Robert A; Madrid, Peter

    2015-01-01

    The search for small molecule inhibitors of Ebola virus (EBOV) has led to several high throughput screens over the past 3 years. These have identified a range of FDA-approved active pharmaceutical ingredients (APIs) with anti-EBOV activity in vitro and several of which are also active in a mouse infection model. There are millions of additional commercially-available molecules that could be screened for potential activities as anti-EBOV compounds. One way to prioritize compounds for testing is to generate computational models based on the high throughput screening data and then virtually screen compound libraries. In the current study, we have generated Bayesian machine learning models with viral pseudotype entry assay and the EBOV replication assay data. We have validated the models internally and externally. We have also used these models to computationally score the MicroSource library of drugs to select those likely to be potential inhibitors. Three of the highest scoring molecules that were not in the model training sets, quinacrine, pyronaridine and tilorone, were tested in vitro and had EC 50 values of 350, 420 and 230 nM, respectively. Pyronaridine is a component of a combination therapy for malaria that was recently approved by the European Medicines Agency, which may make it more readily accessible for clinical testing. Like other known antimalarial drugs active against EBOV, it shares the 4-aminoquinoline scaffold. Tilorone, is an investigational antiviral agent that has shown a broad array of biological activities including cell growth inhibition in cancer cells, antifibrotic properties, α7 nicotinic receptor agonist activity, radioprotective activity and activation of hypoxia inducible factor-1. Quinacrine is an antimalarial but also has use as an anthelmintic. Our results suggest data sets with less than 1,000 molecules can produce validated machine learning models that can in turn be utilized to identify novel EBOV inhibitors in vitro. PMID:26834994

  2. Triplet supercurrent due to spin-active zones in a Josephson junction

    Linder, Jacob; Sudbø, Asle

    2010-07-01

    Motivated by a recent experiment evidencing triplet superconductivity in a ferromagnetic Josephson junction with a Cu2MnAl -Heusler barrier, we construct a theoretical model accounting for this observation. The key ingredients in our model which generate the triplet supercurrent are spin-active zones, characterized by an effective canted interface magnetic moment. Using a numerical solution of the quasiclassical equations of superconductivity with spin-active boundary conditions, we find qualitatively very good agreement with the experimentally observed supercurrent. Further experimental implications of the spin-active zones are discussed.

  3. Water molecule network and active site flexibility of apo protein tyrosine phosphatase 1B

    Pedersen, A.K.; Peters, Günther H.J.; Møller, K.B.;

    2004-01-01

    Protein tyrosine phosphatase 1B (PTP1B) plays a key role as a negative regulator of insulin and leptin signalling and is therefore considered to be an important molecular target for the treatment of type 2 diabetes and obesity. Detailed structural information about the structure of PTP1B, including...... the conformation and flexibility of active-site residues as well as the water-molecule network, is a key issue in understanding ligand binding and enzyme kinetics and in structure-based drug design. A 1.95 Angstrom apo PTP1B structure has been obtained, showing four highly coordinated water molecules...

  4. Facilitating the medical response into an active shooter hot zone

    Tierney, Martin T.

    2016-01-01

    Approved for public release; distribution is unlimited The response to active shooter attacks is not as effective as it could be. People die before receiving care because most jurisdictions have a policy in place that stipulates emergency medical services (EMS) wait to enter a scene until law enforcement (LE) announces that the scene is clear or secure. Since this can take some time, life-saving care is not immediately available to the people who most need it, and consequently, there can b...

  5. CHEMICAL ACTIVATION OF MOLECULES BY METALS: EXPERIMENTAL STUDIES OF ELECTRON DISTRIBUTIONS AND BONDING

    LICHTENBERGER, DENNIS L.

    2002-03-26

    This research program is directed at obtaining detailed experimental information on the electronic interactions between metals and organic molecules. These interactions provide low energy pathways for many important chemical and catalytic processes. A major feature of the program is the continued development and application of our special high-resolution valence photoelectron spectroscopy (UPS), and high-precision X-ray core photoelectron spectroscopy (XPS) instrumentation for study of organometallic molecules in the gas phase. The study involves a systematic approach towards understanding the interactions and activation of bound carbonyls, C-H bonds, methylenes, vinylidenes, acetylides, alkenes, alkynes, carbenes, carbynes, alkylidenes, alkylidynes, and others with various monometal, dimetal, and cluster metal species. Supporting ligands include -aryls, alkoxides, oxides, and phosphines. We are expanding our studies of both early and late transition metal species and electron-rich and electron-poor environments in order to more completely understand the electronic factors that serve to stabilize particular organic fragments and intermediates on metals. Additional new directions for this program are being taken in ultra-high vacuum surface UPS, XPS, scanning tunneling microscopy (STM) and atomic force microscopy (AFM) experiments on both physisorbed and chemisorbed organometallic thin films. The combination of these methods provides additional electronic structure information on surface-molecule and molecule-molecule interactions. A very important general result emerging from this program is the identification of a close relationship between the ionization energies of the species and the thermodynamics of the chemical and catalytic reactions of these systems.

  6. CHEMICAL ACTIVATION OF MOLECULES BY METALS: EXPERIMENTAL STUDIES OF ELECTRON DISTRIBUTIONS AND BONDING; FINAL

    This research program is directed at obtaining detailed experimental information on the electronic interactions between metals and organic molecules. These interactions provide low energy pathways for many important chemical and catalytic processes. A major feature of the program is the continued development and application of our special high-resolution valence photoelectron spectroscopy (UPS), and high-precision X-ray core photoelectron spectroscopy (XPS) instrumentation for study of organometallic molecules in the gas phase. The study involves a systematic approach towards understanding the interactions and activation of bound carbonyls, C-H bonds, methylenes, vinylidenes, acetylides, alkenes, alkynes, carbenes, carbynes, alkylidenes, alkylidynes, and others with various monometal, dimetal, and cluster metal species. Supporting ligands include -aryls, alkoxides, oxides, and phosphines. We are expanding our studies of both early and late transition metal species and electron-rich and electron-poor environments in order to more completely understand the electronic factors that serve to stabilize particular organic fragments and intermediates on metals. Additional new directions for this program are being taken in ultra-high vacuum surface UPS, XPS, scanning tunneling microscopy (STM) and atomic force microscopy (AFM) experiments on both physisorbed and chemisorbed organometallic thin films. The combination of these methods provides additional electronic structure information on surface-molecule and molecule-molecule interactions. A very important general result emerging from this program is the identification of a close relationship between the ionization energies of the species and the thermodynamics of the chemical and catalytic reactions of these systems

  7. Aqueous phase adsorption of different sized molecules on activated carbon fibers: Effect of textural properties.

    Prajapati, Yogendra N; Bhaduri, Bhaskar; Joshi, Harish C; Srivastava, Anurag; Verma, Nishith

    2016-07-01

    The effect that the textural properties of rayon-based activated carbon fibers (ACFs), such as the BET surface area and pore size distribution (PSD), have on the adsorption of differently sized molecules, namely, brilliant yellow (BY), methyl orange (MO) and phenol (PH), was investigated in the aqueous phase. ACF samples with different BET areas and PSDs were produced by steam-activating carbonized fibers for different activation times (0.25, 0.5, and 1 h). The samples activated for 0.25 h were predominantly microporous, whereas those activated for relatively longer times contained hierarchical micro-mesopores. The adsorption capacities of the ACFs for the adsorbate increased with increasing BET surface area and pore volume, and ranged from 51 to 1306 mg/g depending on the textural properties of the ACFs and adsorbate size. The adsorption capacities of the hierarchical ACF samples followed the order BY > MO > PH. Interestingly, the number of molecules adsorbed by the ACFs followed the reverse order: PH > MO > BY. This anomaly was attributed to the increasing molecular weight of the PH, MO and BY molecules. The equilibrium adsorption data were described using the Langmuir isotherm. This study shows that suitable textural modifications to ACFs are required for the efficient aqueous phase removal of an adsorbate. PMID:27107386

  8. Heavy metals contamination characteristics in soil of different mining activity zones

    LIAO Guo-li; LIAO Da-xue; LI Quan-ming

    2008-01-01

    Depending upon the polluted features of various mining activities in a typical nonferrous metal mine, the contaminated soil area was divided into four zones which were polluted by tailings, mine drainage, dust deposition in wind and spreading minerals during vehicle transportation, respectively. In each zone, soil samples were collected. Total 28 soil samples were dug and analyzed by ICP-AES and other relevant methods. The results indicate that the average contents of Zn, Pb, Cd, Cu and As in soils are 508.6, 384.8, 7.53, 356 and 44.6 mg/kg, respectively. But the contents of heavy metals in different zone have distinct differences. The proportion of oxidizing association with organic substance is small. Difference of the association of heavy metals is small in different polluted zones.

  9. Visualizing repetitive diffusion activity of double-strand RNA binding proteins by single molecule fluorescence assays.

    Koh, Hye Ran; Wang, Xinlei; Myong, Sua

    2016-08-01

    TRBP, one of double strand RNA binding proteins (dsRBPs), is an essential cofactor of Dicer in the RNA interference pathway. Previously we reported that TRBP exhibits repetitive diffusion activity on double strand (ds)RNA in an ATP independent manner. In the TRBP-Dicer complex, the diffusion mobility of TRBP facilitates Dicer-mediated RNA cleavage. Such repetitive diffusion of dsRBPs on a nucleic acid at the nanometer scale can be appropriately captured by several single molecule detection techniques. Here, we provide a step-by-step guide to four different single molecule fluorescence assays by which the diffusion activity of dsRBPs on dsRNA can be detected. One color assay, termed protein induced fluorescence enhancement enables detection of unlabeled protein binding and diffusion on a singly labeled RNA. Two-color Fluorescence Resonance Energy Transfer (FRET) in which labeled dsRBPs is applied to labeled RNA, allows for probing the motion of protein along the RNA axis. Three color FRET reports on the diffusion movement of dsRBPs from one to the other end of RNA. The single molecule pull down assay provides an opportunity to collect dsRBPs from mammalian cells and examine the protein-RNA interaction at single molecule platform. PMID:27012177

  10. Single molecule investigation of the onset and minimum size of the calcium-mediated junction zone in alginate.

    Bowman, Kate A; Aarstad, Olav Andreas; Nakamura, Marcela; Stokke, Bjørn Torger; Skjåk-Bræk, Gudmund; Round, Andrew N

    2016-09-01

    One of the principal roles of alginate, both natively and in commercial applications, is gelation via Ca(2+)-mediated crosslinks between blocks of guluronic acid. In this work, single molecule measurements were carried out between well-characterised series of nearly monodisperse guluronic acid blocks ('oligoGs') using dynamic force spectroscopy. The measurements provide evidence that for interaction times on the order of tens of milliseconds the maximum crosslink strength is achieved by pairs of oligoGs long enough to allow the coordination of 4Ca(2+) ions, with both shorter and longer oligomers forming weaker links. Extending the interaction time from tens to hundreds of milliseconds allows longer oligoGs to achieve much stronger crosslinks but does not change the strength of individual links between shorter oligoGs. These results are considered in light of extant models for the onset of cooperative crosslinking in polyelectrolytes and an anisotropic distribution of oligoGs on interacting surfaces and provide a timescale for the formation and relaxation of alginate gels at the single crosslink level. PMID:27185115

  11. Structure Based Discovery of Small Molecules to Regulate the Activity of Human Insulin Degrading Enzyme

    Çakir, Bilal; Dağliyan, Onur; Dağyildiz, Ezgi; Bariş, İbrahim; Kavakli, Ibrahim Halil; Kizilel, Seda; Türkay, Metin

    2012-01-01

    Background Insulin-degrading enzyme (IDE) is an allosteric Zn+2 metalloprotease involved in the degradation of many peptides including amyloid-β, and insulin that play key roles in Alzheimer's disease (AD) and type 2 diabetes mellitus (T2DM), respectively. Therefore, the use of therapeutic agents that regulate the activity of IDE would be a viable approach towards generating pharmaceutical treatments for these diseases. Crystal structure of IDE revealed that N-terminal has an exosite which is ∼30 Å away from the catalytic region and serves as a regulation site by orientation of the substrates of IDE to the catalytic site. It is possible to find small molecules that bind to the exosite of IDE and enhance its proteolytic activity towards different substrates. Methodology/Principal Findings In this study, we applied structure based drug design method combined with experimental methods to discover four novel molecules that enhance the activity of human IDE. The novel compounds, designated as D3, D4, D6, and D10 enhanced IDE mediated proteolysis of substrate V, insulin and amyloid-β, while enhanced degradation profiles were obtained towards substrate V and insulin in the presence of D10 only. Conclusion/Significance This paper describes the first examples of a computer-aided discovery of IDE regulators, showing that in vitro and in vivo activation of this important enzyme with small molecules is possible. PMID:22355395

  12. Structure based discovery of small molecules to regulate the activity of human insulin degrading enzyme.

    Bilal Çakir

    Full Text Available BACKGROUND: Insulin-degrading enzyme (IDE is an allosteric Zn(+2 metalloprotease involved in the degradation of many peptides including amyloid-β, and insulin that play key roles in Alzheimer's disease (AD and type 2 diabetes mellitus (T2DM, respectively. Therefore, the use of therapeutic agents that regulate the activity of IDE would be a viable approach towards generating pharmaceutical treatments for these diseases. Crystal structure of IDE revealed that N-terminal has an exosite which is ∼30 Å away from the catalytic region and serves as a regulation site by orientation of the substrates of IDE to the catalytic site. It is possible to find small molecules that bind to the exosite of IDE and enhance its proteolytic activity towards different substrates. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we applied structure based drug design method combined with experimental methods to discover four novel molecules that enhance the activity of human IDE. The novel compounds, designated as D3, D4, D6, and D10 enhanced IDE mediated proteolysis of substrate V, insulin and amyloid-β, while enhanced degradation profiles were obtained towards substrate V and insulin in the presence of D10 only. CONCLUSION/SIGNIFICANCE: This paper describes the first examples of a computer-aided discovery of IDE regulators, showing that in vitro and in vivo activation of this important enzyme with small molecules is possible.

  13. Nanoscale charge transport in cytochrome c3/DNA network: Comparative studies between redox-active molecules

    Yamaguchi, Harumasa; Che, Dock-Chil; Hirano, Yoshiaki; Suzuki, Masayuki; Higuchi, Yoshiki; Matsumoto, Takuya

    2015-09-01

    The redox-active molecule of a cytochrome c3/DNA network exhibits nonlinear current-voltage (I-V) characteristics with a threshold bias voltage at low temperature and zero-bias conductance at room temperature. I-V curves for the cytochrome c3/DNA network are well matched with the Coulomb blockade network model. Comparative studies of the Mn12 cluster, cytochrome c, and cytochrome c3, which have a wide variety of redox potentials, indicate no difference in charge transport, which suggests that the conduction mechanism is not directly related to the redox states. The charge transport mechanism has been discussed in terms of the newly-formed electronic energy states near the Fermi level, induced by the ionic interaction between redox-active molecules with the DNA network.

  14. Tsunamigenic potential of Mediterranean fault systems and active subduction zones

    Petricca, Patrizio; Babeyko, Andrey

    2016-04-01

    Since the North East Atlantic and Mediterranean Tsunami Warning System (NEAMTWS) is under development by the European scientific community, it becomes necessary to define guidelines for the characterization of the numerous parameters must be taken into account in a fair assessment of the risk. Definition of possible tectonic sources and evaluation of their potential is one of the principal issues. In this study we systematically evaluate tsunamigenic potential of up-to-now known real fault systems and active subduction interfaces in the NEAMTWS region. The task is accomplished by means of numerical modeling of tsunami generation and propagation. We have simulated all possible uniform-slip ruptures populating fault and subduction interfaces with magnitudes ranging from 6.5 up to expected Mmax. A total of 15810 individual ruptures were processed. For each rupture, a tsunami propagation scenario was computed in linear shallow-water approximation on 1-arc minute bathymetric grid (Gebco_08) implying normal reflection boundary conditions. Maximum wave heights at coastal positions (totally - 23236 points of interest) were recorded for four hours of simulation and then classified according to currently adopted warning level thresholds. The resulting dataset allowed us to classify the sources in terms of their tsunamigenic potential as well as to estimate their minimum tsunamigenic magnitude. Our analysis shows that almost every source in the Mediterranean Sea is capable to produce local tsunami at the advisory level (i.e., wave height > 20 cm) starting from magnitude values of Mw=6.6. In respect to the watch level (wave height > 50 cm), the picture is less homogeneous: crustal sources in south-west Mediterranean as well as East-Hellenic arc need larger magnitudes (around Mw=7.0) to trigger watch levels even at the nearby coasts. In the context of the regional warning (i.e., source-to-coast distance > 100 km) faults also behave more heterogeneously in respect to the minimum

  15. Topoisomerase I as a Biomarker: Detection of Activity at the Single Molecule Level

    Proszek, Joanna; Roy, Amit; Jakobsen, Ann-Katrine;

    2014-01-01

    hTopI have been reported to result in CPT resistance. Therefore, hTOPI gene copy number, mRNA level, protein amount, and enzyme activity have been studied to explain differences in cellular response to CPT. We show that Rolling Circle Enhanced Enzyme Activity Detection (REEAD), allowing measurement...... of hTopI cleavage-religation activity at the single molecule level, may be used to detect posttranslational enzymatic differences influencing CPT response. These differences cannot be detected by analysis of hTopI gene copy number, mRNA amount, or protein amount, and only become apparent upon...... measuring the activity of hTopI in the presence of CPT. Furthermore, we detected differences in the activity of the repair enzyme tyrosyl-DNA phosphodiesterase 1, which is involved in repair of hTopI-induced DNA damage. Since increased TDP1 activity can reduce cellular CPT sensitivity we suggest that a...

  16. Discovery of fragment molecules that bind the human peroxiredoxin 5 active site.

    Sarah Barelier

    Full Text Available The search for protein ligands is a crucial step in the inhibitor design process. Fragment screening represents an interesting method to rapidly find lead molecules, as it enables the exploration of a larger portion of the chemical space with a smaller number of compounds as compared to screening based on drug-sized molecules. Moreover, fragment screening usually leads to hit molecules that form few but optimal interactions with the target, thus displaying high ligand efficiencies. Here we report the screening of a homemade library composed of 200 highly diverse fragments against the human Peroxiredoxin 5 protein. Peroxiredoxins compose a family of peroxidases that share the ability to reduce peroxides through a conserved cysteine. The three-dimensional structures of these enzymes ubiquitously found throughout evolution have been extensively studied, however, their biological functions are still not well understood and to date few inhibitors have been discovered against these enzymes. Six fragments from the library were shown to bind to the Peroxiredoxin 5 active site and ligand-induced chemical shift changes were used to drive the docking of these small molecules into the protein structure. The orientation of the fragments in the binding pocket was confirmed by the study of fragment homologues, highlighting the role of hydroxyl functions that hang the ligands to the Peroxiredoxin 5 protein. Among the hit fragments, the small catechol molecule was shown to significantly inhibit Peroxiredoxin 5 activity in a thioredoxin peroxidase assay. This study reports novel data about the ligand-Peroxiredoxin interactions that will help considerably the development of potential Peroxiredoxin inhibitors.

  17. Structure-property relationship of quinuclidinium surfactants--Towards multifunctional biologically active molecules.

    Skočibušić, Mirjana; Odžak, Renata; Štefanić, Zoran; Križić, Ivana; Krišto, Lucija; Jović, Ozren; Hrenar, Tomica; Primožič, Ines; Jurašin, Darija

    2016-04-01

    Motivated by diverse biological and pharmacological activity of quinuclidine and oxime compounds we have synthesized and characterized novel class of surfactants, 3-hydroxyimino quinuclidinium bromides with different alkyl chains lengths (CnQNOH; n=12, 14 and 16). The incorporation of non conventional hydroxyimino quinuclidinium headgroup and variation in alkyl chain length affects hydrophilic-hydrophobic balance of surfactant molecule and thereby physicochemical properties important for its application. Therefore, newly synthesized surfactants were characterized by the combination of different experimental techniques: X-ray analysis, potentiometry, electrical conductivity, surface tension and dynamic light scattering measurements, as well as antimicrobial susceptibility tests. Comprehensive investigation of CnQNOH surfactants enabled insight into structure-property relationship i.e., way in which the arrangement of surfactant molecules in the crystal phase correlates with their solution behavior and biologically activity. The synthesized CnQNOH surfactants exhibited high adsorption efficiency and relatively low critical micelle concentrations. In addition, all investigated compounds showed very potent and promising activity against Gram-positive and clinically relevant Gram-negative bacterial strains compared to conventional antimicrobial agents: tetracycline and gentamicin. The overall results indicate that bicyclic headgroup with oxime moiety, which affects both hydrophilicity and hydrophobicity of CnQNOH molecule in addition to enabling hydrogen bonding, has dominant effect on crystal packing and physicochemical properties. The unique structural features of cationic surfactants with hydroxyimino quinuclidine headgroup along with diverse biological activity have made them promising structures in novel drug discovery. Obtained fundamental understanding how combination of different functionalities in a single surfactant molecule affects its physicochemical

  18. Morbilliviruses Use Signaling Lymphocyte Activation Molecules (CD150) as Cellular Receptors

    Tatsuo, Hironobu; Ono, Nobuyuki; Yanagi, Yusuke

    2001-01-01

    Morbilliviruses comprise measles virus, canine distemper virus, rinderpest virus, and several other viruses that cause devastating human and animal diseases accompanied by severe immunosuppression and lymphopenia. Recently, we have shown that human signaling lymphocyte activation molecule (SLAM) is a cellular receptor for measles virus. In this study, we examined whether canine distemper and rinderpest viruses also use canine and bovine SLAMs, respectively, as cellular receptors. The Onderste...

  19. Identification of intrinsic catalytic activity for electrochemical reduction of water molecules to generate hydrogen

    Shinagawa, Tatsuya

    2015-01-01

    Insufficient hydronium ion activities at near-neutral pH and under unbuffered conditions induce diffusion-limited currents for hydrogen evolution, followed by a reaction with water molecules to generate hydrogen at elevated potentials. The observed constant current behaviors at near neutral pH reflect the intrinsic electrocatalytic reactivity of the metal electrodes for water reduction. This journal is © the Owner Societies.

  20. Anticancer molecule AS1411 exhibits low nanomolar antiviral activity against HIV-1.

    Métifiot, Mathieu; Amrane, Samir; Mergny, Jean-Louis; Andreola, Marie-Line

    2015-11-01

    During clinical trials, a number of fully characterized molecules are dropped along the way because they do not provide enough benefit for the patient. Some of them show limited side effects and might be of great use for other applications. AS1411 is a nucleolin-targeting aptamer that underwent phase II clinical trials as anticancer agent. Here, we show that AS1411 exhibits extremely potent antiviral activity and is therefore an attractive new lead as anti-HIV agent. PMID:26363100

  1. A Novel Accessory Molecule Trim59 Involved in Cytotoxicity of BCG-Activated Macrophages

    Zhao, Xiangfeng; Liu, Qihui; Du, Baiqiu; Li, Peng; Cui, Qu; Han, Xiao; Du, Bairong; Yan, Dongmei; Zhu, Xun

    2012-01-01

    BCG-activated macrophages (BAM) could kill the tumor cells through cell-cell contact. In this process membrane proteins play an important role. However, up to date, few membrane proteins were revealed. In this study, we selected a surface molecule named Trim59, which was specifically expressed on BAM membrane (compared with the negative control). We cloned and prokaryoticly expressed the extracellular domain of Trim59, purified the recombinant protein and generated polyclonal antibodies. Immu...

  2. Chemical activation of molecules by metals: Experimental studies of electron distributions and bonding

    This quarter has witnessed further progress both in our experimental methods of photoelectron spectroscopy and in our understanding the fundamental relationships between ionization energies and the chemistry of transition metal species. Progress continues on the new gas phase photoelectron spectrometer that combine improved capabilities for HeI/HeII UPS, XPS, and Auger investigations of organometallic molecules. Several measurements have been accomplished this year that were not possible previously. We have published the formal relationship between measured molecular ionization energies and thermodynamic bond dissociation energies, and applied the relationships to homonuclear and heteronuclear diatomic molecules, multiple bonds, and metal-ligand bonds. Studies of C-H bond activation have continued with examination of different degrees of Si-H bond addition to metals. the electronic effects of intermolecular interactions have been observed by comparing the ionizations of metal complexes in the gas phase with the ionizations of monolayer solid organometallic films prepared in ultra-high vacuum. The orientations of the molecules have been determined by scanning tunneling microscopy. Especially interesting has been the recent application of these techniques to the characterization of the soccer-ball shaped C60 molecule, buckminsterfullerene. Studies of the following complexes are described : Fe, Os, Nb, Mo, Rh, Re, Al, and Mn. 19 refs

  3. A chlorite mineral surface actively drives the deposition of DNA molecules in stretched conformations

    Muscovite mica is commonly used to immobilize DNA molecules onto a flat surface. This method, however, requires either the use of divalent cations in the buffer solution or the chemical modification of the surface. Here we show that DNA molecules have different binding affinities and assume different conformations when adsorbed to different layered minerals. In particular, the effect of biotite, muscovite, talc, brucite and chlorite upon DNA binding is investigated. Using atomic force microscopy it is possible to quantify the amount of DNA deposited onto a flat surface and it is experimentally confirmed that biotite, talc and brucite have a much higher affinity than muscovite (7-, 20- and 25-fold more volume of DNA deposited, respectively). The deposition of DNA onto chlorite presents areas (brucite-like) with high DNA coverage and areas (mica-like) where DNA molecules are absent. We regularly observed isolated DNA molecules that became stretched across these regions of low affinity. The stretching is not induced by the deposition procedure but is driven by the surface potential gradient between brucite-like and mica-like regions in chlorite. The active stretching of DNA on chlorite is a clear indication of the technological potential carried by these materials when used as substrates for biomolecules

  4. Supported gold catalysis: from small molecule activation to green chemical synthesis.

    Liu, Xiang; He, Lin; Liu, Yong-Mei; Cao, Yong

    2014-03-18

    With diminishing natural resources, there is an ever-increasing demand for cost-effective and sustainable production of fine and commodity chemicals. For this purpose, there is a need for new catalytic methods that can permit efficient and targeted conversion of fossil and biorenewable feedstocks with lower energy requirements and environmental impact. A significant number of industrial catalytic processes are performed by platinum-group-metal (PGM)-based heterogeneous catalysts capable of activating a range of important small molecules, such as CO, O2, H2, and N2. In contrast, there is a general feeling that gold (Au) cannot act as an efficient catalyst because of its inability to activate most molecules, which is essential to any catalytic processes. As a consequence, researchers have long neglected the potential for use of gold as a catalyst. In recent years, however, chemists have put forth tremendous effort and progress in the use of supported gold catalysts to facilitate a variety of useful synthetic transformations. The seminal discovery by Haruta in 1987 that suitably prepared Au-based catalysts were surprisingly active for CO oxidation even at 200 K initiated rapid development of the field. Since then, researchers have widely employed Au-based catalysts in many types of mild chemical processes, with special focus on selective reactions involving small molecules (for example, CO, H2O, O2, or H2) as a reactant. That gold in the form of tiny nanoparticles (NPs, generally less than 5 nm in diameter) can subtly activate the reactant molecules under mild conditions has been evoked to explain the superior effectiveness of gold compared with conventional PGMs. In this context, Au-based catalysts are gaining great significance in developing new green processes with improved selectivity and energy minimization. In this Account, we describe our efforts toward the development of a range of green and selective processes largely through the appropriate choice of Au

  5. Cloning and expression of the receptor for human urokinase plasminogen activator, a central molecule in cell surface, plasmin dependent proteolysis

    Roldan, A L; Cubellis, M V; Masucci, M T;

    1990-01-01

    The surface receptor for urokinase plasminogen activator (uPAR) has been recognized in recent years as a key molecule in regulating plasminogen mediated extracellular proteolysis. Surface plasminogen activation controls the connections between cells, basement membrane and extracellular matrix, an...

  6. Microbial respiration and extracellular enzyme activity in sediments from the Gulf of Mexico hypoxic zone

    This study explores the relationship between sediment chemistry (TC, TN, TP) and microbial respiration (DHA) and extracellular enzyme activity (EEA) across the Gulf of Mexico (GOM) hypoxic zone. TC, TN, and TP were all positively correlated with each other (r=0.19-0.68). DHA was ...

  7. Reduced endogenous Ca2+ buffering speeds active zone Ca2+ signaling.

    Delvendahl, Igor; Jablonski, Lukasz; Baade, Carolin; Matveev, Victor; Neher, Erwin; Hallermann, Stefan

    2015-06-01

    Fast synchronous neurotransmitter release at the presynaptic active zone is triggered by local Ca(2+) signals, which are confined in their spatiotemporal extent by endogenous Ca(2+) buffers. However, it remains elusive how rapid and reliable Ca(2+) signaling can be sustained during repetitive release. Here, we established quantitative two-photon Ca(2+) imaging in cerebellar mossy fiber boutons, which fire at exceptionally high rates. We show that endogenous fixed buffers have a surprisingly low Ca(2+)-binding ratio (∼ 15) and low affinity, whereas mobile buffers have high affinity. Experimentally constrained modeling revealed that the low endogenous buffering promotes fast clearance of Ca(2+) from the active zone during repetitive firing. Measuring Ca(2+) signals at different distances from active zones with ultra-high-resolution confirmed our model predictions. Our results lead to the concept that reduced Ca(2+) buffering enables fast active zone Ca(2+) signaling, suggesting that the strength of endogenous Ca(2+) buffering limits the rate of synchronous synaptic transmission. PMID:26015575

  8. Dynamical Organization of Syntaxin-1A at the Presynaptic Active Zone.

    Ullrich, Alexander; Böhme, Mathias A; Schöneberg, Johannes; Depner, Harald; Sigrist, Stephan J; Noé, Frank

    2015-09-01

    Synaptic vesicle fusion is mediated by SNARE proteins forming in between synaptic vesicle (v-SNARE) and plasma membrane (t-SNARE), one of which is Syntaxin-1A. Although exocytosis mainly occurs at active zones, Syntaxin-1A appears to cover the entire neuronal membrane. By using STED super-resolution light microscopy and image analysis of Drosophila neuro-muscular junctions, we show that Syntaxin-1A clusters are more abundant and have an increased size at active zones. A computational particle-based model of syntaxin cluster formation and dynamics is developed. The model is parametrized to reproduce Syntaxin cluster-size distributions found by STED analysis, and successfully reproduces existing FRAP results. The model shows that the neuronal membrane is adjusted in a way to strike a balance between having most syntaxins stored in large clusters, while still keeping a mobile fraction of syntaxins free or in small clusters that can efficiently search the membrane or be traded between clusters. This balance is subtle and can be shifted toward almost no clustering and almost complete clustering by modifying the syntaxin interaction energy on the order of only 1 kBT. This capability appears to be exploited at active zones. The larger active-zone syntaxin clusters are more stable and provide regions of high docking and fusion capability, whereas the smaller clusters outside may serve as flexible reserve pool or sites of spontaneous ectopic release. PMID:26367029

  9. Early-Late Heterobimetallic Complexes Linked by Phosphinoamide Ligands. Tuning Redox Potentials and Small Molecule Activation

    Thomas, Christine M. [Brandeis Univ., Waltham, MA (United States)

    2015-08-01

    Recent attention in the chemical community has been focused on the energy efficient and environmentally benign conversion of abundant small molecules (CO2, H2O, etc.) to useful liquid fuels. This project addresses these goals by examining fundamental aspects of catalyst design to ultimately access small molecule activation processes under mild conditions. Specifically, Thomas and coworkers have targetted heterobimetallic complexes that feature metal centers with vastly different electronic properties, dictated both by their respective positions on the periodic table and their coordination environment. Unlike homobimetallic complexes featuring identical or similar metals, the bonds between metals in early/late heterobimetallics are more polarized, with the more electron-rich late metal center donating electron density to the more electron-deficient early metal center. While metal-metal bonds pose an interesting strategy for storing redox equivalents and stabilizing reactive metal fragments, the polar character of metal-metal bonds in heterobimetallic complexes renders these molecules ideally poised to react with small molecule substrates via cleavage of energy-rich single and double bonds. In addition, metal-metal interactions have been shown to dramatically affect redox potentials and promote multielectron redox activity, suggesting that metal-metal interactions may provide a mechanism to tune redox potentials and access substrate reduction/activation at mild overpotentials. This research project has provided a better fundamental understanding of how interactions between transition metals can be used as a strategy to promote and/or control chemical transformations related to the clean production of fuels. While this project focused on the study of homogeneous systems, it is anticipated that the broad conclusions drawn from these investigations will be applicable to heterogeneous catalysis as well, particularly on heterogeneous processes that occur at interfaces in

  10. Green Oxygenation Degradation of Rhodamine B by Using Activated Molecule Oxygen

    Ke Jian DENG; Fei HUANG; Duo Yuan WANG; Zheng He PENG; Yun Hong ZHOU

    2004-01-01

    Iron(Ⅱ) tetra-(1,4-dithin)-porphyrazine, (FePz(dtn)4) is able to activate molecule oxygen for oxygenation degradation of rhodamine B (RhB) in an extensive pH region without light excitation. Experiments indicate that the RhB can be degraded nearly 52% in alkaline aqueous solution, bubbling with dioxygen for seven hours in the presence of FePz(dtn)4 and the hydrogen peroxides as an actve intermediate were determined by DPD method. The catalyst is recyclable and the catalyst activity was maintained after l0 recycles.

  11. Intercellular Cell Adhesion Molecule-1, Vascular Cell Adhesion Molecule-1, and Regulated on Activation Normal T Cell Expressed and Secreted Are Expressed by Human Breast Carcinoma Cells and Support Eosinophil Adhesion and Activation

    Ali, Shahina; Kaur, Jaswinder; Patel, Kamala D.

    2000-01-01

    Eosinophils are usually associated with parasitic and allergic diseases; however, eosinophilia is also observed in several types of human tumors, including breast carcinomas. In this study we examined several human breast carcinoma cell lines for adhesion molecule expression and the ability to bind and activate eosinophils. MDA-MB-435S and MDA-MB-468 cells constitutively expressed both intercellular adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule-1 (VCAM-1) and this expressio...

  12. Earthquake doublet in an active shear zone, southwest Japan: Constraints from geophysical and geochemical findings

    Umeda, Koji; Asamori, Koichi; Makuuchi, Ayumu; Kobori, Kazuo

    2014-11-01

    In 1997, the Kagoshima earthquake doublet, consisting of two closely associated Mw ~ 6 strike-slip events, five km and 48 days apart, has occurred in southwest Japan. The location is where an E-W trending discontinuity along 32°N latitude on southern Kyushu Island is clearly defined in GPS velocities, indicating the presence of a highly active left-lateral shear zone. However, there have not been any obvious indications of active faulting at the surface prior to the earthquake doublet, which could be associated with this shear zone. Three-dimensional inversion of magnetotelluric sounding data obtained in the source region of the earthquake doublet reveals a near-vertical conductive zone with a width of 20 km, extending down to the base of the crust and perhaps into the upper mantle toward the Okinawa trough. The prominent conductor corresponds to the western part of the active shear zone. Elevated 3He/4He ratios in groundwaters sampled from hot spring and drinking water wells suggest the emission of mantle-derived helium from the seismic source region. The geophysical and geochemical observations are significant indications that the invasion of mantle fluids into the crust, driven by upwelling asthenosphere from the Okinawa trough, triggers the notable left-lateral shearing in the zone in the present-day subduction system. In addition, the existence of aqueous fluids in and below the seismogenic layer could change the strength of the zones, and alter the local stress regime, resulting in the occurrence of the 1997 earthquake doublet.

  13. Geophysical and Geochemical Signatures Associated with Mantle Fluids Beneath an Active Shear Zone, Southwest Japan

    Umeda, K.; Asamori, K.; Sueoka, S.; Tamura, H.; Shimizu, M.

    2014-12-01

    In 1997, the Kagoshima earthquake doublet, consisting of two closely associated Mw ~ 6 strike-slip events, five km and 48 days apart, has occurred in southwest Japan. The location is where an E-W trending discontinuity along 32°N latitude on southern Kyushu Island is clearly defined in GPS velocities, indicating the presence of a highly active left-lateral shear zone. However, there have not been any obvious indications of active faulting at the surface prior to the earthquake doublet, which could be associated with this shear zone. Three-dimensional inversion of magnetotelluric sounding data obtained in the source region of the earthquake doublet reveals a near-vertical conductive zone with a width of 20 km, extending down to the base of the crust and perhaps into the upper mantle toward the Okinawa trough. The prominent conductor corresponds to the western part of the active shear zone. Elevated 3He/4He ratios in groundwaters sampled from hot spring and drinking water wells suggest the emission of mantle-derived helium from the seismic source region. The geophysical and geochemical observations are significant indications that the invasion of mantle fluids into the crust, driven by upwelling asthenosphere from the Okinawa trough, triggers the notable left-lateral shearing in the zone in the present-day subduction system. In addition, the existence of aqueous fluids in and below the seismogenic layer could change the strength of the zones, and alter the local stress regime, resulting in the occurrence of the 1997 earthquake doublet.

  14. Ethosomes for the delivery of anti-HSV-1 molecules: preparation, characterization and in vitro activity.

    Cortesi, R; Ravani, L; Zaid, A N; Menegatti, E; Romagnoli, R; Drechsler, M; Esposito, E

    2010-10-01

    This paper describes the production, characterization and in vitro activity of ethosomes containing two molecules with antiviral activity, such as acyclovir (ACY) and N1-beta-D-ribofuranosyl-pyrazole [3,4d]pyridazin-7(6p-chlorine-phenyl)-one nucleoside (N1CP). Ethosomes were prepared and morphologically characterized by Cryo-TEM. The encapsulation efficiency was 92.3 +/- 2.5% for ACY and 94.2 +/- 2.8% for N1CP. The release of the drug from vesicles, determined by a Franz cell method, indicated that both drugs were released in a controlled manner. In order to possibly guarantee the stability during long-term storage ethosome suspensions was freeze-dried. It was found that the freeze-dried ethosomes' cakes were compact, glassy characterized by low density and quick re-hydration. However, the storage time slightly influences the percentage of drug encapsulation within ethosomes showing a drug leakage after re-hydration around 10%. The antiviral activity against HSV-1 of both drugs was tested by plaque reduction assay in monolayer cultures of Vero cells. Data showed that ethosomes allowed a reduction of the ED50 of N1CP evidencing an increase of its antiviral activity. However, ACY remains more active than N1CP. No differences are appreciable between drug-containing ethosomes before and after freeze-drying. Taken together these results, ethosomal formulation could be possibly proposed as mean for topical administration of anti-herpetic molecules. PMID:21105576

  15. Single-molecule kinetics under force: probing protein folding and enzymatic activity with optical tweezers

    Wong, Wesley

    2010-03-01

    Weak non-covalent bonds between and within single molecules govern many aspects of biological structure and function (e.g. DNA base-paring, receptor-ligand binding, protein folding, etc.) In living systems, these interactions are often subject to mechanical forces, which can greatly alter their kinetics and activity. My group develops and applies novel single-molecule manipulation techniques to explore and quantify these force-dependent kinetics. Using optical tweezers, we have quantified the force-dependent unfolding and refolding kinetics of different proteins, including the cytoskeletal protein spectrin in collaboration with E. Evans's group [1], and the A2 domain of the von Willebrand factor blood clotting protein in collaboration with T. Springer's group [2]. Furthermore, we have studied the kinetics of the ADAMTS13 enzyme acting on a single A2 domain, and have shown that physiolgical forces in the circulation can act as a cofactor for enzymatic cleavage, regulating hemostatic activity [2]. References: 1. E. Evans, K. Halvorsen, K. Kinoshita, and W.P. Wong, Handbook of Single Molecule Biophysics, P. Hinterdorfer, ed., Springer (2009). 2. X. Zhang, K. Halvorsen, C.-Z. Zhang, W.P. Wong, and T.A. Springer, Science 324 (5932), 1330-1334 (2009).

  16. Theoretical investigation of the degradation mechanisms in host and guest molecules used in OLED active layers

    Winget, Paul

    2014-10-08

    A feature of OLEDs that has to date received little attention is the prediction of the stability of the molecules involved in the electrical and optical processes. Here, we present computational results intended to aid in the development of stable systems. We identify degradation pathways and define new strategies to guide the synthesis of stable materials for OLED applications for both phosphorescent emitters and organic host materials. The chemical reactivity of these molecules in the active layers of the devices is further complicated by the fact that, during operation, they can be either oxidized or reduced (as they localize a hole or an electron) in addition to forming both singlet and triplet excitons. © (2014) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

  17. Stellar Activity Masquerading as Planets in the Habitable Zone of the M dwarf Gliese 581

    Robertson, Paul; Endl, Michael; Roy, Arpita

    2014-01-01

    The M dwarf Gliese 581 is believed to host four planets, including one (GJ 581d) near the habitable zone that could possibly support liquid water on its surface if it is a rocky planet. The detection of another habitable-zone planet--GJ 581g--is disputed, as its significance depends on the eccentricity assumed for d. Analyzing stellar activity using the H-alpha line, we measure a stellar rotation period of 130+/-2 days and a correlation for H-alpha modulation with radial velocity. Correcting for activity greatly diminishes the signal of GJ 581d (to 1.5 sigma), while significantly boosting the signals of the other known super-Earth planets. GJ 581d does not exist, but is an artifact of stellar activity which, when incompletely corrected, causes the false detection of planet g.

  18. 78 FR 7395 - Foreign-Trade Zone 129-Bellingham, WA; Notification of Proposed Production Activity; T.C. Trading...

    2013-02-01

    ... Foreign-Trade Zones Board Foreign-Trade Zone 129--Bellingham, WA; Notification of Proposed Production Activity; T.C. Trading Company, Inc. (Eyeglass Assembly and Kitting); Blaine, WA The Port of Bellingham, grantee of FTZ 129, submitted a notification of proposed production activity on behalf of T.C....

  19. 34 CFR 299.3 - What priority may the Secretary establish for activities in an Empowerment Zone or Enterprise...

    2010-07-01

    ... activities in an Empowerment Zone or Enterprise Community? For any ESEA discretionary grant program, the Secretary may establish a priority, as authorized by 34 CFR 75.105(b), for projects that will— (a) Use a... activities in an Empowerment Zone or Enterprise Community? 299.3 Section 299.3 Education Regulations of...

  20. Influence of the water molecules near surface of viral protein on virus activation process

    The infection of a cell with influenza virus comprises the stages of receptor binding to the cell membrane, endocytosis of virus particle, and fusion of the virus envelope and cell endosome membrane, which is determined by the conformational changes in hemagglutinin, a virus envelope protein, caused by pH decrease within the endosome. The pH value that induces conformation rearrangements of hemagglutinin molecule considerably varies for different influenza virus strains, first and foremost, due to the differences in amino acid structure of the corresponding proteins. The main goal of this study was to construct a model making it possible to assess the critical pH value characterizing the fusogenic activity of influenza virus hemagglutinin from the data on hemagglutinin structure and experimental verification of this model. Under this model, we assume that when the electrostatic force between interacting hemagglutinin molecules in the virus envelop exceeds a certain value, the hemagglutinin HA1 subunits are arranged so that they form a cavity sufficient for penetration of water molecules. This event leads to an irreversible hydration of the inner fragments of hemagglutinin molecule in a trimer and to the completion of conformational changes. The geometry of electrostatic field in hemagglutinin trimer was calculated taking into account the polarization effects near the interface of two dielectrics, aqueous medium and protein macromolecule. The critical pH values for the conformational changes in hemagglutinin were measured by the erythrocyte hemolysis induced by influenza virus particles when decreasing pH. The critical pH value conditionally separating the pH range into the regions with and without the conformational changes was calculated for several influenza virus H1N1 and H3N2 strains based on the data on the amino acid structure of the corresponding hemagglutinin molecules. Comparison of the theoretical and experimental values of critical pH values for

  1. High Throughput Extraction of Plant, Marine and Fungal Specimens for Preservation of Biologically Active Molecules

    Thomas G. McCloud

    2010-06-01

    Full Text Available The Developmental Therapeutics Program (DTP of the U.S. National Cancer Institute (NCI, at its NCI-Frederick facility, has built perhaps the largest and most diverse natural products screening library in the world for drug discovery. Composed of plant, marine organism and microbial extracts, it currently contains in excess of 230,000 unique materials. From the inception of this program to identify new anticancer chemotherapeutics from natural products sources in 1987, two extracts have been sequentially prepared from each specimen: one produced by organic solvent extraction, which yields a complex material that contains non- to moderately polar small molecules, and a water-soluble extract, a milieu largely unexplored for useful drugs in earlier years, which contains polar small to medium-sized molecules. Plant specimens and microbial ferments are extracted by modified traditional methods, while the method developed to produce extracts from marine organisms is unique and very different from that used by marine natural products chemists previously, but again yields both an organic solvent soluble and a water soluble material for inclusion into the screening library. Details of high throughput extract production for preservation of biologically active molecules are presented.

  2. Effect of methylprednisolone on the oxidative burst activity, adhesion molecules and clinical outcome following open heart surgery

    Toft, P; Christiansen, K; Tønnesen, Else Kirstine; Nielsen, C H; Lillevang, S

    1997-01-01

    cytometrically using 123-dihydrorhodamine. A panel of adhesion molecules was measured using monoclonal antibodies. Following CPB the oxidative burst activity and the expression of the adhesion molecule L-selectin more than doubled compared to initial values. There was no difference between the steroid group and...

  3. In vitro and in vivo activity of a novel antifungal small molecule against Candida infections.

    Sarah Sze Wah Wong

    Full Text Available Candida is the most common fungal pathogen of humans worldwide and has become a major clinical problem because of the growing number of immunocompromised patients, who are susceptible to infection. Moreover, the number of available antifungals is limited, and antifungal-resistant Candida strains are emerging. New and effective antifungals are therefore urgently needed. Here, we discovered a small molecule with activity against Candida spp. both in vitro and in vivo. We screened a library of 50,240 small molecules for inhibitors of yeast-to-hypha transition, a major virulence attribute of Candida albicans. This screening identified 20 active compounds. Further examination of the in vitro antifungal and anti-biofilm properties of these compounds, using a range of Candida spp., led to the discovery of SM21, a highly potent antifungal molecule (minimum inhibitory concentration (MIC 0.2-1.6 µg/ml. In vitro, SM21 was toxic to fungi but not to various human cell lines or bacterial species and was active against Candida isolates that are resistant to existing antifungal agents. Moreover, SM21 was relatively more effective against biofilms of Candida spp. than the current antifungal agents. In vivo, SM21 prevented the death of mice in a systemic candidiasis model and was also more effective than the common antifungal nystatin at reducing the extent of tongue lesions in a mouse model of oral candidiasis. Propidium iodide uptake assay showed that SM21 affected the integrity of the cell membrane. Taken together, our results indicate that SM21 has the potential to be developed as a novel antifungal agent for clinical use.

  4. Affinity of Drugs and Small Biologically Active Molecules to Carbon Nanotubes: A Pharmacodynamics and Nanotoxicity Factor?

    Liu, John; Yang, Liu; Hopfinger, Anton J.

    2009-01-01

    The MM-PBSA MD method was used to estimate the affinity, as represented by log kb, of each of a variety of biologically active molecules to a carbon nanotube in an aqueous environment. These ligand-receptor binding simulations were calibrated by first estimating the log kb values for eight ligands to human serum albumin, HSA, whose log kb values have been observed. A validation linear correlation equation was established [R2 = 0.888 Q2 = 0.603] between the observed and estimated log kb values...

  5. Benzimidazole-1,2,3-triazole Hybrid Molecules: Synthesis and Evaluation for Antibacterial/Antifungal Activity

    Ouahrouch, Abdelaaziz; Ighachane, Hana; Taourirte, Moha; Joachim W. Engels; Sedra, My Hassan; Lazrek, Hassan B.

    2014-01-01

    A novel series of hybrid molecules 4a–i and 5a–i were prepared by condensation of 4-(trimethylsilylethynyl)benzaldehyde 1 with substituted o-phenylenediamines. These in turn were reacted with 2-(azidomethoxy)ethyl acetate in a Cu alkyne–azide cycloaddition (CuAAC) to generate the 1,2,3-triazole pharmacophore under microwave assistance. The newly synthesized compounds were examined for their in vitro antimicrobial activities against Gram-positive and Gram-negative bacteria and the phytopathoge...

  6. Structure Based Discovery of Small Molecules to Regulate the Activity of Human Insulin Degrading Enzyme

    Bilal Çakir; Onur Dağliyan; Ezgi Dağyildiz; İbrahim Bariş; Ibrahim Halil Kavakli; Seda Kizilel; Metin Türkay

    2012-01-01

    Structure Based Discovery of Small Molecules to Regulate the Activity of Human Insulin Degrading Enzyme Bilal C¸ akir1, Onur Dag˘ liyan1, Ezgi Dag˘ yildiz1, I˙brahim Baris¸1, Ibrahim Halil Kavakli1,2*, Seda Kizilel1*, Metin Tu¨ rkay3* 1 Department of Chemical and Biological Engineering, Koc¸ University, Sariyer, Istanbul, Turkey, 2 Department of Molecular Biology and Genetics, Koc¸ University, Sariyer, Istanbul, Turkey, 3 Department of Industrial Engineering, Koc¸ University...

  7. Small molecule activators of SIRT1 replicate signaling pathways triggered by calorie restriction in vivo

    Lavu Siva

    2009-03-01

    Full Text Available Abstract Background Calorie restriction (CR produces a number of health benefits and ameliorates diseases of aging such as type 2 diabetes. The components of the pathways downstream of CR may provide intervention points for developing therapeutics for treating diseases of aging. The NAD+-dependent protein deacetylase SIRT1 has been implicated as one of the key downstream regulators of CR in yeast, rodents, and humans. Small molecule activators of SIRT1 have been identified that exhibit efficacy in animal models of diseases typically associated with aging including type 2 diabetes. To identify molecular processes induced in the liver of mice treated with two structurally distinct SIRT1 activators, SIRT501 (formulated resveratrol and SRT1720, for three days, we utilized a systems biology approach and applied Causal Network Modeling (CNM on gene expression data to elucidate downstream effects of SIRT1 activation. Results Here we demonstrate that SIRT1 activators recapitulate many of the molecular events downstream of CR in vivo, such as enhancing mitochondrial biogenesis, improving metabolic signaling pathways, and blunting pro-inflammatory pathways in mice fed a high fat, high calorie diet. Conclusion CNM of gene expression data from mice treated with SRT501 or SRT1720 in combination with supporting in vitro and in vivo data demonstrates that SRT501 and SRT1720 produce a signaling profile that mirrors CR, improves glucose and insulin homeostasis, and acts via SIRT1 activation in vivo. Taken together these results are encouraging regarding the use of small molecule activators of SIRT1 for therapeutic intervention into type 2 diabetes, a strategy which is currently being investigated in multiple clinical trials.

  8. Mechanically activated switching of Si-based single-molecule junction as imaged with three-dimensional dynamic probe

    Nakamura, Miki; Yoshida, Shoji; Katayama, Tomoki; Taninaka, Atsushi; Mera, Yutaka; Okada, Susumu; Takeuchi, Osamu; Shigekawa, Hidemi

    2015-10-01

    Understanding and extracting the full functions of single-molecule characteristics are key factors in the development of future device technologies, as well as in basic research on molecular electronics. Here we report a new methodology for realizing a three-dimensional (3D) dynamic probe of single-molecule conductance, which enables the elaborate 3D analysis of the conformational effect on molecular electronics, by the formation of a Si/single molecule/Si structure using scanning tunnelling microscopy (STM). The formation of robust covalent bonds between a molecule and Si electrodes, together with STM-related techniques, enables the stable and repeated control of the conformational modulation of the molecule. By 3D imaging of the conformational effect on a 1,4-diethynylbenzene molecule, a binary change in conductance with hysteresis is observed for the first time, which is considered to originate from a mechanically activated conformational change.

  9. Traumatic Brain Injury Activation of the Adult Subventricular Zone Neurogenic Niche

    Chang, Eun Hyuk; Adorjan, Istvan; Mundim, Mayara V.; Sun, Bin; Dizon, Maria L. V.; Szele, Francis G.

    2016-01-01

    Traumatic brain injury (TBI) is common in both civilian and military life, placing a large burden on survivors and society. However, with the recognition of neural stem cells in adult mammals, including humans, came the possibility to harness these cells for repair of damaged brain, whereas previously this was thought to be impossible. In this review, we focus on the rodent adult subventricular zone (SVZ), an important neurogenic niche within the mature brain in which neural stem cells continue to reside. We review how the SVZ is perturbed following various animal TBI models with regards to cell proliferation, emigration, survival, and differentiation, and we review specific molecules involved in these processes. Together, this information suggests next steps in attempting to translate knowledge from TBI animal models into human therapies for TBI. PMID:27531972

  10. Small-molecule CFTR activators increase tear secretion and prevent experimental dry eye disease.

    Flores, Alyssa M; Casey, Scott D; Felix, Christian M; Phuan, Puay W; Verkman, A S; Levin, Marc H

    2016-05-01

    Dry eye disorders, including Sjögren's syndrome, constitute a common problem in the aging population, with limited effective therapeutic options available. The cAMP-activated Cl(-) channel cystic fibrosis transmembrane conductance regulator (CFTR) is a major prosecretory channel at the ocular surface. We investigated whether compounds that target CFTR can correct the abnormal tear film in dry eye. Small-molecule activators of human wild-type CFTR identified by high-throughput screening were evaluated in cell culture and in vivo assays, to select compounds that stimulate Cl(-)-driven fluid secretion across the ocular surface in mice. An aminophenyl-1,3,5-triazine, CFTRact-K089, fully activated CFTR in cell cultures with EC50 ∼250 nM and produced an ∼8.5 mV hyperpolarization in ocular surface potential difference. When delivered topically, CFTRact-K089 doubled basal tear volume for 4 h and had no effect in CF mice. CFTRact-K089 showed sustained tear film bioavailability without detectable systemic absorption. In a mouse model of aqueous-deficient dry eye produced by lacrimal ablation, topical administration of 0.1 nmol CFTRact-K089 3 times daily restored tear volume to basal levels, preventing corneal epithelial disruption when initiated at the time of surgery and reversing it when started after development of dry eye. Our results support the potential utility of CFTR-targeted activators as a novel prosecretory treatment for dry eye.-Flores, A. M., Casey, S. D., Felix, C. M., Phuan, P. W., Verkman, A. S., Levin, M. H. Small-molecule CFTR activators increase tear secretion and prevent experimental dry eye disease. PMID:26842854

  11. Influence of platelet activating factor on expression of adhesion molecules in experimental pancreatitis

    Hua Zhao; Ji-Wei Chen; Ya-Kui Zhou; Xue-Feng Zhou; Pei-Yun Li

    2003-01-01

    AIM: To determine whether Platelet activating factor (PAF)has a regulation role in the expression of adhesion moleculesand accumulation of neutrophils in a murine model of acutepancreatitis.METHODS: One hundred twenty-eight Kunming mice weredivided into four groups. Group 1 received 0.1 mi saline s.c.every hour for three hours (sham). Group 2 received cerulein(50 μg/kg dose s.c.) every hour for three hours. Group 3received AP and additional challenge of PAF (50 rg/kg inabsolute ethanol) (AP/PAF). Group 4 received AP, plustherapeutic treatment with GAB (25 mg dose i.p.) immediatelyafter the first challenge of cerulein (AP/GAB). Animals weresacrificed at 12 h after the first challenge of saline or cerulein.Adhesion molecules of pancreas were semi-quantified bySP methods. Standard assays were performed for serumamylase and myeloperoxidase activity (MPO) of pancreas.Histology of pancreas was scored in a blind manner. Watercontent of pancreas was also measured at the same time.RESULTS: Control pancreata showed negligible adhesionmolecule expression and neutrophil accumulation. Therewere evident adhesion molecules expression and neutrophilaccumulation in AP and AP/PAF compared with sham (P<0.05).AP/GAB had a lower level of adhesion molecules, neutrophils,and water content versus AP and AP/PAF (P<0.05). Histologyshowed a trend toward improvement in AP/GAB, but didnot reach statistical significance.CONCLUSION: PAF can induce the expression of adhesionmolecules that mediate neutrophil accumulation. The PAFantagonist reduces the expression of adhesion moleculesand the severity of inflammation when given immediatelyafter the induction of mild AP in mice. These results suggestthat PAF antagonism may be useful in the treatment of mildpancreatitis after its clinical onset.

  12. Outcome of early active mobilization after flexor tendons repair in zones II–V in hand

    Saini Narender; Kundnani Vishal; Patni Purnima; Gupta S

    2010-01-01

    Background: The functional outcome of a flexor tendon injury after repair depends on multiple factors. The postoperative management of tendon injuries has paved a sea through many mobilization protocols. The improved understanding of splinting techniques has promoted the understanding and implication of these mobilization protocols. We conducted a study to observe and record the results of early active mobilization of repaired flexor tendons in zones II-V. Materials and Methods: 25 cases w...

  13. Effect of methylprednisolone on the oxidative burst activity, adhesion molecules and clinical outcome following open heart surgery

    Toft, P; Christiansen, K; Tønnesen, Else Kirstine;

    1997-01-01

    Following cardiac surgery with cardiopulmonary bypass (CPB), activated granulocytes may be involved with ischaemia/ reperfusion injury. The purpose of this study was to investigate whether steroids could reduce the oxidative burst activity of granulocytes, the expression of adhesion molecules on...... cytometrically using 123-dihydrorhodamine. A panel of adhesion molecules was measured using monoclonal antibodies. Following CPB the oxidative burst activity and the expression of the adhesion molecule L-selectin more than doubled compared to initial values. There was no difference between the steroid group and...... the control group regarding the expression of adhesion molecules or the oxidative burst activity. In the steroid group the fluid gain during extracorporeal circulation (ECC) was 683 ml (median) compared to 1488 ml in the control group. Steroids prevented hyperthermia in the postoperative period but...

  14. Expression of activated molecules on CD5(+)B lymphocytes in autoimmune hemolytic anemia.

    Zhu, Hongli; Xu, Wenyan; Liu, Hong; Wang, Huaquan; Fu, Rong; Wu, Yuhong; Qu, Wen; Wang, Guojin; Guan, Jing; Song, Jia; Xing, Limin; Shao, Zonghong

    2016-05-01

    To investigate the expression of activation molecules on CD5(+)B lymphocytes in peripheral blood of autoimmune hemolytic anemia (AIHA)/Evans patients. The expression of CD80, CD86, and CD69 on CD5(+)B lymphocytes was detected using flow cytometry in 30 AIHA/Evans patients, 18 normal controls (NC) and nine chronic lymphocytic leukemia (CLL) patients. CD80 on CD5(+)B lymphocytes in untreated patients was higher than that in remission patients (P  0.05), but lower than those of CD5(-)B lymphocytes in remission patients and NC (P  0.05). CD80 and CD86 on CD5(+)B lymphocytes was negatively correlated with hemoglobin (HB), C3, C4 (P < 0.05) and positively correlated with reticulocyte (Ret) (P < 0.05). CD69 on CD5(+) and CD5(-)B lymphocytes of CLL was higher than those of AIHA/Evans patients and NC (P < 0.05). The active molecules on CD5(+)B lymphocytes in peripheral blood of AIHA/Evans patients differ from those on CD5(-) and clonal CD5(+)B lymphocytes. PMID:26968550

  15. Tungsten polyoxometalate molecules as active nodes for dynamic carrier exchange in hybrid molecular/semiconductor capacitors

    In this work we study the utilization of molecular transition metal oxides known as polyoxometalates (POMs), in particular the Keggin structure anions of the formula PW12O403−, as active nodes for potential switching and/or fast writing memory applications. The active molecules are being integrated in hybrid Metal-Insulator/POM molecules-Semiconductor capacitors, which serve as prototypes allowing investigation of critical performance characteristics towards the design of more sophisticated devices. The charging ability as well as the electronic structure of the molecular layer is probed by means of electrical characterization, namely, capacitance-voltage and current-voltage measurements, as well as transient capacitance measurements, C (t), under step voltage polarization. It is argued that the transient current peaks observed are manifestations of dynamic carrier exchange between the gate electrode and specific molecular levels, while the transient C (t) curves under conditions of molecular charging can supply information for the rate of change of the charge that is being trapped and de-trapped within the molecular layer. Structural characterization via surface and cross sectional scanning electron microscopy as well as atomic force microscopy, spectroscopic ellipsometry, UV and Fourier-transform IR spectroscopies, UPS, and XPS contribute to the extraction of accurate electronic structure characteristics and open the path for the design of new devices with on-demand tuning of their interfacial properties via the controlled preparation of the POM layer.

  16. Neutron-activation analysis for investigation of biochemical manganese in soils cotton soweol zone of Uzbekistan

    Full text: For many years we neutron activation analysis of soils sampled from different areas of landscape-geochemical regions of Uzbekistan including zone of extreme ecological catastrophe of Aral. Content of manganese and some other elements in the 'soil-cotton' system was investigated. Neutron-activation method of manganese determining with productivity up to 400 samples on shift with detection limit of 1,1 10-5 % and discrepancies not more than 10%. Was developed extremely uniform distribution of manganese in cotton sowed soils of the Republic (340-1800mg/kg) is determined. Practically all soils of cotton-sowed zone of Republic are with lack of manganese. Distribution of manganese on soil profile of separate organs of cotton (leaves seeds etc.) was studied. Correlation between gross concentration of manganese and its active part extracted by distilled water on the basis of quantity analysis was found. Successive comparison of gross content of manganese in the soil with crop capacity of cotton in different zones of Republic made it possible to find interconnection between these quantities, which proves necessity of using micro-additions of manganese in the soils where its low concentration is detected

  17. A model of ischemia-induced neuroblast activation in the adult subventricular zone.

    Davide Vergni

    Full Text Available We have developed a rat brain organotypic culture model, in which tissue slices contain cortex-subventricular zone-striatum regions, to model neuroblast activity in response to in vitro ischemia. Neuroblast activation has been described in terms of two main parameters, proliferation and migration from the subventricular zone into the injured cortex. We observed distinct phases of neuroblast activation as is known to occur after in vivo ischemia. Thus, immediately after oxygen/glucose deprivation (6-24 hours, neuroblasts reduce their proliferative and migratory activity, whereas, at longer time points after the insult (2 to 5 days, they start to proliferate and migrate into the damaged cortex. Antagonism of ionotropic receptors for extracellular ATP during and after the insult unmasks an early activation of neuroblasts in the subventricular zone, which responded with a rapid and intense migration of neuroblasts into the damaged cortex (within 24 hours. The process is further enhanced by elevating the production of the chemoattractant SDf-1alpha and may also be boosted by blocking the activation of microglia. This organotypic model which we have developed is an excellent in vitro system to study neurogenesis after ischemia and other neurodegenerative diseases. Its application has revealed a SOS response to oxygen/glucose deprivation, which is inhibited by unfavorable conditions due to the ischemic environment. Finally, experimental quantifications have allowed us to elaborate a mathematical model to describe neuroblast activation and to develop a computer simulation which should have promising applications for the screening of drug candidates for novel therapies of ischemia-related pathologies.

  18. Small-Molecule Inhibition and Activation-Loop Trans-Phosphorylation of the IGF1 Receptor

    Wu,J.; Li, W.; Craddock, B.; Foreman, K.; Mulvihill, M.; Ji, Q.; Miller, W.; Hubbard, S.

    2008-01-01

    The insulin-like growth factor-1 receptor (IGF1R) is a receptor tyrosine kinase (RTK) that has a critical role in mitogenic signalling during embryogenesis and an antiapoptotic role in the survival and progression of many human tumours. Here, we present the crystal structure of the tyrosine kinase domain of IGF1R (IGF1RK), in its unphosphorylated state, in complex with a novel compound, cis-3-[3-(4-methyl-piperazin-l-yl)-cyclobutyl]-1-(2-phenyl-quinolin-7-yl)-imidazo[1, 5-a]pyrazin-8-ylamine (PQIP), which we show is a potent inhibitor of both the unphosphorylated (basal) and phosphorylated (activated) states of the kinase. PQIP interacts with residues in the ATP-binding pocket and in the activation loop, which confers specificity for IGF1RK and the highly related insulin receptor (IR) kinase. In this crystal structure, the IGF1RK active site is occupied by Tyr1135 from the activation loop of an symmetry (two-fold)-related molecule. This dimeric arrangement affords, for the first time, a visualization of the initial trans-phosphorylation event in the activation loop of an RTK, and provides a molecular rationale for a naturally occurring mutation in the activation loop of the IR that causes type II diabetes mellitus.

  19. Discovery of novel small molecule activators of β-catenin signaling.

    Folkert Verkaar

    Full Text Available Wnt/β-catenin signaling plays a major role in embryonic development and adult stem cell maintenance. Reduced activation of the Wnt/β-catenin pathway underlies neurodegenerative disorders and aberrations in bone formation. Screening of a small molecule compound library with a β-galactosidase fragment complementation assay measuring β-catenin nuclear entry revealed bona fide activators of β-catenin signaling. The compounds stabilized cytoplasmic β-catenin and activated β-catenin-dependent reporter gene activity. Although the mechanism through which the compounds activate β-catenin signaling has yet to be determined, several key regulators of Wnt/β-catenin signaling, including glycogen synthase kinase 3 and Frizzled receptors, were excluded as the molecular target. The compounds displayed remarkable selectivity, as they only induced β-catenin signaling in a human osteosarcoma U2OS cell line and not in a variety of other cell lines examined. Our data indicate that differences in cellular Wnt/β-catenin signaling machinery can be exploited to identify cell type-specific activators of Wnt/β-catenin signaling.

  20. Novel small-molecule AMPK activator orally exerts beneficial effects on diabetic db/db mice

    Li, Yuan-Yuan; Yu, Li-Fang; Zhang, Li-Na; Qiu, Bei-Ying; Su, Ming-Bo; Wu, Fang; Chen, Da-Kai; Pang, Tao; Gu, Min; Zhang, Wei; Ma, Wei-Ping; Jiang, Hao-Wen; Li, Jing-Ya, E-mail: jyli@mail.shcnc.ac.cn; Nan, Fa-Jun, E-mail: fjnan@mail.shcnc.ac.cn; Li, Jia, E-mail: jli@mail.shcnc.ac.cn

    2013-12-01

    AMP-activated protein kinase (AMPK), which is a pivotal guardian of whole-body energy metabolism, has become an attractive therapeutic target for metabolic syndrome. Previously, using a homogeneous scintillation proximity assay, we identified the small-molecule AMPK activator C24 from an optimization based on the original allosteric activator PT1. In this paper, the AMPK activation mechanism of C24 and its potential beneficial effects on glucose and lipid metabolism on db/db mice were investigated. C24 allosterically stimulated inactive AMPK α subunit truncations and activated AMPK heterotrimers by antagonizing autoinhibition. In primary hepatocytes, C24 increased the phosphorylation of AMPK downstream target acetyl-CoA carboxylase dose-dependently without changing intracellular AMP/ATP ratio, indicating its allosteric activation in cells. Through activating AMPK, C24 decreased glucose output by down-regulating mRNA levels of phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6Pase) in primary hepatocytes. C24 also decreased the triglyceride and cholesterol contents in HepG2 cells. Due to its improved bioavailability, chronic oral treatment with multiple doses of C24 significantly reduced blood glucose and lipid levels in plasma, and improved the glucose tolerance of diabetic db/db mice. The hepatic transcriptional levels of PEPCK and G6Pase were reduced. These results demonstrate that this orally effective activator of AMPK represents a novel approach to the treatment of metabolic syndrome. - Highlights: • C24 activates AMPK through antagonizing autoinhibition within α subunit. • C24 activates AMPK in hepatocytes and decreases glucose output via AMPK. • C24 exerts beneficial effects on diabetic db/db mice. • C24 represents a novel therapeutic for treatment of metabolic syndrome.

  1. Novel small-molecule AMPK activator orally exerts beneficial effects on diabetic db/db mice

    AMP-activated protein kinase (AMPK), which is a pivotal guardian of whole-body energy metabolism, has become an attractive therapeutic target for metabolic syndrome. Previously, using a homogeneous scintillation proximity assay, we identified the small-molecule AMPK activator C24 from an optimization based on the original allosteric activator PT1. In this paper, the AMPK activation mechanism of C24 and its potential beneficial effects on glucose and lipid metabolism on db/db mice were investigated. C24 allosterically stimulated inactive AMPK α subunit truncations and activated AMPK heterotrimers by antagonizing autoinhibition. In primary hepatocytes, C24 increased the phosphorylation of AMPK downstream target acetyl-CoA carboxylase dose-dependently without changing intracellular AMP/ATP ratio, indicating its allosteric activation in cells. Through activating AMPK, C24 decreased glucose output by down-regulating mRNA levels of phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6Pase) in primary hepatocytes. C24 also decreased the triglyceride and cholesterol contents in HepG2 cells. Due to its improved bioavailability, chronic oral treatment with multiple doses of C24 significantly reduced blood glucose and lipid levels in plasma, and improved the glucose tolerance of diabetic db/db mice. The hepatic transcriptional levels of PEPCK and G6Pase were reduced. These results demonstrate that this orally effective activator of AMPK represents a novel approach to the treatment of metabolic syndrome. - Highlights: • C24 activates AMPK through antagonizing autoinhibition within α subunit. • C24 activates AMPK in hepatocytes and decreases glucose output via AMPK. • C24 exerts beneficial effects on diabetic db/db mice. • C24 represents a novel therapeutic for treatment of metabolic syndrome

  2. Small Molecule-Induced Allosteric Activation of the Vibrio Cholerae RTX Cysteine Protease Domain

    Lupardus, P.J.; Shen, A.; Bogyo, M.; Garcia, K.C.

    2009-05-19

    Vibrio cholerae RTX (repeats in toxin) is an actin-disrupting toxin that is autoprocessed by an internal cysteine protease domain (CPD). The RTX CPD is efficiently activated by the eukaryote-specific small molecule inositol hexakisphosphate (InsP{sub 6}), and we present the 2.1 angstrom structure of the RTX CPD in complex with InsP{sub 6}. InsP{sub 6} binds to a conserved basic cleft that is distant from the protease active site. Biochemical and kinetic analyses of CPD mutants indicate that InsP{sub 6} binding induces an allosteric switch that leads to the autoprocessing and intracellular release of toxin-effector domains.

  3. ACTIVITY AND Vp/Vs RATIO OF VOLCANO-TECTONIC SEISMIC SWARM ZONES AT NEVADO DEL RUIZ VOLCANO, COLOMBIA

    Londoño B. John Makario

    2010-06-01

    Full Text Available An analysis of the seismic activity for volcano-tectonic earthquake (VT swarms zones at Nevado del Ruiz Volcano (NRV was carried out for the interval 1985- 2002, which is the most seismic active period at NRV until now (2010. The swarm-like seismicity of NRV was frequently concentrated in very well defined clusters around the volcano. The seismic swarm zone located at the active crater was the most active during the entire time. The seismic swarm zone located to the west of the volcano suggested some relationship with the volcanic crises. It was active before and after the two eruptions occurred in November 1985 and September 1989. It is believed that this seismic activity may be used as a monitoring tool of volcanic activity. For each seismic swarm zone the Vp/Vs ratio was also calculated by grouping of earthquakes and stations. It was found that each seismic swarm zone had a distinct Vp/Vs ratio with respect to the others, except for the crater and west swarm zones, which had the same value. The average Vp/Vs ratios for the seismic swarm zones located at the active crater and to the west of the volcano are about 6-7% lower than that for the north swarm zone, and about 3% lower than that for the south swarm zone. We suggest that the reduction of the Vp/Vs ratio is due to degassing phenomena inside the central and western earthquake swarm zones, or due to the presence of microcracks inside the volcano. This supposition is in agreement with other studies of geophysics, geochemistry and drilling surveys carried out at NRV.

  4. Transcriptome Analysis of Tomato Flower Pedicel Tissues Reveals Abscission Zone-Specific Modulation of Key Meristem Activity Genes

    Wang, Xiang; Liu, Danmei; Li, Aili; Sun, Xiuli; Zhang, Rongzhi; Wu, Liang; Liang, Yanchun; Mao, Long

    2013-01-01

    Tomato flower abscises at the anatomically distinct abscission zone that separates the pedicel into basal and apical portions. During abscission, cell separation occurs only at the abscission zone indicating distinctive molecular regulation in its cells. We conducted a transcriptome analysis of tomato pedicel tissues during ethylene promoted abscission. We found that the abscission zone was the most active site with the largest set of differentially expressed genes when compared with basal an...

  5. Micro 3D ERT tomography for data assimilation modelling of active root zone

    Vanella, Daniela; Busato, Laura; Boaga, Jacopo; Cassiani, Giorgio; Binley, Andrew; Putti, Mario; Consoli, Simona

    2016-04-01

    Within the soil-plant-atmosphere system, root activity plays a fundamental role, as it connects different domains and allows a large part of the water and nutrient exchanges necessary for plant sustenance. The understanding of these processes is not only useful from an environmental point of view, making a fundamental contribution to the understanding of the critical zone dynamics, but also plays a pivotal role in precision agriculture, where the optimisation of water resources exploitation is mandatory and often carried out through deficit irrigation techniques. In this work, we present the results of non-invasive monitoring of the active root zone of two orange trees (Citrus sinensis, cv Tarocco Ippolito) located in an orange orchard in eastern Sicily (Italy) and drip irrigated with two different techniques: partial root drying and 100% crop evapotranspiration. The main goal of the monitoring activity is to assess possible differences between the developed root systems and the root water uptake between the two irrigation strategies. The monitoring is conducted using 3D micro-electrical resistivity tomography (ERT) based on an apparatus composed of a number of micro-boreholes (about 1.2 m deep) housing 12 electrodes each, plus a number of surface electrodes. Time-lapse measurements conducted both with long-term periodicity and short-term repetition before and after irrigation clearly highlight the presence and distribution of root water uptake zone both at shallow and larger depth, likely to correspond to zones utilized during the irrigation period (shallow) and during the time when the crop is not irrigated (deep). Subsidiary information is available in terms of precipitation, sap flow measurements and micrometeorological evapotranspiration estimates. This data ensemble lends itself to the assimilation into a variably saturated flow model, where both soil hydraulic parameters and root distribution shall be identified. Preliminary results in this directions show

  6. Dendrimers and Polyamino-Phenolic Ligands: Activity of New Molecules Against Legionella pneumophila Biofilms

    Andreozzi, Elisa; Barbieri, Federica; Ottaviani, Maria F.; Giorgi, Luca; Bruscolini, Francesca; Manti, Anita; Battistelli, Michela; Sabatini, Luigia; Pianetti, Anna

    2016-01-01

    Legionnaires’ disease is a potentially fatal pneumonia caused by Legionella pneumophila, an aquatic bacterium often found within the biofilm niche. In man-made water systems microbial biofilms increase the resistance of legionella to disinfection, posing a significant threat to public health. Disinfection methods currently used in water systems have been shown to be ineffective against legionella over the long-term, allowing recolonization by the biofilm-protected microorganisms. In this study, the anti-biofilm activity of previously fabricated polyamino-phenolic ligands and polyamidoamine dendrimers was investigated against legionella mono-species and multi-species biofilms formed by L. pneumophila in association with other bacteria that can be found in tap water (Aeromonas hydrophila, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae). Bacterial ability to form biofilms was verified using a crystal violet colorimetric assay and testing cell viability by real-time quantitative PCR and Plate Count assay. The concentration of the chemicals tested as anti-biofilm agents was chosen based on cytotoxicity assays: the highest non-cytotoxic chemical concentration was used for biofilm inhibition assays, with dendrimer concentration 10-fold higher than polyamino-phenolic ligands. While Macrophen and Double Macrophen were the most active substances among polyamino-phenolic ligands, dendrimers were overall twofold more effective than all other compounds with a reduction up to 85 and 73% of legionella and multi-species biofilms, respectively. Chemical interaction with matrix molecules is hypothesized, based on SEM images and considering the low or absent anti-microbial activity on planktonic bacteria showed by flow cytometry. These data suggest that the studied compounds, especially dendrimers, could be considered as novel molecules in the design of research projects aimed at the development of efficacious anti-biofilm disinfection treatments of water systems

  7. Dendrimers and polyamino-phenolic ligands: activity of new molecules against Legionella pneumophila biofilms.

    Elisa Andreozzi

    2016-03-01

    Full Text Available Legionnaires’ disease is a potentially fatal pneumonia caused by Legionella pneumophila, an aquatic bacterium often found within the biofilm niche. In man-made water systems microbial biofilms increase the resistance of legionella to disinfection, posing a significant threat to public health. Disinfection methods currently used in water systems have been shown to be ineffective against legionella over the long-term, allowing recolonization by the biofilm-protected microorganisms. In this study, the anti-biofilm activity of previously fabricated polyamino-phenolic ligands and polyamidoamine dendrimers was investigated against legionella mono-species and multi-species biofilms formed by L. pneumophila in association with other bacteria that can be found in tap water (Aeromonas hydrophila, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae. Bacterial ability to form biofilms was verified using a crystal violet colorimetric assay and testing cell viability by real-time quantitative PCR and Plate Count assay. The concentration of the chemicals tested as anti-biofilm agents was chosen based on cytotoxicity assays: the highest non-cytotoxic chemical concentration was used for biofilm inhibition assays, with dendrimer concentration ten-fold higher than polyamino-phenolic ligands. While Macrophen and Double Macrophen were the most active substances among polyamino-phenolic ligands, dendrimers were overall two-fold more effective than all other compounds with a reduction up to 85% and 73% of legionella and multi-species biofilms, respectively. Chemical interaction with matrix molecules is hypothesized, based on SEM images and considering the low or absent anti-microbial activity on planktonic bacteria showed by flow cytometry. These data suggest that the studied compounds, especially dendrimers, could be considered as novel molecules in the design of research projects aimed at the development of efficacious anti-biofilm disinfection

  8. Dendrimers and Polyamino-Phenolic Ligands: Activity of New Molecules Against Legionella pneumophila Biofilms.

    Andreozzi, Elisa; Barbieri, Federica; Ottaviani, Maria F; Giorgi, Luca; Bruscolini, Francesca; Manti, Anita; Battistelli, Michela; Sabatini, Luigia; Pianetti, Anna

    2016-01-01

    Legionnaires' disease is a potentially fatal pneumonia caused by Legionella pneumophila, an aquatic bacterium often found within the biofilm niche. In man-made water systems microbial biofilms increase the resistance of legionella to disinfection, posing a significant threat to public health. Disinfection methods currently used in water systems have been shown to be ineffective against legionella over the long-term, allowing recolonization by the biofilm-protected microorganisms. In this study, the anti-biofilm activity of previously fabricated polyamino-phenolic ligands and polyamidoamine dendrimers was investigated against legionella mono-species and multi-species biofilms formed by L. pneumophila in association with other bacteria that can be found in tap water (Aeromonas hydrophila, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae). Bacterial ability to form biofilms was verified using a crystal violet colorimetric assay and testing cell viability by real-time quantitative PCR and Plate Count assay. The concentration of the chemicals tested as anti-biofilm agents was chosen based on cytotoxicity assays: the highest non-cytotoxic chemical concentration was used for biofilm inhibition assays, with dendrimer concentration 10-fold higher than polyamino-phenolic ligands. While Macrophen and Double Macrophen were the most active substances among polyamino-phenolic ligands, dendrimers were overall twofold more effective than all other compounds with a reduction up to 85 and 73% of legionella and multi-species biofilms, respectively. Chemical interaction with matrix molecules is hypothesized, based on SEM images and considering the low or absent anti-microbial activity on planktonic bacteria showed by flow cytometry. These data suggest that the studied compounds, especially dendrimers, could be considered as novel molecules in the design of research projects aimed at the development of efficacious anti-biofilm disinfection treatments of water systems in

  9. Stellar activity mimics a habitable-zone planet around Kapteyn's star

    Robertson, Paul; Mahadevan, Suvrath

    2015-01-01

    Kapteyn's star is an old M subdwarf believed to be a member of the Galactic halo population of stars. A recent study has claimed the existence of two super-Earth planets around the star based on radial velocity (RV) observations. The innermost of these candidate planets--Kapteyn b (P = 48 days)--resides within the circumstellar habitable zone. Given recent progress in understanding the impact of stellar activity in detecting planetary signals, we have analyzed the observed HARPS data for signatures of stellar activity. We find that while Kapteyn's star is photometrically very stable, a suite of spectral activity indices reveals a large-amplitude rotation signal, and we determine the stellar rotation period to be 143 days. The spectral activity tracers are strongly correlated with the purported RV signal of "planet b," and the 48-day period is an integer fraction (1/3) of the stellar rotation period. We conclude that Kapteyn b is not a planet in the Habitable Zone, but an artifact of stellar activity.

  10. 78 FR 66330 - Foreign-Trade Zone (FTZ) 235-Lakewood, New Jersey, Notification of Proposed Production Activity...

    2013-11-05

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE Foreign-Trade Zones Board Foreign-Trade Zone (FTZ) 235--Lakewood, New Jersey, Notification of Proposed Production Activity, Cosmetic Essence Innovations, LLC, (Fragrance Bottling), Holmdel, New Jersey...

  11. 78 FR 56655 - Foreign-Trade Zone (FTZ) 203-Moses Lake, Washington; Notification of Proposed Production Activity...

    2013-09-13

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE Foreign-Trade Zones Board Foreign-Trade Zone (FTZ) 203--Moses Lake, Washington; Notification of Proposed Production Activity; AREVA Inc. (Fuel Rod Assemblies); Richland, Washington The Moses Lake Public...

  12. 78 FR 65963 - Foreign-Trade Zone 44-Mt. Olive, New Jersey; Authorization of Production Activity; Givaudan...

    2013-11-04

    ... notice in the Federal Register inviting public comment (78 FR 39707, 07-02-2013). The FTZ Board has... Foreign-Trade Zones Board Foreign-Trade Zone 44--Mt. Olive, New Jersey; Authorization of Production Activity; Givaudan Fragrances Corporation (Fragrance and Flavor Products); Mt. Olive, New Jersey On June...

  13. 77 FR 28568 - Foreign-Trade Zone 216-Olympia, WA; Notification of Proposed Production Activity; Callisons, Inc...

    2012-05-15

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE Foreign-Trade Zones Board Foreign-Trade Zone 216--Olympia, WA; Notification of Proposed Production Activity; Callisons, Inc., (Mint Products), Lacey and Chehalis, WA The Port of Olympia, grantee of FTZ...

  14. 77 FR 28851 - Foreign-Trade Zone 126-Reno, NV; Notification of Proposed Production Activity; Brightpoint North...

    2012-05-16

    ... Foreign-Trade Zones Board Foreign-Trade Zone 126--Reno, NV; Notification of Proposed Production Activity; Brightpoint North America L.P. (Cell Phone Kitting and Distribution); Reno, NV The Economic Development... behalf of Brightpoint North America L.P (Brightpoint), located in Reno, Nevada. The Brightpoint...

  15. Activation-induced deoxycytidine deaminase (AID) co-transcriptional scanning at single-molecule resolution

    Senavirathne, Gayan; Bertram, Jeffrey G.; Jaszczur, Malgorzata; Chaurasiya, Kathy R.; Pham, Phuong; Mak, Chi H.; Goodman, Myron F.; Rueda, David

    2015-12-01

    Activation-induced deoxycytidine deaminase (AID) generates antibody diversity in B cells by initiating somatic hypermutation (SHM) and class-switch recombination (CSR) during transcription of immunoglobulin variable (IgV) and switch region (IgS) DNA. Using single-molecule FRET, we show that AID binds to transcribed dsDNA and translocates unidirectionally in concert with RNA polymerase (RNAP) on moving transcription bubbles, while increasing the fraction of stalled bubbles. AID scans randomly when constrained in an 8 nt model bubble. When unconstrained on single-stranded (ss) DNA, AID moves in random bidirectional short slides/hops over the entire molecule while remaining bound for ~5 min. Our analysis distinguishes dynamic scanning from static ssDNA creasing. That AID alone can track along with RNAP during transcription and scan within stalled transcription bubbles suggests a mechanism by which AID can initiate SHM and CSR when properly regulated, yet when unregulated can access non-Ig genes and cause cancer.

  16. Nucleic Acid Chaperone Activity of HIV-1 NC Proteins Investigated by Single Molecule DNA Stretching

    Williams, Mark C.; Gorelick, Robert J.; Musier-Forsyth, Karin; Bloomfield, Victor A.

    2002-03-01

    HIV-1 Nucleocapsid Protein (NC) is a nucleic acid chaperone protein that is responsible for facilitating numerous nucleic acid rearrangements throughout the reverse transcription cycle of HIV-1. To understand the mechanism of NC’s chaperone function, we carried out single molecule DNA stretching studies in the presence of NC and mutant forms of NC. Using an optical tweezers instrument, we stretch single DNA molecules from the double-stranded helical state to the single-stranded (coil) state. Based on the observed cooperativity of DNA force-induced melting, we find that the fraction of melted base pairs at room temperature is increased dramatically in the presence of NC. Thus, upon NC binding, increased thermal fluctuations cause continuous melting and reannealing of base pairs so that DNA strands are able to rapidly sample configurations in order to find the lowest energy state. While NC destabilizes the double-stranded form of DNA, a mutant form of NC that lacks the zinc finger structures does not. DNA stretching experiments carried out in the presence of NC variants containing more subtle changes in the zinc finger structures were conducted to elucidate the contribution of each individual finger to NC’s chaperone activity, and these results will be reported.

  17. A Method of Permeabilization of Drosophila Embryos for Assays of Small Molecule Activity

    Rand, Matthew D.

    2014-01-01

    The Drosophila embryo has long been a powerful laboratory model for elucidating molecular and genetic mechanisms that control development. The ease of genetic manipulations with this model has supplanted pharmacological approaches that are commonplace in other animal models and cell-based assays. Here we describe recent advances in a protocol that enables application of small molecules to the developing fruit fly embryo. The method details steps to overcome the impermeability of the eggshell while maintaining embryo viability. Eggshell permeabilization across a broad range of developmental stages is achieved by application of a previously described d-limonene embryo permeabilization solvent (EPS1) and by aging embryos at reduced temperature (18 °C) prior to treatments. In addition, use of a far-red dye (CY5) as a permeabilization indicator is described, which is compatible with downstream applications involving standard red and green fluorescent dyes in live and fixed preparations. This protocol is applicable to studies using bioactive compounds to probe developmental mechanisms as well as for studies aimed at evaluating teratogenic or pharmacologic activity of uncharacterized small molecules. PMID:25046169

  18. Topical Anti-inflammatory Activity of New Hybrid Molecules of Terpenes and Synthetic Drugs

    Cristina Theoduloz

    2015-06-01

    Full Text Available The aim of the study was to assess changes in the activity of anti-inflammatory terpenes from Chilean medicinal plants after the formation of derivatives incorporating synthetic anti-inflammatory agents. Ten new hybrid molecules were synthesized combining terpenes (ferruginol (1, imbricatolic acid (2 and oleanolic acid (3 with ibuprofen (4 or naproxen (5. The topical anti-inflammatory activity of the compounds was assessed in mice by the arachidonic acid (AA and 12-O-tetradecanoyl phorbol 13-acetate (TPA induced ear edema assays. Basal cytotoxicity was determined towards human lung fibroblasts, gastric epithelial cells and hepatocytes. At 1.4 µmol/mouse, a strong anti-inflammatory effect in the TPA assay was observed for oleanoyl ibuprofenate 12 (79.9% and oleanoyl ibuprofenate methyl ester 15 (80.0%. In the AA assay, the best activity was observed for 12 at 3.2 µmol/mouse, with 56.8% reduction of inflammation, in the same range as nimesulide (48.9%. All the terpenyl-synthetic anti-inflammatory hybrids showed better effects in the TPA assay, with best activity for 6, 12 and 15. The cytotoxicity of the compounds 8 and 10 with a free COOH, was higher than that of 2. The derivatives from 3 were less toxic than the triterpene. Several of the new compounds presented better anti-inflammatory effect and lower cytotoxicity than the parent terpenes.

  19. A Pipeline for Screening Small Molecules with Growth Inhibitory Activity against Burkholderia cenocepacia.

    Carrie Selin

    Full Text Available Infections with the bacteria Burkholderia cepacia complex (Bcc are very difficult to eradicate in cystic fibrosis patients due the intrinsic resistance of Bcc to most available antibiotics and the emergence of multiple antibiotic resistant strains during antibiotic treatment. In this work, we used a whole-cell based assay to screen a diverse collection of small molecules for growth inhibitors of a relevant strain of Bcc, B. cenocepacia K56-2. The primary screen used bacterial growth in 96-well plate format and identified 206 primary actives among 30,259 compounds. From 100 compounds with no previous record of antibacterial activity secondary screening and data mining selected a total of Bce bioactives that were further analyzed. An experimental pipeline, evaluating in vitro antibacterial and antibiofilm activity, toxicity and in vivo antibacterial activity using C. elegans was used for prioritizing compounds with better chances to be further investigated as potential Bcc antibacterial drugs. This high throughput screen, along with the in vitro and in vivo analysis highlights the utility of this experimental method to quickly identify bioactives as a starting point of antibacterial drug discovery.

  20. Screening and characterization of molecules that modulate the biological activity of IFNs-I.

    Bürgi, Milagros; Zapol'skii, Viktor A; Hinkelmann, Bettina; Köster, Mario; Kaufmann, Dieter E; Sasse, Florenz; Hauser, Hansjörg; Etcheverrigaray, Marina; Kratje, Ricardo; Bollati-Fogolín, Mariela; Oggero, Marcos

    2016-09-10

    Type I Interferons (IFNs-I) are species-specific glycoproteins which play an important role as primary defence against viral infections and that can also modulate the adaptive immune system. In some autoimmune diseases, interferons (IFNs) are over-produced. IFNs are widely used as biopharmaceuticals for a variety of cancer indications, chronic viral diseases, and for their immuno-modulatory action in patients with multiple sclerosis; therefore, increasing their therapeutic efficiency and decreasing their side effects is of high clinical value. In this sense, it is interesting to find molecules that can modulate the activity of IFNs. In order to achieve that, it was necessary to establish a simple, fast and robust assay to analyze numerous compounds simultaneously. We developed four reporter gene assays (RGAs) to identify IFN activity modulator compounds by using WISH-Mx2/EGFP, HeLa-Mx2/EGFP, A549-Mx2/EGFP, and HEp2-Mx2/EGFP reporter cell lines (RCLs). All of them present a Z' factor higher than 0.7. By using these RGAs, natural and synthetic compounds were analyzed simultaneously. A total of 442 compounds were studied by the Low Throughput Screening (LTS) assay using the four RCLs to discriminate between their inhibitory or enhancing effects on IFN activity. Some of them were characterized and 15 leads were identified. Finally, one promising candidate with enhancing effect on IFN-α/-β activity and five compounds with inhibitory effect were described. PMID:27346232

  1. Broadband standoff detection of large molecules by mid-infrared active coherent laser spectrometry.

    Macleod, Neil A; Molero, Francisco; Weidmann, Damien

    2015-01-26

    A widely tunable active coherent laser spectrometer (ACLaS) has been demonstrated for standoff detection of broadband absorbers in the 1280 to 1318 cm-1 spectral region using an external cavity quantum cascade laser as a mid-infrared source. The broad tuning range allows detection and quantification of vapor phase molecules, such as dichloroethane, ethylene glycol dinitrate, and tetrafluoroethane. The level of confidence in molecular mixing ratios retrieved from interfering spectral measurements is assessed in a quantitative manner. A first qualitative demonstration of condensed phase chemical detection on nitroacetanilide has also been conducted. Detection performances of the broadband ACLaS have been placed in the context of explosive detection and compared to that obtained using distributed feedback quantum cascade lasers. PMID:25835851

  2. Activation energy of fractional vortices and spectroscopy of a vortex molecule in long Josephson junction

    This thesis is divided into two parts, the measurement of the activation energy of a fractional vortex and the spectroscopy of a vortex-molecule. Fractional vortices can be studied in long 0-κ Josephson junctions, where a jump of the Josephson phase is created artificially with a pair of tiny current injectors. To compensate for this phase discontinuity, a ρ vortex is formed. Here, ρ describes the vortex's so called topological charge. The ρ vortices are pinned at the discontinuity and they carry the fraction (ρ/2).Φ0 of magnetic flux, with the magnetic flux quantum Φ0 2.07.10-15. Two stable vortex configurations are possible, a direct Vortex and a complementary one. ρ depends on the injector current. When the bias current of the junction exceeds a characteristic threshold, which dependents on ρ, the Lorentz force is bigger than the pinning force of the vortex and a fluxon is pulled away. In this case a complementary (ρ-2π) vortex is left behind. This switching of the ρ vortex and the resulting emission of a fluxon can be described as a Kramers like escape of a particle out of a tilted washboard potential. The washboard potential is tilted to the point where the barrier is small enough, so that the particle can escape via thermal or quantum fluctuations. In the case of thermal fluctuations the barrier height is called activation energy. The activation energy can be determined by measuring the junction's switching current statistics. In this thesis, the activation energy, necessary for the vortex escape, was measured as a function of ρ and a homogenous external magnetic field perpendicular to the junction. The main focus was the investigation of 0-π junctions. The temperature dependence of the activation energy was investigated, too. It turns out, that the transition-state-theory is convenient to describe the switching probability of the standard Nb-AlOx-Nb junctions at 4.2 K. For the measurements at 0.5 K a model of low to intermediate damping results

  3. Counteracting Interactions between Lipopolysaccharide Molecules with Differential Activation of Toll-Like Receptors

    Hajishengallis, George; Martin, Michael; Schifferle, Robert E.; Genco, Robert J.

    2002-01-01

    We investigated counteracting interactions between the lipopolysaccharides (LPS) from Escherichia coli (Ec-LPS) and Porphyromonas gingivalis (Pg-LPS), which induce cellular activation through Toll-like receptor 4 (TLR4) and TLR2, respectively. We found that Ec-LPS induced tolerance in THP-1 cells to subsequent tumor necrosis factor alpha (TNF-α) and interleukin 1 beta (IL-1β) induction by Pg-LPS, though the reverse was not true, and looked for explanatory differential effects on the signal transduction pathway. Cells exposed to Pg-LPS, but not to Ec-LPS, displayed persisting expression of IL-1 receptor-associated kinase without apparent degradation, presumably allowing prolonged relay of downstream signals. Accordingly, cells pretreated with Pg-LPS, but not with Ec-LPS, were effectively activated in response to subsequent exposure to either LPS molecule, as evidenced by assessing nuclear factor (NF)-κB activity. In fact, Pg-LPS primed THP-1 cells for enhanced NF-κB activation and TNF-α release upon restimulation with the same LPS. This was a dose-dependent effect and correlated with upregulation of surface TLR2 expression. Furthermore, we observed inhibition of NF-κB-dependent transcription in a reporter cell line pretreated with Ec-LPS and restimulated with Pg-LPS (compared to cells pretreated with medium only and restimulated with Pg-LPS), but not when the reverse treatment was made. Although Pg-LPS could not make cells tolerant to subsequent activation by Ec-LPS, Pg-LPS inhibited Ec-LPS-induced TNF-α and IL-6 release when the two molecules were added simultaneously into THP-1 cell cultures. Pg-LPS also suppressed P. gingivalis FimA protein-induced NF-κB-dependent transcription in the 3E10/huTLR4 reporter cell line, which does not express TLR2. This rules out competition for common signaling intermediates, suggesting that Pg-LPS may block component(s) of the TLR4 receptor complex. Interactions between TLR2 and TLR4 agonists may be important in the

  4. Active Crustal Faults in the Forearc Region, Guerrero Sector of the Mexican Subduction Zone

    Gaidzik, Krzysztof; Ramírez-Herrera, Maria Teresa; Kostoglodov, Vladimir

    2016-01-01

    This work explores the characteristics and the seismogenic potential of crustal faults on the overriding plate in an area of high seismic hazard associated with the occurrence of subduction earthquakes and shallow earthquakes of the overriding plate. We present the results of geomorphic, structural, and fault kinematic analyses conducted on the convergent margin between the Cocos plate and the forearc region of the overriding North American plate, within the Guerrero sector of the Mexican subduction zone. We aim to determine the active tectonic processes in the forearc region of the subduction zone, using the river network pattern, topography, and structural data. We suggest that in the studied forearc region, both strike-slip and normal crustal faults sub-parallel to the subduction zone show evidence of activity. The left-lateral offsets of the main stream courses of the largest river basins, GPS measurements, and obliquity of plate convergence along the Cocos subduction zone in the Guerrero sector suggest the activity of sub-latitudinal left-lateral strike-slip faults. Notably, the regional left-lateral strike-slip fault that offsets the Papagayo River near the town of La Venta named "La Venta Fault" shows evidence of recent activity, corroborated also by GPS measurements (4-5 mm/year of sinistral motion). Assuming that during a probable earthquake the whole mapped length of this fault would rupture, it would produce an event of maximum moment magnitude Mw = 7.7. Even though only a few focal mechanism solutions indicate a stress regime relevant for reactivation of these strike-slip structures, we hypothesize that these faults are active and suggest two probable explanations: (1) these faults are characterized by long recurrence period, i.e., beyond the instrumental record, or (2) they experience slow slip events and/or associated fault creep. The analysis of focal mechanism solutions of small magnitude earthquakes in the upper plate, for the period between 1995

  5. DEFORMATION WAVES AS A TRIGGER MECHANISM OF SEISMIC ACTIVITY IN SEISMIC ZONES OF THE CONTINENTAL LITHOSPHERE

    S. I. Sherman

    2015-09-01

    Full Text Available Deformation waves as a trigger mechanism of seismic activity and migration of earthquake foci have been under discussion by researchers in seismology and geodynamics for over 50 years. Four sections of this article present available principal data on impacts of wave processes on seismicity and new data. The first section reviews analytical and experimental studies aimed at identification of relationships between wave processes in the lithosphere and seismic activity manifested as space-and-time migration of individual earthquake foci or clusters of earthquakes. It is concluded that with a systematic approach, instead of using a variety of terms to denote waves that trigger seismic process in the lithosphere, it is reasonable to apply the concise definition of ‘deformation waves’, which is most often used in fact.The second section contains a description of deformation waves considered as the trigger mechanism of seismic activity. It is concluded that a variety of methods are applied to identify deformation waves, and such methods are based on various research methods and concepts that naturally differ in sensitivity concerning detection of waves and/or impact of the waves on seismic process. Epicenters of strong earthquakes are grouped into specific linear or arc-shaped systems, which common criterion is the same time interval of the occurrence of events under analysis. On site the systems compose zones with similar time sequences, which correspond to the physical notion of moving waves (Fig. 9. Periods of manifestation of such waves are estimated as millions of years, and a direct consideration of the presence of waves and wave parameters is highly challenging. In the current state-of-the-art, geodynamics and seismology cannot provide any other solution yet.The third section presents a solution considering record of deformation waves in the lithosphere. With account of the fact that all the earthquakes with М≥3.0 are associated with

  6. Along strike variation of tremor activities and thermal structures in various subduction zones

    Yabe, S.; Ide, S.; Yoshioka, S.

    2012-12-01

    A family of slow earthquakes, e.g., deep low frequency tremors, low frequency earthquakes (LFEs), very low frequency earthquakes (VLFs) and slow slip events (SSEs), are observed in various subduction zones. These phenomena represent shear slip on the plate interface, and they are thought to be related to brittle-ductile transition behavior on the plate interface because they are often located near the transition zones of interplate coupling estimated from GPS data. Such slip behavior along the plate interface would be controlled by temperature. Furthermore, tremors are considered to be related to fluid dehydrated from the subducting slab, through temperature dependent chemical reactions. Therefore, tremors occurrences are expected to be influenced by temperature, though some studies have questioned about the relationship between tremor activity and temperature. Here we investigate the source locations of deep tremor using an envelope correlation method and compare them with the temperature and shear strength profiles along the plate interface calculated using a numerical model (Yoshioka and Sanshadokoro, 2002). The study areas include New Zealand, southern Chile, and Mexico, where tremor behavior changes significantly along the strike of the plate interface. Investigating such along-strike variation in individual subduction zone may clarify the temperature dependence of tremor because environmental conditions affecting tremor occurrence are similar, unlike the comparison between different subduction zones. In the Hikurangi subduction zone beneath the North Island, New Zealand, the depth of SSE are quite different along the strike, e.g., deeper in the central region and shallower in the northern region (e.g. Wallace and Beavan, 2010). We reanalyze tremors detected by previous studies (Kim et al., 2011; Ide, 2012) to estimate their absolute depth and confirm that tremors in North Island are on the plate interface in both the central and the northern regions. Thermal

  7. Bioorthogonal cyclization-mediated in situ self-assembly of small-molecule probes for imaging caspase activity in vivo.

    Ye, Deju; Shuhendler, Adam J; Cui, Lina; Tong, Ling; Tee, Sui Seng; Tikhomirov, Grigory; Felsher, Dean W; Rao, Jianghong

    2014-06-01

    Directed self-assembly of small molecules in living systems could enable a myriad of applications in biology and medicine, and already this has been used widely to synthesize supramolecules and nano/microstructures in solution and in living cells. However, controlling the self-assembly of synthetic small molecules in living animals is challenging because of the complex and dynamic in vivo physiological environment. Here we employ an optimized first-order bioorthogonal cyclization reaction to control the self-assembly of a fluorescent small molecule, and demonstrate its in vivo applicability by imaging caspase-3/7 activity in human tumour xenograft mouse models of chemotherapy. The fluorescent nanoparticles assembled in situ were imaged successfully in both apoptotic cells and tumour tissues using three-dimensional structured illumination microscopy. This strategy combines the advantages offered by small molecules with those of nanomaterials and should find widespread use for non-invasive imaging of enzyme activity in vivo. PMID:24848238

  8. Crust-mantle structure feature and the seismic activity of the main tectonic units in the North Tanlu fault zone

    2000-01-01

    Using recent data of geoscience transaction in Northeast China, the author analyses and studies the crust-upper mantle structure feature of the North Tanlu fault zone. The result shows the crust-mantle structure are obvious difference at both sides of the North Tanlu fault zone. The fault activity and segmentation are closely related with abruptly change zone of the crust-upper mantle structure. There is a clear mirror image relationship between the big geomorphic shape and asthenosphere undulate, the former restricts tectonic stability and tectonic style of different crustal units. The significantly strengthening seismicity of north set and south set in the North Tanlu fault zone just correspond to the low-velocity and high conductivity layer of crust-upper mantle. In the North Tanlu fault zone, the main controlling structure of the mid-strong seismic generally consists of the active fault sectors, whose crust-mantle structure is more complicated in rigidity massif.

  9. Small molecule inhibition of 6-phosphofructo-2-kinase suppresses t cell activation

    Telang Sucheta

    2012-05-01

    Full Text Available Abstract Background T cell activation is associated with a rapid increase in intracellular fructose-2,6-bisphosphate (F2,6BP, an allosteric activator of the glycolytic enzyme, 6-phosphofructo-1-kinase. The steady state concentration of F2,6BP in T cells is dependent on the expression of the bifunctional 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatases (PFKFB1-4 and the fructose-2,6-bisphosphatase, TIGAR. Of the PFKFB family of enzymes, PFKFB3 has the highest kinase:bisphosphatase ratio and has been demonstrated to be required for T cell proliferation. A small molecule antagonist of PFKFB3, 3-(3-pyridinyl-1-(4-pyridinyl-2-propen-1-one (3PO, recently has been shown to reduce F2,6BP synthesis, glucose uptake and proliferation in transformed cells. We hypothesized that the induction of PFKFB3 expression may be required for the stimulation of glycolysis in T cells and that exposure to the PFKFB3 antagonist, 3PO, would suppress T cell activation. Methods We examined PFKFB1-4 and TIGAR expression and F2,6BP concentration in purified CD3+ T cells stimulated with microbead-conjugated agonist antibodies specific for CD3 and the co-stimulatory receptor, CD28. We then determined the effect of 3PO on anti-CD3/anti-CD28-induced T cell activation, F2,6BP synthesis, 2-[1-14C]-deoxy-d-glucose uptake, lactate secretion, TNF-α secretion and proliferation. Finally, we examined the effect of 3PO administration on the development of delayed type hypersensitivity to methylated BSA and on imiquimod-induced psoriasis in mice. Results We found that purified human CD3+ T cells express PFKFB2, PFKFB3, PFKFB4 and TIGAR, and that anti-CD3/anti-CD28 conjugated microbeads stimulated a >20-fold increase in F2,6BP with a coincident increase in protein expression of the PFKFB3 family member and a decrease in TIGAR protein expression. We then found that exposure to the PFKFB3 small molecule antagonist, 3PO (1–10 μM, markedly attenuated the stimulation of F2,6BP

  10. High pressure chemistry of red phosphorus by photo-activated simple molecules

    High pressure (HP) is very effective in reducing intermolecular distances and inducing unexpected chemical reactions. In addition the photo-activation of the reactants in HP conditions can lead to very efficient and selective processes. The chemistry of phosphorus is currently based on the white molecular form. The red polymeric allotrope, despite more stable and much less toxic, has not attracted much attention so far. However, switching from the white to the red form would benefit any industrial procedure, especially from an environmental point of view. On the other side, water and ethanol are renewable, environmental friendly and largely available molecules, usable as reactants and photo-activators in HP conditions. Here we report a study on the HP photo-induced reactivity of red phosphorus with water and ethanol, showing the possibility of very efficient and selective processes, leading to molecular hydrogen and valuable phosphorus compounds. The reactions have been studied by means of FTIR and Raman spectroscopy and pressure has been generated using membrane Diamond (DAC) and Sapphire (SAC) anvil cells. HP reactivity has been activated by the two-photon absorption of near-UV wavelengths and occurred in total absence of solvents, catalysts and radical initiators, at room T and mild pressure conditions (0.2–1.5 GPa).

  11. High pressure chemistry of red phosphorus by photo-activated simple molecules

    Ceppatelli, M.; Fanetti, S.; Bini, R.; Caporali, M.; Peruzzini, M.

    2014-05-01

    High pressure (HP) is very effective in reducing intermolecular distances and inducing unexpected chemical reactions. In addition the photo-activation of the reactants in HP conditions can lead to very efficient and selective processes. The chemistry of phosphorus is currently based on the white molecular form. The red polymeric allotrope, despite more stable and much less toxic, has not attracted much attention so far. However, switching from the white to the red form would benefit any industrial procedure, especially from an environmental point of view. On the other side, water and ethanol are renewable, environmental friendly and largely available molecules, usable as reactants and photo-activators in HP conditions. Here we report a study on the HP photo-induced reactivity of red phosphorus with water and ethanol, showing the possibility of very efficient and selective processes, leading to molecular hydrogen and valuable phosphorus compounds. The reactions have been studied by means of FTIR and Raman spectroscopy and pressure has been generated using membrane Diamond (DAC) and Sapphire (SAC) anvil cells. HP reactivity has been activated by the two-photon absorption of near-UV wavelengths and occurred in total absence of solvents, catalysts and radical initiators, at room T and mild pressure conditions (0.2-1.5 GPa).

  12. Single molecule analysis of B cell receptor motion during signaling activation

    Rey Suarez, Ivan; Koo, Peter; Mochrie, Simon; Song, Wenxia; Upadhyaya, Arpita

    B cells are an essential part of the adaptive immune system. They patrol the body looking for signs of infection in the form of antigen on the surface of antigen presenting cells. The binding of the B cell receptor (BCR) to antigen induces signaling cascades that lead to B cell activation and eventual production of high affinity antibodies. During activation, BCR organize into signaling microclusters, which are platforms for signal amplification. The physical processes underlying receptor movement and aggregation are not well understood. Here we study the dynamics of single BCRs on activated murine primary B cells using TIRF imaging and single particle tracking. The tracks obtained are analyzed using perturbation expectation-maximization (pEM) a systems-level analysis that allows the identification of different short-time diffusive states from a set of single particle tracks. We identified five different diffusive states on wild type cells, which correspond to different molecular states of the BCR. By using actin polymerization inhibitors and mutant cells lacking important actin regulators we were able to identify the BCR molecule configuration associated with each diffusive state.

  13. Auroral Electrojet Indices Designed to Provide a Global Measure, 2.5-Minute Intervals, of Auroral Zone Magnetic Activity

    National Oceanic and Atmospheric Administration, Department of Commerce — The Auroral Electrojet index (AE) is designed to provide a global quantitative measure of auroral zone magnetic activity produced by enhanced ionospheric currents...

  14. Auroral Electrojet Index Designed to Provide a Global Measure, l-minute Intervals, of Auroral Zone Magnetic Activity

    National Oceanic and Atmospheric Administration, Department of Commerce — The Auroral Electrojet index (AE) is designed to provide a global quantitative measure of auroral zone magnetic activity produced by enhanced ionospheric currents...

  15. Studies of Active Ingredients in Cough Syrup by Capillary Zone Electrophoresis with Amperometric Detection

    ZHOU Tian-shu; WANG Ai-fang; WU Fang; SHI Guo-yue; FANG Yu-zhi

    2003-01-01

    The present paper covers a simple, reliable and reproducible method, based on capillary zone electrophoresis(CZE) with amperometric detection(AD), for the separation and the determination of ephedrine hydrochloride, promethazine hydrochloride and codeine phosphate. Under the optimal conditions, the three analytes were base-line separated completely within 16 min. Good linear relationships between the peak heights and the concentrations of the three analytes were obtained with the correlation coefficients better than 0.9993. The method was directly applied to the determination of the active ingredients in pharmaceutical preparations and the assay results were satisfactory.

  16. Oscillatory dynamics of the biologically active zone in in situ bioremediation

    Murray, Regan E.; Luce, Benjamin P.

    2002-10-01

    In situ bioremediation is a promising biotechnology for removing aqueous phase contaminants from groundwater. The system of three partial differential equations used to model bioremediation has a traveling wave solution which loses stability in a Hopf bifurcation, giving rise to oscillating fronts. To understand the origin of these oscillations, we construct a simplified model of the biologically active zone, a time delay differential equation with state-dependent delay. Despite its simplicity the new model mimics the dynamical characteristics of the bioremediation equations remarkably well and yields an approximate parametric expression for the oscillation onset point.

  17. Neotectonic Model of Formation of Oil and Gas Fields and Mineragenic Role of Geodynamic Active Zones

    I. S. Kopylov

    2014-03-01

    Full Text Available The article considers the importance of role of geodynamic active zones in formation of mineral deposits, their distribution, and mineragenic characteristics. Geodynamic model of formation of the oil and gas fields is developed. It reflects the evolution of formation of oil and gas fields and, after the stage of learning, allows predicting the petroleum potential of local areas. The model building procedure uses the integrated analysis of all the available information and determining the most informative indicators for forecasting the oil and gas reserves. The article presents an example of model worked out for oil and gas fields of the Perm Kray.

  18. Analysis of protein phosphorylation in nerve terminal reveals extensive changes in active zone proteins upon exocytosis.

    Kohansal-Nodehi, Mahdokht; Chua, John Je; Urlaub, Henning; Jahn, Reinhard; Czernik, Dominika

    2016-01-01

    Neurotransmitter release is mediated by the fast, calcium-triggered fusion of synaptic vesicles with the presynaptic plasma membrane, followed by endocytosis and recycling of the membrane of synaptic vesicles. While many of the proteins governing these processes are known, their regulation is only beginning to be understood. Here we have applied quantitative phosphoproteomics to identify changes in phosphorylation status of presynaptic proteins in resting and stimulated nerve terminals isolated from the brains of Wistar rats. Using rigorous quantification, we identified 252 phosphosites that are either up- or downregulated upon triggering calcium-dependent exocytosis. Particularly pronounced were regulated changes of phosphosites within protein constituents of the presynaptic active zone, including bassoon, piccolo, and RIM1. Additionally, we have mapped kinases and phosphatases that are activated upon stimulation. Overall, our study provides a snapshot of phosphorylation changes associated with presynaptic activity and provides a foundation for further functional analysis of key phosphosites involved in presynaptic plasticity. PMID:27115346

  19. Inhibition of Streptococcus mutans polysaccharide synthesis by molecules targeting glycosyltransferase activity

    Zhi Ren

    2016-04-01

    Full Text Available Glycosyltransferase (Gtf is one of the crucial virulence factors of Streptococcus mutans, a major etiological pathogen of dental caries. All the available evidence indicates that extracellular polysaccharide, particularly glucans produced by S. mutans Gtfs, contribute to the cariogenicity of dental biofilms. Therefore, inhibition of Gtf activity and the consequential polysaccharide synthesis may impair the virulence of cariogenic biofilms, which could be an alternative strategy to prevent the biofilm-related disease. Up to now, many Gtf inhibitors have been recognized in natural products, which remain the major and largely unexplored source of Gtf inhibitors. These include catechin-based polyphenols, flavonoids, proanthocyanidin oligomers, polymeric polyphenols, and some other plant-derived compounds. Metal ions, oxidizing agents, and some other synthetic compounds represent another source of Gtf inhibitors, with some novel molecules either discovered by structure-based virtual screening or synthesized based on key structures of known inhibitors as templates. Antibodies that inhibit one or more Gtfs have also been developed as topical agents. Although many agents have been shown to possess potent inhibitory activity against glucan synthesis by Gtfs, bacterial cell adherence, and caries development in animal models, much research remains to be performed to find out their mechanism of action, biological safety, cariostatic efficacies, and overall influence on the entire oral community. As a strategy to inhibit the virulence of cariogenic microbes rather than eradicate them from the microbial community, Gtf inhibition represents an approach of great potential to prevent dental caries.

  20. A novel molecule with notable activity against multi-drug resistant tuberculosis.

    Nair, Vasu; Okello, Maurice O; Mangu, Naveen K; Seo, Byung I; Gund, Machhindra G

    2015-03-15

    Multi-drug resistant tuberculosis (MDR-TB) is emerging as a serious global health problem, which has been elevated through co-infection involving HIV and MDR-Mtb. The discovery of new compounds with anti-MDR TB efficacy and favorable metabolism profiles is an important scientific challenge. Using computational biology and ligand docking data, we have conceived a multifunctional molecule, 2, as a potential anti-MDR TB agent. This compound was produced through a multi-step synthesis. It exhibited significant in vitro activity against MDR-TB (MIC 1.56μg/mL) and its half-life (t1/2) in human liver microsomes was 14.4h. The metabolic profiles of compound 2 with respect to human cytochrome P450 (CYP) and uridine 5'-diphospho-glucuronosyltransferase (UGT) isozymes were favorable. Compound 2 also had relatively low in vitro cytotoxicity in uninfected macrophages. It displayed synergistic behavior against MDR-TB in combination with PA-824. Interestingly, compound 2 also displayed in vitro anti-HIV activity. PMID:25677656

  1. Therapeutic potential of an orally effective small molecule inhibitor of plasminogen activator inhibitor for asthma.

    Liu, Rui-Ming; Eldridge, Stephanie; Watanabe, Nobuo; Deshane, Jessy; Kuo, Hui-Chien; Jiang, Chunsun; Wang, Yong; Liu, Gang; Schwiebert, Lisa; Miyata, Toshio; Thannickal, Victor J

    2016-02-15

    Asthma is one of the most common respiratory diseases. Although progress has been made in our understanding of airway pathology and many drugs are available to relieve asthma symptoms, there is no cure for chronic asthma. Plasminogen activator inhibitor 1 (PAI-1), a primary inhibitor of tissue-type and urokinase-type plasminogen activators, has pleiotropic functions besides suppression of fibrinolysis. In this study, we show that administration of TM5275, an orally effective small-molecule PAI-1 inhibitor, 25 days after ovalbumin (OVA) sensitization-challenge, significantly ameliorated airway hyperresponsiveness in an OVA-induced chronic asthma model. Furthermore, we show that TM5275 administration significantly attenuated OVA-induced infiltration of inflammatory cells (neutrophils, eosinophils, and monocytes), the increase in the levels of OVA-specific IgE and Th2 cytokines (IL-4 and IL-5), the production of mucin in the airways, and airway subepithelial fibrosis. Together, the results suggest that the PAI-1 inhibitor TM5275 may have therapeutic potential for asthma through suppressing eosinophilic allergic response and ameliorating airway remodeling. PMID:26702150

  2. Small-molecule nociceptin receptor agonist ameliorates mast cell activation and pain in sickle mice.

    Vang, Derek; Paul, Jinny A; Nguyen, Julia; Tran, Huy; Vincent, Lucile; Yasuda, Dennis; Zaveri, Nurulain T; Gupta, Kalpna

    2015-12-01

    Treatment of pain with morphine and its congeners in sickle cell anemia is suboptimal, warranting the need for analgesics devoid of side effects, addiction and tolerance liability. Small-molecule nociceptin opioid receptor ligands show analgesic efficacy in acute and chronic pain models. We show that AT-200, a high affinity nociceptin opioid receptor agonist with low efficacy at the mu opioid receptor, ameliorated chronic and hypoxia/reoxygenation-induced mechanical, thermal and deep tissue/musculoskeletal hyperalgesia in HbSS-BERK sickle mice. The antinociceptive effect of AT-200 was antagonized by SB-612111, a nociceptin opioid receptor antagonist, but not naloxone, a non-selective mu opioid receptor antagonist. Daily 7-day treatment with AT-200 did not develop tolerance and showed a sustained anti-nociceptive effect, which improved over time and led to reduced plasma serum amyloid protein, neuropeptides, inflammatory cytokines and mast cell activation in the periphery. These data suggest that AT-200 ameliorates pain in sickle mice via the nociceptin opioid receptor by reducing inflammation and mast cell activation without causing tolerance. Thus, nociceptin opioid receptor agonists are promising drugs for treating pain in sickle cell anemia. PMID:26294734

  3. Simultaneous measurement of DNA motor protein conformation and activity with combined optical trap and single-molecule fluorescence

    Chemla, Yann

    2013-03-01

    We present single-molecule measurements of Superfamily 1 UvrD helicase DNA unwinding that reveal directly how helicase stoichiometry and conformation regulate motor activity. Using a new instrument that combines high resolution optical tweezers with single-molecule fluorescence microscopy, we record DNA unwinding activity with base pair-scale resolution (via optical tweezers) simultaneously with helicase stoichiometry and conformation (via fluorescence). Quantifying the fluorescence signal from labeled UvrD, we observe that pairs of UvrD molecules are required for long distance unwinding but that individual molecules exhibit limited, non-processive unwinding activity. UvrD is also known to exhibit two different conformations, `closed' and `open', based on the orientation of its 2B regulatory domain. The function of these conformations has remained elusive. Measuring the fluorescence of FRET labeled proteins, we detect directly the conformation of the 2B domain of individual UvrD molecules during unwinding activity. We observe that UvrD is in the `closed' conformation during DNA unwinding but surprisingly switches to the `open' conformation upon reversal of helicase direction, i.e. when UvrD switches strands and translocates on the opposing strand with the DNA junction rezipping behind it. We hypothesize that the 2B domain acts as a conformational switch that controls DNA unwinding vs. re-annealing. Work supported by NSF (PHY-082261, Center for the Physics of Living Cells) and NIH (R21 RR025341A)

  4. Impacts of stellar evolution and dynamics on the habitable zone: The role of rotation and magnetic activity

    Florian, Gallet; Louis, Amard; Sacha, Brun; Ana, Palacios; Stephane, Mathis

    2016-01-01

    In this article, we aim to provide the community with the dependence of the habitable zone upon the stellar mass, metallicity, rotation, and for various prescriptions of the limits of the habitable zone. We use the STAREVOL code to study the evolution of the habitable zone and of the continuously habitable zone limits. Mass and metallicity are the stellar parameters that have the most dramatic effects on the habitable zone limits. Conversely, for a given stellar mass and metallicity, stellar rotation has only a marginal effect on these limits and does not modify the width of the habitable zone. The evolution of the habitable zone limits is also correlated to the evolution of the stellar activity (through the Rossby number) that depends on the stellar mass considered. While the magnetic activity has negligible consequence in the case of more massive stars, these effects may have a strong impact on the habitability of a planet around M dwarf stars. Thus, stellar activity cannot be neglected and may have strong ...

  5. Antimicrobial activity of innate immune molecules against Streptococcus pneumoniae, Moraxella catarrhalis and nontypeable Haemophilus influenzae

    Teufert Karen

    2004-05-01

    Full Text Available Abstract Background Despite its direct connection to the nasopharynx which harbors otitis media pathogens as part of its normal flora, the middle ear cavity is kept free of these bacteria by as yet unknown mechanisms. Respiratory mucosal epithelia, including those of the middle ear and eustachian tube, secrete antimicrobial effectors including lysozyme, lactoferrin and β defensins-1 and -2. To elucidate the role of these innate immune molecules in the normal defense and maintenance of sterility of respiratory mucosa such as that of the middle ear, we assessed their effect on the respiratory pathogens nontypeable Haemophilus influenzae (NTHi 12, Moraxella catarrhalis 035E, and Streptococcus pneumoniae 3, and 6B. Methods Two assay methods, the radial assay and the liquid broth assay, were employed for testing the antimicrobial activity of the molecules. This was done in order to minimize the possibility that the observed effects were artifacts of any single assay system employed. Also, transmission electron microscopy (TEM was employed to evaluate the effect of antimicrobial innate immune molecules on OM pathogens. For the statistical analysis of the data, Student's t-test was performed. Results Results of the radial diffusion assay showed that β defensin-2 was active against all four OM pathogens tested, while treatment with β defensin-1 appeared to only affect M. catarrhalis. The radial assay results also showed that lysozyme was quite effective against S. pneumoniae 3 and 6B and was partially bacteriostatic/bactericidal against M. catarrhalis. Lysozyme however, appeared not to affect the growth of NTHi. Thus, lysozyme seems to have a more pronounced impact on the growth of the Gram-positive S. pneumoniae as compared to that of Gram-negative pathogens. Lactoferrin on the other hand, enhanced the growth of the bacteria tested. The results of the radial assays were confirmed using liquid broth assays for antimicrobial activity, and showed that

  6. Characteristics of Relocated Quiet Zones Using Virtual Microphone Algorithm in an Active Headrest System

    Seokhoon Ryu

    2016-01-01

    Full Text Available This study displays theoretical and experimental investigation on the characteristics of the relocated zone of quiet by a virtual microphone (VM based filtered-x LMS (FxLMS algorithm which can be embedded in a real-time digital controller for an active headrest system. The attenuation changes at the relocated zones of quiet by the variation of the distance between the ear and the error microphone are mainly examined. An active headrest system was implemented for the control experiment at a chair and consists of two (left and right secondary loudspeakers, two error microphones, two observer microphones at ear positions in a HATS, and other electronics including a dSPACE 1401 controller. The VM based FxLMS algorithm achieved an attenuation of about 22 dB in the control experiment against a narrowband primary noise by the variation of the distance between the ear and the error microphone. The important factors for the algorithm are discussed as well.

  7. Study on Integrated Recurrence Behaviors of Strong Earthquakes Along Entire Active Fault Zones in the Sichuan-Yunnan Region, China

    Yi Guixi; Wen Xueze; Xu Xiwei

    2003-01-01

    Based on historical earthquake data, we use statistical methods to study integrated recurrencebehaviors of strong earthquakes along 7 selected active fault zones in the Sichuan-Yunnanregion. The results show that recurrences of strong earthquakes in the 7 fault zones displaynear-random, random and clustering behaviors. The recurrence processes are never quasi-periodic, and are neither strength-time nor time-strength dependent. The more independentsegments for strong earthquake rupturing a fault zone has, the more complicated thecorresponding recurrence process is. And relatively active periods and quiescent periods forearthquake activity occur alternatively. Within the active periods, the distribution ofrecurrence time intervals between earthquakes has relatively large discretion, and can bemodelled well by a Weibull distribution. The time distribution of the quiescent periods hasrelatively small discretion, and can be approximately described by some distributions as thenormal. Both the durations of the active periods and the numbers of strong earthquakes withinthe active periods vary obviously cycle by cycle, leading to the relatively active periods havingnever repeated quasi-periodically. Therefore, the prohabilistic assessment for middle- and long-term seismic hazard for entireties of active fault zones based on data of historical strongearthquakes on the fault zones still faces difficulty.

  8. Proapoptotic and antiinvasive activity of Rac1 small molecule inhibitors on malignant glioma cells

    Cardama GA

    2014-10-01

    Full Text Available Georgina A Cardama,1 Nazareno Gonzalez,1 Matias Ciarlantini,2 Lucia Gandolfi Donadío,2 María Julieta Comin,2 Daniel F Alonso,1 Pablo Lorenzano Menna,1,* Daniel E Gomez1,*1Laboratory of Molecular Oncology, National University of Quilmes, Buenos Aires, Argentina; 2Laboratory of Organic Synthesis, Center of Research and Development in Chemistry, National Institute of Industrial Technology, San Martín, Argentina, *These authors contributed equally to this workAbstract: Malignant gliomas are characterized by an intrinsic ability to invade diffusely throughout the normal brain tissue. This feature contributes mainly to the failure of existing therapies. Deregulation of small GTPases signaling, in particular Rac1 activity, plays a key role in the invasive phenotype of gliomas. Here we report the effect of ZINC69391, a specific Rac1 inhibitor developed by our group, on human glioma cell lines LN229 and U-87 MG. ZINC69391 is able to interfere with the interaction of Rac1 with Dock180, a relevant Rac1 activator in glioma invasion, and to reduce Rac1-GTP levels. The kinase Pak1, a downstream effector of Dock180–Rac1 signaling, was also downregulated upon ZINC69391 treatment. ZINC69391 reduced cell proliferation, arrested cells in G1 phase, and triggered apoptosis in glioma cells. Importantly, ZINC69391 dramatically affected cell migration and invasion in vitro, interfering with actin cytoskeleton dynamics. We also evaluated the effect of analog 1A-116, a compound derived from ZINC69391 structure. 1A-116 showed an improved antiproliferative and antiinvasive activity on glioma cells. These findings encourage further preclinical testing in clinically relevant animal models.Keywords: GTPases. invasion, Dock180, small molecule

  9. Antiviral activity of a small molecule deubiquitinase inhibitor occurs via induction of the unfolded protein response.

    Jeffrey W Perry

    Full Text Available Ubiquitin (Ub is a vital regulatory component in various cellular processes, including cellular responses to viral infection. As obligate intracellular pathogens, viruses have the capacity to manipulate the ubiquitin (Ub cycle to their advantage by encoding Ub-modifying proteins including deubiquitinases (DUBs. However, how cellular DUBs modulate specific viral infections, such as norovirus, is poorly understood. To examine the role of DUBs during norovirus infection, we used WP1130, a small molecule inhibitor of a subset of cellular DUBs. Replication of murine norovirus in murine macrophages and the human norovirus Norwalk virus in a replicon system were significantly inhibited by WP1130. Chemical proteomics identified the cellular DUB USP14 as a target of WP1130 in murine macrophages, and pharmacologic inhibition or siRNA-mediated knockdown of USP14 inhibited murine norovirus infection. USP14 is a proteasome-associated DUB that also binds to inositol-requiring enzyme 1 (IRE1, a critical mediator of the unfolded protein response (UPR. WP1130 treatment of murine macrophages did not alter proteasome activity but activated the X-box binding protein-1 (XBP-1 through an IRE1-dependent mechanism. In addition, WP1130 treatment or induction of the UPR also reduced infection of other RNA viruses including encephalomyocarditis virus, Sindbis virus, and La Crosse virus but not vesicular stomatitis virus. Pharmacologic inhibition of the IRE1 endonuclease activity partially rescued the antiviral effect of WP1130. Taken together, our studies support a model whereby induction of the UPR through cellular DUB inhibition blocks specific viral infections, and suggest that cellular DUBs and the UPR represent novel targets for future development of broad spectrum antiviral therapies.

  10. Fault mirrors in seismically active fault zones: A fossil of small earthquakes at shallow depths

    Kuo, Li-Wei; Song, Sheng-Rong; Suppe, John; Yeh, En-Chao

    2016-03-01

    Fault mirrors (FMs) are naturally polished and glossy fault slip surfaces that can record seismic deformation at shallow depths. They are important for investigating the processes controlling dynamic fault slip. We characterize FMs in borehole samples from the hanging wall damage zone of the active Hsiaotungshi reverse fault, Taiwan. Here we report the first documented occurrence of the combination of silica gel and melt patches coating FMs, with the silica gel resembling those observed on experimentally formed FMs that were cataclastically generated. In addition, the melt patches, which are unambiguous indicators of coseismic slip, suggest that the natural FMs were produced at seismic rates, presumably resulting from flash heating at asperities on the slip surfaces. Since flash heating is efficient at small slip, we propose that these natural FMs represent fossils of small earthquakes, formed in either coseismic faulting and folding or aftershock deformation in the active Taiwan fold-and-thrust belt.

  11. Activation of human ether-a-go-go related gene (hERG) potassium channels by small molecules

    Ping-zheng ZHOU; Joseph BABCOCK; Lian-qing LIU; Min LI; Zhao-bing GAO

    2011-01-01

    Human ether-a-go-go related gene (hERG) potassium (K+) channels play a critical role in cardiac action potential repolarlzatlon. Mutations that reduce hERG conductance or surface expression may cause congenital long QT syndrome (LQTS). Moreover, the channels can be inhibited by structurally diverse small molecules, resulting in an acquired form of LQTS. Consequently, small molecules that increase the hERG current may be of value for treatment of LQTS. So far, nine hERG activators have been reported. The aim of this review is to discuss recent advances concerning the identification and action mechanism of hERG activators.

  12. Active faults in the deformation zone off Noto Peninsula, Japan, revealed by high- resolution seismic profiles

    Inoue, T.; Okamura, Y.; Murakami, F.; Kimura, H.; Ikehara, K.

    2008-12-01

    Recently, a lot of earthquakes occur in Japan. The deformation zone which many faults and folds have concentrated exists on the Japan Sea side of Japan. The 2007 Noto Hanto Earthquake (MJMA 6.9) and 2007 Chuetsu-oki Earthquake (MJMA 6.8) were caused by activity of parts of faults in this deformation zone. The Noto Hanto Earthquake occurred on 25 March, 2007 under the northwestern coast of Noto Peninsula, Ishikawa Prefecture, Japan. This earthquake is located in Quaternary deformation zone that is continued from northern margin of Noto Peninsula to southeast direction (Okamura, 2007a). National Institute of Advanced Industrial Science and Technology (AIST) carried out high-resolution seismic survey using Boomer and 12 channels short streamer cable in the northern part off Noto Peninsula, in order to clarify distribution and activities of active faults in the deformation zone. A twelve channels short streamer cable with 2.5 meter channel spacing developed by AIST and private corporation is designed to get high resolution seismic profiles in shallow sea area. The multi-channel system is possible to equip on a small fishing boat, because the data acquisition system is based on PC and the length of the cable is short and easy to handle. Moreover, because the channel spacing is short, this cable is very effective for a high- resolution seismic profiling survey in the shallow sea, and seismic data obtained by multi-channel cable can be improved by velocity analysis and CDP stack. In the northern part off Noto Peninsula, seismic profiles depicting geologic structure up to 100 meters deep under sea floor were obtained. The most remarkable reflection surface recognized in the seismic profiles is erosion surface at the Last Glacial Maximum (LGM). In the western part, sediments about 30 meters (40 msec) thick cover the erosional surface that is distributed under the shelf shallower than 100m in depth and the sediments thin toward offshore and east. Flexures like deformation in

  13. Endoplasmic reticulum stress-independent activation of unfolded protein response kinases by a small molecule ATP-mimic.

    Mendez, Aaron S; Alfaro, Jennifer; Morales-Soto, Marisol A; Dar, Arvin C; McCullagh, Emma; Gotthardt, Katja; Li, Han; Acosta-Alvear, Diego; Sidrauski, Carmela; Korennykh, Alexei V; Bernales, Sebastian; Shokat, Kevan M; Walter, Peter

    2015-01-01

    Two ER membrane-resident transmembrane kinases, IRE1 and PERK, function as stress sensors in the unfolded protein response. IRE1 also has an endoribonuclease activity, which initiates a non-conventional mRNA splicing reaction, while PERK phosphorylates eIF2α. We engineered a potent small molecule, IPA, that binds to IRE1's ATP-binding pocket and predisposes the kinase domain to oligomerization, activating its RNase. IPA also inhibits PERK but, paradoxically, activates it at low concentrations, resulting in a bell-shaped activation profile. We reconstituted IPA-activation of PERK-mediated eIF2α phosphorylation from purified components. We estimate that under conditions of maximal activation less than 15% of PERK molecules in the reaction are occupied by IPA. We propose that IPA binding biases the PERK kinase towards its active conformation, which trans-activates apo-PERK molecules. The mechanism by which partial occupancy with an inhibitor can activate kinases may be wide-spread and carries major implications for design and therapeutic application of kinase inhibitors. PMID:25986605

  14. Small Molecule Activation by Intermolecular Zr(IV)-Phosphine Frustrated Lewis Pairs.

    Metters, Owen J; Forrest, Sebastian J K; Sparkes, Hazel A; Manners, Ian; Wass, Duncan F

    2016-02-17

    We report intermolecular transition metal frustrated Lewis pairs (FLPs) based on zirconocene aryloxide and phosphine moieties that exhibit a broad range of small molecule activation chemistry that has previously been the preserve of only intramolecular pairs. Reactions with D2, CO2, THF, and PhCCH are reported. By contrast with previous intramolecular examples, these systems allow facile access to a variety of steric and electronic characteristics at the Lewis acidic and Lewis basic components, with the three-step syntheses of 10 new intermolecular transition metal FLPs being reported. Systematic variation to the phosphine Lewis base is used to unravel steric considerations, with the surprising conclusion that phosphines with relatively small Tolman steric parameters not only give highly reactive FLPs but are often seen to have the highest selectivity for the desired product. DOSY NMR spectroscopic studies on these systems reveal for the first time the nature of the Lewis acid/Lewis base interactions in transition metal FLPs of this type. PMID:26788963

  15. Evaluation of Activated Leukocyte Cell Adhesion Molecule as a Biomarker for Breast Cancer in Egyptian Patients

    In this study, serum activated leukocyte cell adhesion molecule (ALCAM) levels were evaluated in 41 primary breast cancer patients and 20 healthy females, and its diagnostic value was quantified, and compared with those of carbohydrate antigen 15-3 (CA15-3) and carcinoembryonic antigen (CEA). Also, its prognostic value was examined. Serum ALCAM levels were also evaluated before and after surgical treatment. Serum levels of ALCAM and CA 15-3 were significantly higher in breast cancer patients than healthy controls (P=0.002, P=0.043 respectively), but the difference in serum CEA levels did not reach statistical significance. Serum ALCAM levels had significant area under the curve (AUC) (P=0.002), but serum levels of CA 15-3 and CEA had nonsignificant AUCs, and various combinations between them did not result in any improvement. A significant association was found between serum levels of ALCAM and CEA with age and menopausal status in breast cancer patients. Non-significant difference was shown in serum levels of ALCAM, CA 15-3 and CEA before and after surgical treatment. In conclusion, this study suggests that serum ALCAM may represent a novel diagnostic bio marker for breast cancer

  16. Kinetics of T cell-activation molecules in response to Mycobacterium tuberculosis antigens

    Antas Paulo RZ

    2002-01-01

    Full Text Available The phenotypic features acquired subsequent to antigen-specific stimulation in vitro were evaluated by means of the kinetic expressions of CD69 and CD25 activation molecules on T lymphocytes and assayed by flow cytometry in response to PPD, Ag85B, and ferritin in PPD-positive healthy control individuals. In response to PHA, CD69 staining on both CD4+ and CD8+ T cells became initially marked after 4 h, peaked at 24 h, and quickly decreased after 120 h. For CD25, a latter expression was detected around 8 h, having increased after 96 h. As expected, the response rate to the mycobacterial antigens was much lower than that to the mitogen. Positive staining was high after 96 h for CD25 and after 24 h for CD69. CD69 expression was significantly enhanced (p < 0.05 on CD8+ as compared to CD4+ T cells. High levels were also found between 96-120 h. Regarding Ag85B, CD25+ cells were mostly CD4+ instead of CD8+ T cells. Moreover, in response to ferritin, a lower CD25 expression was noted. The present data will allow further characterization of the immune response to new mycobacterial-specific antigens and their evaluation for possible inclusion in developing new diagnostic techniques for tuberculosis as well in a new vaccine to prevent the disease.

  17. The new generation drug candidate molecules: Spectral, electrochemical, DNA-binding and anticancer activity properties

    Gölcü, Ayşegül; Muslu, Harun; Kılıçaslan, Derya; Çeşme, Mustafa; Eren, Özge; Ataş, Fatma; Demirtaş, İbrahim

    2016-09-01

    The new generation drug candidate molecules [Cu(5-Fu)2Cl2H2O] (NGDCM1) and [Zn(5-Fu)2(CH3COO)2] (NGDCM2) were obtained from the reaction of copper(II) and zinc(II) salts with the anticancer drug 5-fluoracil (5-Fu). These compounds have been characterized by spectroscopic and analytical techniques. Thermal behavior of the compounds were also investigated. The electrochemical properties of the compounds have been investigated by cyclic voltammetry (CV) using glassy carbon electrode. The biological activity of the NGDCM1 and NGDCM2 has been evaluated by examining their ability to bind to fish sperm double strand DNA (FSdsDNA) with UV spectroscopy. UV studies of the interaction of the 5-Fu and metal derivatives with FSdsDNA have shown that these compounds can bind to FSdsDNA. The binding constants of the compounds with FSdsDNA have also been calculated. Thermal decomposition of the compounds lead to the formation of CuO and ZnO as final products. The effect of proliferation 5-Fu, NGDCM1 and NGDCM2 were examined on the HeLa cells using real-time cell analyzer with three different concentrations.

  18. Dimeric aluminum-phosphorus compounds as masked frustrated Lewis pairs for small molecule activation.

    Roters, Steffi; Appelt, Christian; Westenberg, Hauke; Hepp, Alexander; Slootweg, J Chris; Lammertsma, Koop; Uhl, Werner

    2012-08-14

    Hydroalumination of aryldialkynylphosphines RP(C≡C-(t)Bu)(2) (R = Ph, Mes) with equimolar quantities of diethylaluminum hydride afforded mixed alkenyl-alkynyl cyclic dimers in which the dative aluminum-phosphorus bonds are geminal to the exocyclic alkenyl groups. Addition of triethylaluminum to isolated 1 (R = Ph) or to the in situ generated species (R = Mes) caused diethylaluminum ethynide elimination to yield the arylethylphosphorus dimers 2 and 3. These possess a chair-like Al(2)C(2)P(2) heterocycle with intermolecular Al-P interactions. The boat conformation (4) was obtained by the reaction of (t)Bu-P(C≡C-(t)Bu)(2) with di(tert-butyl)aluminum hydride. Despite being dimeric, 2 behaves as a frustrated Lewis pair and activates small molecules. The reaction with carbon dioxide gave cis/trans isomeric AlPC(2)O heterocycles that differ only by the configuration of the exocyclic alkenyl unit. Four isomers resulted from the reaction with phenyl isocyanate. This is caused by cis/trans isomerization of the initial C=O adduct and subsequent rearrangement to the AlPC(2)N heterocycle, being the C=N adduct. PMID:22411491

  19. NMDA modulates oligodendrocyte differentiation of subventricular zone cells through PKC activation

    Fabio eCavaliere

    2013-12-01

    Full Text Available Multipotent cells from the juvenile subventricular zone (SVZ possess the ability to differentiate into new neural cells. Depending on local signals, SVZ can generate new neurons, astrocytes or oligodendrocytes. We previously demonstrated that activation of NMDA receptors in SVZ progenitors increases the rate of oligodendrocyte differentiation. Here we investigated the mechanisms involved in NMDA receptor-dependent differentiation. Using functional studies performed with the reporter gene luciferase we found that activation of NMDA receptor stimulates PKC. In turn, stimulation of PKC precedes the activation of NADPH oxidase (NOX as demonstrated by translocation of the p67phox subunit to the cellular membrane. We propose that NOX2 is involved in the transduction of the signal from NMDA receptors through PKC activation as the inhibitor gp91 reduced their pro-differentiation effect. In addition, our data and that from other groups suggest that signaling through the NMDA receptor/PKC/NOX2 cascade generates ROS that activate the PI3/mTOR pathway and finally leads to the generation of new oligodendrocytes.

  20. Determination of the Absolute Number of Cytokine mRNA Molecules within Individual Activated Human T Cells

    Karr, Laurel J.; Marshall, Gwen; Hockett, Richard D.; Bucy, R. Pat; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    A primary function of activated T cells is the expression and subsequent secretion of cytokines, which orchestrate the differentiation of other lymphocytes, modulate antigen presenting cell activity, and alter vascular endothelium to mediate an immune response. Since many features of immune regulation probably result from modest alterations of endogenous rates of multiple interacting processes, quantitative analysis of the frequency and specific activity of individual T cells is critically important. Using a coordinated set of quantitative methods, the absolute number of molecules of several key cytokine mRNA species in individual T cells has been determined. The frequency of human blood T cells activated in vitro by mitogens and recall protein antigens was determined by intracellular cytokine protein staining, in situ hybridization for cytokine mRNA, and by limiting dilution analysis for cytokine mRNA+ cells. The absolute number of mRNA molecules was simultaneously determined in both homogenates of the entire population of cells and in individual cells obtained by limiting dilution, using a quantitative, competitive RT-PCR assay. The absolute numbers of mRNA molecules in a population of cells divided by the frequency of individual positive cells, yielded essentially the same number of mRNA molecules per cell as direct analysis of individual cells by limiting dilution analysis. Mean numbers of mRNA per positive cell from both mitogen and antigen activated T cells, using these stimulation conditions, were 6000 for IL-2, 6300 for IFN-gamma, and 1600 for IL-4.

  1. Outcome of early active mobilization after flexor tendons repair in zones II-V in hand

    Saini Narender

    2010-01-01

    Full Text Available Background: The functional outcome of a flexor tendon injury after repair depends on multiple factors. The postoperative management of tendon injuries has paved a sea through many mobilization protocols. The improved understanding of splinting techniques has promoted the understanding and implication of these mobilization protocols. We conducted a study to observe and record the results of early active mobilization of repaired flexor tendons in zones II-V. Materials and Methods: 25 cases with 75 digits involving 129 flexor tendons including 8 flexor pollicis longus (FPL tendons in zones II-V of thumb were subjected to the early active mobilization protocol. Eighteen (72% patients were below 30 years of age. Twenty-four cases (96% sustained injury by sharp instrument either accidentally or by assault. Ring and little finger were involved in 50% instances. In all digits, either a primary repair (n=26 or a delayed primary repair (n=49 was done. The repair was done with the modified Kessler core suture technique with locking epitendinous sutures with a knot inside the repair site, using polypropylene 3-0/4-0 sutures. An end-to-end repair of the cut nerves was done under loupe magnification using a 6-0/8-0 polyamide suture. The rehabilitation program adopted was a modification of Kleinert′s regimen, and Silfverskiold regimen. The final assessment was done at 14 weeks post repair using the Louisville system of Lister et al. Results: Eighteen of excellent results were attributed to ring and little fingers where there was a flexion lag of < 1 cm and an extension lag of < 15o. FPL showed 75% (n=6 excellent flexion. 63% (n=47 digits showed excellent results whereas good results were seen in 19% (n=14 digits. Nine percent (n=7 digits showed fair and the same number showed poor results. The cases where the median (n=4 or ulnar nerve (n=6 or both (n=3 were involved led to some deformity (clawing/ape thumb at 6 months postoperatively. The cases with digital

  2. Transcriptome analysis of tomato flower pedicel tissues reveals abscission zone-specific modulation of key meristem activity genes.

    Xiang Wang

    Full Text Available Tomato flower abscises at the anatomically distinct abscission zone that separates the pedicel into basal and apical portions. During abscission, cell separation occurs only at the abscission zone indicating distinctive molecular regulation in its cells. We conducted a transcriptome analysis of tomato pedicel tissues during ethylene promoted abscission. We found that the abscission zone was the most active site with the largest set of differentially expressed genes when compared with basal and apical portions. Gene Ontology analyses revealed enriched transcription regulation and hydrolase activities in the abscission zone. We also demonstrate coordinated responses of hormone and cell wall related genes. Besides, a number of ESTs representing homologs of key Arabidopsis shoot apical meristem activity genes were found to be preferentially expressed in the abscission zone, including WUSCHEL (WUS, KNAT6, LATERAL ORGAN BOUNDARIES DOMAIN PROTEIN 1(LBD1, and BELL-like homeodomain protein 1 (BLH1, as well as tomato axillary meristem genes BLIND (Bl and LATERAL SUPPRESSOR (Ls. More interestingly, the homologs of WUS and the potential functional partner OVATE FAMILIY PROTEIN (OFP were subsequently down regulated during abscission while Bl and AGL12 were continuously and specifically induced in the abscission zone. The expression patterns of meristem activity genes corroborate the idea that cells of the abscission zone confer meristem-like nature and coincide with the course of abscission and post-abscission cell differentiation. Our data therefore propose a possible regulatory scheme in tomato involving meristem genes that may be required not only for the abscission zone development, but also for abscission.

  3. An enzymatic deconjugation method for the analysis of small molecule active drugs on antibody-drug conjugates.

    Li, Yi; Gu, Christine; Gruenhagen, Jason; Yehl, Peter; Chetwyn, Nik P; Medley, Colin D

    2016-01-01

    Antibody-drug conjugates (ADCs) are complex therapeutic agents that use the specific targeting properties of antibodies and the highly potent cytotoxicity of small molecule drugs to selectively eliminate tumor cells while limiting the toxicity to normal healthy tissues. Two critical quality attributes of ADCs are the purity and stability of the active small molecule drug linked to the ADC, but these are difficult to assess once the drug is conjugated to the antibody. In this study, we report a enzyme deconjugation approach to cleave small molecule drugs from ADCs, which allows the drugs to be subsequently characterized by reversed-phase high performance liquid chromatography. The model ADC we used in this study utilizes a valine-citrulline linker that is designed to be sensitive to endoproteases after internalization by tumor cells. We screened several proteases to determine the most effective enzyme. Among the 3 cysteine proteases evaluated, papain had the best efficiency in cleaving the small molecule drug from the model ADC. The deconjugation conditions were further optimized to achieve complete cleavage of the small molecule drug. This papain deconjugation approach demonstrated excellent specificity and precision. The purity and stability of the active drug on an ADC drug product was evaluated and the major degradation products of the active drug were identified. The papain deconjugation method was also applied to several other ADCs, with the results suggesting it could be applied generally to ADCs containing a valine-citrulline linker. Our results indicate that the papain deconjugation method is a powerful tool for characterizing the active small molecule drug conjugated to an ADC, and may be useful in ensuring the product quality, efficacy and the safety of ADCs. PMID:26891281

  4. Activated platelets form protected zones of adhesion on fibrinogen and fibronectin-coated surfaces

    1993-01-01

    Leukocytes form zones of close apposition when they adhere to ligand- coated surfaces. Because plasma proteins are excluded from these contact zones, we have termed them protected zones of adhesion. To determine whether platelets form similar protected zones of adhesion, gel-filtered platelets stimulated with thrombin or ADP were allowed to adhere to fibrinogen- or fibronectin-coated surfaces. The protein- coated surfaces with platelets attached were stained with either fluorochrome-conjugate...

  5. Zeolite H-BEA catalysed multicomponent reaction: One-pot synthesis of amidoalkyl naphthols - Biologically active drug-like molecules

    Sunil R Mistry; Rikesh S Joshi; Kalpana C Maheria

    2011-07-01

    Zeolite has been used as an efficient and a novel heterogeneous catalyst for one-pot synthesis of biologically active drug-like molecules, amidoalkyl naphthols. This green route involves multicomponent reaction of 2-naphthol, aromatic aldehydes and amide in the presence of a catalytic amount of zeolite H-Beta (H-BEA) under solvent reflux as well as solvent-free conditions.

  6. Machine learning models identify molecules active against the Ebola virus in vitro [version 1; referees: 2 approved

    Sean Ekins

    2015-10-01

    Full Text Available The search for small molecule inhibitors of Ebola virus (EBOV has led to several high throughput screens over the past 3 years. These have identified a range of FDA-approved active pharmaceutical ingredients (APIs with anti-EBOV activity in vitro and several of which are also active in a mouse infection model. There are millions of additional commercially-available molecules that could be screened for potential activities as anti-EBOV compounds. One way to prioritize compounds for testing is to generate computational models based on the high throughput screening data and then virtually screen compound libraries. In the current study, we have generated Bayesian machine learning models with viral pseudotype entry assay and the EBOV replication assay data. We have validated the models internally and externally. We have also used these models to computationally score the MicroSource library of drugs to select those likely to be potential inhibitors. Three of the highest scoring molecules that were not in the model training sets, quinacrine, pyronaridine and tilorone, were tested in vitro and had EC50 values of 350, 420 and 230 nM, respectively. Pyronaridine is a component of a combination therapy for malaria that was recently approved by the European Medicines Agency, which may make it more readily accessible for clinical testing. Like other known antimalarial drugs active against EBOV, it shares the 4-aminoquinoline scaffold. Tilorone, is an investigational antiviral agent that has shown a broad array of biological activities including cell growth inhibition in cancer cells, antifibrotic properties, α7 nicotinic receptor agonist activity, radioprotective activity and activation of hypoxia inducible factor-1. Quinacrine is an antimalarial but also has use as an anthelmintic. Our results suggest data sets with less than 1,000 molecules can produce validated machine learning models that can in turn be utilized to identify novel EBOV inhibitors in

  7. Machine learning models identify molecules active against the Ebola virus in vitro [version 2; referees: 2 approved

    Sean Ekins

    2016-01-01

    Full Text Available The search for small molecule inhibitors of Ebola virus (EBOV has led to several high throughput screens over the past 3 years. These have identified a range of FDA-approved active pharmaceutical ingredients (APIs with anti-EBOV activity in vitro and several of which are also active in a mouse infection model. There are millions of additional commercially-available molecules that could be screened for potential activities as anti-EBOV compounds. One way to prioritize compounds for testing is to generate computational models based on the high throughput screening data and then virtually screen compound libraries. In the current study, we have generated Bayesian machine learning models with viral pseudotype entry assay and the EBOV replication assay data. We have validated the models internally and externally. We have also used these models to computationally score the MicroSource library of drugs to select those likely to be potential inhibitors. Three of the highest scoring molecules that were not in the model training sets, quinacrine, pyronaridine and tilorone, were tested in vitro and had EC50 values of 350, 420 and 230 nM, respectively. Pyronaridine is a component of a combination therapy for malaria that was recently approved by the European Medicines Agency, which may make it more readily accessible for clinical testing. Like other known antimalarial drugs active against EBOV, it shares the 4-aminoquinoline scaffold. Tilorone, is an investigational antiviral agent that has shown a broad array of biological activities including cell growth inhibition in cancer cells, antifibrotic properties, α7 nicotinic receptor agonist activity, radioprotective activity and activation of hypoxia inducible factor-1. Quinacrine is an antimalarial but also has use as an anthelmintic. Our results suggest data sets with less than 1,000 molecules can produce validated machine learning models that can in turn be utilized to identify novel EBOV inhibitors in

  8. Radon variations in an active landslide zone from Himalaya: A preliminary study

    The radon concentration was measured in soil and water samples from an active landslide zone in the Garhwal Himalaya. The landslide is compound in nature i.e. slump in the crown portion and debris slide in the lower part. The measured radon concentration varies from 3.1 to 18.3 Bq/l in water whereas in soil/debris samples it varies from 2.3 to 12.2 kBq/m3. The crown portion (upper portion) show higher radon values in comparison to distal portion. The higher radon concentration in crown portion may be because of the failure plane of landslide associated with high fracturing and crushing whereas, increased porosity of debris of slide does not allow radon to accumulate in soil and water in the lower portion. (author)

  9. Determination of dissociation constants of pharmacologically active xanthones by capillary zone electrophoresis with diode array detection.

    Wu, Xiaomu; Gong, Suxuan; Bo, Tao; Liao, Yiping; Liu, Huwei

    2004-12-24

    In this article, the dissociation constants (pKa) of 10 pharmacologically active xanthones isolated from herbal medicine Securidaca inappendiculata were determined by capillary zone electrophoresis with diode array detection. The pKa values determined by the method based on the electrophoretic mobilities (calculated from migration times) have been proved by the method based on UV absorbance calculated from the online spectra corresponding peaks. No conspicuous difference was observed between the two methods with acceptable reproducibility. Two pKa values (pKa1 and pKa2) were found for four xanthones while generally the 10 compounds possess the pKa values ranging from 6.4 to 9.2. PMID:15641365

  10. Growth of the active zone in nitride based long wavelength laser structures

    Rossow, U.; Jönen, H.; Brendel, M.; Dräger, A.; Langer, T.; Hoffmann, L.; Bremers, H.; Hangleiter, A.

    2011-01-01

    In xGa 1- xN/GaN quantum well (QW) structures grown on c-plane surfaces for long wavelength light emitters have been investigated intended. We reached indium concentrations of xIn≥0.35 with good optical and structural quality. For QW thicknesses dQW≤2 nm a fully strained layer structure is observed. QWs of such high indium concentrations, however, are very sensitive to the growth conditions of the subsequent layers and thermal stability/degradation becomes an important issue. We modified the growth of the QWs to avoid or minimize V-pit formation without temperature ramping in the barriers and showed that their properties were unchanged when used in the active zone of a laser structure.

  11. Structure-activity relationship studies of strigolactone-related molecules for branching inhibition in garden pea: molecule design for shoot branching.

    Boyer, François-Didier; de Saint Germain, Alexandre; Pillot, Jean-Paul; Pouvreau, Jean-Bernard; Chen, Victor Xiao; Ramos, Suzanne; Stévenin, Arnaud; Simier, Philippe; Delavault, Philippe; Beau, Jean-Marie; Rameau, Catherine

    2012-08-01

    Initially known for their role in the rhizosphere in stimulating the seed germination of parasitic weeds such as the Striga and Orobanche species, and later as host recognition signals for arbuscular mycorrhizal fungi, strigolactones (SLs) were recently rediscovered as a new class of plant hormones involved in the control of shoot branching in plants. Herein, we report the synthesis of new SL analogs and, to our knowledge, the first study of SL structure-activity relationships for their hormonal activity in garden pea (Pisum sativum). Comparisons with their action for the germination of broomrape (Phelipanche ramosa) are also presented. The pea rms1 SL-deficient mutant was used in a SL bioassay based on axillary bud length after direct SL application on the bud. This assay was compared with an assay where SLs were fed via the roots using hydroponics and with a molecular assay in which transcript levels of BRANCHED1, the pea homolog of the maize TEOSINTE BRANCHED1 gene were quantified in axillary buds only 6 h after application of SLs. We have demonstrated that the presence of a Michael acceptor and a methylbutenolide or dimethylbutenolide motif in the same molecule is essential. It was established that the more active analog 23 with a dimethylbutenolide as the D-ring could be used to control the plant architecture without strongly favoring the germination of P. ramosa seeds. Bold numerals refer to numbers of compounds. PMID:22723084

  12. APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone.

    Laßek, Melanie; Weingarten, Jens; Wegner, Martin; Mueller, Benjamin F; Rohmer, Marion; Baeumlisberger, Dominic; Arrey, Tabiwang N; Hick, Meike; Ackermann, Jörg; Acker-Palmer, Amparo; Koch, Ina; Müller, Ulrike; Karas, Michael; Volknandt, Walter

    2016-04-01

    The hallmarks of Alzheimer's disease (AD) are characterized by cognitive decline and behavioral changes. The most prominent brain region affected by the progression of AD is the hippocampal formation. The pathogenesis involves a successive loss of hippocampal neurons accompanied by a decline in learning and memory consolidation mainly attributed to an accumulation of senile plaques. The amyloid precursor protein (APP) has been identified as precursor of Aβ-peptides, the main constituents of senile plaques. Until now, little is known about the physiological function of APP within the central nervous system. The allocation of APP to the proteome of the highly dynamic presynaptic active zone (PAZ) highlights APP as a yet unknown player in neuronal communication and signaling. In this study, we analyze the impact of APP deletion on the hippocampal PAZ proteome. The native hippocampal PAZ derived from APP mouse mutants (APP-KOs and NexCreAPP/APLP2-cDKOs) was isolated by subcellular fractionation and immunopurification. Subsequently, an isobaric labeling was performed using TMT6 for protein identification and quantification by high-resolution mass spectrometry. We combine bioinformatics tools and biochemical approaches to address the proteomics dataset and to understand the role of individual proteins. The impact of APP deletion on the hippocampal PAZ proteome was visualized by creating protein-protein interaction (PPI) networks that incorporated APP into the synaptic vesicle cycle, cytoskeletal organization, and calcium-homeostasis. The combination of subcellular fractionation, immunopurification, proteomic analysis, and bioinformatics allowed us to identify APP as structural and functional regulator in a context-sensitive manner within the hippocampal active zone network. PMID:27092780

  13. APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone

    Mueller, Benjamin F.; Rohmer, Marion; Baeumlisberger, Dominic; Arrey, Tabiwang N.; Hick, Meike; Ackermann, Jörg; Acker-Palmer, Amparo; Koch, Ina; Müller, Ulrike; Karas, Michael; Volknandt, Walter

    2016-01-01

    The hallmarks of Alzheimer’s disease (AD) are characterized by cognitive decline and behavioral changes. The most prominent brain region affected by the progression of AD is the hippocampal formation. The pathogenesis involves a successive loss of hippocampal neurons accompanied by a decline in learning and memory consolidation mainly attributed to an accumulation of senile plaques. The amyloid precursor protein (APP) has been identified as precursor of Aβ-peptides, the main constituents of senile plaques. Until now, little is known about the physiological function of APP within the central nervous system. The allocation of APP to the proteome of the highly dynamic presynaptic active zone (PAZ) highlights APP as a yet unknown player in neuronal communication and signaling. In this study, we analyze the impact of APP deletion on the hippocampal PAZ proteome. The native hippocampal PAZ derived from APP mouse mutants (APP-KOs and NexCreAPP/APLP2-cDKOs) was isolated by subcellular fractionation and immunopurification. Subsequently, an isobaric labeling was performed using TMT6 for protein identification and quantification by high-resolution mass spectrometry. We combine bioinformatics tools and biochemical approaches to address the proteomics dataset and to understand the role of individual proteins. The impact of APP deletion on the hippocampal PAZ proteome was visualized by creating protein-protein interaction (PPI) networks that incorporated APP into the synaptic vesicle cycle, cytoskeletal organization, and calcium-homeostasis. The combination of subcellular fractionation, immunopurification, proteomic analysis, and bioinformatics allowed us to identify APP as structural and functional regulator in a context-sensitive manner within the hippocampal active zone network. PMID:27092780

  14. APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone.

    Melanie Laßek

    2016-04-01

    Full Text Available The hallmarks of Alzheimer's disease (AD are characterized by cognitive decline and behavioral changes. The most prominent brain region affected by the progression of AD is the hippocampal formation. The pathogenesis involves a successive loss of hippocampal neurons accompanied by a decline in learning and memory consolidation mainly attributed to an accumulation of senile plaques. The amyloid precursor protein (APP has been identified as precursor of Aβ-peptides, the main constituents of senile plaques. Until now, little is known about the physiological function of APP within the central nervous system. The allocation of APP to the proteome of the highly dynamic presynaptic active zone (PAZ highlights APP as a yet unknown player in neuronal communication and signaling. In this study, we analyze the impact of APP deletion on the hippocampal PAZ proteome. The native hippocampal PAZ derived from APP mouse mutants (APP-KOs and NexCreAPP/APLP2-cDKOs was isolated by subcellular fractionation and immunopurification. Subsequently, an isobaric labeling was performed using TMT6 for protein identification and quantification by high-resolution mass spectrometry. We combine bioinformatics tools and biochemical approaches to address the proteomics dataset and to understand the role of individual proteins. The impact of APP deletion on the hippocampal PAZ proteome was visualized by creating protein-protein interaction (PPI networks that incorporated APP into the synaptic vesicle cycle, cytoskeletal organization, and calcium-homeostasis. The combination of subcellular fractionation, immunopurification, proteomic analysis, and bioinformatics allowed us to identify APP as structural and functional regulator in a context-sensitive manner within the hippocampal active zone network.

  15. Classical complement pathway activation by antipneumococcal antibodies leads to covalent binding of C3b to antibody molecules.

    Brown, E J; Berger, M.; Joiner, K A; Frank, M. M.

    1983-01-01

    We have examined whether or not a physical relationship exists between antipneumococcal antibodies (Ab) and C3b when Ab activate the classical complement pathway on the surface of pneumococci (Pn). After sensitization with 125I-labeled Ab, Pn were sequentially incubated with purified C1, C4, C2, and biotinylated C3. Ab molecules were then eluted from Pn, and C3b-associated molecules were purified on avidin-Sepharose. Both 125I-labeled immunoglobulin G (IgG) and [125I]IgM bound to C3b; the ass...

  16. Instrumental neutron activation analysis of well sediments from the costal zone of Kurzeme

    Full text: The coastal zone of Kurzeme 2-4 km wide is located in different economical regions. Geologically this zone is under the influence of the sea. Through the sandy soil the chemical compounds infiltrate very well in the underground waters and so it is possible from the condition of underground waters to judge about the state of the zone. The purpose of this work is to get the information about the influence of the human activities on the coastal zone and also to estimate the influence of the penetration of seawater on the chemical composition of underground waters in wells. As the sediments integrate the chemical composition of water over a longer period of time, then in the first stage for the characterisation of water the sediments were chosen. To solve the mentioned problems it is necessary to obtain information about large amounts of chemical elements (V, Mn, Co, Ni, Cu, Zn, As, Sb, Th, U, lanthanide, a.o., about 30-40 at all) in macro, micro and trace concentrations. It is possible only by use one of the methods of multielement analysis. We chose the instrumental neutron activation analysis (INAA), because it is one of the most sensitive allows to determine elements in wide range of concentrations (from % to ppb) and do not need complicated sample preparation. The INAA was carried out in the Laboratory of Neutron Activation Analysis in the Nuclear Research Center of the Latvian Academy of Sciences, by the use of nuclear reactor as neutron source. For the determination of elements two modes of irradiation and three of measurements were used. 1. The irradiation of samples in reactors horizontal experimental channel neutron flux 1.6 · 1013 n/cm2 s by use of pneumotransporter. The irradiation time was 30 s, cooling time 8 min, measuring time of the gamma-spectrums - 200/s. Under such conditions radionuclides with half periods less than 30 n were determined: Mg, Cl, V, Mn, a.o. 2. The irradiation of samples in reactors vertical experimental channel (neutron

  17. Calculations of Induced Activity in the ATLAS Experiment for Nuclear Waste Zoning.

    Morev, M N

    2007-01-01

    Extensive calculations were performed with the general activation formula using the fluxes of high-energy hadrons and low-energy neutrons previously obtained from simulations with the GCALOR code of the ATLAS detector. Three sets of proton cross-sections were used for hadrons energy above 20 MeV: (a) one set calculated with the YIELDX code (i.e., the Silberberg-Tsao formula of partial proton spallation cross-sections), (b) one set calculated with the Rudstam formula, and (c) the ‘best-estimate' dataset which was a compilation of the available experimental and calculated data. In the energy region below 20 MeV, neutron activation cross-sections were taken from evaluated nuclear data files. The activity of each nuclide for a predefined operation scenario (i.e., number and duration of irradiation and shutdown cycles) was normalized to reference values taken from the European or Swiss legislations, to obtain an aggregate estimate of the radiological hazard comparable with a nuclear waste zoning definition cr...

  18. Underground Corrosion of Activated Metals in an Arid Vadose Zone Environment

    The subsurface radioactive disposal site located at the Idaho National Engineering and Environmental Laboratory contains neutron-activated metals from nonfuel nuclear-reactor- core components. A long-term corrosion test is being conducted to obtain site-specific corrosion rates to support efforts to more accurately estimate the transfer of activated elements in an arid vadose zone environment. The tests use nonradioactive metal coupons representing the prominent neutron-activated material buried at the disposal location, namely, Type 304L stainless steel, Type 315L stainless steel, nickel-chromium alloy (UNS NO7718), beryllium, aluminum 6061-T6, and a zirconium alloy, (UNS R60804). In addition, carbon steel (the material presently used in the cask disposal liners and other disposal containers) and a duplex stainless steel (UNS S32550) (the proposed material for the high- integrity disposal containers) are also included in the test program. This paper briefly describes the test program and presents the early corrosion rate results after 1 year and 3 years of underground exposure

  19. NORM activity concentration in sediment cores from the Peninsular Malaysia East Coast Exclusive Economic Zone

    Study for distribution of Naturally Occurring Radioactive Materials (NORM) i.e. 226Ra, 228Ra and 40K in the east coast of Peninsular Malaysia Exclusive Economic Zone (EEZ) was carried out as part of the national marine environment project. Sixteen marine sediment cores from selected locations within the EEZ were collected for determination of NORM activity concentrations using high-purity germanium (HPGe) gamma spectrometer. From the measurement, the activity concentration of 226Ra, 228Ra and 40K is ranged from 16 ± 4 Bq/kg to 46 ± 6 Bq/kg (total mean 30), 28 ± 7 Bq/kg to 87 ± 11 Bq/kg (total mean 56) and 171 ± 33 Bq/kg to 690 ± 89 Bq/kg (total mean 420), dry wt., respectively. The activity concentrations of radionuclides in most of the core were quite uniform suggesting that there were thorough vertical mixed of sediment throughout the core. The results obtained were also in good agreement with those previous reported from other countries in the region and therefore can be used to enhance present radioactivity database. The calculated external hazard values were ranged from 0.25 to 0.51 with the mean of 0.38 (less than unity) showed little risk of external hazard to the workers handling the sediments and it was likely low level of the mainland natural gamma-radiation in the east coast of Peninsular Malaysia. (author)

  20. Phosphate Activation via Reduced Oxidation State Phosphorus (P. Mild Routes to Condensed-P Energy Currency Molecules

    Claire R. Cousins

    2013-07-01

    Full Text Available The emergence of mechanisms for phosphorylating organic and inorganic molecules is a key step en route to the earliest living systems. At the heart of all contemporary biochemical systems reside reactive phosphorus (P molecules (such as adenosine triphosphate, ATP as energy currency molecules to drive endergonic metabolic processes and it has been proposed that a predecessor of such molecules could have been pyrophosphate [P2O74−; PPi(V]. Arguably the most geologically plausible route to PPi(V is dehydration of orthophosphate, Pi(V, normally a highly endergonic process in the absence of mechanisms for activating Pi(V. One possible solution to this problem recognizes the presence of reactive-P containing mineral phases, such as schreibersite [(Fe,Ni3P] within meteorites whose abundance on the early Earth would likely have been significant during a putative Hadean-Archean heavy bombardment. Here, we propose that the reduced oxidation state P-oxyacid, H-phosphite [HPO32−; Pi(III] could have activated Pi(V towards condensation via the intermediacy of the condensed oxyacid pyrophosphite [H2P2O52−; PPi(III]. We provide geologically plausible provenance for PPi(III along with evidence of its ability to activate Pi(V towards PPi(V formation under mild conditions (80 °C in water.

  1. Conformational, spectroscopic and nonlinear optical properties of biologically active N,N-dimethyltryptamine molecule: A theoretical study

    Öner, Nazmiye; Tamer, Ömer; Avcı, Davut; Atalay, Yusuf

    2014-12-01

    The effective psychoactive properties of N,N-dimethyltryptamine (DMT) known as the near-death molecule have encouraged the imagination of many research disciplines for several decades. Although there is no theoretical study, a number of paper composed by experimental techniques have been reported for DMT molecule. In this study, the molecular modeling of DMT was carried out using B3LYP and HSEh1PBE levels of density functional theory (DFT). Our calculations showed that the energy gap between HOMO and LUMO is low, demonstrating that DMT is a biologically active molecule. Large hyperconjugation interaction energies imply that molecular charge transfer occurs in DMT. Moreover, NLO analysis indicates that DMT can be used an effective NLO material.

  2. How water molecules affect the catalytic activity of hydrolases - A XANES study of the local structures of peptide deformylase

    Cui, Peixin; Wang, Yu; Chu, Wangsheng; Guo, Xiaoyun; Yang, Feifei; Yu, Meijuan; Zhao, Haifeng; Dong, Yuhui; Xie, Yaning; Gong, Weimin; Wu, Ziyu

    2014-12-01

    Peptide deformylase (PDF) is a prokaryotic enzyme that catalyzes the deformylation of nascent peptides generated during protein synthesis and water molecules play a key role in these hydrolases. Using X-ray absorption near edge spectroscopy (XANES) and ab initio calculations we accurately probe the local atomic environment of the metal ion binding in the active site of PDF at different pH values and with different metal ions. This new approach is an effective way to monitor existing correlations among functions and structural changes. We show for the first time that the enzymatic activity depends on pH values and metal ions via the bond length of the nearest coordinating water (Wat1) to the metal ion. Combining experimental and theoretical data we may claim that PDF exhibits an enhanced enzymatic activity only when the distance of the Wat1 molecule with the metal ion falls in the limited range from 2.15 to 2.55 Å.

  3. Biochemical and toxicological evaluation of nano-heparins in cell functional properties, proteasome activation and expression of key matrix molecules.

    Piperigkou, Zoi; Karamanou, Konstantina; Afratis, Nikolaos A; Bouris, Panagiotis; Gialeli, Chrysostomi; Belmiro, Celso L R; Pavão, Mauro S G; Vynios, Dimitrios H; Tsatsakis, Aristidis M

    2016-01-01

    The glycosaminoglycan heparin and its derivatives act strongly on blood coagulation, controlling the activity of serine protease inhibitors in plasma. Nonetheless, there is accumulating evidence highlighting different anticancer activities of these molecules in numerous types of cancer. Nano-heparins may have great biological significance since they can inhibit cell proliferation and invasion as well as inhibiting proteasome activation. Moreover, they can cause alterations in the expression of major modulators of the tumor microenvironment, regulating cancer cell behavior. In the present study, we evaluated the effects of two nano-heparin formulations: one isolated from porcine intestine and the other from the sea squirt Styela plicata, on a breast cancer cell model. We determined whether these nano-heparins are able to affect cell proliferation, apoptosis and invasion, as well as proteasome activity and the expression of extracellular matrix molecules. Specifically, we observed that nano-Styela compared to nano-Mammalian analogue has higher inhibitory role on cell proliferation, invasion and proteasome activity. Moreover, nano-Styela regulates cell apoptosis, expression of inflammatory molecules, such as IL-6 and IL-8 and reduces the expression levels of extracellular matrix macromolecules, such as the proteolytic enzymes MT1-MMP, uPA and the cell surface proteoglycans syndecan-1 and -2, but not on syndecan-4. The observations reported in the present article indicate that nano-heparins and especially ascidian heparin are effective agents for heparin-induced effects in critical cancer cell functions, providing an important possibility in pharmacological targeting. PMID:26476401

  4. Variation of radon flux along active fault zones in association with earthquake occurrence

    Radon flux measurements were carried out at three radon stations along an active fault zone in the Langadas basin, Northern Greece by various techniques for earthquake prediction studies. Specially made devices with alpha track-etch detectors (ATDs) were installed by using LR-115, type II, non-strippable cellulose nitrate films (integrating method of measurements). Continuous monitoring of radon gas exhaling from the ground was also performed by using silicon diode detectors, Barasol and Clipperton type, in association with various probes and sensors including simultaneously registration of the meteorological parameters, such as precipitation height (rainfall events), temperature and barometric pressure. The obtained radon data were studied in parallel with the data of seismic events, such as the magnitude, ML of earthquakes, the epicentral distance, the hypocentral distance and the energy released during the earthquake event occurred at the fault zone during the period of measurements to find out any association between the rad on flux and the meteorological and seismological parameters. Seismic events with magnitude ML ≥ 4.0 appeared to be preceded by large precursory signals produced a well-defined 'anomaly' (peak) of radon flux prior to the event. In the results, the radon peaks in the obtained spectra appeared to be sharp and narrow. The rise time of a radon peak, that is the time period from the onset of a radon peak until the time of radon flux maximum is about a week, while the after time, that is the time interval between the time of radon flux maximum and the time of a seismic event ranges from about 3 weeks or more.

  5. Impaired hippocampal activity at the goal zone on the place preference task in a DISC1 mouse model.

    Hayashi, Yuichiro; Sawa, Akira; Hikida, Takatoshi

    2016-05-01

    Learning deficit is a clinical feature of many mental disorders and is hypothesized to result from an inability to integrate information in neural systems. We showed that transgenic mice expressing a dominant-negative form of DISC1, a risk gene for neuropsychiatric disorders, exhibited impaired performance in a reward-place association task when combined with a mild isolation stress. CA1 cells in the mutant mice showed normal place cell properties, but their activity at the goal zone was diminished. This abnormality in hippocampal activity at the goal zone during the task may underlie the learning deficit observed in the DISC1 mutant mice. PMID:26497623

  6. Active faults and related Late Quaternary deformation along the Northwestern Himalayan Frontal Zone, India

    T. Nakata

    2003-06-01

    Full Text Available Numerous newly-identified traces of active faults in the Himalayan foothill zone along the HFF around Chandigarh, in Pinjore Dun, along the piedmont zone of the Lower Siwalik hill front and within the Lower Tertiary hill range reveal the pattern of thrust and strike-slip faulting, striking parallel to the principal structural trend (NNW-SSE of the orogenic belt. The active Chandigarh Fault, Pinjore Garden Fault and Barsar thrust have vertically dislocated, warped and backtilted fluvial and alluvial-fan surfaces made up of Late Pleistocene-Holocene sediments. West- and southwest-facing fault scarplets with heights ranging from 12 to 50 m along these faults suggest continued tectonic movement through Late Pleistocene to recent times. Gentle warping and backtilting of the terraces on the hanging wall sides of the faults indicate fault-bend folding. These active faults are the manifestation of north-dipping imbricated thrust faults branching out from the major fault systems like the Main Boundary Fault (MBF and Himalayan Frontal Fault (HFF, probably merging down northward into a décollement. The Taksal Fault, striking NNW-SSE, shows prominent right-lateral movement marked by lateral offset of streams and younger Quaternary terraces and occupies a narrow deep linear valley along the fault trace. Right stepping along this fault has resulted in formation of a small pull-apart basin. Fault scarplets facing ENE and WSW are the manifestation of dip-slip movement. This fault is an example of slip-partitioning between the strike-slip and thrust faults, suggesting ongoing oblique convergence of the Indian plate and northward migration of a tectonic sliver. Slip rate along the Taksal Fault has been calculated as 2.8 mm/yr. Preliminary trench investigation at the base of the Chandigarh Fault Scarp has revealed total displacement of 3.5 m along a low angle thrust fault with variable dip of 20° to 46° due northeast, possibly the result of one

  7. Activation of Carbonyl-Containing Molecules with Solid Lewis Acids in Aqueous Media

    Román-Leshkov, Yuriy [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Chemical Engineering; Davis, Mark E. [California Inst. of Technology (CalTech), Pasadena, CA (United States). Chemical Engineering

    2011-09-28

    Current interest in reacting carbonyl-containing molecules in aqueous media is primarily due to the growing emphasis on conversion of biomass to fuels and chemicals. Recently, solid Lewis acids have been shown to perform catalytic reactions with carbonyl-containing molecules such as sugars in aqueous media. Here, catalysis mediated by Lewis acids is briefly discussed, Lewis acid solids that perform catalysis in aqueous media are then described, and the review is concluded with a few comments on the outlook for the future.

  8. Interaction of an immunodominant epitope with Ia molecules in T-cell activation

    Adorini, L; Sette, A; Buus, S;

    1988-01-01

    The amino acid sequence corresponding to residues 107-116 of hen egg-white lysozyme (HEL) has been identified as containing an immunodominant T-cell epitope recognized in association with the I-Ed molecule. The immunodominance of this epitope in HEL-primed H-2d mice was demonstrated by analysis o......-120)-peptide was found to be immunogenic in H-2d mice. Thus, a single semiconservative substitution drastically reduces binding capacity and abolishes immunogenicity, suggesting that a strict correlation exists between binding of a peptide to Ia molecules and its immunogenicity....

  9. New insights on the seismogenic potential of the Eastern Betic Shear Zone (SE Iberia): Quaternary activity and paleoseismicity of the SW segment of the Carrascoy Fault Zone

    Martín-Banda, Raquel; García-Mayordomo, Julián.; Insua-Arévalo, Juan M.; Salazar, Ángel E.; Rodríguez-Escudero, Emilio; Álvarez-Gómez, Jose A.; Medialdea, Alicia; Herrero, María. J.

    2016-01-01

    The Carrascoy Fault (CAF) is one of the main active faults that form part of the Eastern Betic Shear Zone, a 450 km fault system that accommodates most of the convergence between the Eurasian (Iberia) and Nubian plates in the Betic Cordillera, south Spain. Although the CAF represents a major earthquake threat to the nearby City of Murcia, studies on its Quaternary tectonics and seismogenic potential are scarce to date. We present evidence that supports the division of the CAF into two overlapping segments with contrasting tectonic structure, Quaternary activity, and landform control: a SW segment, characterized by a broad fold-and-thrust zone similar to the forebergs defined in the Gobi-Altai region, and a NE segment, characterized by a sharp mountain front controlled by strike-slip tectonics. We attribute the differentiation into these two segments to the stresses associated with topography, which in turn is a consequence of the shortening component, at the middle Pleistocene, after circa 217.4 ka. For the SW segment we infer the occurrence of 9 to 11, Mw 6.7 paleoearthquakes in the last 30.2 kyr, and a slip rate of 0.37 ± 0.08 m/kyr. We date the occurrence of the last surface rupture event after 2750 B.P., and we estimate an average recurrence period of major events of 3.3 ± 0.7 kyr.

  10. Activation of a water molecule coordinated to manganese: four study cases

    The daunting energy consumption of western societies calls for the development of renewable energies. Among them, hydrogen stands as a major candidate. The cleanest way of producing hydrogen is water electro- or photolysis. This reaction is carried out in natural photosynthesis by a manganese-oxo cluster, the functioning of which remains unknown. Insight into this mechanism would greatly help the search for low-cost water splitting catalysts. Our contribution to this field is the understanding of the fundamental processes that govern the activation of water by manganese complexes. This manuscript describes our attempts to generate electrochemically mononuclear manganese(IV) complexes bearing a fully deprotonated water molecule (oxo ligand). We have studied four different cases, which reflect different possible coordination spheres capable of stabilizing such species. In the first chapter, we will give a brief overview of the present energetic challenges faced by western societies. In the second chapter, we will present general considerations about manganese chemistry and a description of the structure and functioning of the water oxidizing enzyme. We will also describe the basic requirements for the splitting of water and present the goals of our work. In the third chapter, we will present the synthesis of a new family of tetradentate ligands, together with the synthesis and full characterization of the corresponding nickel(II) complexes. The first results obtained with the manganese analogue will also be shown. Chapter four presents the formation and the full characterization of a mononuclear manganese(IV)-oxo complex, by electrochemical oxidation of a manganese(II)-aqua complex. We will present different pathways to generate this species and show which intermediates are involved in this 2 e-, 2 H+ reaction. Chapter five describes the formation of a mononuclear manganese(IV) complex, by electrochemical oxidation of a manganese(III)-hydroxo complex. The manganese

  11. An Assessment of Variation in Active Ingredients of Ampucare from Different Zones of India

    Naveen Pathak

    2010-04-01

    Full Text Available The present study was designed to assess the variation in curcumin content of Curcuma longa rhizome and total polyphenols in Azadirachta indica bark samples procured from different zones of India. Physico-chemical tests such as total ash, acid insoluble ash, alcohol soluble extractive, water soluble extractive, volatile oil content etc. were also determined. A slight variation was seen in the bark samples of Azadirachta indica. Total ash ranged from 4.25±0.15 (East zone to 5.57±0.20 (Central zone whereas acid insoluble ash ranged from 0.80±0.07 (East zone to 1.52±0.06 (Central zone. Alcohol soluble extractive value of East zone sample was found to be more than 4 times higher 16.95±0.80 than that of central zone 3.85±0.12, where lowest value was recorded. Water soluble extractive value was also found to be highest in East zone sample 17.80±1.10 which was 2 times more than that of Central zone sample 8.45±0.15. This variation may be due to variation in climatic conditions, soil type, pollution stress etc. All the results were within the limits as given in The Ayurvedic Pharmacopoeia of India. Total Polyphenols ranged from 190.0 mgGAE/g of dry weight (Central zone to 510.0 mgGAE/g of dry weight (East zone. All the samples were found to be rich in total polyphenols. In Curcuma longa samples, Total ash ranged from 3.10±0.20 (South zone to 4.80±0.25 (North zone whereas acid insoluble ash ranged from 0.55±0.04 (South zone to 1.24±0.06 (North zone. Alcohol soluble extractive value was found to be highest in South zone sample 14.80±0.30 which was found to be more than 3 times higher than that of central zone 4.28±0.19 where lowest value was recorded. Water soluble extractive value was also found to be highest in West zone sample 12.55±0.69 and lowest in Central zone sample 8.90±0.37. Volatile oil ranged from 3.50±0.21 North zone sample to 5.50±0.20 South zone sample, where highest volatile oil was recovered. All the results were within

  12. Rabies Virus Expressing Dendritic Cell-Activating Molecules Enhances the Innate and Adaptive Immune Response to Vaccination ▿

    Wen, Yongjun; Wang, Hualei; Wu, Hua; Yang, Fuhe; Tripp, Ralph A.; Hogan, Robert J.; Fu, Zhen F.

    2010-01-01

    Our previous studies indicated that recruitment and/or activation of dendritic cells (DCs) is important in enhancing the protective immune responses against rabies virus (RABV) (L. Zhao, H. Toriumi, H. Wang, Y. Kuang, X. Guo, K. Morimoto, and Z. F. Fu, J. Virol. 84:9642-9648). To address the importance of DC activation for RABV vaccine efficacy, the genes for several DC recruitment and/or activation molecules, e.g., granulocyte-macrophage colony-stimulating factor (GM-CSF), macrophage-derived...

  13. Persistent downregulation of the pancarcinoma-associated epithelial cell adhesion molecule via active intranuclear methylation

    van der Gun, Bernardina T. F.; Wasserkort, Reinhold; Monami, Amelie; Jeltsch, Albert; Rasko, Tamits; Slaska-Kiss, Krystyna; Cortese, Rene; Rots, Marianne G.; de Leij, Lou F. M. H.; Ruiters, Marcel H. J.; Kiss, Antal; Weinhold, Elmar; McLaughlin, Pamela M. J.

    2008-01-01

    The epithelial cell adhesion molecule (EpCAM) is expressed at high levels on the surface of most carcinoma cells. SiRNA silencing of EpCAM expression leads to reduced metastatic potential of tumor cells demonstrating its importance in oncogenesis and tumor progression. However, siRNA therapy require

  14. Unequal Activities of Enantiomers via Biological Receptors: Examples of Chiral Drug, Pesticide, and Fragrance Molecules

    Mannschreck, Albrecht; Kiesswetter, Roland; von Angerer, Erwin

    2007-01-01

    A molecule coming from outside an organism can form a ligand-receptor complex. Upon its formation, a message is transmitted, for example, to certain cells. In this way, two enantiomers can emit messages that differ, either quantitatively or qualitatively. In the present article, these facts are taken as a common basis for the actions of chiral…

  15. Synthesis of Zn-MOF incorporating titanium-hydrides as active sites binding H2 molecules

    Kim, Jongsik; Ok Kim, Dong; Wook Kim, Dong; Sagong, Kil

    2015-10-01

    This paper describes the synthetic effort for a Zn-MOF imparting Ti-H as a preferential binding site potentially capturing H2 molecules via Kubas-type interaction. The formation mechanism of Ti-H innate to the final material was potentially demonstrated to follow a radical dissociation rather than a β-hydrogen elimination and a C-H reductive elimination.

  16. Active tectonics west of New Zealand's Alpine Fault: South Westland Fault Zone activity shows Australian Plate instability

    De Pascale, Gregory P.; Chandler-Yates, Nicholas; Dela Pena, Federico; Wilson, Pam; May, Elijah; Twiss, Amber; Cheng, Che

    2016-04-01

    The 300 km long South Westland Fault Zone (SWFZ) is within the footwall of the Central Alpine Fault (<20 km away) and has 3500 m of dip-slip displacement, but it has been unknown if the fault is active. Here the first evidence for SWFZ thrust faulting in the "stable" Australian Plate is shown with cumulative dip-slip displacements up to 5.9 m (with 3 m throw) on Pleistocene and Holocene sediments and gentle hanging wall anticlinal folding. Cone penetration test (CPT) stratigraphy shows repeated sequences within the fault scarp (consistent with thrusting). Optically stimulated luminescence (OSL) dating constrains the most recent rupture post-12.1 ± 1.7 ka with evidence for three to four events during earthquakes of at least Mw 6.8. This study shows significant deformation is accommodated on poorly characterized Australian Plate structures northwest of the Alpine Fault and demonstrates that major active and seismogenic structures remain uncharacterized in densely forested regions on Earth.

  17. Isolation and Molecular Characterization of Biofouling Bacteria and Profiling of Quorum Sensing Signal Molecules from Membrane Bioreactor Activated Sludge

    Harshad Lade; Diby Paul; Ji Hyang Kweon

    2014-01-01

    The formation of biofilm in a membrane bioreactor depends on the production of various signaling molecules like N-acyl homoserine lactones (AHLs). In the present study, a total of 200 bacterial strains were isolated from membrane bioreactor activated sludge and screened for AHLs production using two biosensor systems, Chromobacterium violaceum CV026 and Agrobacterium tumefaciens A136. A correlation between AHLs production and biofilm formation has been made among screened AHLs producing strai...

  18. Functional role of HLA class I cell-surface molecules in human T-lymphocyte activation and proliferation.

    Taylor, D S; Nowell, P C; Kornbluth, J

    1986-01-01

    This investigation addressed the role of major histocompatibility complex-encoded class I molecules in the activation and proliferation of human lymphocytes. We studied the effect of antibodies specific for HLA-A and HLA-B locus gene products on mitogen-stimulated peripheral blood mononuclear cell (PBMC) subpopulations. Three individually derived, well-characterized anti-HLA class I monoclonal antibodies were demonstrated to inhibit the proliferation of human PBMC stimulated by either OKT3 or...

  19. Distribution of 210Pb activity concentrations in marine surface sediments within East Coast Peninsula Malaysia Exclusive Economic Zone (EEZ)

    A sampling expedition into the East Coast Peninsula Malaysia Exclusive Economic Zone (EEZ) was carried in June 2008. Marine surface sediment samples were taken and the activity concentrations of 210Pb have been determined. Its distribution was plotted and the findings show that the activity concentrations decline from north to south. On the other hand, the activity concentrations are increasing from west to east right to the edge of the EEZ. The highest activity concentrations were found to be near offshore oil platforms. The 210Pb activity concentrations were found to be in the range of 18.3 - 123.1 Bq/ kg. (author)

  20. Cyclosporine A affects the in vitro expression of T cell activation-related molecules and cytokines in dogs.

    Fellman, C L; Stokes, J V; Archer, T M; Pinchuk, L M; Lunsford, K V; Mackin, A J

    2011-04-15

    Cyclosporine is a powerful immunosuppressive drug that is being used with increasing frequency to treat a wide range of immune-mediated diseases in the dog. To date, ideal dosing protocols that will achieve immunosuppression with cyclosporine in dogs remain unclear, and standard methods that can measure effectiveness of immunosuppression have not been established. The aim of our study was to evaluate the effects of in vitro cyclosporine exposure on a panel of molecules expressed by activated T cells to ascertain their potential as biomarkers of immunosuppression in dogs. Blood was drawn from six healthy dogs, and peripheral blood mononuclear cells (PBMC) were isolated and activated. Half of the cells were incubated with 200 ng/mL cyclosporine prior to activation, and the other half were not exposed to cyclosporine. Samples were analyzed using flow cytometry, and the expression of intracellular cytokines IL-2, IL-4, and IFN-γ was evaluated after 6, 12, and 24h of drug exposure. Each cytokine exhibited a time-dependent suppression profile, and all but two samples activated in the presence of cyclosporine showed lower cytokine expression than untreated controls. We also evaluated the expression of the surface T cell activation molecules CD25 and CD95 by flow cytometry after 36 h of drug exposure. Expression of these surface molecules decreased significantly when activated in the presence of cyclosporine. Our results suggest that suppressed expression of the markers related to T cell activation could potentially be utilized as an indicator of the efficacy of cyclosporine therapy in dogs. PMID:21227512

  1. Major histocompatibility complex class II (DR) antigen and costimulatory molecules on in vitro and in vivo activated human polymorphonuclear neutrophils

    Sandilands, Gavin P; McCrae, Jame; Hill, Kathryn; Perry, Martin; Baxter, Derek

    2006-01-01

    We have previously shown that normal human peripheral blood polymorphonuclear neutrophils (PMNs) contain cytoplasmic ‘stores’ of three key molecules normally associated with antigen presentation and T-cell costimulation, i.e. major histocompatibility complex class II (DR) antigen, CD80 (B7-1) and CD86 (B7-2). These cytoplasmic molecules were found to translocate to the cell surface within a few minutes following cross-linking (X-L) of Mac-1: an early neutrophil activation signal. In this study we have compared X-L of Mac −1 in parallel with four other well documented in vitro neutrophil activators: phorbol myristate acetate, N-formyl methionyl leucyl phenylalanine, lipopolysaccharide, and phagocytosis of immunoglobulin G–Latex particles. In addition, we have used paired samples of neutrophils obtained from peripheral blood (as a control) and synovial fluid from patients with rheumatoid arthritis as a source of in vivo activated cells. With the exception of phagocytosis, all activators resulted in the rapid (within 30 min) generation of two populations of activated neutrophils (designated P1 and P2) based on flow-cytometry measurements of size, granularity and phenotype. Significant up-regulation of DR and costimulatory molecules was observed, predominantly on P2 cells, with all activators except phagocytosis. CD80 and CD86 were noted to respond to the various activation signals in a different pattern suggesting that their intracellular granule location may be different. Dual-staining confocal laser microscopy studies showed that CD80 is largely confined to secretory vesicles (SVs) while CD86 appears to have a much wider distribution being found in SVs and within secondary (specific) and primary (azurophilic) granules. Increased surface expression of these antigens was also observed on P2 synovial fluid neutrophils appearing as large heterogeneous clusters on the cell surface when visualized by confocal laser microscopy. PMID:17034427

  2. Single molecule measurements of DNA helicase activity with magnetic tweezers and t-test based step-finding analysis.

    Seol, Yeonee; Strub, Marie-Paule; Neuman, Keir C

    2016-08-01

    Magnetic tweezers is a versatile and easy to implement single-molecule technique that has become increasingly prevalent in the study of nucleic acid based molecular motors. Here, we provide a description of the magnetic tweezers instrument and guidelines for measuring and analyzing DNA helicase activity. Along with experimental methods, we describe a robust method of single-molecule trajectory analysis based on the Student's t-test that accommodates continuous transitions in addition to the discrete transitions assumed in most widely employed analysis routines. To illustrate the single-molecule unwinding assay and the analysis routine, we provide DNA unwinding measurements of Escherichia coli RecQ helicase under a variety of conditions (Na+, ATP, temperature, and DNA substrate geometry). These examples reveal that DNA unwinding measurements under various conditions can aid in elucidating the unwinding mechanism of DNA helicase but also emphasize that environmental effects on DNA helicase activity must be considered in relation to in vivo activity and mechanism. PMID:27131595

  3. SET7/9 catalytic mutants reveal the role of active site water molecules in lysine multiple methylation.

    Del Rizzo, Paul A; Couture, Jean-François; Dirk, Lynnette M A; Strunk, Bethany S; Roiko, Marijo S; Brunzelle, Joseph S; Houtz, Robert L; Trievel, Raymond C

    2010-10-01

    SET domain lysine methyltransferases (KMTs) methylate specific lysine residues in histone and non-histone substrates. These enzymes also display product specificity by catalyzing distinct degrees of methylation of the lysine ε-amino group. To elucidate the molecular mechanism underlying this specificity, we have characterized the Y245A and Y305F mutants of the human KMT SET7/9 (also known as KMT7) that alter its product specificity from a monomethyltransferase to a di- and a trimethyltransferase, respectively. Crystal structures of these mutants in complex with peptides bearing unmodified, mono-, di-, and trimethylated lysines illustrate the roles of active site water molecules in aligning the lysine ε-amino group for methyl transfer with S-adenosylmethionine. Displacement or dissociation of these solvent molecules enlarges the diameter of the active site, accommodating the increasing size of the methylated ε-amino group during successive methyl transfer reactions. Together, these results furnish new insights into the roles of active site water molecules in modulating lysine multiple methylation by SET domain KMTs and provide the first molecular snapshots of the mono-, di-, and trimethyl transfer reactions catalyzed by these enzymes. PMID:20675860

  4. SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation*

    Del Rizzo, Paul A.; Couture, Jean-François; Dirk, Lynnette M. A.; Strunk, Bethany S.; Roiko, Marijo S.; Brunzelle, Joseph S.; Houtz, Robert L.; Trievel, Raymond C.

    2010-01-01

    SET domain lysine methyltransferases (KMTs) methylate specific lysine residues in histone and non-histone substrates. These enzymes also display product specificity by catalyzing distinct degrees of methylation of the lysine ϵ-amino group. To elucidate the molecular mechanism underlying this specificity, we have characterized the Y245A and Y305F mutants of the human KMT SET7/9 (also known as KMT7) that alter its product specificity from a monomethyltransferase to a di- and a trimethyltransferase, respectively. Crystal structures of these mutants in complex with peptides bearing unmodified, mono-, di-, and trimethylated lysines illustrate the roles of active site water molecules in aligning the lysine ϵ-amino group for methyl transfer with S-adenosylmethionine. Displacement or dissociation of these solvent molecules enlarges the diameter of the active site, accommodating the increasing size of the methylated ϵ-amino group during successive methyl transfer reactions. Together, these results furnish new insights into the roles of active site water molecules in modulating lysine multiple methylation by SET domain KMTs and provide the first molecular snapshots of the mono-, di-, and trimethyl transfer reactions catalyzed by these enzymes. PMID:20675860

  5. SET7/9 Catalytic Mutants Reveal the Role of Active Site Water Molecules in Lysine Multiple Methylation

    Del Rizzo, Paul A.; Couture, Jean-François; Dirk, Lynnette M.A.; Strunk, Bethany S.; Roiko, Marijo S.; Brunzelle, Joseph S.; Houtz, Robert L.; Trievel, Raymond C. (Michigan); (NWU); (Kentucky)

    2010-11-15

    SET domain lysine methyltransferases (KMTs) methylate specific lysine residues in histone and non-histone substrates. These enzymes also display product specificity by catalyzing distinct degrees of methylation of the lysine {epsilon}-amino group. To elucidate the molecular mechanism underlying this specificity, we have characterized the Y245A and Y305F mutants of the human KMT SET7/9 (also known as KMT7) that alter its product specificity from a monomethyltransferase to a di- and a trimethyltransferase, respectively. Crystal structures of these mutants in complex with peptides bearing unmodified, mono-, di-, and trimethylated lysines illustrate the roles of active site water molecules in aligning the lysine {epsilon}-amino group for methyl transfer with S-adenosylmethionine. Displacement or dissociation of these solvent molecules enlarges the diameter of the active site, accommodating the increasing size of the methylated {epsilon}-amino group during successive methyl transfer reactions. Together, these results furnish new insights into the roles of active site water molecules in modulating lysine multiple methylation by SET domain KMTs and provide the first molecular snapshots of the mono-, di-, and trimethyl transfer reactions catalyzed by these enzymes.

  6. Determination of Four Active Ingredients in Vc Yinqiao Tablets by Capillary Zone Electrophoresis with Amperometric Detection

    L(U),Jin; WANG,Qing-Jiang; CHENG,Xi; LIU,Hai-Yan; HE,Pin-Gang; FANG,Yu-Zhi

    2006-01-01

    A simple, reliable and reproducible method, based on capillary zone electrophoresis with amperometric detection (CZE-AD), has been developed for simultaneous determination of four active ingredients in Vc Yinqiao tablets including paracetamol, vitamin C, caffeic acid and chlorogenic acid. A carbon-disk electrode was used as working electrode and 0.95 V (versus SCE) was selected as detection potential. The optimal conditions of CZE experiment were 30 mmol·L-1 borate solution (pH 9.5) as running buffer, 14 kV as separation voltage and 8 s (14 kV) as electro-kinetic sampling time. Under the selected optimum conditions, paracetamol, vitamin C, caffeic acid and chlorogenic acid could be perfectly separated within 22 min, and their detection limits (S/N=3) ranged from 5 × 10-7 to 1×10-6 mol·L-1. This proposed method demonstrated good reproducibility with relative standard deviations of less than 3% for both migration time and peak current (n=7). The utility of this method was demonstrated by monitoring a kind of compound medicine named Vc Yinqiao tablets and the assay results were satisfactory.

  7. Liparid and macrourid fishes of the hadal zone: in situ observations of activity and feeding behaviour.

    Jamieson, A J; Fujii, T; Solan, M; Matsumoto, A K; Bagley, P M; Priede, I G

    2009-03-22

    Using baited camera landers, the first images of living fishes were recorded in the hadal zone (6000-11000 m) in the Pacific Ocean. The widespread abyssal macrourid Coryphaenoides yaquinae was observed at a new depth record of approximately 7000 m in the Japan Trench. Two endemic species of liparid were observed at similar depths: Pseudoliparis amblystomopsis in the Japan Trench and Notoliparis kermadecensis in the Kermadec Trench. From these observations, we have documented swimming and feeding behaviour of these species and derived the first estimates of hadal fish abundance. The liparids intercepted bait within 100-200 min but were observed to preferentially feed on scavenging amphipods. Notoliparis kermadecensis act as top predators in the hadal food web, exhibiting up to nine suction-feeding events per minute. Both species showed distinctive swimming gaits: P. amblystomopsis (mean length 22.5 cm) displayed a mean tail-beat frequency of 0.47 Hz and mean caudal:pectoral frequency ratio of 0.76, whereas N. kermadecensis (mean length 31.5 cm) displayed respective values of 1.04 and 2.08 Hz. Despite living at extreme depths, these endemic liparids exhibit similar activity levels compared with shallow-water liparids. PMID:19129104

  8. Synaptophysin 1 Clears Synaptobrevin 2 from the Presynaptic Active Zone to Prevent Short-Term Depression

    Rajit Rajappa

    2016-02-01

    Full Text Available Release site clearance is an important process during synaptic vesicle (SV recycling. However, little is known about its molecular mechanism. Here we identify self-assembly of exocytosed Synaptobrevin 2 (Syb2 and Synaptophysin 1 (Syp1 by homo- and hetero-oligomerization into clusters as key mechanisms mediating release site clearance for preventing cis-SNARE complex formation at the active zone (AZ. In hippocampal neurons from Syp1 knockout mice, neurons expressing a monomeric Syb2 mutant, or after acute block of the ATPase N-ethylmaleimide-sensitive factor (NSF, responsible for cis-SNARE complex disassembly, we found strong frequency-dependent short-term depression (STD, whereas retrieval of Syb2 by compensatory endocytosis was only affected weakly. Defects in Syb2 endocytosis were stimulus- and frequency-dependent, indicating that Syp1 is not essential for Syb2 retrieval, but for its efficient clearance upstream of endocytosis. Our findings identify an SV protein as a release site clearance factor.

  9. Photochemical activation and reactivity of polynuclear transition metal complex molecules. Final report

    Several bi- and trinuclear metal complexes containing ligands from β-polyketonates have been synthesized and characterized including homo- and hetero-polynuclear complexes. New synthetic approaches to the preparation of heterobi- and trinuclear complexes have been developed that allow the preparation of a large number of molecules containing heavy-metal ions such as Pd2+ or UO22+ and a first-row transition-metal ion. The electrochemical properties of these complexes have been investigated and many exhibit the ability to transfer two electrons at very nearly the same potential. Photochemical studies on binuclear Cu(II) and Ni(II) showed that these compounds yielded reduced metal species and decomposition upon irradiation. Luminescence of hetero-complexes of uranyl polyketonates is observed at 770K with the UO22+ moiety functioning as an isolated chromophore in which emission is observed only on direct excitation of UO22+ and energy transfer to lower states in the molecule is not observed

  10. Tautocrowns: a concept for a sensing molecule with an active side-arm

    Antonov, Liudmil M.; Kurteva, Vanya B.; Simeonov, Svilen P.; Deneva, Vera V.; Crochet, Aurelien; Katharina M. Fromm

    2010-01-01

    A new sensing molecule containing aza-15-crown-5 as a receptor and 4-(phenyldiazenyl)naphthalen-1-ol as a signal converter has been synthesized. In the free ligand, the hydrogen bonding between the tautomeric OH group and the nitrogen atom from the macrocycle fully shifts the tautomeric equilibrium towards the enol form. The complexation reverses the equilibrium as a result of the strong interaction between the metal ion captured in the macrocyclic moiety and the tautomeric carbonyl group. Th...

  11. Platelet endothelial cell adhesion molecule-1 signaling inhibits the activation of human platelets

    Cicmil, Milenko; Stevens, Jo; Leduc, Mireille; Bon, Cassian; Gibbins, Jonathan M.

    2002-01-01

    Platelet endothelial cell adhesion molecule-1 (PECAM-1/CD31) is a 130-kd transmembrane glycoprotein and a member of the growing family of receptors with immunoreceptor tyrosine-based inhibitory motifs (ITIMs). PECAM-1 is expressed on platelets, certain T cells, monocytes, neutrophils, and vascular endothelial cells and is involved in a range of cellular processes, though the role of PECAM-1 in platelets is unclear. Cross-linking of PECAM-1 results in phosphorylation of the ITIM allowing the r...

  12. Activation of CO2 and Related Small Molecules by Neopentyl-Derivatized Uranium Complexes

    Schmidt, Anna-Corina

    2015-01-01

    The world´s concern about the environment has continued to intensify as the effects of greenhouse gases or complicated work-up and disposal of radioactive substances become more obvious and profound. Unsurprisingly, the number of publications related to the solution of these issues has greatly increased in the last 15 years. Thus, a basic understanding of the specific properties and behavior of small molecules is crucial for the reduction of greenhouse gases, which may be realized through act...

  13. Cuticular transport of hydrophilic molecules with special focus on primary metabolites and active ingredients

    Popp, Christian

    2005-01-01

    The plant cuticle as an interface between the plant interior and the adjoining atmosphere plays an important role in any interaction between the plant and its environment. Transport processes across the cuticles were the object of countless research since many decades. However, bulk of the work done was focused on transport of lipophilic molecules. It is highly plausible to examine the penetration of lipophilic compounds, since the cuticle is dominated by lipophilic compartments itself, and t...

  14. Chemical activation of molecules by metals: Experimental studies of electron distributions and bonding

    The formal relationship between measured molecular ionization energies and thermodynamic bond dissociation energies has been developed into a single equation which unifies the treatment of covalent bonds, ionic bonds, and partially ionic bonds. This relationship has been used to clarify the fundamental thermodynamic information relating to metal-hydrogen, metal-alkyl, and metal-metal bond energies. We have been able to obtain a direct observation and measurement of the stabilization energy provided by the agostic interaction of the C-H bond with the metal. The ionization energies have also been used to correlate the rates of carbonyl substitution reactions of (η5-C5H4X)Rh(CO)2 complexes, and to reveal the electronic factors that control the stability of the transition state. The extent that the electronic features of these bonding interactions transfer to other chemical systems is being investigated in terms of the principle of additivity of ligand electronic effects. Specific examples under study include metal- phosphines, metal-halides, and metallocenes. Especially interesting has been the recent application of these techniques to the characterization of the soccer-ball shaped C60 molecule, buckminsterfullerene, and its interaction with a metal surface. The high-resolution valence ionizations in the gas phase reveal the high symmetry of the molecule, and studies of thin films of C60 reveal weak intermolecular interactions. Scanning tunneling and atomic force microscopy reveal the arrangement of spherical molecules on gold substrates, with significant delocalization of charge from the metal surface. 21 refs

  15. Shoreline changes and its impact on activities in the coastal zone in Greenland

    Kroon, A.; Bendixen, M.; Elberling, B.

    2015-12-01

    Almost all coastal environments in Greenland are developed in high-relief areas, along fjords, or hard-rock cliffs. The sedimentary shores often fringe these areas and a large number of small deltas (areal delta surface temperatures, ice and snow. There is a seasonal variation with open waters and active rivers in summer and ice-covered coastal waters and frozen rivers in winter. The coastal processes by waves and tides are thus often limited to summer and early fall. Nowadays, global climate changes induce many changes along the arctic coasts. Global sea-levels are rising due to thermal expansion and an increased fresh water flux from the glaciers and land ice masses, while ice coverage of the coastal waters decreases and the open water periods in summer extend. However, it is still unknown if the extra input of fluvial sediments can cope with increased erosion rates at the shores. Besides, the rate of actual sea-level rise in West Greenland is probably less than the local rate of isostatic uplift, leading to local relative sea level fall.The focus in this presentation is on shoreline changes and its impact on two coastal environments in Greenland: the Young Sound area (fjord environment in North-East Greenland), and the southern shore of Disko Island (open sea embayment in West Greenland). These coastal environments exhibit a wide variety of coastal landforms like deltas, spits, barriers, etc. The coastal landforms were mapped and aerial images, orthogonal photos, and satellite images were used to digitize successive shorelines. The shoreline changes were estimated using the digital shoreline analysis system (DSAS) of the USGS. The spatial variability of accumulation and erosion patterns was detected and shows a surprising thread for ancient settlements and present-day activities in the coastal zone. The same patterns are finally discussed in terms of coastal risk assessment.

  16. Structural Insights into the Activation of Human Relaxin Family Peptide Receptor 1 by Small-Molecule Agonists.

    Hu, Xin; Myhr, Courtney; Huang, Zaohua; Xiao, Jingbo; Barnaeva, Elena; Ho, Brian A; Agoulnik, Irina U; Ferrer, Marc; Marugan, Juan J; Southall, Noel; Agoulnik, Alexander I

    2016-03-29

    The GPCR relaxin family peptide receptor 1 (RXFP1) mediates the action of relaxin peptide hormone, including its tissue remodeling and antifibrotic effects. The peptide has a short half-life in plasma, limiting its therapeutic utility. However, small-molecule agonists of human RXFP1 can overcome this limitation and may provide a useful therapeutic approach, especially for chronic diseases such as heart failure and fibrosis. The first small-molecule agonists of RXFP1 were recently identified from a high-throughput screening, using a homogeneous cell-based cAMP assay. Optimization of the hit compounds resulted in a series of highly potent and RXFP1 selective agonists with low cytotoxicity, and excellent in vitro ADME and pharmacokinetic properties. Here, we undertook extensive site-directed mutagenesis studies in combination with computational modeling analysis to probe the molecular basis of the small-molecule binding to RXFP1. The results showed that the agonists bind to an allosteric site of RXFP1 in a manner that closely interacts with the seventh transmembrane domain (TM7) and the third extracellular loop (ECL3). Several residues were determined to play an important role in the agonist binding and receptor activation, including a hydrophobic region at TM7 consisting of W664, F668, and L670. The G659/T660 motif within ECL3 is crucial to the observed species selectivity of the agonists for RXFP1. The receptor binding and activation effects by the small molecule ML290 were compared with the cognate ligand, relaxin, providing valuable insights on the structural basis and molecular mechanism of receptor activation and selectivity for RXFP1. PMID:26866459

  17. Living microbial ecosystems within the active zone of catagenesis: Implications for feeding the deep biosphere

    Horsfield, B.; Schenk, H. J.; Zink, K.; Ondrak, R.; Dieckmann, V.; Kallmeyer, J.; Mangelsdorf, K.; di Primio, R.; Wilkes, H.; Parkes, R. J.; Fry, J.; Cragg, B.

    2006-06-01

    Earth's largest reactive carbon pool, marine sedimentary organic matter, becomes increasingly recalcitrant during burial, making it almost inaccessible as a substrate for microorganisms, and thereby limiting metabolic activity in the deep biosphere. Because elevated temperature acting over geological time leads to the massive thermal breakdown of the organic matter into volatiles, including petroleum, the question arises whether microorganisms can directly utilize these maturation products as a substrate. While migrated thermogenic fluids are known to sustain microbial consortia in shallow sediments, an in situ coupling of abiotic generation and microbial utilization has not been demonstrated. Here we show, using a combination of basin modelling, kinetic modelling, geomicrobiology and biogeochemistry, that microorganisms inhabit the active generation zone in the Nankai Trough, offshore Japan. Three sites from ODP Leg 190 have been evaluated, namely 1173, 1174 and 1177, drilled in nearly undeformed Quaternary and Tertiary sedimentary sequences seaward of the Nankai Trough itself. Paleotemperatures were reconstructed based on subsidence profiles, compaction modelling, present-day heat flow, downhole temperature measurements and organic maturity parameters. Today's heat flow distribution can be considered mainly conductive, and is extremely high in places, reaching 180 mW/m 2. The kinetic parameters describing total hydrocarbon generation, determined by laboratory pyrolysis experiments, were utilized by the model in order to predict the timing of generation in time and space. The model predicts that the onset of present day generation lies between 300 and 500 m below sea floor (5100-5300 m below mean sea level), depending on well location. In the case of Site 1174, 5-10% conversion has taken place by a present day temperature of ca. 85 °C. Predictions were largely validated by on-site hydrocarbon gas measurements. Viable organisms in the same depth range have been

  18. Evolution of surface motor activation zones in hemiplegic patients during 20 sessions of FES therapy with multi-pad electrodes

    Jovana Malešević

    2016-06-01

    Full Text Available The purpose of this study was to examine surface motor activation zones for wrist, fingers and thumb extension movements and their temporal change during 20 therapy sessions using advanced multi-pad functional electrical stimulation system. Results from four hemiplegic patients indicate that certain zones have higher probability of eliciting each of the target movements. However, mutual overlap and variations of the zones are present not just between the subjects, but also on the intrasubject level, reflected through these session to session transformations of the selected virtual electrodes. The obtained results could be used as a priori knowledge for semi-automated optimization algorithm and could shorten the time required for calibration of the multi-pad electrode.

  19. Discovery of a small-molecule binder of the oncoprotein gankyrin that modulates gankyrin activity in the cell

    Chattopadhyay, Anasuya; O’Connor, Cornelius J.; Zhang, Fengzhi; Galvagnion, Celine; Galloway, Warren R. J. D.; Tan, Yaw Sing; Stokes, Jamie E.; Rahman, Taufiq; Verma, Chandra; Spring, David R.; Itzhaki, Laura S.

    2016-04-01

    Gankyrin is an ankyrin-repeat oncoprotein whose overexpression has been implicated in the development of many cancer types. Elevated gankyrin levels are linked to aberrant cellular events including enhanced degradation of tumour suppressor protein p53, and inhibition of gankyrin activity has therefore been identified as an attractive anticancer strategy. Gankyrin interacts with several partner proteins, and a number of these protein-protein interactions (PPIs) are of relevance to cancer. Thus, molecules that bind the PPI interface of gankyrin and interrupt these interactions are of considerable interest. Herein, we report the discovery of a small molecule termed cjoc42 that is capable of binding to gankyrin. Cell-based experiments demonstrate that cjoc42 can inhibit gankyrin activity in a dose-dependent manner: cjoc42 prevents the decrease in p53 protein levels normally associated with high amounts of gankyrin, and it restores p53-dependent transcription and sensitivity to DNA damage. The results represent the first evidence that gankyrin is a “druggable” target with small molecules.

  20. Auroral Electrojet (AE, AL, AO, AU) - A Global Measure of Auroral Zone Magnetic Activity

    National Oceanic and Atmospheric Administration, Department of Commerce — The AE index is derived from geomagnetic variations in the horizontal component observed at selected (10-13) observatories along the auroral zone in the northern...

  1. Immobilisation of redox active molecules as precursors for nanowire self-assembly

    Campagnoli, Elena

    2007-01-01

    Spontaneously adsorbed monolayers of [Co(ttp-CH2-SH)2](PF6)2 have been formed on platinum microelectrodes by exposure to micromolar solutions of the complex in 0.1 M TBABF4 in acetonitrile, ttp-CH2-SH is 4'-(p-(thiolmethyl)-phenyl)-2,2':6',2''- terpyridine. Resonance Raman spectroscopy on roughened polycrystalline platinum macro electrodes show that the molecule undergoes adsorption by sulphur atom onto the platinum surface. The monolayers show reversible and well defined cyclic voltammetry w...

  2. Depth-dependent activity of non-volcanic tremor and other slow earthquake in the Nankai subduction zone

    Obara, K.

    2010-12-01

    In the Nankai subduction zone, some types of slow earthquakes have been detected by dense seismic/geodetic observation network. At the deeper part in the transition zone between the locked and stable sliding zones, the tremor is distributed within a narrow belt with a 600 km along the strike of the subducting Philippine Sea plate (Obara, 2002). The major tremor burst is often accompanied by the short-term slow slip event (Obara et al., 2004) and deep very low frequency earthquake (Ito et al., 2007). Between the belt-like tremor zone and locked zone, the long-term slow slip event occurs at eastern and western edges of the tremor belt-like zone. These slow earthquakes represent a clear depth-dependent property. The slip behavior in time is drastically different between the shallower long-term slow slip event and deeper coupling events. Within the tremor source area, the temporal behavior of tremor activity is different in depth. In western Shikoku and northeastern Kii where major tremor bursts associated with short-term slow slip events frequently occur, the tremor distribution is separated into double peaks at shallower and deeper edge in the dip direction (Obara et al., 2010). The updip tremor activity is modulated by the major tremor burst occurring at regular recurrence interval. On the other hand, the downdip tremor activity is composed of more frequent occurrence of minor burst. The nucleation of the tremor activity often occurs from the deeper part and migrates updip direction, then propagates along strike laterally. In Bungo channel between Shikoku and Kyushu islands at the western edge of the tremor source belt, the long-term slow slip event with duration from a half to one year occurs every 6 years in 1997, 2003 and 2010. The transient slip event strongly affect to the tremor activity. Especially, the updip part of the tremor activity in Bungo channel is clearly correlated to the GPS displacement caused by the long-term slow slip event; however, the downdip

  3. Coordinated trafficking of synaptic vesicle and active zone proteins prior to synapse formation

    Sabo Shasta L

    2011-05-01

    Full Text Available Abstract Background The proteins required for synaptic transmission are rapidly assembled at nascent synapses, but the mechanisms through which these proteins are delivered to developing presynaptic terminals are not understood. Prior to synapse formation, active zone proteins and synaptic vesicle proteins are transported along axons in distinct organelles referred to as piccolo-bassoon transport vesicles (PTVs and synaptic vesicle protein transport vesicles (STVs, respectively. Although both PTVs and STVs are recruited to the same site in the axon, often within minutes of axo-dendritic contact, it is not known whether or how PTV and STV trafficking is coordinated before synapse formation. Results Here, using time-lapse confocal imaging of the dynamics of PTVs and STVs in the same axon, we show that vesicle trafficking is coordinated through at least two mechanisms. First, a significant proportion of STVs and PTVs are transported together before forming a stable terminal. Second, individual PTVs and STVs share pause sites within the axon. Importantly, for both STVs and PTVs, encountering the other type of vesicle increases their propensity to pause. To determine if PTV-STV interactions are important for pausing, PTV density was reduced in axons by expression of a dominant negative construct corresponding to the syntaxin binding domain of syntabulin, which links PTVs with their KIF5B motor. This reduction in PTVs had a minimal effect on STV pausing and movement, suggesting that an interaction between STVs and PTVs is not responsible for enhancing STV pausing. Conclusions Our results indicate that trafficking of STVs and PTVs is coordinated even prior to synapse development. This novel coordination of transport and pausing might provide mechanisms through which all of the components of a presynaptic terminal can be rapidly accumulated at sites of synapse formation.

  4. The Active and Periactive Zone Organization and the Functional Properties of Small and Large Synapses.

    Cano, Raquel; Tabares, Lucia

    2016-01-01

    The arrival of an action potential (AP) at a synaptic terminal elicits highly synchronized quanta release. Repetitive APs produce successive synaptic vesicle (SV) fusions that require management of spent SV components in the presynaptic membrane with minimum disturbance of the secretory apparatus. To this end, the synaptic machinery is structured accordingly to the strength and the range of frequencies at which each particular synapse operates. This results in variations in the number and dimension of Active Zones (AZs), amount and distribution of SVs, and probably, in the primary endocytic mechanisms they use. Understanding better how these structural differences determine the functional response in each case has been a matter of long-term interest. Here we review the structural and functional properties of three distinct types of synapses: the neuromuscular junction (NMJ; a giant, highly reliable synapse that must exocytose a large number of quanta with each stimulus to guarantee excitation of the postsynaptic cell), the hippocampal excitatory small synapse (which most often has a single release site and a relatively small pool of vesicles), and the cerebellar mossy fiber-granule cell synapse (which possesses hundreds of release sites and is able to translocate, dock and prime vesicles at high speed). We will focus on how the release apparatus is organized in each case, the relative amount of vesicular membrane that needs to be accommodated within the periAZ upon stimulation, the different mechanisms for retrieving the excess of membrane and finally, how these factors may influence the functioning of the release sites. PMID:27252645

  5. Simultaneous Segmentation of Prostatic Zones Using Active Appearance Models With Multiple Coupled Levelsets.

    Toth, Robert; Ribault, Justin; Gentile, John; Sperling, Dan; Madabhushi, Anant

    2013-09-01

    In this work we present an improvement to the popular Active Appearance Model (AAM) algorithm, that we call the Multiple-Levelset AAM (MLA). The MLA can simultaneously segment multiple objects, and makes use of multiple levelsets, rather than anatomical landmarks, to define the shapes. AAMs traditionally define the shape of each object using a set of anatomical landmarks. However, landmarks can be difficult to identify, and AAMs traditionally only allow for segmentation of a single object of interest. The MLA, which is a landmark independent AAM, allows for levelsets of multiple objects to be determined and allows for them to be coupled with image intensities. This gives the MLA the flexibility to simulataneously segmentation multiple objects of interest in a new image. In this work we apply the MLA to segment the prostate capsule, the prostate peripheral zone (PZ), and the prostate central gland (CG), from a set of 40 endorectal, T2-weighted MRI images. The MLA system we employ in this work leverages a hierarchical segmentation framework, so constructed as to exploit domain specific attributes, by utilizing a given prostate segmentation to help drive the segmentations of the CG and PZ, which are embedded within the prostate. Our coupled MLA scheme yielded mean Dice accuracy values of .81, .79 and .68 for the prostate, CG, and PZ, respectively using a leave-one-out cross validation scheme over 40 patient studies. When only considering the midgland of the prostate, the mean DSC values were .89, .84, and .76 for the prostate, CG, and PZ respectively. PMID:23997571

  6. Gold nano-island arrays on silicon as SERS active substrate for organic molecule detection

    Gold islands forming highly controlled arrays have been fabricated by two potential step electrochemical deposition method using nanopatterned Si surface templates. In the present work, the Raman scattering studies realized using 11-mercaptoundecanoic probe molecule showed that such structures exhibit an enhanced Raman signal compared with nanostructured physical deposited thin gold film on flat silicon substrate and can be valued as surface-enhanced Raman scattering substrates. Besides the more appropriate management of nano-island arrays distribution, the high ratio of their Raman signals can be explain by the epitaxial-like growth mechanism of the metallic nano-islands, clearly showed by X-ray diffraction studies. Furthermore, the substrates enabled reproducibility and stability detection due to the chemically assembling of organothiol molecules, the X-ray photoelectron spectroscopy studies confirming formation of the thiolate species which corresponds to Au-S bonds, and also, the unwanted ‘hot-spots’ are missing, which make them suitable for high sensitivity biosensing applications. - Highlights: • Gold nano-islands are electrochemical deposited on nanopatterned silicon. • The X-ray diffraction studies revealed the epitaxial-like growth mechanism. • Enhanced Raman signal of Au nano-islands was observed compared with Au nano-film

  7. Synthesis of Zn-MOF incorporating titanium-hydrides as active sites binding H2 molecules

    This paper describes the synthetic effort for a Zn-MOF imparting Ti-H as a preferential binding site potentially capturing H2 molecules via Kubas-type interaction. The formation mechanism of Ti-H innate to the final material was potentially demonstrated to follow a radical dissociation rather than a β-hydrogen elimination and a C-H reductive elimination. - Graphical abstract: This study details the synthesis and the formation mechanism of Zn-MOF adsorbent site-isolating TiH3 that can potentially capture H2 molecules via Kubas-binding mechanism. - Highlights: • OH-functionalized Zn-MOF was employed as a reactive template to site-isolate TiH3. • This MOF was post-synthetically modified using a tetracyclohexyl titanium (IV). • This intermediate was hydrogenolyzed to change ligand from cyclohexyl to hydride. • Formation mechanism of TiH3 was investigated via two control GC–MS experiments. • Final Zn-MOF potentially site-isolating TiH3 species was used as a H2 adsorbent

  8. The Activation of Macrophage and Upregulation of CD40 Costimulatory Molecule in Lipopolysaccharide-Induced Acute Lung Injury

    Wenxiang Bi

    2008-04-01

    Full Text Available To study the activation of macrophage and upregulation of costimulatory molecule of CD40 in lipopolysaccharide- (LPS- induced acute lung injury (ALI model, and to investigate the pathogenecy of ALI, mice were randomly divided into two groups. ALI model was created by injecting 0.2 mg/kg LPS in phosphate saline (PBS in trachea. The pathologic changes of mice lungs were observed by HE staining at 24 and 48 hours after LPS treatment, then the alveolar septum damage, abnormal contraction, alveolar space hyperemia, and neutrophils or other inflammatory cells infiltration in the LPS group, but not in the control group, were observed. The expression of CD40 mRNA and CD40 protein molecules were higher in LPS group as compared to the control group by Northern blot and flow cytometry, respectively. Expression of Toll-like receptor-4 (TLR4 in activated macrophage (AMΦ was higher in LPS group as compared to the control group by RT-PCR. The activation of NF-κB binding to NF-κB consensus oligos increased in LPS group by EMSA in macrophage. The concentrations of TNF-α, MIP-2, and IL-1β cytokines from bronchoalveolar lavage fluid (BALF were increased significantly in LPS group as compared to the control group by ELISA. The activation of AM and upregulation of costimulatory molecule CD40 induced all kinds of inflammatory cytokines releasing, then led to ALI. Therefore, both of them played vital role in the process of development of ALI.

  9. Communities on the move: Pedestrian-oriented zoning as a facilitator of adult active travel to work in the United States

    Jamie Friedman Chriqui

    2016-04-01

    Full Text Available Background: Communities across the United States have been reforming their zoning codes to create pedestrian-friendly neighborhoods with increased street connectivity, mixed-use and higher density, open space, transportation infrastructure, and a traditional neighborhood structure. Zoning code reforms include new urbanist zoning such as the SmartCode, form-based codes, transects, transportation and pedestrian-oriented developments, and traditional neighborhood developments.Purpose: To examine the relationship of zoning code reforms and more active living-oriented zoning provisions with adult active travel to work via walking, biking, or by using public transit.Methods: Zoning codes effective as of 2010 were compiled for 3,914 municipal-level jurisdictions located in 471 counties and 2 consolidated cities in 48 states and the District of Columbia, and that collectively covered 72.9% of the U.S. population. Zoning codes were evaluated for the presence of code reform zoning and nine pedestrian-oriented zoning provisions (1=yes: sidewalks, crosswalks, bike-pedestrian connectivity, street connectivity, bike lanes, bike parking, bike-pedestrian trails/paths, mixed use development, and other walkability/pedestrian-orientation. A zoning scale reflected the number of provisions addressed (out of 10. Five continuous outcome measures were constructed using 2010-2014 American Community Survey municipal-level 5-year estimates to assess the percentage of workers: walking, biking, walking or biking, or taking public transit to work OR engaged in any active travel to work. Regression models controlled for municipal-level socioeconomic characteristics and a GIS-constructed walkability scale and were clustered on county with robust standard errors. Results: Adjusted models indicated that several pedestrian-oriented zoning provisions were statistically associated (p<.05 or lower with increased rates of walking, biking, or engaging in any active travel (walking

  10. Raman and surface enhanced Raman spectroscopic studies of specific, small molecule activator of histone acetyltransferase p300

    Kundu, Partha P.; Pavan Kumar, G. V.; Mantelingu, Kempegowda; Kundu, Tapas K.; Narayana, Chandrabhas

    2011-07-01

    We report for the first time, the Raman and surface enhanced Raman scattering (SERS) studies of N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-benzamide (CTB). This molecule is specific activator of human histone acetyltransferase (HAT), p300, and serves as lead molecule to design anti-neoplastic therapeutics. A detailed Raman and SERS band assignments have been performed for CTB, which are compared with the density functional theory calculations. The observed red shift of N sbnd H stretching frequency from the computed wavenumber indicates the weakening of N sbnd H bond resulting from proton transfer to the neighboring oxygen atom. We observe Ag sbnd N vibrational mode at 234 cm -1 in SERS of CTB. This indicates there is a metal-molecule bond leading to chemical enhancement in SERS. We also observe, enhancement in the modes pertaining to substituted benzene rings and methyl groups. Based on SERS analysis we propose the adsorption sites and the orientation of CTB on silver surface.