Science.gov

Sample records for gnnqqny heptapeptide decamer

  1. The DECam Legacy Survey

    NASA Astrophysics Data System (ADS)

    Blum, Robert D.; Burleigh, Kaylan; Dey, Arjun; Schlegel, David J.; Meisner, Aaron M.; Levi, Michael; Myers, Adam D.; Lang, Dustin; Moustakas, John; Patej, Anna; Valdes, Francisco; Kneib, Jean-Paul; Huanyuan, Shan; Nord, Brian; Olsen, Knut A.; Delubac, Timothée; Saha, Abi; James, David; Walker, Alistair R.; DECaLS Team

    2016-06-01

    The DECam Legacy Survey (DECaLS) is conducting a 3-band imaging survey of the Sloan Digital Sky Survey (SDSS) extragalactic footprint as part of the Legacy Survey, which is associated with the Dark Energy Spectroscopic Instrument (DESI) redshift survey. The Legacy Survey covers 14000 square degrees in the g, r, and z bands and is being executed on the Blanco 4-m, Mayall 4-m, and Bok 2.3-m telescopes. For DECaLS, the Dark Energy Camera (DECam) will image the footprint overlapping SDSS in the region -20 < Dec < +30 deg, to depths of g=24.7, r=23.9, z=23.0 and will eventually cover a total of 7500 square degrees. The survey began in 2014 and will run through Spring 2017. Images and catalogs were introduced in Public Data Release 2 (DR2), which occurred in January 2016. The algorithm "Tractor" applies multi-wavelength forced photometry to DECam and WISE data to produce galaxy (and star) magnitudes (as well as shape and other information) for the catalogs. In total, the optical data in DR2 cover a disjoint footprint in 2078, 2141 and 5322 square degrees in g, r, and z bands, respectively; 1807 square degrees has been observed in all three optical filters. There are approximately 260 million unique sources in DR2 spread over 97,554 0.25 x 0.25 square degree bricks.The Dark Energy Spectroscopic Instrument (DESI) will observe 30+ million galaxies and quasars in a 14,000 square degree extragalactic footprint. The targeting in that footprint will be provided by a combination of these DECam data, the MOSAIC camera on the Mayall 4-meter, and the 90Prime camera on the Bok telescope.

  2. On cooperative effects and aggregation of GNNQQNY and NNQQNY peptides

    NASA Astrophysics Data System (ADS)

    Nochebuena, Jorge; Ireta, Joel

    2015-10-01

    Some health disturbances like neurodegenerative diseases are associated to the presence of amyloids. GNNQQNY and NNQQNY peptides are considered as prototypical examples for studying the formation of amyloids. These exhibit quite different aggregation behaviors despite they solely differ in size by one residue. To get insight into the reasons for such difference, we have examined association energies of aggregates (parallel β-sheets, fibril-spines, and crystal structures) from GNNQQNY and NNQQY using density functional theory. As we found that GNNQQNY tends to form a zwitterion in the crystal structure, we have investigated the energetics of parallel β-sheets and fibril-spines in the canonical and zwitterionic states. We found that the formation of GNNQQNY aggregates is energetically more favored than the formation of the NNQQNY ones. We show that the latter is connected to the network of hydrogen bonds formed by each aggregate. Moreover, we found that the formation of some NNQQNY aggregates is anticooperative, whereas cooperative with GNNQQNY. These results have interesting implications for deciphering the factors determining peptide aggregation propensities.

  3. Spectrophotometric Calibration System for DECam

    NASA Astrophysics Data System (ADS)

    Rheault, Jean-Philippe; DePoy, D.; Marshall, J.; Carona, D.; Cook, K.; Behm, T.; Allen, R.

    2011-01-01

    We present a spectrophotometric calibration system that will be implemented as part of the DES DECam project at the Blanco 4 meter at CTIO. Our calibration system uses a 2nm wide tunable source to measure the instrumental response function of the telescope from 300nm up to 1100nm. This calibration will be performed at regular interval during the survey to monitor any change in the transmission function. The system consists of a monochromator based tunable light source that provides illumination on a dome flat that is monitored by calibrated photodiodes and allow us to measure the throughput as a function of wavelength. Our system has an output power of 2 mW, equivalent to a flux of approximately 800 photons/s per pixel on DECam. We also present results from the deployment of a prototype of this system at the Swope and DuPont telescopes at Las Campanas Observatory for the calibration of the photometric equipment used in the Carnegie Supernova Project.

  4. The DECam Minute Cadence Survey

    NASA Astrophysics Data System (ADS)

    Belardi, C.; Kilic, M.; Munn, J. A.; Gianninas, A.; Barber, S. D.; Dey, A.; Stetson, P. B.

    2017-03-01

    We present the first results from a minute cadence survey of a 3 deg2 field obtained with the Dark Energy Camera. We imaged part of the Canada- France-Hawaii Telescope Legacy Survey area over eight half-nights. We use the stacked images to identify 111 high proper motion white dwarf candidates with g≤ 24.5 mag and search for eclipse-like events and other sources of variability. We find a new g=20.64 mag pulsating ZZ Ceti star with pulsation periods of 11-13 min. However, we do not find any transiting planetary companions in the habitable zone of our target white dwarfs. Given the probability of eclipses of 1% and our observing window from the ground, the non-detection of such companions in this first field is not surprising. Minute cadence DECam observations of additional fields will provide stringent constraints on the frequency of planets in the white dwarf habitable zone.

  5. Characterization of DECam focal plane detectors

    SciTech Connect

    Diehl, H.Thomas; Angstadt, Robert; Campa, Julia; Cease, Herman; Derylo, Greg; Emes, John H.; Estrada, Juan; Kibik, Donna; Flaugher, Brenna L.; Holland, Steve E.; Jonas, Michelle; /Fermilab /Madrid, CIEMAT /LBL, Berkeley /Argonne /Pennsylvania U.

    2008-06-01

    DECam is a 520 Mpix, 3 square-deg FOV imager being built for the Blanco 4m Telescope at CTIO. This facility instrument will be used for the 'Dark Energy Survey' of the southern galactic cap. DECam has chosen 250 ?m thick CCDs, developed at LBNL, with good QE in the near IR for the focal plane. In this work we present the characterization of these detectors done by the DES team, and compare it to the DECam technical requirements. The results demonstrate that the detectors satisfy the needs for instrument.

  6. Centaur size distribution with DECam

    NASA Astrophysics Data System (ADS)

    Fuentes, Cesar; Trilling, David E.; Schlichting, Hilke

    2014-11-01

    We present the results of the 2014 centaur search campaign on the Dark Energy Camera (DECam) in Tololo, Chile. This is the largest debiased Centaur survey to date, measuring for the first time the size distribution of small Centaurs (1-10km) and the first time the sizes of planetesimals from which the entire Solar System formed are directly detected.The theoretical model for the coagulation and collisional evolution of the outer solar system proposed in Schlichting et al. 2013 predicts a steep rise in the size distribution of TNOs smaller than 10km. These objects are below the detection limit of current TNO surveys but feasible for the Centaur population. By constraining the number of Centaurs and this feature in their size distribution we can confirm the collisional evolution of the Solar System and estimate the rate at which material is being transferred from the outer to the inner Solar System. If the shallow power law behavior from the TNO size distribution at ~40km can be extrapolated to 1km, the size of the Jupiter Family of Comets (JFC), there would not be enough small TNOs to supply the JFC population (Volk & Malhotra, 2008), debunking the link between TNOs and JFCs.We also obtain the colors of small Centaurs and TNOs, providing a signature of collisional evolution by measuring if there is in fact a relationship between color and size. If objects smaller than the break in the TNO size distribution are being ground down by collisions then their surfaces should be fresh, and then appear bluer in the optical than larger TNOs that are not experiencing collisions.

  7. DECam Integration Tests on Telescope Simulator

    NASA Astrophysics Data System (ADS)

    Soares-Santos, M.; Annis, J.; Bonati, M.; Buckley-Geer, E.; Cease, H.; DePoy, D.; Derylo, G.; Diehl, H. T.; Elliott, A.; Estrada, J.; Finley, D.; Flaugher, B.; Frieman, J.; Hao, J.; Honscheid, K.; Karliner, I.; Krempetz, K.; Kuehn, K.; Kuhlmann, S.; Kuk, K.; Lin, H.; Merrit, W.; Neilsen, E.; Scott, L.; Serrano, S.; Shaw, T.; Schultz, K.; Stuermer, W.; Sypniewski, A.; Thaler, J.; Walker, A.; Walton, J.; Wester, W.; Yanny, B.; Des Collaboration

    The Dark Energy Survey (DES) is a next generation optical survey aimed at measuring the expansion history of the universe using four probes: weak gravitational lensing, galaxy cluster counts, baryon acoustic oscillations, and Type Ia supernovae. To perform the survey, the DES Collaboration is building the Dark Energy Camera (DECam), a 3 square degree, 570 Megapixel CCD camera which will be mounted at the Blanco 4-meter telescope at the Cerro Tololo Inter-American Observatory. DES will survey 5000 square degrees of the southern galactic cap in 5 filters (g, r, i, z, Y). DECam will be comprised of 74 250 micron thick fully depleted CCDs: 62 2k x 4k CCDs for imaging and 12 2k x 2k CCDs for guiding and focus. Construction of DECam is nearing completion. In order to verify that the camera meets technical specifications for DES and to reduce the time required to commission the instrument, we have constructed a full sized telescope simulator and performed full system testing and integration prior to shipping. To complete this comprehensive test phase we have simulated a DES observing run in which we have collected 4 nights worth of data. We report on the results of these unique tests performed for the DECam and its impact on the experiment's progress.

  8. Status of the Dark Energy Survey Camera (DECam) Project

    SciTech Connect

    Flaugher, Brenna L.; Abbott, Timothy M.C.; Angstadt, Robert; Annis, Jim; Antonik, Michelle, L.; Bailey, Jim; Ballester, Otger.; Bernstein, Joseph P.; Bernstein, Rebbeca; Bonati, Marco; Bremer, Gale; /Fermilab /Cerro-Tololo InterAmerican Obs. /ANL /Texas A-M /Michigan U. /Illinois U., Urbana /Ohio State U. /University Coll. London /LBNL /SLAC /IFAE

    2012-06-29

    The Dark Energy Survey Collaboration has completed construction of the Dark Energy Camera (DECam), a 3 square degree, 570 Megapixel CCD camera which will be mounted on the Blanco 4-meter telescope at CTIO. DECam will be used to perform the 5000 sq. deg. Dark Energy Survey with 30% of the telescope time over a 5 year period. During the remainder of the time, and after the survey, DECam will be available as a community instrument. All components of DECam have been shipped to Chile and post-shipping checkout finished in Jan. 2012. Installation is in progress. A summary of lessons learned and an update of the performance of DECam and the status of the DECam installation and commissioning will be presented.

  9. DECal: A Spectrophotometric Calibration System for DECam

    NASA Astrophysics Data System (ADS)

    Marshall, J. L.; Rheault, J.-P.; DePoy, D. L.; Prochaska, T.; Allen, R.; Behm, T. W.; Martin, E. C.; Veal, B.; Villanueva, S., Jr.; Williams, P.; Wise, J.

    2016-05-01

    DECal is a new calibration system for the CTIO 4 m Blanco telescope. It is currently being installed as part of the Dark Energy Survey and will provide both broadband flat fields and narrowband (˜1 nm bandwidth) spectrophotometric calibration for the new Dark Energy Camera (DECam). Both of these systems share a new Lambertian flat field screen. The broadband flat field system uses LEDs to illuminate each photometric filter. The spectrophotometric calibration system consists of a monochromator-based tunable light source that is projected onto the flat field screen using a custom line-to-spot fiber bundle and an engineered diffuser. Several calibrated photodiodes positioned along the beam monitor the telescope throughput as a function of wavelength. This system will measure the wavelength-dependent instrumental response function of the total telescope+instrument system in the range 300 <λ< 1100nm. The spectrophotometric calibration will be performed regularly (roughly once per month) to determine the spectral response of the DECam system and to monitor changes in instrumental throughput during the five year Dark Energy Survey project.

  10. Terahertz absorption of DNA decamer duplex.

    PubMed

    Li, Xiaowei; Globus, Tatiana; Gelmont, Boris; Salay, Luiz C; Bykhovski, Alexei

    2008-11-27

    This work combines experimental and theoretical approaches to investigate terahertz absorption spectra of the DNA formed by the sequence oligomer 5'-CCGGCGCCGG-3'. The three-dimensional structure of this self-complimentary DNA decamer has been well-studied, permitting us to perform direct identification of the low-frequency phonon modes associated with specific conformation and to conduct comprehensive computer simulations. Two modeling techniques, normal-mode analysis and nanosecond molecular dynamics with explicit solvent molecules, were employed to extract the low-frequency vibrational modes based on which the absorption spectra were calculated. The absorption spectra of the DNA decamer in aqueous solution were measured in the frequency range 10-25 cm(-1) using the terahertz Fourier transform infrared spectroscopy. Multiple well-resolved and reproducible resonance modes were observed. When calculated and experimental spectra were compared, the spectrum based on molecular dynamics simulations showed a better correlation with the experimental spectra than the one based on normal-mode analysis. These results demonstrate that there exist a considerable number of active low-frequency phonon modes in this short DNA duplex.

  11. Comparison of LSST and DECam wavefront recovery algorithms

    NASA Astrophysics Data System (ADS)

    Xin, Bo; Roodman, Aaron; Angeli, George; Claver, Chuck; Thomas, Sandrine

    2016-07-01

    We make a detailed quantitative comparison of the wavefront recovery algorithms between those developed for Dark Energy Camera (DECam) and the Large Synoptic Survey Telescope (LSST). Samples used in this study include images of out of focus stars collected by the DECam at the Blanco 4-meter telescope and artificial simulated donut images. The data from DECam include wavefront images collected by the wavefront sensors and out-of-focus images where the entire DECam sensor array is used. For simulated images, we have used both the forward Fraunhofer diffraction and a LSST-like ZEMAX optical model where the images are convolved with Kolmogorov atmosphere. All samples are analyzed with the forward wavefront retrieval algorithm developed for DECam and the transport of intensity algorithm for LSST. Good quantitative agreement between results by the two implemented algorithms is observed.

  12. Automated characterization of CCD detectors for DECam

    NASA Astrophysics Data System (ADS)

    Kubik, D.; Alvarez, R.; Abbott, T.; Annis, J.; Bonati, M.; Buckley-Geer, E.; Campa, J.; Cease, H.; Chappa, S.; DePoy, D.; Derylo, G.; Diehl, H. T.; Estrada, J.; Flaugher, B.; Hao, J.; Holland, S.; Huffman, D.; Karliner, I.; Kuhlmann, S.; Kuk, K.; Lin, H.; Montes, J.; Roe, N.; Scarpine, V.; Schmidt, R.; Schultz, K.; Shaw, T.; Simaitis, V.; Spinka, H.; Stuermer, W.; Tucker, D.; Walker, A.; Wester, W.

    2010-07-01

    The Dark Energy Survey Camera (DECam) will be comprised of a mosaic of 74 charge-coupled devices (CCDs). The Dark Energy Survey (DES) science goals set stringent technical requirements for the CCDs. The CCDs are provided by LBNL with valuable cold probe data at 233 K, providing an indication of which CCDs are more likely to pass. After comprehensive testing at 173 K, about half of these qualify as science grade. Testing this large number of CCDs to determine which best meet the DES requirements is a very time-consuming task. We have developed a multistage testing program to automatically collect and analyze CCD test data. The test results are reviewed to select those CCDs that best meet the technical specifications for charge transfer efficiency, linearity, full well capacity, quantum efficiency, noise, dark current, cross talk, diffusion, and cosmetics.

  13. Serinocyclins A and B, Cyclic Heptapeptides from Metarhizium anisopliae

    USDA-ARS?s Scientific Manuscript database

    Two new cyclic heptapeptides, serinocyclins A (1) and B (2), were isolated from conidia of the entomopathogenic fungus Metarhizium anisopliae. Structures were elucidated by a combination of mass spectrometric, NMR, and X-ray diffraction techniques. Serinocyclin A (1) contains three serine units, a...

  14. Structural characterization of GNNQQNY amyloid fibrils by magic angle spinning NMR.

    PubMed

    van der Wel, Patrick C A; Lewandowski, Józef R; Griffin, Robert G

    2010-11-09

    Several human diseases are associated with the formation of amyloid aggregates, but experimental characterization of these amyloid fibrils and their oligomeric precursors has remained challenging. Experimental and computational analysis of simpler model systems has therefore been necessary, for instance, on the peptide fragment GNNQQNY7−13 of yeast prion protein Sup35p. Expanding on a previous publication, we report here a detailed structural characterization of GNNQQNY fibrils using magic angle spinning (MAS) NMR. On the basis of additional chemical shift assignments we confirm the coexistence of three distinct peptide conformations within the fibrillar samples, as reflected in substantial chemical shift differences. Backbone torsion angle measurements indicate that the basic structure of these coexisting conformers is an extended β-sheet. We structurally characterize a previously identified localized distortion of the β-strand backbone specific to one of the conformers. Intermolecular contacts are consistent with each of the conformers being present in its own parallel and in-register sheet. Overall the MAS NMR data indicate a substantial difference between the structure of the fibrillar and crystalline forms of these peptides, with a clearly increased complexity in the GNNQQNY fibril structure. These experimental data can provide guidance for future work, both experimental and theoretical, and provide insights into the distinction between fibril growth and crystal formation.

  15. The DECam minute cadence survey - I

    NASA Astrophysics Data System (ADS)

    Belardi, Claudia; Kilic, Mukremin; Munn, Jeffrey A.; Gianninas, A.; Barber, Sara D.; Dey, Arjun; Stetson, Peter B.

    2016-11-01

    We present the first results from a minute cadence survey of a 3 deg2 field obtained with the Dark Energy Camera. We imaged part of the Canada-France-Hawaii Telescope Legacy Survey area over eight half-nights. We use the stacked images to identify 111 high proper motion white dwarf candidates with g ≤ 24.5 mag and search for eclipse-like events and other sources of variability. We find a new g = 20.64 mag pulsating ZZ Ceti star with pulsation periods of 11-13 min. However, we do not find any transiting planetary companions in the habitable zone of our target white dwarfs. Given the probability of eclipses of 1 per cent and our observing window from the ground, the non-detection of such companions in this first field is not surprising. Minute cadence DECam observations of additional fields will provide stringent constraints on the frequency of planets in the white dwarf habitable zone.

  16. DECam Observations of the Tidal Shells Around NGC 3923

    NASA Astrophysics Data System (ADS)

    Miller, Bryan; Grooms, Connor; Puzia, Thomas H.; Matthew, Taylor; Graeme, Candlish; McGaugh, Stacy S.; Mihos, Chris; Smith, Rory; Schirmer, Mischa

    2016-01-01

    Stellar shells around elliptical galaxies are thought to be the results of near-radial mergers with low mass companions. Thus, the shell systems contain information about the merger history and gravitational potential of the elliptical galaxy. We present a preliminary census of the shell system of NGC 3923 from extremely deep g and i-band DECam imaging. NGC 3923 has the largest know shell system, with different studies finding between 27 and 42 shells. We present an overview of the DECam data reduction and an initial analysis of the shell system.

  17. Kinetics of amyloid aggregation: a study of the GNNQQNY prion sequence.

    PubMed

    Nasica-Labouze, Jessica; Mousseau, Normand

    2012-01-01

    The small amyloid-forming GNNQQNY fragment of the prion sequence has been the subject of extensive experimental and numerical studies over the last few years. Using unbiased molecular dynamics with the OPEP coarse-grained potential, we focus here on the onset of aggregation in a 20-mer system. With a total of 16.9 μs of simulations at 280 K and 300 K, we show that the GNNQQNY aggregation follows the classical nucleation theory (CNT) in that the number of monomers in the aggregate is a very reliable descriptor of aggregation. We find that the critical nucleus size in this finite-size system is between 4 and 5 monomers at 280 K and 5 and 6 at 300 K, in overall agreement with experiment. The kinetics of growth cannot be fully accounted for by the CNT, however. For example, we observe considerable rearrangements after the nucleus is formed, as the system attempts to optimize its organization. We also clearly identify two large families of structures that are selected at the onset of aggregation demonstrating the presence of well-defined polymorphism, a signature of amyloid growth, already in the 20-mer aggregate.

  18. Kinetics of Amyloid Aggregation: A Study of the GNNQQNY Prion Sequence

    PubMed Central

    Nasica-Labouze, Jessica; Mousseau, Normand

    2012-01-01

    The small amyloid-forming GNNQQNY fragment of the prion sequence has been the subject of extensive experimental and numerical studies over the last few years. Using unbiased molecular dynamics with the OPEP coarse-grained potential, we focus here on the onset of aggregation in a 20-mer system. With a total of 16.9 of simulations at 280 K and 300 K, we show that the GNNQQNY aggregation follows the classical nucleation theory (CNT) in that the number of monomers in the aggregate is a very reliable descriptor of aggregation. We find that the critical nucleus size in this finite-size system is between 4 and 5 monomers at 280 K and 5 and 6 at 300 K, in overall agreement with experiment. The kinetics of growth cannot be fully accounted for by the CNT, however. For example, we observe considerable rearrangements after the nucleus is formed, as the system attempts to optimize its organization. We also clearly identify two large families of structures that are selected at the onset of aggregation demonstrating the presence of well-defined polymorphism, a signature of amyloid growth, already in the 20-mer aggregate. PMID:23209391

  19. The DECam Gravitational Waves Follow-up Program

    NASA Astrophysics Data System (ADS)

    Soares-Santos, Marcelle; Dark Energy Survey Collaboration

    2016-03-01

    We report on the status of a program to search for the optical counterparts of gravitational wave sources using the Dark Energy camera (DECam) on the Blanco 4-m telescope at CTIO. This program is a joint effort between the community and the Dark Energy Survey (DES). DECam has a 3 sq-deg field of view, and typically reaches a limiting magnitude of i,z = 23 for 90 sec exposure times. As such it is one of the most efficient and rapid instruments for deep searches of the large gravitational wave error regions. In this talk we describe our observing strategies and on-going efforts based on the first Advanced LIGO science run.

  20. A Novel Heptapeptide with Tyrosinase Inhibitory Activity Identified from a Phage Display Library.

    PubMed

    Nie, Huali; Liu, Lin; Yang, Huiqin; Guo, Hongzhen; Liu, Xiang; Tan, Yuanhao; Wang, Wen; Quan, Jing; Zhu, Limin

    2017-01-01

    Peptidic inhibition of the enzyme tyrosinase, responsible for skin pigmentation and food browning, would be extremely useful for the food, cosmetics, and pharmaceutical industries. In order to identify novel inhibitory peptides, a library of short sequence oligopeptides was screened to reveal direct interaction with the tyrosinase. A phage displaying heptapeptide (IQSPHFF) was found to bind most strongly to tyrosinase. The inhibitory activity of the heptapeptide was evaluated using mushroom tyrosinase. The results showed that the peptide inhibited both the monophenolase and diphenolase activities of mushroom tyrosinase with IC50 values of 1.7 and 4.0 mM, respectively. The heptapeptide is thought to be a reversible competitive inhibitor of diphenolase with the inhibition constants (Ki) of 0.765 mM. To further investigate how the heptapeptide exerts its inhibitory effect, a docking study between tyrosinase and heptapeptide was performed. The simulation showed that the heptapeptide binds in the active site of the enzyme near the catalytically active Cu ions and forms hydrogen bonds with five histidine residues on the active site. Phage display technology is thus a useful approach for the screening of potential tyrosinase inhibitors and could be widely applicable to a much wider range of enzymes.

  1. Identifying Electromagnetic Counterparts to Gravitational Wave Triggers With DECam

    NASA Astrophysics Data System (ADS)

    Cowperthwaite, Philip

    2016-03-01

    Identifying the electromagnetic counterpart to a gravitational wave (GW) event is one of the great observational challenges in modern astronomy. We report on our work to overcome this challenge by investigating the theoretical and practical issues associated with optical follow-up of a GW event. This includes a systematic study of the potential contaminant population and their impact on counterpart detectability in simulated observations. Additionally, we utilize data taken with the Dark Energy Camera (DECam) on the Blanco 4-m telescope at CTIO. These data serve as a mock follow-up to a GW event and assist in the characterization of contamination not captured in simulations. P.S.C. is grateful for support provided by the NSF through the Graduate Research Fellowship Program, Grant DGE1144152.

  2. The Dark Energy Spectroscopic Instrument (DESI): The NOAO DECam Legacy Imaging Survey and DESI Target Selection

    NASA Astrophysics Data System (ADS)

    Schlegel, David J.; Blum, Robert D.; Castander, Francisco Javier; Dey, Arjun; Finkbeiner, Douglas P.; Foucaud, Sebastien; Honscheid, Klaus; James, David; Lang, Dustin; Levi, Michael; Moustakas, John; Myers, Adam D.; Newman, Jeffrey; Nord, Brian; Nugent, Peter E.; Patej, Anna; Reil, Kevin; Rudnick, Gregory; Rykoff, Eli S.; Ford Schlafly, Eddie; Stark, Casey; Valdes, Francisco; Walker, Alistair R.; Weaver, Benjamin; DECam Legacy Survey Collaboration

    2015-01-01

    The DECam Legacy Survey will conduct a 3-band imaging survey of the Sloan Digital Sky Survey (SDSS) extragalactic footprint. The Dark Energy Camera (DECam) will be used to image the 6700 square degree footprint overlapping SDSS in the region -20 < Dec < +30 deg, to depths of g=24.7, r=23.9, z=23.0. The survey will be conducted from Fall 2014 through Spring 2017, with periodic data releases beginning in March 2015. These releases will include catalogs constructed with the Tractor-based multi-wavelength forced photometry applied to the DECam and WISE satellite data.The Dark Energy Spectroscopic Instrument (DESI) will observe 24 million galaxies and quasars in a 14,000 square degree extragalactic footprint. The targeting in that footprint will be provided by a combination of these DECam data, the MOSAIC camera on the Mayall 4-meter, and the 90Prime camera on the Bok Telescope.

  3. Bonnevillamides, Linear Heptapeptides Isolated from a Great Salt Lake-Derived Streptomyces sp.

    PubMed Central

    Wu, Guangwei; Nielson, Jason R.; Peterson, Randall T.; Winter, Jaclyn M.

    2017-01-01

    Streptomyces sp. GSL-6B was isolated from sediment collected from the Great Salt Lake and investigation of its organic extract led to the isolation of three new linear heptapeptides, bonnevillamides A (1), B (2), and C (3). The bonnevillamides represent a new class of linear peptides featuring unprecedented non-proteinogenic amino acids. All three peptides contain the newly characterized bonnevillic acid moiety (3-(3,5-dichloro-4-methoxyphenyl)-2-hydroxyacrylic acid), as well as a heavily modified proline residue. Moreover, in bonnevillamide A, the terminal proline residue found in bonnevillamides B and C is replaced with 4-methyl-azetidine-2-carboxylic acid methyl ester. The structures of the three heptapeptides were elucidated by NMR, high-resolution electrospray ionization mass spectroscopy (HRESIMS), and LC-MS/MS, and the absolute configuration of all proteinogenic amino acid residues were determined by advanced Marfey’s method. Bonnevillamides A, B and C were evaluated for their effects on zebrafish embryo development. All three heptapeptides were shown to modulate heart growth and cardiac function, with bonnevillamide B having the most pronounced effect. PMID:28672784

  4. Heptapeptide mimic of ohmefentanyl binding in the discontinuous mu-opiod receptor.

    PubMed

    Gawley, Robert E; Dukh, Mykhaylo; Cardona, Claudia M; Jannach, Stephan H; Greathouse, Denise

    2005-07-07

    [reaction: see text] Ohmefentanyl binds to the rat mu-opiod receptor via two dipeptide sequences (Trp-His and Asp-Tyr) that are separated by 170 residues. A turn-inducing tripeptide, Pro-Aib-Aib, holds the dipeptides in a conformation that binds the narcotic (K(b) = 7.1 x 10(4) M(-)(1)) in THF. Binding is specific for ohmefentanyl over morphine and is accompanied by a conformational change in the heptapeptide host. Control experiments with a Gly-Gly-Gly tripeptide linking the dipeptides show no evidence of binding.

  5. A variational model for oligomer-formation process of GNNQQNY peptide from yeast prion protein Sup35.

    PubMed

    Qi, Xianghong; Hong, Liu; Zhang, Yang

    2012-02-08

    Many human neurodegenerative diseases are associated with the aggregation of insoluble amyloid-like fibrous proteins. However, the processes by which the randomly diffused monomer peptides aggregate into the highly regulated amyloid fibril structures are largely unknown. We proposed a residue-level coarse-grained variational model for the investigation of the aggregation pathway for a small assembly of amyloid proteins, the peptide GNNQQNY from yeast prion protein Sup35. By examining the free energy surface, we identified the residue-level sequential pathways for double parallel and antiparallel β-peptides, which show that the central dry polar zipper structure is the major folding core in both cases. The critical nucleus size is determined to be three peptides for the homogeneous nucleation process, whereas the zig-zag growth pattern appears most favorably for heterogeneous nucleation. Consistent with the dock-and-lock mechanism, the aggregation process of free peptides to the fibril core was found to be highly cooperative. The quantitative validation with the computational simulations and experimental data demonstrated the usefulness of the proposed model in understanding the general mechanism of the amyloid fibril system. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  6. A Variational Model for Oligomer-Formation Process of GNNQQNY Peptide from Yeast Prion Protein Sup35

    PubMed Central

    Qi, Xianghong; Hong, Liu; Zhang, Yang

    2012-01-01

    Many human neurodegenerative diseases are associated with the aggregation of insoluble amyloid-like fibrous proteins. However, the processes by which the randomly diffused monomer peptides aggregate into the highly regulated amyloid fibril structures are largely unknown. We proposed a residue-level coarse-grained variational model for the investigation of the aggregation pathway for a small assembly of amyloid proteins, the peptide GNNQQNY from yeast prion protein Sup35. By examining the free energy surface, we identified the residue-level sequential pathways for double parallel and antiparallel β-peptides, which show that the central dry polar zipper structure is the major folding core in both cases. The critical nucleus size is determined to be three peptides for the homogeneous nucleation process, whereas the zig-zag growth pattern appears most favorably for heterogeneous nucleation. Consistent with the dock-and-lock mechanism, the aggregation process of free peptides to the fibril core was found to be highly cooperative. The quantitative validation with the computational simulations and experimental data demonstrated the usefulness of the proposed model in understanding the general mechanism of the amyloid fibril system. PMID:22325283

  7. A single mutation in the hepta-peptide active site of Aspergillus niger PhyA phytase leads to myriad of biochemical changes

    USDA-ARS?s Scientific Manuscript database

    The active site motif of proteins belonging to ‘Histidine Acid Phosphatase’ (HAP) contains a hepta-peptide region, RHGXRXP. A close comparison among fungal and yeast HAPs has revealed the fourth residue of the hepta-peptide to be E instead of A, which is the case with A. niger phyA phytase. However,...

  8. The Search for Light Echoes of Historic SNe in the Southern Hemisphere with DECam

    NASA Astrophysics Data System (ADS)

    Rest, Armin; Bianco, Federica; Chornock, Ryan; Clocchiatti, Alejandro; Foley, Ryan J.; James, David; Matheson, Thomas; Narayan, Gautham; Olsen, Knut A.; Points, Sean; Prieto, Jose Luis; Smith, R. Chris; Smith, Nathan; Suntzeff, Nicholas B.; Welch, Douglas L.; Zenteno, Alfredo

    2015-01-01

    In recent years, light echoes of ancient SNe have been discovered with the Mosaic II cameras at the CTIO Blanco and KPNO Mayall telescopes. We have found light echoes in the LMC (Rest et al. 2005, 2008a) and near the historical Galactic events Cas A, Tycho, and Eta Car (Rest et al. 2008b, 2011a, 2012). However, searches for light echoes near the Kepler SN and SN 1006 have not yet been successful. We have started a search for light echoes in the southern hemisphere using DECam at the CTIO Blanco telescope. DECam is an excellent light echo detection system with its larger field of view and much faster read time compared to Mosaic II. This increases the efficiency of the search by more than a factor of 10, allowing us to cover significantly larger areas of the sky. We report on strategy, progress, current coverage, and first results of our project.

  9. A Search for Extremely Distant Sedna-Like Objects Using DECam

    NASA Astrophysics Data System (ADS)

    Trujillo, Chadwick A.; Sheppard, S. S.

    2013-10-01

    We present initial results of a survey for the most distant objects in the solar system. Our survey utilizes the Dark Energy Camera (DECam) on the prime focus of the Cerro Tololo Inter-American Observatory (CTIO) 4m Blanco telescope. DECam, with its 3 square degree field of view, is the largest camera in the world on a 4 meter class (or larger) telescope. Our primary survey goal is to find new Sedna-like objects. Sedna has a perihelion of 76 AU, significantly larger than any other object in the solar system. It is difficult to explain the formation of such objects without invoking external dynamical interactions, such as a primordial close passage between our young solar system and another star. Conservative assumptions suggest that a Sedna-like population could easily outnumber the Kuiper Belt Objects (KBOs). To date, Sedna is the only member of its class. Our goal is to find more Sedna-like bodies to measure basic population and orbital statistics of this interesting dynamical class. DECam provides a unique combination of survey depth (red magnitudes of 24 or deeper) and breadth (a large 3 square degree field of view) allowing unparalleled constraints on the Sedna population. We discuss our basic survey methodology and analysis methods for this data-intensive campaign; roughly 120 Gigabytes of survey field data are collected per clear night. We also present object statistics from a few nights of DECam observations where we surveyed a few hundred square degrees to depths beyond red magnitude 24. In addition to detecting hundreds of KBOs, we have found several objects beyond 60 AU. We are refining the orbits of these distant objects to determine if they could be newly discovered members of the elusive Sedna population.

  10. Structures of the Lowest Energy Nonamer and Decamer Water Clusters from Chirped-Pulse Rotational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Perez, Cristobal; Pate, Brooks H.; Kisiel, Zbigniew; Temelso, Berhane; Shields, George C.

    2013-06-01

    In the breakthrough paper reporting observation and analysis of pure rotational spectra of the hexamer, heptamer and nonamer water clusters only one nonamer species was identified. The advances in this experiment, as described in the previous talk, allowed identification, among others, of five different nonamer, (H_2O)_9, conformers and of four different decamer, (H_2O)_{10}, conformers. Analysis of ^{18}O enriched spectra resulted in determination of oxygen framework geometries for three of the water nonamers and two of the water decamers. Determination of experimental geometries proved considerably more challenging than for the lighter clusters since isotopic changes to moments of inertia are proportionally smaller, and there are multiple instances of near-zero principal coordinates. There are also more indications of the effect of internal motions. These problems have been overcome by careful application of r_s and least-squares r_m techniques in concert with ab initio calculations so that it was possible to match the experimental and theoretical geometries unambiguously. The precise oxygen framework geometries obtained from chirped-pulse spectroscopy for water clusters ranging in size from the hexamer to the decamer allow, for the first time, to identify some common features of the underlying hydrogen bonding from direct experimental evidence. C. Perez, M. T. Muckle, D. P. Zaleski, N. A. Seifert, B. Temelso, G. C. Shields, Z. Kisiel, and B. H. Pate, Science {336}, 897 (2012).

  11. Hydrogen Bond Network Isomers of the Water Nonamer and Decamer Observed by Broadband Rotational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Perez, Cristobal; Zaleski, Daniel P.; Seifert, Nathan A.; Pate, Brooks H.; Kisiel, Zbigniew; Temelso, Berhane; Shields, George C.

    2013-06-01

    After our previous study of the rotational spectrum of water clusters in the 6-18 GHz region, in order to study clusters of larger size (>8 water molecules), a chirped-pulse Fourier transform microwave spectrometer in the 2-8 GHz frequency range has been used to obtain the broadband rotational spectra of five water nonamer isomers and four water decamer isomers in a pulsed molecular beam. The oxygen atom framework geometries for three nonamers and two decamers have also been unambiguously identified from isotopic labeling measurements using an H_{2}^{18}O enriched sample. Three of the four observed water decamer show tunneling effect associated with the internal dynamics of hydrogen-bond network in a similar fashion as the prism water hexamer. These tunneling paths are quenched upon a single incorporation of a H_{2}^{18}O molecule in the cluster. Due the large amount of closely-spaced rotational transitions in the H_{2}^{18}O spectrum, automated fitting tools were employed to extract the corresponding rotational spectra, which will be also briefly described. C. Perez, M. T. Muckle, D. P. Zaleski, N. A. Seifert, B. Temelso, G. C. Shields, Z. Kisiel, and B. H. Pate, Science 336, 897 (2012).

  12. A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35

    PubMed Central

    Nasica-Labouze, Jessica; Meli, Massimiliano; Derreumaux, Philippe; Colombo, Giorgio; Mousseau, Normand

    2011-01-01

    The self-organization of peptides into amyloidogenic oligomers is one of the key events for a wide range of molecular and degenerative diseases. Atomic-resolution characterization of the mechanisms responsible for the aggregation process and the resulting structures is thus a necessary step to improve our understanding of the determinants of these pathologies. To address this issue, we combine the accelerated sampling properties of replica exchange molecular dynamics simulations based on the OPEP coarse-grained potential with the atomic resolution description of interactions provided by all-atom MD simulations, and investigate the oligomerization process of the GNNQQNY for three system sizes: 3-mers, 12-mers and 20-mers. Results for our integrated simulations show a rich variety of structural arrangements for aggregates of all sizes. Elongated fibril-like structures can form transiently in the 20-mer case, but they are not stable and easily interconvert in more globular and disordered forms. Our extensive characterization of the intermediate structures and their physico-chemical determinants points to a high degree of polymorphism for the GNNQQNY sequence that can be reflected at the macroscopic scale. Detailed mechanisms and structures that underlie amyloid aggregation are also provided. PMID:21625573

  13. A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35.

    PubMed

    Nasica-Labouze, Jessica; Meli, Massimiliano; Derreumaux, Philippe; Colombo, Giorgio; Mousseau, Normand

    2011-05-01

    The self-organization of peptides into amyloidogenic oligomers is one of the key events for a wide range of molecular and degenerative diseases. Atomic-resolution characterization of the mechanisms responsible for the aggregation process and the resulting structures is thus a necessary step to improve our understanding of the determinants of these pathologies. To address this issue, we combine the accelerated sampling properties of replica exchange molecular dynamics simulations based on the OPEP coarse-grained potential with the atomic resolution description of interactions provided by all-atom MD simulations, and investigate the oligomerization process of the GNNQQNY for three system sizes: 3-mers, 12-mers and 20-mers. Results for our integrated simulations show a rich variety of structural arrangements for aggregates of all sizes. Elongated fibril-like structures can form transiently in the 20-mer case, but they are not stable and easily interconvert in more globular and disordered forms. Our extensive characterization of the intermediate structures and their physico-chemical determinants points to a high degree of polymorphism for the GNNQQNY sequence that can be reflected at the macroscopic scale. Detailed mechanisms and structures that underlie amyloid aggregation are also provided.

  14. A Novel Carboxyl-Terminal Heptapeptide Initiates the Regulated Secretion of LH from Unique Sub-Domains of the ER

    PubMed Central

    Jablonka-Shariff, Albina; Boime, Irving

    2013-01-01

    The coordinated secretion of LH and FSH are critical for reproductive functions. After translocation into the endoplasmic reticulum (ER), their biosynthetic routes diverge at a determinative step prior to sorting in the regulated (LH) and constitutive (FSH) secretion pathways. Recently, we identified a C-terminal heptapeptide sequence, present only in the LHβ subunit, as a critical signal for entry of the LH dimer into the regulated pathway. We showed that an LHβ mutant lacking the heptapeptide (LHβΔT) assembled more efficiently with the α subunit than wild-type LHβ subunit, and this LHΔT dimer was secreted constitutively. Thus, an association exists between the presence of the C-terminal heptapeptide and sorting of the LH heterodimer to the regulated pathway. To study how this delayed LHβ subunit assembly is related to the trafficking of LH, we exploited the single subunit transfection model in rat somatotrope-derived GH3 cells with the use of immunofluorescence confocal microscopy. The LHβ subunit showed a distinct immunofluorescent localization as compared to the FSHβ subunit and LHβ mutants. The wild-type LHβ subunit exhibited a perinuclear staining corresponding to the ER/nuclear envelope region. In contrast, the wild-type FSHβ subunit and the mutants LHβΔT and LHβL119A displayed no detectable perinuclear staining; only peripheral ER puncta were observed. Also, no perinuclear fluorescence was detected in cells expressing the LH heterodimer. We propose that the C-terminal heptapeptide is responsible for delayed heterodimer assembly within an ER sub-domain of the nuclear envelope, as an early partitioning event necessary for the entrance of LH into the regulated secretory pathway, whereas FSHβ does not traverse the nuclear envelope region. These data suggest that, at least for LH, the molecular decision to enter the regulated secretory pathway is a pre-Golgi event controlled by the novel C-terminal heptapeptide. PMID:23734233

  15. Anion Transport in Liposomes Responds to Variations in the Anchor Chains and the Fourth Amino Acid of Heptapeptide Ion Channels

    PubMed Central

    Ferdani, Riccardo; Pajewski, Robert; Djedovič, Natasha; Pajewska, Jolanta; Schlesinger, Paul H.; Gokel, George W.

    2008-01-01

    Seven heptapeptide derivatives have been prepared. The peptide structure is (Gly)3Xxx(Gly)3 in which Xxx stands for a variable amino acid. The amino acid variations include azetidine carboxylic acid, pipecolic acid, meta-aminobenzoic acid, proline, and leucine. All seven compounds have a C-terminal benzyl group. In all cases, the heptapeptide's N-terminus was linked to diglycolic acid and a dialkylamine. In five cases, the N-terminal group was didecylamine and in two cases, N-ethyl-N-decyl. Chloride and carboxyfluorescein release from phospholipid vesicles was studied with the result that C10H21N(C2H5) COCH2OCH2CO-NH-(Gly)3Leu(Gly)3-OCH2Ph was the most active. Hill analysis showed that this compound involves pore formation by four monomer units rather than two, as previously found for other members of this family. PMID:19169373

  16. Immunometric assay of BN 52080, a heptapeptide C-terminal analogue of sorbin.

    PubMed

    Ezan, E; Tarrade, T; Cazenave, C; Ardouin, T; Genet, R; Grassi, J; Grognet, J M; Pradelles, P

    1995-01-01

    A novel type of enzyme immunometric assay has been developed for a heptapeptide, BN 52080. This compound is a short C-terminal analogue of sorbin and is under clinical evaluation for treatment of chronic diarrhea. In this solid-phase immobilized epitope immunoassay (SPIE-IA), the peptide is first immunologically bound to polyclonal antibodies adsorbed to a solid phase and then, after covalent immobilization with glutaraldehyde, is released from the antibody paratope by NaOH. The peptide linked to the solid phase is further quantified with a tracer consisting of the same antibodies purified by affinity chromatography and coupled to acetylcholinesterase. This assay has a detection limit of 10 pg/ml and is therefore five times more sensitive than competitive enzyme immunoassay using the same antibodies and BN 52080 coupled to acetylcholinesterase as tracer. The assay is specific and allows direct measurement of peptide in human plasma after subcutaneous or intravenous administration of 200 micrograms of BN 52080 to volunteers.

  17. DECam Survey for Substellar and Low-mass Stellar Members of Sco-Cen

    NASA Astrophysics Data System (ADS)

    Mamajek, Eric E.; Moolekamp, Fred; James, David; Luhman, Kevin; Pecaut, Mark; Metchev, Stanimir A.; Denbo, Sara; Bell, Cameron P. M.

    2017-01-01

    We present the results of a DECam imaging survey for low-mass stellar and substellar objects in the nearby Sco-Cen OB association. The DECam survey was taken in izY bands in 2013 and 2015 and covered $\\sim$87 deg$^2$ in the two nearest and oldest subgroups, Upper Cen-Lup ($\\sim$142 pc) and Lower Cen-Cru ($\\sim$118 pc; both with mean ages $\\sim$16 Myr). Using color-magnitude and proper motion selection, we identify 391 candidate Sco-Cen members with masses ranging from near the D-burning limit of $\\sim$13 M$_{Jup}$, through the H-burning limit, up to $\\sim$0.4 M$_\\odot$. Our initial spectroscopic follow-up with the ARCoIRIS and COSMOS spectrographs for 19 objects have yielded young M dwarfs showing signatures of low surface-gravity. Our survey yields the first constraints on the substellar and low-mass initial mass function and disk fraction in the two oldest Sco-Cen subgroups, and will yield a large sample of young, low-surface gravity M and L-type objects of constrained age, distance, and chemical composition. We acknowledge support from NSF award AST-1313029 and the REU Site in Physics and Astrophysics at the University of Rochester supported by NSF award PHY-1156339.

  18. Solid-state NMR study of amyloid nanocrystals and fibrils formed by the peptide GNNQQNY from yeast prion protein Sup35p.

    PubMed

    van der Wel, Patrick C A; Lewandowski, Józef R; Griffin, Robert G

    2007-04-25

    Sup35p is a prion protein found in yeast that contains a prion-forming domain characterized by a repetitive sequence rich in Gln, Asn, Tyr, and Gly amino acid residues. The peptide GNNQQNY7-13 is one of the shortest segments of this domain found to form amyloid fibrils, in a fashion similar to the protein itself. Upon dissolution in water, GNNQQNY displays a concentration-dependent polymorphism, forming monoclinic and orthorhombic crystals at low concentrations and amyloid fibrils at higher concentrations. We prepared nanocrystals of both space groups as well as fibril samples that reproducibly contain three (coexisting) structural forms and examined the specimens with magic angle spinning (MAS) solid-state nuclear magnetic resonance. 13C and 15N MAS spectra of both nanocrystals and fibrils reveal narrow resonances indicative of a high level of microscopic sample homogeneity that permitted resonance assignments of all five species. We observed variations in chemical shift among the three dominant forms of the fibrils which were indicated by the presence of three distinct, self-consistent sets of correlated NMR signals. Similarly, the monoclinic and orthorhombic crystals exhibit chemical shifts that differ from one another and from the fibrils. Collectively, the chemical shift data suggest that the peptide assumes five conformations in the crystals and fibrils that differ from one another in subtle but distinct ways. This includes variations in the mobility of the aromatic Tyr ring. The data also suggest that various structures assumed by the peptide may be correlated to the "steric zipper" observed in the monoclinic crystals.

  19. Nonribosomal biosynthesis of vancomycin-type antibiotics: a heptapeptide backbone and eight peptide synthetase modules.

    PubMed

    Recktenwald, Jürgen; Shawky, Riham; Puk, Oliver; Pfennig, Frank; Keller, Ulrich; Wohlleben, Wolfgang; Pelzer, Stefan

    2002-04-01

    During analysis of the recently identified gene cluster for the glycopeptide antibiotic balhimycin, produced by Amycolatopsis mediterranei DSM 5908, novel genes were identified and characterized in detail. The gene products of four of the identified genes (bpsA, bpsB, bpsC and bpsD) are nonribosomal peptide synthetases (NRPSs); one (Orf1-protein) shows similarities to small proteins associated with several NRPSs without an assigned function. BpsA and BpsB are composed of three modules each (modules 1-6), BpsC of one module (module 7) and BpsD of a minimal module (module 8). Thus, the balhimycin gene cluster encodes eight modules, whereas its biosynthetic product is a heptapeptide. Non-producing mutants were created by a gene disruption of bpsB, an in-frame deletion of bpsC and a gene replacement of bpsD. After establishment of a gene complementation system for Amycolatopsis strains, the replacement mutant of bpsD was complemented, demonstrating for the first time that BpsD, encoding the eighth module, is indeed involved in balhimycin biosynthesis. After feeding with beta-hydroxytyrosine the capability of the bpsD mutant to produce balhimycin was restored, demonstrating the participation of BpsD in the biosynthesis of this amino acid. The specificity of four of the eight adenylation domains was determined by ATP/PP(i) exchange assays: modules 4 and 5 activated L-4-hydroxyphenylglycine, module 6 activated beta-hydroxytyrosine and module 7 activated L-3,5-dihydroxyphenylglycine, which is in accordance with the sequence of the non-proteogenic amino acids 4 to 7 of the balhimycin backbone.

  20. Heptapeptide-loaded solid lipid nanoparticles for cosmetic anti-aging applications.

    PubMed

    Suter, Franz; Schmid, Daniel; Wandrey, Franziska; Zülli, Fred

    2016-11-01

    The cosmetic industry requires more and more expensive actives and ingredients such as retinol, coenzyme Q10, proteins, peptides and biotechnologically produced molecules. In this study, we demonstrate the development of a cost effective formulation of a nanostructured lipid carrier (NLC) or solid lipid nanoparticles (SLN) improving peptide delivery into skin. NLC or SLN are very suitable vehicles for the delivery of active ingredients into skin. The SLN, produced by using hot high pressure homogenization method combine advantages such as physical stability, protection of incorporated labile actives and controlled release. By the used method we dispersed the amorphous heptapeptide DEETGEF in shea butter and homogenized this pre-dispersion at 60°C together with the water phase using a Microfluidizer at 1000bar. The analysis of the obtained SLN-P7 showed a particle size of 173nm, incorporated peptide of 0.014%, entrapment efficiency of 90.8%, melting peak (DSC) of the core lipid of 27°C and a zeta potential of -54mV. By an ex vivo study with skin explants we could stimulate NQO1 (NAD(P)H quinone oxidoreductase), HMOX1 (Heme oxygenase-1) and PRDX1 (Peroxiredoxin-1) genes all of which are cell protecting enzymes. In a multicellular protection against UV induced stress study with skin explants we detected the formation of sun burn cells and the number and morphology of Langerhans cells. The application of our SLN-P7 formulation on skin explants led to a significant and dose dependent protection against UV irradiation. In the clinical suction blister study, irradiation with UVA light for two hours after final product application led to a statistically significant increase of the 8-OhdG (8-hydroxy-2'-deoxyguanosine) concentration in the human epidermis. The skin treated with our verum formulation showed a statistically significant 20% decrease in DNA damage compared to placebo. In conclusion, it was demonstrated that SLN technology enabled peptide delivery into skin

  1. DECam z and Y-band Imaging of the H-ATLAS SDP Field

    NASA Astrophysics Data System (ADS)

    Yan, Haojing; Stefanon, Mauro

    2014-02-01

    The very-wide-field Herschel surveys have resulted in hundreds of thousands of bright FIR/sub-mm sources awaiting further exploration. However many of them are still lacking optical identifications, which severely hampers the follow-up studies. Intertwined with the problem that lots of these FIR sources are intrinsically optical-faint due to their dusty nature, the source blending problem due to the large beam sizes of the Herschel instruments is a severe limitation. Nevertheless, the blended sources can be decomposed if the positions of the major components can be determined from the higher resolution optical data. For this purpose, optical images much deeper than the SDSS are in demand, and ideally they should cover the entire optical range in multiple bands for ease of studying their properties. We propose to do medium-deep DECam z and Y-band imaging of the H-ATLAS SDP field, which is currently the only wide, equatorial Herschel survey field that has public data in both PACS and SPIRE passbands and can be accessed from both hemispheres. While it was designed primarily for science at z<1, the H-ATLAS is sensitive enough to detect non-lensed ULIRG to z>3 and beyond. In particular, its multiple FIR bands will enable direct measurement of the total IR luminosities without relying on extrapolation. Our DECam request in z and Y-bands is part of a larger program to acquire multi-wavelength data (optical to radio) in its SDP field to add to its legacy value. The counterpart program is to acquire imaging data in ugri-bands at the CFHT/Megacam, and the u- band component will be executed in the coming Nov-Jan season. Combining all these data with the WISE images after the similar source deblending procedures, we will construct reliable UV-to-FIR SEDs for future studies. In particular, we will be able to study the relation between the ULIRG phase and the underlying stellar populations, and the contribution of ULIRG to the global star formation rate density at z>1.

  2. The conformation of a B-DNA decamer is mainly determined by its sequence and not by crystal environment.

    PubMed Central

    Heinemann, U; Alings, C

    1991-01-01

    By comparing the conformations adopted by a double-stranded decameric B-DNA fragment in different crystal environments, we address the question of the degree of deformability of DNA helices. The three-dimensional structure of the self-complementary DNA decamer CCAGGCmeCTGG has been determined from crystals of space group P6 at 2.25 A resolution with an R value of 17.2% for 2407 1 sigma structure amplitudes. The oligonucleotide forms a B-type double helix with a characteristic sequence-dependent conformation closely resembling that of the corresponding unmethylated decamer, the structure of which is known from a high-resolution analysis of crystals of space group C2. Evidently, both the effects of single-site methylation and altered crystal environment on the DNA conformation are small. Therefore, double-helical DNA may possess sequence-determined conformational features that are less deformable than previously thought. Images PMID:1989887

  3. HRMAS 1H NMR conformational study of the resin-bound amyloid-forming peptide GNNQQNY from the yeast prion Sup35.

    PubMed

    Andrey, Samuel B; Chan, Michael L; Power, William P

    2010-03-18

    The conversion of soluble proteins to insoluble amyloid fibrils is associated with numerous human diseases. The peptide GNNQQNY is a short segment of the yeast prion protein Sup35 that previously has been found to form amyloid fibrils in a similar manner to the protein itself. The approach taken in this work was to attach this peptide sequence to an insoluble polymer matrix through solid phase peptide synthesis and give it the internal freedom to fold into its local conformation in an organic solvent. Observation of its monomeric structure, free from the effects of aggregation, entropic solvent effects, and neighboring molecules, was possible by two-dimensional high-resolution magic angle spinning (1)H NMR spectroscopy. Analysis of the through-bond correlations and through-space interactions observed in the spectra, combined with global energy minimization via computational studies, led to the observation that the peptide chain adopts a compact beta-like turn at the central hydrophilic residues. The technique of peptide attachment to a polymer resin and observation by NMR may allow for future study of single peptide fragments prone to aggregation.

  4. The size distribution of Near-Earth Asteroids from the DECam NEO Survey

    NASA Astrophysics Data System (ADS)

    Allen, Lori; Valdes, Francisco; Trilling, David; James, David; Herrera, David; Fuentes, Cesar; Axelrod, Tim; Rajagopal, Jayadev; IAU Minor Planet Center, Cerro Tololo Inter-American Observatory

    2016-10-01

    We analyzed data from the first year of a survey for Near Earth Objects (NEOs) that we are carrying out with the Dark Energy Camera (DECam) on the 4 meter Blanco telescope at the Cerro Tololo Inter-American Observatory. We implanted synthetic NEOs into the data stream to derive our nightly detection efficiency as a function of magnitude and rate of motion. Using these measured efficiencies and the Solar System absolute magnitudes derived by the Minor Planet Center for the 1377 measurements of 235 unique NEOs detected, we directly derive, for the first time from a single observational data set, the NEO size distribution from 1 km down to 10 meters. We find that there are 106.6 NEOs larger than 10 meters. This result implies a factor of ten fewer small NEOs than some previous results (e.g., Harris & D'Abramo 2015, Boslough et al. 2015) but a factor of ten more than Tricarico (2016). This result also implies that the impact risk for small- and medium-sized NEOs is less than previously thought.

  5. Characterization and correction of charge-induced pixel shifts in DECam

    SciTech Connect

    Gruen, D.; Bernstein, G. M.; Jarvis, M.; Rowe, B.; Vikram, V.; Plazas, A. A.; Seitz, S.

    2015-05-01

    Interaction of charges in CCDs with the already accumulated charge distribution causes both a flux dependence of the point-spread function (an increase of observed size with flux, also known as the brighter/fatter effect) and pixel-to-pixel correlations of the {Poissonian} noise in flat fields. We describe these effects in the Dark Energy Camera (DECam) with charge dependent shifts of effective pixel borders, i.e. the Antilogus et al. (2014) model, which we fit to measurements of flat-field {Poissonian} noise correlations. The latter fall off approximately as a power-law r(-)(2.5) with pixel separation r, are isotropic except for an asymmetry in the direct neighbors along rows and columns, are stable in time, and are weakly dependent on wavelength. They show variations from chip to chip at the 20% level that correlate with the silicon resistivity. The charge shifts predicted by the model cause biased shape measurements, primarily due to their effect on bright stars, at levels exceeding weak lensing science requirements. We measure the flux dependence of star images and show that the effect can be mitigated by applying the reverse charge shifts at the pixel level during image processing. Differences in stellar size, however, remain significant due to residuals at larger distance from the centroid.

  6. Characterization and correction of charge-induced pixel shifts in DECam

    DOE PAGES

    Gruen, D.; Bernstein, G. M.; Jarvis, M.; ...

    2015-05-28

    Interaction of charges in CCDs with the already accumulated charge distribution causes both a flux dependence of the point-spread function (an increase of observed size with flux, also known as the brighter/fatter effect) and pixel-to-pixel correlations of the Poissonian noise in flat fields. We describe these effects in the Dark Energy Camera (DECam) with charge dependent shifts of effective pixel borders, i.e. the Antilogus et al. (2014) model, which we fit to measurements of flat-field Poissonian noise correlations. The latter fall off approximately as a power-law r-2.5 with pixel separation r, are isotropic except for an asymmetry in the directmore » neighbors along rows and columns, are stable in time, and are weakly dependent on wavelength. They show variations from chip to chip at the 20% level that correlate with the silicon resistivity. The charge shifts predicted by the model cause biased shape measurements, primarily due to their effect on bright stars, at levels exceeding weak lensing science requirements. We measure the flux dependence of star images and show that the effect can be mitigated by applying the reverse charge shifts at the pixel level during image processing. Differences in stellar size, however, remain significant due to residuals at larger distance from the centroid.« less

  7. Characterization and correction of charge-induced pixel shifts in DECam

    SciTech Connect

    Gruen, D.; Bernstein, G. M.; Jarvis, M.; Rowe, B.; Vikram, V.; Plazas, A. A.; Seitz, S.

    2015-05-28

    Interaction of charges in CCDs with the already accumulated charge distribution causes both a flux dependence of the point-spread function (an increase of observed size with flux, also known as the brighter/fatter effect) and pixel-to-pixel correlations of the Poissonian noise in flat fields. We describe these effects in the Dark Energy Camera (DECam) with charge dependent shifts of effective pixel borders, i.e. the Antilogus et al. (2014) model, which we fit to measurements of flat-field Poissonian noise correlations. The latter fall off approximately as a power-law r-2.5 with pixel separation r, are isotropic except for an asymmetry in the direct neighbors along rows and columns, are stable in time, and are weakly dependent on wavelength. They show variations from chip to chip at the 20% level that correlate with the silicon resistivity. The charge shifts predicted by the model cause biased shape measurements, primarily due to their effect on bright stars, at levels exceeding weak lensing science requirements. We measure the flux dependence of star images and show that the effect can be mitigated by applying the reverse charge shifts at the pixel level during image processing. Differences in stellar size, however, remain significant due to residuals at larger distance from the centroid.

  8. Sailing under the Magellanic Clouds: a DECam view of the Carina dwarf

    NASA Astrophysics Data System (ADS)

    McMonigal, B.; Bate, N. F.; Lewis, G. F.; Irwin, M. J.; Battaglia, G.; Ibata, R. A.; Martin, N. F.; McConnachie, A. W.; Guglielmo, M.; Conn, A. R.

    2014-11-01

    We present deep optical photometry from the DECam imager on the 4 m Blanco telescope of over 12 deg2 around the Carina dwarf spheroidal, with complete coverage out to 1 deg and partial coverage extending out to 2.6 deg. Using a Poisson-based matched-filter analysis to identify stars from each of the three main stellar populations, old, intermediate, and young, we confirm the previously identified radial age gradient, distance, tidal radius, stellar radial profiles, relative stellar population sizes, ellipticity, and position angle. We find an angular offset between the three main elliptical populations of Carina, and find only tentative evidence for tidal debris, suggesting that past tidal interactions could not have significantly influenced the Carina dwarf. We detect stars in the vicinity of, but distinct to, the Carina dwarf, and measure their distance to be 46±2 kpc. We determine this population to be part of the halo of the Large Magellanic Cloud at an angular radius of over 20 deg. Due to overlap in colour-magnitude space with Magellanic stars, previously detected tidal features in the old population of Carina are likely weaker than previously thought.

  9. Adsorption of peptide nucleic acid and DNA decamers at electrically charged surfaces.

    PubMed Central

    Fojta, M; Vetterl, V; Tomschik, M; Jelen, F; Nielsen, P; Wang, J; Palecek, E

    1997-01-01

    Adsorption behavior of peptide nucleic acid (PNA) and DNA decamers (GTAGATCACT and the complementary sequence) on a mercury surface was studied by means of AC impedance measurements at a hanging mercury drop electrode. The nucleic acid was first attached to the electrode by adsorption from a 5-microliter drop of PNA (or DNA) solution, and the electrode with the adsorbed nucleic acid layer was then washed and immersed in the blank background electrolyte where the differential capacity C of the electrode double layer was measured as a function of the applied potential E. It was found that the adsorption behavior of the PNA with an electrically neutral backbone differs greatly from that of the DNA (with a negatively charged backbone), whereas the DNA-PNA hybrid shows intermediate behavior. At higher surface coverage PNA molecules associate at the surface, and the minimum value of C is shifted to negative potentials because of intermolecular interactions of PNA at the surface. Prolonged exposure of PNA to highly negative potentials does not result in PNA desorption, whereas almost all of the DNA is removed from the surface at these potentials. Adsorption of PNA decreases with increasing NaCl concentration in the range from 0 to 50 mM NaCl, in contrast to DNA, the adsorption of which increases under the same conditions. PMID:9129832

  10. First Discoveries of z > 6 Quasars with the DECam Legacy Survey and UKIRT Hemisphere Survey

    NASA Astrophysics Data System (ADS)

    Wang, Feige; Fan, Xiaohui; Yang, Jinyi; Wu, Xue-Bing; Yang, Qian; Bian, Fuyan; McGreer, Ian D.; Li, Jiang-Tao; Li, Zefeng; Ding, Jiani; Dey, Arjun; Dye, Simon; Findlay, Joseph R.; Green, Richard; James, David; Jiang, Linhua; Lang, Dustin; Lawrence, Andy; Myers, Adam D.; Ross, Nicholas P.; Schlegel, David J.; Shanks, Tom

    2017-04-01

    We present the first discoveries from a survey of z ≳ 6 quasars using imaging data from the DECam Legacy Survey (DECaLS) in the optical, the UKIRT Deep Infrared Sky Survey (UKIDSS) and a preliminary version of the UKIRT Hemisphere Survey (UHS) in the near-IR, and ALLWISE in the mid-IR. DECaLS will image 9000 deg2 of sky down to z AB ˜ 23.0, and UKIDSS and UHS will map the northern sky at 0 < decl. < +60°, reaching J VEGA ˜ 19.6 (5-σ). The combination of these data sets allows us to discover quasars at redshift z ≳ 7 and to conduct a complete census of the faint quasar population at z ≳ 6. In this paper, we report on the selection method of our search, and on the initial discoveries of two new, faint z ≳ 6 quasars and one new z = 6.63 quasar in our pilot spectroscopic observations. The two new z ˜ 6 quasars are at z = 6.07 and z = 6.17 with absolute magnitudes at rest-frame wavelength 1450 Å being M 1450 = -25.83 and M 1450 = -25.76, respectively. These discoveries suggest that we can find quasars close to or fainter than the break magnitude of the Quasar Luminosity Function (QLF) at z ≳ 6. The new z = 6.63 quasar has an absolute magnitude of M 1450 = -25.95. This demonstrates the potential of using the combined DECaLS and UKIDSS/UHS data sets to find z ≳ 7 quasars. Extrapolating from previous QLF measurements, we predict that these combined data sets will yield ˜200 z ˜ 6 quasars to z AB < 21.5, ˜1000 z ˜ 6 quasars to z AB < 23, and ˜30 quasars at z > 6.5 to J VEGA < 19.5.

  11. A DECam search for an optical counterpart to the LIGO gravitational-wave event GW151226

    SciTech Connect

    Cowperthwaite, P. S.; Berger, E.; Soares-Santos, M.; Annis, J.; Brout, D.; Brown, D. A.; Buckley-Geer, E.; Cenko, S. B.; Chen, H. Y.; Chornock, R.; Diehl, H. T.; Doctor, Z.; Drlica-Wagner, A.; Drout, M. R.; Farr, B.; Finley, D. A.; Foley, R. J.; Fong, W.; Fox, D. B.; Frieman, J.; Garcia-Bellido, J.; Gill, M. S. S.; Gruendl, R. A.; Herner, K.; Holz, D. E.; Kasen, D.; Kessler, R.; Lin, H.; Margutti, R.; Marriner, J.; Matheson, T.; Metzger, B. D.; Neilsen Jr., E. H.; Quataert, E.; Rest, A.; Sako, M.; Scolnic, D.; Smith, N.; Sobreira, F.; Strampelli, G. M.; Villar, V. A.; Walker, A. R.; Wester, W.; Williams, P. K. G.; Yanny, B.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Armstrong, R.; Bechtol, K.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Burke, D. L.; Rosell, A. Carnero; Kind, M. Carrasco; Carretero, J.; Castander, F. J.; Cunha, C. E.; D’Andrea, C. B.; Costa, L. N. da; Desai, S.; Dietrich, J. P.; Evrard, A. E.; Neto, A. Fausti; Fosalba, P.; Gerdes, D. W.; Giannantonio, T.; Goldstein, D. A.; Gruen, D.; Gutierrez, G.; Honscheid, K.; James, D. J.; Johnson, M. W. G.; Johnson, M. D.; Krause, E.; Kuehn, K.; Kuropatkin, N.; Lima, M.; Maia, M. A. G.; Marshall, J. L.; Menanteau, F.; Miquel, R.; Mohr, J. J.; Nichol, R. C.; Nord, B.; Ogando, R.; Plazas, A. A.; Reil, K.; Romer, A. K.; Sanchez, E.; Scarpine, V.; Sevilla-Noarbe, I.; Smith, R. C.; Suchyta, E.; Tarle, G.; Thomas, D.; Thomas, R. C.; Tucker, D. L.; Weller, J.

    2016-07-29

    We report the results of a Dark Energy Camera (DECam) optical follow-up of the gravitational wave (GW) event GW151226, discovered by the Advanced LIGO detectors. Our observations cover 28.8 deg2 of the localization region in the i and z bands (containing 3% of the BAYESTAR localization probability), starting 10 hours after the event was announced and spanning four epochs at 2–24 days after the GW detection. We achieve 5σ point-source limiting magnitudes of i ≈ 21.7 and z ≈ 21.5 , with a scatter of 0.4 mag, in our difference images. Given the two day delay, we search this area for a rapidly declining optical counterpart with ≳3σ significance steady decline between the first and final observations. We recover four sources that pass our selection criteria, of which three are cataloged AGN. The fourth source is offset by 5.8 arcsec from the center of a galaxy at a distance of 187 Mpc, exhibits a rapid decline by 0.5 mag over 4 days, and has a red color of i–z ≈ 0.3 mag. These properties roughly match the expectations for a kilonova. However, this source was detected several times, starting 94 days prior to GW151226, in the Pan-STARRS Survey for Transients (dubbed as PS15cdi) and is therefore unrelated to the GW event. Given its long-term behavior, PS15cdi is likely a Type IIP supernova that transitioned out of its plateau phase during our observations, mimicking a kilonova-like behavior. As a result, we comment on the implications of this detection for contamination in future optical follow-up observations.

  12. First Discoveries of z > 6 Quasars with the DECam Legacy Survey and UKIRT Hemisphere Survey

    DOE PAGES

    Wang, Feige; Fan, Xiaohui; Yang, Jinyi; ...

    2017-04-11

    In this paper, we present the first discoveries from a survey of z ≳ 6 quasars using imaging data from the DECam Legacy Survey (DECaLS) in the optical, the UKIRT Deep Infrared Sky Survey (UKIDSS) and a preliminary version of the UKIRT Hemisphere Survey (UHS) in the near-IR, and ALLWISE in the mid-IR. DECaLS will image 9000 deg2 of sky down to z AB ~ 23.0, and UKIDSS and UHS will map the northern sky at 0 < decl. < +60°, reaching J VEGA ~ 19.6 (5-σ). The combination of these data sets allows us to discover quasars at redshiftmore » z ≳ 7 and to conduct a complete census of the faint quasar population at z ≳ 6. In this paper, we report on the selection method of our search, and on the initial discoveries of two new, faint z ≳ 6 quasars and one new z = 6.63 quasar in our pilot spectroscopic observations. The two new z ~ 6 quasars are at z = 6.07 and z = 6.17 with absolute magnitudes at rest-frame wavelength 1450 Å being M 1450 = -25.83 and M 1450 = -25.76, respectively. These discoveries suggest that we can find quasars close to or fainter than the break magnitude of the Quasar Luminosity Function (QLF) at z ≳ 6. The new z = 6.63 quasar has an absolute magnitude of M 1450 = -25.95. This demonstrates the potential of using the combined DECaLS and UKIDSS/UHS data sets to find z ≳ 7 quasars. Finally, extrapolating from previous QLF measurements, we predict that these combined data sets will yield ~200 z ~ 6 quasars to z AB < 21.5, ~1000 z ~ 6 quasars to z AB < 23, and ~30 quasars at z > 6.5 to J VEGA < 19.5.« less

  13. Heparin decamer bridges a growth factor and an oligolysine by different charge-driven interactions.

    PubMed

    Minsky, Burcu Baykal; Nguyen, Thuy V; Peyton, Shelly R; Kaltashov, Igor A; Dubin, Paul L

    2013-11-11

    Full-length heparin is widely used in tissue engineering applications due its multiple protein-binding sites that allow it to retain growth factor affinity while associating with oligopeptide components of the tissue scaffold. However, the extent to which oligopeptide coupling interferes with cognate protein binding is difficult to predict. To investigate such simultaneous interactions, we examined a well-defined ternary system comprised of acidic fibroblast growth factor (FGF), tetralysine (K4), with a heparin decamer (dp10) acting as a noncovalent coupler. Electrospray ionization mass spectrometry was used to assess binding affinities and complex stoichiometries as a function of ionic strength for dp10·K4 and FGF·dp10. The ionic strength dependence of K4·dp10 formation is qualitatively consistent with binding driven by the release of condensed counterions previously suggested for native heparin with divalent oligopeptides (Mascotti, D. P.; Lohman, T. M. Biochemistry 1995, 34, 2908-2915). On the other hand, FGF binding displays more complex ionic strength dependence, with higher salt resistance. Remarkably, dp10 that can bind two FGF molecules can only bind one tetralysine. The limited binding of K4 to dp10 suggests that the tetralysine might not block growth factor binding, and the 1:1:1 ternary complex is indeed observed. The analysis of mass distribution of the bound dp10 chains in FGF·dp10, FGF2·dp10, and FGF·dp10·K4 complexes indicated that higher degrees of dp10 sulfation promote the formation of FGF2·dp10 and FGF·dp10·K4. Thus, the selectivity of appropriately chosen short heparin chains could be used to modulate growth factor sequestration and release in a way not feasible with heterogeneous native heparin. In support of this, human hepatocellular carcinoma cells (HEP3Bs) treated with FGF·dp10·K4 were found to exhibit biological activity similar to cells treated with FGF.

  14. Incorporation of local structure into kriging models for the prediction of atomistic properties in the water decamer

    PubMed Central

    Davie, Stuart J; Di Pasquale, Nicodemo

    2016-01-01

    Machine learning algorithms have been demonstrated to predict atomistic properties approaching the accuracy of quantum chemical calculations at significantly less computational cost. Difficulties arise, however, when attempting to apply these techniques to large systems, or systems possessing excessive conformational freedom. In this article, the machine learning method kriging is applied to predict both the intra‐atomic and interatomic energies, as well as the electrostatic multipole moments, of the atoms of a water molecule at the center of a 10 water molecule (decamer) cluster. Unlike previous work, where the properties of small water clusters were predicted using a molecular local frame, and where training set inputs (features) were based on atomic index, a variety of feature definitions and coordinate frames are considered here to increase prediction accuracy. It is shown that, for a water molecule at the center of a decamer, no single method of defining features or coordinate schemes is optimal for every property. However, explicitly accounting for the structure of the first solvation shell in the definition of the features of the kriging training set, and centring the coordinate frame on the atom‐of‐interest will, in general, return better predictions than models that apply the standard methods of feature definition, or a molecular coordinate frame. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:27535711

  15. Incorporation of local structure into kriging models for the prediction of atomistic properties in the water decamer.

    PubMed

    Davie, Stuart J; Di Pasquale, Nicodemo; Popelier, Paul L A

    2016-10-15

    Machine learning algorithms have been demonstrated to predict atomistic properties approaching the accuracy of quantum chemical calculations at significantly less computational cost. Difficulties arise, however, when attempting to apply these techniques to large systems, or systems possessing excessive conformational freedom. In this article, the machine learning method kriging is applied to predict both the intra-atomic and interatomic energies, as well as the electrostatic multipole moments, of the atoms of a water molecule at the center of a 10 water molecule (decamer) cluster. Unlike previous work, where the properties of small water clusters were predicted using a molecular local frame, and where training set inputs (features) were based on atomic index, a variety of feature definitions and coordinate frames are considered here to increase prediction accuracy. It is shown that, for a water molecule at the center of a decamer, no single method of defining features or coordinate schemes is optimal for every property. However, explicitly accounting for the structure of the first solvation shell in the definition of the features of the kriging training set, and centring the coordinate frame on the atom-of-interest will, in general, return better predictions than models that apply the standard methods of feature definition, or a molecular coordinate frame. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  16. Absolute Magnitudes and Colors of RR Lyrae Stars in DECam Passbands from Photometry of the Globular Cluster M5

    NASA Astrophysics Data System (ADS)

    Vivas, A. Katherina; Saha, Abhijit; Olsen, Knut; Blum, Robert; Olszewski, Edward W.; Claver, Jennifer; Valdes, Francisco; Axelrod, Tim; Kaleida, Catherine; Kunder, Andrea; Narayan, Gautham; Matheson, Thomas; Walker, Alistair

    2017-09-01

    We characterize the absolute magnitudes and colors of RR Lyrae stars in the globular cluster M5 in the ugriz filter system of the Dark Energy Camera (DECam). We provide empirical period-luminosity (P-L) relationships in all five bands based on 47 RR Lyrae stars of the type ab and 14 stars of the type c. The P-L relationships were found to be better constrained for the fundamental-mode RR Lyrae stars in the riz passbands, with dispersions of 0.03, 0.02 and 0.02 mag, respectively. The dispersion of the color at minimum light was found to be small, supporting the use of this parameter as a means to obtain accurate interstellar extinctions along the line of sight up to the distance of the RR Lyrae star. We found a trend of color at minimum light with a pulsational period that, if taken into account, brings the dispersion in color at minimum light to ≤slant 0.016 mag for the (r-i), (i-z), and (r-z) colors. These calibrations will be very useful for using RR Lyrae stars from DECam observations as both standard candles for distance determinations and color standards for reddening measurements.

  17. Development of an Automated System to Test and Select CCDs for the Dark Energy Survey Camera (DECam)

    NASA Astrophysics Data System (ADS)

    Kubik, Donna; Dark Energy Survey Collaboration

    2009-01-01

    The Dark Energy Survey (DES) is a next generation sky survey aimed directly at understanding why the universe is expanding at an accelerating rate. The survey will use the Dark Energy Camera (DECam), a 3 square degree, 500 Megapixel mosaic camera mounted at the prime focus of the Blanco 4-meter telescope at the Cerro Tololo Inter-American Observatory, to observe 5000 square-degrees of sky through 5 filters (g, r, i, z, Y). DECam will be comprised of 74 CCDs: 62 2k x 4k CCDs for imaging and 12 2k x 2k CCDs for guiding and focus. The goal of the DES is to provide a factor of 3-5 improvement in the Dark Energy Task Force Figure of Merit using four complementary methods: weak gravitational lensing, galaxy cluster counts, baryon acoustic oscillations, and Type IA supernovae. This goal sets stringent technical requirements for the CCDs. Testing a large number of CCDs to determine which best meet the DES requirements would be a very time-consuming manual task. We have developed a system to automatically collect and analyze CCD test data. The test results are entered into an online SQL database which facilitates selection of those CCDs that best meet the technical specifications for charge transfer efficiency, linearity, full well, quantum efficiency, noise, dark current, cross talk, diffusion, and cosmetics.

  18. Intragenic and Extragenic Suppressors of Mutations in the Heptapeptide Repeat Domain of Saccharomyces Cerevisiae RNA Polymerase II

    PubMed Central

    Nonet, M. L.; Young, R. A.

    1989-01-01

    The largest subunit of RNA polymerase II contains a repeated heptapeptide sequence at its carboxy terminus. Yeast mutants with certain partial deletions of the carboxy-terminal repeat (CTR) domain are temperature-sensitive, cold-sensitive and are inositol auxotrophs. Intragenic and extragenic suppressors of the cold-sensitive phenotype of CTR domain deletion mutants were isolated and studied to investigate the function of this domain. Two types of intragenic suppressing mutations suppress the temperature-sensitivity, cold-sensitivity and inositol auxotrophy of CTR domain deletion mutants. Most intragenic mutations enlarge the repeat domain by duplicating various portions of the repeat coding sequence. Other intragenic suppressing mutations are point mutations in a conserved segment of the large subunit. An extragenic suppressing mutation (SRB2-1) was isolated that strongly suppresses the conditional and auxotrophic phenotypes of CTR domain mutations. The SRB2 gene was isolated and mapped, and an SRB2 partial deletion mutation (srb2Δ10) was constructed. The srb2Δ10 mutants are temperature-sensitive, cold-sensitive and are inositol auxotrophs. These phenotypes are characteristic of mutations in genes encoding components of the transcription apparatus. We propose that the SRB2 gene encodes a factor that is involved in RNA synthesis and may interact with the CTR domain of the large subunit of RNA polymerase II. PMID:2693207

  19. Membrane-associated precursor to poliovirus VPg identified by immunoprecipitation with antibodies directed against a synthetic heptapeptide

    SciTech Connect

    Semelr, B.L.; Anderson, C.W.; Hanecak, R.; Dorner, L.F.; Wimmer, E.

    1982-02-01

    A synthetic heptapeptide corresponding to the C-terminal sequence of the poliovirus genome protein (VPg) has been linked to bovine serum albumin and used to raise antibodies in rabbits. These antibodies precipitate not only VPg but also at least two more virus-specific polypeptides. The smaller polypeptide, denoted P3-9 (12,000 daltons), has been mapped by Edman degradation and by fragmentation with cyanogen bromide and determined to be the N-terminal cleavage product of polypeptide P3-1b, a precursor to the RNA polymerase. P3-9 contains the sequence of the basic protein VPg (22 amino acids) at its C terminus. As predicted by the known RNA sequence of poliovirus, P3-9 also contains a hydrophobic region of 22 amino acids preceding VPg, an observation suggesting that P3-9 may be membrane-associated. This was confirmed by fractionation of infected cells in the presence or absence of detergent. We speculate that P3-9 may be the donor of VPg to RNA chains in the membrane-bound RNA replication complex.

  20. Spatial structure of heptapeptide Glu-Ile-Leu-Asn-His-Met-Lys, a fragment of the HIV enhancer prostatic acid phosphatase, in aqueous and SDS micelle solutions

    NASA Astrophysics Data System (ADS)

    Bloсhin, Dmitri S.; Aganova, Oksana V.; Yulmetov, Aidar R.; Filippov, Andrei V.; Gizatullin, Bulat I.; Afonin, Sergii; Antzutkin, Oleg N.; Klochkov, Vladimir V.

    2013-02-01

    Prostatic acid phosphatase (PAP) is a protein abundantly present in human seminal fluid. PAP plays important role in fertilization. Its 39-amino-acid fragment, PAP(248-286), is effective in enhancing infectivity of HIV virus. In this work, we determined the spatial structure in aqueous solution of a heptapeptide within the PAP fragment, containing amino acid residues 266-272 (Glu-Ile-Leu-Asn-His-Met-Lys). We also report the structure of the complex formed by this heptapeptide with sodium dodecyl sulfate micelles, a model of a biological membrane, as determined by 1H NMR spectroscopy and 2D NMR (TOCSY, HSQC-HECADE, NOESY) spectroscopy. Complex formation was confirmed by chemical shift alterations in the 1H NMR spectra of the heptapeptide, as well as by the signs and values of NOE effects. We also present a comparison of the spatial structure of Glu-Ile-Leu-Asn-His-Met-Lys in water and in complex with sodium dodecyl sulfate.

  1. Binding profile of the endogenous novel heptapeptide Met-enkephalin-Gly-tyr in zebrafish and rat brain.

    PubMed

    González-Nuñez, V; Arsequell, G; Szemenyei, E; Toth, G; Valencia, G; Rodriguez, R E

    2005-08-01

    Zebrafish is considered a model organism, not only for the study of the biological functions of vertebrates but also as a tool to analyze the effects of some drugs or toxic agents. Five opioid precursor genes homologous to the mammalian opioid propeptide genes have recently been identified; one of these, the zebrafish proenkephalin, codes a novel heptapeptide, the Met-enkephalin-Gly-Tyr (MEGY). To analyze the pharmacological properties of this novel ligand, we have labeled it with tritium ([(3)H]MEGY). In addition, we have also synthesized two analogs: (d-Ala(2))-MEGY (Y-d-Ala-GFMGY) and (d-Ala(2), Val(5))-MEGY (Y-d-Ala-GFVGY). The binding profile of these three agents has been studied in zebrafish and rat brain membranes. [(3)H]MEGY presents one binding site in zebrafish, as well as in rat brain membranes, although it shows a slight higher affinity in zebrafish brain. The observed saturable binding is displaced by naloxone, thus confirming the opioid nature of the binding sites. Competition binding assays indicate that the methionine residue is essential for high-affinity binding of MEGY and probably of other peptidic agonists in zebrafish, whereas the change of a Gly for a d-Ala does not dramatically affect the ligand affinity. Our results show that the percentage of [(3)H]MEGY displaced by all the ligands studied is higher than 100%, thus inferring that naloxone (used to determine nonspecific binding) does not bind to all the sites labeled by [(3)H]MEGY. Therefore, we can deduct that some of the MEGY binding sites should not be considered classical opioid sites.

  2. Synthesis and biological activity of 2-phenylethyl ester analogues of C-terminal heptapeptide of cholecystokinin modified in Trp 30 region.

    PubMed

    Rolland, M; Rodriguez, M; Lignon, M F; Galas, M C; Laur, J; Aumelas, A; Martinez, J

    1991-08-01

    We have tried to evaluate the significance of the tryptophan side chain residue and of the surrounding peptide bonds in the antagonist activity of cholecystokinin analogues lacking the C-terminal amide function and having a D-tryptophan. In order to perform this study, analogues of the C-terminal heptapeptide of cholecystokinin were synthesized by replacing the C-terminal phenylalanine residue with 2-phenylethyl alcohol and by either replacing the tryptophan residue with an alanine, a norleucine and a phenylalanine residue, or introducing a "reduced peptide bond" in the tryptophan 30 region. Most of these compounds were able to reproduce only part of the response of cholecystokinin in stimulating amylase release from rat pancreatic acini, as was already observed for 2-phenylethyl ester analogues of CCK. These results point out the key role of tryptophan 30 in the biological response of cholecystokinin.

  3. How pH modulates the dimer-decamer interconversion of 2-Cys peroxiredoxins from the Prx1 subfamily.

    PubMed

    Morais, Mariana A B; Giuseppe, Priscila O; Souza, Tatiana A C B; Alegria, Thiago G P; Oliveira, Marcos A; Netto, Luis E S; Murakami, Mario T

    2015-03-27

    2-Cys peroxiredoxins belonging to the Prx1 subfamily are Cys-based peroxidases that control the intracellular levels of H2O2 and seem to assume a chaperone function under oxidative stress conditions. The regulation of their peroxidase activity as well as the observed functional switch from peroxidase to chaperone involves changes in their quaternary structure. Multiple factors can modulate the oligomeric transitions of 2-Cys peroxiredoxins such as redox state, post-translational modifications, and pH. However, the molecular basis for the pH influence on the oligomeric state of these enzymes is still elusive. Herein, we solved the crystal structure of a typical 2-Cys peroxiredoxin from Leishmania in the dimeric (pH 8.5) and decameric (pH 4.4) forms, showing that conformational changes in the catalytic loop are associated with the pH-induced decamerization. Mutagenesis and biophysical studies revealed that a highly conserved histidine (His(113)) functions as a pH sensor that, at acidic conditions, becomes protonated and forms an electrostatic pair with Asp(76) from the catalytic loop, triggering the decamerization. In these 2-Cys peroxiredoxins, decamer formation is important for the catalytic efficiency and has been associated with an enhanced sensitivity to oxidative inactivation by overoxidation of the peroxidatic cysteine. In eukaryotic cells, exposure to high levels of H2O2 can trigger intracellular pH variations, suggesting that pH changes might act cooperatively with H2O2 and other oligomerization-modulator factors to regulate the structure and function of typical 2-Cys peroxiredoxins in response to oxidative stress. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. How pH Modulates the Dimer-Decamer Interconversion of 2-Cys Peroxiredoxins from the Prx1 Subfamily*

    PubMed Central

    Morais, Mariana A. B.; Giuseppe, Priscila O.; Souza, Tatiana A. C. B.; Alegria, Thiago G. P.; Oliveira, Marcos A.; Netto, Luis E. S.; Murakami, Mario T.

    2015-01-01

    2-Cys peroxiredoxins belonging to the Prx1 subfamily are Cys-based peroxidases that control the intracellular levels of H2O2 and seem to assume a chaperone function under oxidative stress conditions. The regulation of their peroxidase activity as well as the observed functional switch from peroxidase to chaperone involves changes in their quaternary structure. Multiple factors can modulate the oligomeric transitions of 2-Cys peroxiredoxins such as redox state, post-translational modifications, and pH. However, the molecular basis for the pH influence on the oligomeric state of these enzymes is still elusive. Herein, we solved the crystal structure of a typical 2-Cys peroxiredoxin from Leishmania in the dimeric (pH 8.5) and decameric (pH 4.4) forms, showing that conformational changes in the catalytic loop are associated with the pH-induced decamerization. Mutagenesis and biophysical studies revealed that a highly conserved histidine (His113) functions as a pH sensor that, at acidic conditions, becomes protonated and forms an electrostatic pair with Asp76 from the catalytic loop, triggering the decamerization. In these 2-Cys peroxiredoxins, decamer formation is important for the catalytic efficiency and has been associated with an enhanced sensitivity to oxidative inactivation by overoxidation of the peroxidatic cysteine. In eukaryotic cells, exposure to high levels of H2O2 can trigger intracellular pH variations, suggesting that pH changes might act cooperatively with H2O2 and other oligomerization-modulator factors to regulate the structure and function of typical 2-Cys peroxiredoxins in response to oxidative stress. PMID:25666622

  5. Altered decamer and nonamer from an HLA-A0201-restricted epitope of Survivin differentially stimulate T-cell responses in different individuals

    PubMed Central

    Bernatchez, Chantale; Zhu, Kuichin; Li, Yufeng; Andersson, Helen; Ionnides, Constantin; Fernandez-Vina, Marcelo; Cano, Pedro; Cooper, Laurence; Abbruzzese, James; Hwu, Patrick; Chang, David Z.; Radvanyi, Laszlo G.

    2011-01-01

    Survivin is a universal tumor antigen that is being currently targeted in vaccine app roaches against cancer. Our study here examined the immunogenicity of a novel variant of an HLA-A0201-binding decamer peptide from region 95-104 of Survivin (ELMLGEFLKL) with a T→M modification at position 3 in the peptide. We found that this new modified 10-mer peptide had enhanced HLA-A0201 binding and induced a stronger T-cell response over its wild type counterpart peptide (ELTLGEFLKL) in select HLA-A0201+ normal donors. In addition, when compared to the previously characterized altered 96-104 peptide (LMLGEFLKL) from the same region of Survivin currently used in vaccine trials, we found that both peptides had similar immunogenicity, but donor T cells preferentially reacted strongly to either one or the other, but not strongly to both. These results suggest that these two closely related Survivin peptides yield distinct T-cell responses and that most individuals dominantly respond to one or the other altered peptide. We also found a novel association between positive reactivity to the new altered decamer Survivin peptide in some individuals and their expression of the HLA-C0701 allele along with HLA-A0201. Thus, vaccinating with both the 10-mer and 9-mer peptides would be required to immunize a maximum number of individuals in the HLA-A0201+ population and could lead to more consistent T-cell responses against this region of Survivin. PMID:21320548

  6. Structure-Based Design of a Br Halogen Bond at the Complex Interface of the Human Placental HtrA1 PDZ Domain with Its Heptapeptide Ligand.

    PubMed

    Dou, Shuo-Fen; Liu, Hong; Cao, Tong-Mei; Wen, Qing-Li; Li, Jie; Shao, Qing-Chun

    2016-04-01

    The shock-induced serine protease HtrA1 is a potential regulator of human placenta development during pregnancy. The protein contains a functional PDZ domain that has been solved in complex with a phage display-derived heptapeptide: Asp-6 Ser-5 Arg-4 Ile-3 Trp-2 Trp-1 Val0 . In this study, a rationally designed halogen bond was introduced to the domain-peptide complex based on its NMR structure in solution. We computationally compared the stabilization energies and hindrance effects due to the presence of different halogens X (X = F, Cl, Br, or I), using a hybrid quantum mechanics/molecular mechanics (QM/MM) approach, and found that the Br atom could considerably promote the peptide binding free energy (ΔΔG = -5.2 kcal/mol). Fluorescence assays confirmed that the peptide affinity to the HtrA1 PDZ domain was improved by approximately sevenfold upon bromination. Structural analysis identified a geometrically perfect halogen bond between the Br atom of the peptide Trp-1 residue and the carbonyl O atom of the HtrA1 Ile385 residue, with a bond length and an interaction energy of d = 3.20 Å and ΔE = -3.7 kcal/mol, respectively.

  7. [The binding of Semax, ACTH 4-10 heptapeptide, to plasma membranes of the rat forebrain basal nuclei and its biodegradation].

    PubMed

    Dolotov, O V; Zolotarev, Iu A; Dorokhova, E M; Andreeva, L A; Alfeeva, L Iu; Grivennikov, I A; Miasoedov, N F

    2004-01-01

    The binding characteristics of the peptide Semax (Met-Glu-His-Phe-Pro-Gly-Pro) to plasma membranes of basal nuclei of the rat forebrain and the dynamics of its degradation during its incubation with these membranes were studied. Binding of the homogeneously labeled [G-3H]Semax was shown to be time-dependent, specific, and reversible. Specific binding of the heptapeptide depended on calcium ions and was characterized by the dissociation constant of the ligand-receptor complex Kd = 2.41 +/- 1.02 x 10(-9) M and by the concentration of binding sites Bmax = 33.5 +/- 7.9 x 10(-15) mol/mg of protein. A method of studying Semax biodegradation in the presence of plasma membranes of rat brain was developed. It is based on the use of the peptide homogeneously labeled with tritium and on an HPLC analysis with UV detection at 220 and 254 nm of the peptide fragments formed. The half-life of Semax in the presence of the plasma membranes was demonstrated to be longer than 1 h. Dipeptidylaminopeptidases are considered to be the main enzymes responsible for its biodegradation; they successively cleave Semax to the HFPGP pentapeptide and the PGP tripeptide. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2004, vol. 30, no. 3; see also http://www.maik.ru.

  8. Synthesis and biological activities of pseudopeptide analogues of the C-terminal heptapeptide of cholecystokinin. On the importance of the peptide bonds.

    PubMed

    Rodriguez, M; Lignon, M F; Galas, M C; Fulcrand, P; Mendre, C; Aumelas, A; Laur, J; Martinez, J

    1987-08-01

    A series of pseudopeptide analogues of the C-terminal heptapeptide of cholecystokinin in which each peptide bond, one at a time, has been replaced by a CH2NH bond were synthesized: Z-Tyr(SO3-)-Nle-Gly-Trp-Nle-Asp psi-(CH2NH)Phe-NH2 (1), Z-Tyr(SO3-)-Nle-Gly-Trp-Nle psi (CH2NH)Asp-Phe-NH2 (2), Z-Tyr(SO3-)-Nle-Gly-Trp psi-(CH2NH)Nle-Asp-Phe-NH2 (3), Z-Tyr(SO3-)-Nle-Gly psi(CH2NH)Trp-Nle-Asp-Phe-NH2 (4), Z-Tyr(SO3-)-Nle psi-(CH2NH)Gly-Trp-Nle-Asp-Phe-NH2 (5), Z-Tyr(SO3-)-Met-Gly-Trp-Nle-Asp psi (CH2NH)Phe-NH2 (6), Z-Tyr-(SO3-)-Met-Gly-Trp-Nle psi (CH2NH)Asp-Phe-NH2 (7), Z-Tyr(SO3-)-Met-Gly-Trp psi (CH2NH)Nle-Asp-Phe-NH2 (8). These derivatives were studied for their ability to stimulate amylase release from rat pancreatic acini and to inhibit the binding of labeled CCK-9 to rat pancreatic acini and to guinea pig brain membrane CCK receptors. They were compared to the potent CCK-8 analogue Boc-Asp-Tyr(SO3-)-Nle-Gly-Trp-Nle-Asp-Phe-NH2. All of these pseudopeptides were able to stimulate amylase secretion with the same efficacy as CCK-8 but with varying potencies. These compounds were also potent in inhibiting the binding of labeled CCK-9 to CCK receptors from rat pancreatic acini and from guinea pig brain membranes.

  9. Heat Shock Protein 27-Targeted Heptapeptide of the PKC{Delta} Catalytic V5 Region Sensitizes Tumors With Radio- and Chemoresistance

    SciTech Connect

    Lee, Hae-June; Kim, Eun-Ho; Seo, Woo Duck; Choi, Tae Hyun; Cheon, Gi-Jeong; Lee, Yoon-Jin; Lee, Yun-Sil

    2011-05-01

    Purpose: Previous data suggest that the PKC{delta} catalytic V5 (PKC{delta}-V5) heptapeptide (HEPT) (FEQFLDI) binds HSP27 and blocks HSP27-mediated radio- or chemoresistance. Here we investigated further the in vivo function of the PKC{delta}-V5 HEPT. Methods and Materials: Labeling of HEPT with Cy5.5 or fluorescein isothiocyanate was performed to evaluate in vitro or in vivo distribution of HEPT. A clonogenic survival assay, flow cytometry, and Western blotting of cleaved caspase-3 were performed to determine in vitro sensitization effects of HEPT plus ionizing radiation (IR) versus IR alone or those of HEPT plus cisplatin(Cis) versus Cis alone. A nude mouse xenografting system was also applied to detect in vivo sensitizing effects of HEPT. Results: HEPT efficiently bound to HSP27 and showed sensitization after combined treatment with IR versus treatment with Cis alone in NCI-H1299 lung carcinoma cells, with higher HSP27 expression, which was similar to that of combined treatment with IR or with Cis alone in NCI-H460 lung carcinoma cells with lower HSP27 expression. In vivo image analysis using Cy5.5-labeled HEPT showed that HEPT was retained in HSP27-overexpressing cancer cells after xenografting to nude mice. Combined treatment of HEPT with IR versus that with Cis alone in xenografted mice showed that HEPT increased radio- or chemosensitization in NCI-H1299 cells compared to that in mice xenografted with NCI-H460 cells. Conclusions: The novel PKC{delta}-V5 HEPT may help overcome HSP27-mediated radio- or chemoresistance.

  10. Blood pressure and hepatocellular effects of the cyclic heptapeptide toxin produced by the freshwater cyanobacterium (blue-green alga) Microcystis aeruginosa strain PCC-7820.

    PubMed

    Theiss, W C; Carmichael, W W; Wyman, J; Bruner, R

    1988-01-01

    Laboratory rats and mice were used to investigate the hepatotoxicity caused by the cyclic heptapeptide (mol. wt 994) termed microcystin-LR. Microcystin-LR (also known as cyanoginosin-LR) is produced by the freshwater cyanobacterium (blue-green alga) M. aeruginosa strain PCC-7820. In time course histopathology studies with mice significant liver damage, with an absence of pulmonary emboli, were observed after 15 min. Pulmonary emboli did not appear until 1 hr. In rats, significant liver damage and the presence of occasional emboli were observed at 20 min. Pulmonary emboli did not contain fibrin nor appear life-threatening in any case and resembled the globular eosinophilic debris found in the liver sinusoids and central veins. Measurements of rat femoral arterial, jugular venous and hepatic portal venous blood pressures during the course of toxicity revealed a slowly declining arterial pressure and stable, normal venous pressures. Blood lactic acid levels rose in parallel with the fall in arterial pressure, a pattern typical of hemorrhagic shock. There was no indication of venous congestion that would accompany right heart failure. Isolated, perfused rat livers dosed with toxin showed rapid changes in the liver, including cessation of bile flow within 10 min and complete obliteration of normal lobular architecture within 60 min. No effect of the toxin was observed in isolated perfused rat heart. We conclude that in the mouse and rat, microcystin-LR is a potent, rapid-acting, direct hepatotoxin, with the immediate cause of death in acute toxicities being hemorrhagic shock secondary to massive hepatocellular necrosis and collapse of hepatic parenchyma.

  11. Highly stable, fluorescence-labeled heptapeptides substituted with a D-amino acid for the specific detection of oxidized low-density lipoprotein in plasma.

    PubMed

    Sato, Akira; Yamanaka, Hikaru; Oe, Keitaro; Yokoyama, Izumi; Yamazaki, Yoji; Ebina, Keiichi

    2015-03-01

    Probes that can detect oxidized low-density lipoprotein (ox-LDL) in plasma and in atherosclerotic plaques can be useful for the diagnosis, prevention, and treatment of atherosclerosis. Recently, we have reported that two heptapeptides (Lys-Trp-Tyr-Lys-Asp-Gly-Asp, KP6) coupled to fluorescein isothiocyanate (FITC) through the ε-amino group of N-terminus Lys in the absence/presence of 6-amino-n-caproic acid (AC) linker to FITC-(FITC)KP6 and (FITC-AC)KP6-can be useful as fluorescent probes for the specific detection of ox-LDL. In this study, to develop the fluorescent peptides with high plasma stability for the specific detection of ox-LDL, we investigated the interaction of (FITC)KP6 and (FITC-AC)KP6 substituted with D-Lys at the N-terminus-(FITC)dKP6 and (FITC-AC)dKP6-with ox-LDL, and the in vitro stability of these peptides in mouse plasma. (FITC)dKP6 and (FITC-AC)dKP6 bound with high specificity to ox-LDL in a dose-dependent manner, and also to ox-LDL in the mouse plasma. Furthermore, (FITC)dKP6 was more stable than (FITC)KP6 in mouse plasma (102.1% versus 69.0% remained after 1 h). These findings strongly suggest that (FITC)dKP6 and (FITC-AC)dKP6 may be effective fluorescent probes with higher plasma stability than (FITC)KP6 and (FITC-AC)KP6 for the specific detection of ox-LDL.

  12. MicroRNA Profiling of the Effect of the Heptapeptide Angiotensin-(1-7) in A549 Lung Tumor Cells Reveals a Role for miRNA149-3p in Cellular Migration Processes

    PubMed Central

    da Silva, Brenda de Oliveira; Lima, Kelvin Furtado; Gonçalves, Letícia Rocha; da Silveira, Marina Bonfogo; Moraes, Karen C. M.

    2016-01-01

    Lung cancer is one of the most frequent types of cancer in humans and a leading cause of death worldwide. The high mortality rates are correlated with late diagnosis, which leads to high rates of metastasis found in patients. Thus, despite all the improvement in therapeutic approaches, the development of new drugs that control cancer cell migration and metastasis are required. The heptapeptide angiotensin-(1–7) [ang-(1–7)] has demonstrated the ability to control the growth rates of human lung cancer cells in vitro and in vivo, and the elucidation of central elements that control the fine-tuning of cancer cells migration in the presence of the ang-(1–7), will support the development of new therapeutic approaches. Ang-(1–7) is a peptide hormone of the renin-angiotensin system (RAS) and this study investigates the modulatory effect of the heptapeptide on the expression pattern of microRNAs (miRNAs) in lung tumor cells, to elucidate mechanistic concerns about the effect of the peptide in the control of tumor migratory processes. Our primary aim was to compare the miRNA profiling between treated and untreated-heptapeptide cells to characterize the relevant molecule that modulates cellular migration rates. The analyses selected twenty one miRNAs, which are differentially expressed between the groups; however, statistical analyses indicated miRNA-149-3p as a relevant molecule. Once functional analyses were performed, we demonstrated that miRNA-149-3p plays a role in the cellular migration processes. This information could be useful for future investigations on drug development. PMID:27598578

  13. Solution structure of a DNA decamer containing the antiviral drug ganciclovir: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement.

    PubMed

    Foti, M; Marshalko, S; Schurter, E; Kumar, S; Beardsley, G P; Schweitzer, B I

    1997-05-06

    The nucleoside analog 9-[(1,3-dihydroxy-2-propoxy)methyl]guanine (ganciclovir, DHPG) is an antiviral drug that is used in the treatment of a variety of herpes viruses in immunocompromised patients and in a gene therapy protocol that has shown promising activity for the treatment of cancer. To probe the structural effects of ganciclovir when incorporated into DNA, we determined and compared the solution structure of a modified ganciclovir-containing decamer duplex [d(CTG)(ganciclovir)d(ATCCAG)]2 and a control duplex d[(CTGGATCCAG)]2 using nuclear magnetic resonance techniques. 1H and 31P resonances in both duplexes were assigned using a combination of 2-D 1H and 31P NMR experiments. Proton-proton distances determined from NOESY data and dihedral angles determined from DQF-COSY data were used in restrained molecular dynamics simulations starting from canonical A- and B-form DNA models. Both the control and ganciclovir sets of simulations converged to B-type structures. These structures were subjected to full relaxation matrix refinement to produce final structures that were in excellent agreement with the observed NOE intensities. Examination of the final ganciclovir-containing structures reveals that the base of the ganciclovir residue is hydrogen bonded to its complementary dC and is stacked in the helix; in fact, the base of ganciclovir exhibits increased stacking with the 5' base relative to the control. Interestingly, some of the most significant distortions in the structures occur 3' to the lesion site, including a noticeable kink in the sugar-phosphate backbone at this position. Further examination reveals that the backbone conformation, sugar pucker, and glycosidic torsion angle of the residue 3' to the lesion site all indicate an A-type conformation at this position. A possible correlation of these structural findings with results obtained from earlier biochemical studies will be discussed.

  14. Structures of HLA-A*1101 complexed with immunodominant nonamer and decamer HIV-1 epitopes clearly reveal the presence of a middle, secondary anchor residue.

    PubMed

    Li, Lenong; Bouvier, Marlene

    2004-05-15

    HLA-A*1101 is one of the most common human class I alleles worldwide. An increased frequency of HLA-A*1101 has been observed in cohorts of female sex workers from Northern Thailand who are highly exposed to HIV-1 and yet have remained persistently seronegative. In view of this apparent association of HLA-A*1101 with resistance to acquisition of HIV-1 infection, and given the importance of eliciting strong CTL responses to control and eliminate HIV-1, we have determined the crystal structure of HLA-A*1101 complexed with two immunodominant HIV-1 CTL epitopes: the nonamer reverse transcriptase(313-321) (AIFQSSMTK) and decamer Nef(73-82) (QVPLRPMTYK) peptides. The structures confirm the presence of primary anchor residues P2-Ile/-Val and P9-/P10-Lys, and also clearly reveal the presence of secondary anchor residues P6-Ser for reverse transcriptase and P7-Met for Nef. The overall backbone conformation of both peptides is defined as two bulges that are separated by a more buried middle residue. In this study, we discuss how this topology may offer functional advantages in the selection and presentation of HIV-1 CTL epitopes by HLA-A*1101. Overall, this structural analysis permits a more accurate definition of the peptide-binding motif of HLA-A*1101, the characterization of its antigenic surface, and the correlation of molecular determinants with resistance to HIV-1 infection. These studies are relevant for the rational design of HLA-A*1101-restricted CTL epitopes with improved binding and immunological properties for the development of HIV-1 vaccines.

  15. The crystal structure of the C45S mutant of annelid Arenicola marina peroxiredoxin 6 supports its assignment to the mechanistically typical 2-Cys subfamily without any formation of toroid-shaped decamers

    PubMed Central

    Smeets, Aude; Loumaye, Eléonore; Clippe, André; Rees, Jean-François; Knoops, Bernard; Declercq, Jean-Paul

    2008-01-01

    The peroxiredoxins (PRDXs) define a superfamily of thiol-dependent peroxidases able to reduce hydrogen peroxide, alkyl hydroperoxides, and peroxynitrite. Besides their cytoprotective antioxidant function, PRDXs have been implicated in redox signaling and chaperone activity, the latter depending on the formation of decameric high-molecular-weight structures. PRDXs have been mechanistically divided into three major subfamilies, namely typical 2-Cys, atypical 2-Cys, and 1-Cys PRDXs, based on the number and position of cysteines involved in the catalysis. We report the structure of the C45S mutant of annelid worm Arenicola marina PRDX6 in three different crystal forms determined at 1.6, 2.0, and 2.4 Å resolution. Although A. marina PRDX6 was cloned during the search of annelid homologs of mammalian 1-Cys PRDX6s, the crystal structures support its assignment to the mechanistically typical 2-Cys PRDX subfamily. The protein is composed of two distinct domains: a C-terminal domain and an N-terminal domain exhibiting a thioredoxin fold. The subunits are associated in dimers compatible with the formation of intersubunit disulfide bonds between the peroxidatic and the resolving cysteine residues in the wild-type enzyme. The packing of two crystal forms is very similar, with pairs of dimers associated as tetramers. The toroid-shaped decamers formed by dimer association and observed in most typical 2-Cys PRDXs is not present. Thus, A. marina PRDX6 presents structural features of typical 2-Cys PRDXs without any formation of toroid-shaped decamers, suggesting that it should function more like a cytoprotective antioxidant enzyme or a modulator of peroxide-dependent cell signaling rather than a molecular chaperone. PMID:18359859

  16. Acylated heptapeptide binds albumin with high affinity and application as tag furnishes long-acting peptides

    NASA Astrophysics Data System (ADS)

    Zorzi, Alessandro; Middendorp, Simon J.; Wilbs, Jonas; Deyle, Kaycie; Heinis, Christian

    2017-07-01

    The rapid renal clearance of peptides in vivo limits this attractive platform for the treatment of a broad range of diseases that require prolonged drug half-lives. An intriguing approach for extending peptide circulation times works through a `piggy-back' strategy in which peptides bind via a ligand to the long-lived serum protein albumin. In accordance with this strategy, we developed an easily synthesized albumin-binding ligand based on a peptide-fatty acid chimera that has a high affinity for human albumin (Kd=39 nM). This ligand prolongs the elimination half-life of cyclic peptides in rats 25-fold to over seven hours. Conjugation to a peptide factor XII inhibitor developed for anti-thrombotic therapy extends the half-life from 13 minutes to over five hours, inhibiting coagulation for eight hours in rabbits. This high-affinity albumin ligand could potentially extend the half-life of peptides in human to several days, substantially broadening the application range of peptides as therapeutics.

  17. RDC-enhanced structure calculation of a β-heptapeptide in methanol.

    PubMed

    Rigling, Carla; Ebert, Marc-Olivier

    2017-07-01

    Residual dipolar couplings (RDCs) are a rich source of structural information that goes beyond the range covered by the nuclear Overhauser effect or scalar coupling constants. They can only be measured in partially oriented samples. RDC studies of peptides in organic solvents have so far been focused on samples in chloroform or DMSO. Here, we show that stretched poly(vinyl acetate) can be used for the partial alignment of a linear β-peptide with proteinogenic side chains in methanol. (1) DCH , (1) DNH , and (2) DHH RDCs were collected with this sample and included as restraints in a simulated annealing calculation. Incorporation of RDCs in the structure calculation process improves the long-range definition in the backbone of the resulting 314 -helix and uncovers side-chain mobility. Experimental side-chain RDCs of the central leucine and valine residues are in good agreement with predicted values from a local three-state model. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  18. Specific high-affinity binding sites for a synthetic gliadin heptapeptide of human peripheral blood lymphocytes

    SciTech Connect

    Payan, D.G.; Horvath, K.; Graf, L.

    1987-03-23

    The synthetic peptide containing residues 43-49 of ..cap alpha..-gliadin, the major protein component of gluten, has previously been shown to inhibit the production of lymphokine activities by mononuclear leukocytes. The authors demonstrate using radiolabeled ..cap alpha..-gliadin(43-49) that human peripheral blood lymphocytes express approximately 20,000-25,000 surface receptors for this peptide, with a dissociation constant (K/sub D/) of 20 nM. In addition, binding is inhibited by naloxone and an enkephalin analog, thus confirming the functional correlate which demonstrates inhibition by these agents of ..cap alpha..-gliadin(43-49) functional effects. Furthermore, B-lymphocytes bind specifically a greater amount of (/sup 125/I)..cap alpha..-gliadin(43-49) than T-lymphocytes. The lymphocyte ..cap alpha..-gliadin(43-49) receptor may play an important role in mediating the immunological response to ..cap alpha..-gliadin. 16 references, 4 figures.

  19. A DECam Search for an Optical Counterpart to the LIGO Gravitational Wave Event GW151226

    DOE PAGES

    Cowperthwaite, P.S.; et al.

    2016-07-29

    We report the results of a Dark Energy Camera optical follow-up of the gravitational-wave (GW) event GW151226, discovered by the Advanced Laser Interferometer Gravitational-wave Observatory detectors. Our observations cover 28.8 deg(2) of the localization region in the i and z bands (containing 3% of the BAYESTAR localization probability), starting 10 hr after the event was announced and spanning four epochs at 2–24 days after the GW detection. We achievemore » $$5\\sigma $$ point-source limiting magnitudes of $$i\\approx 21.7$$ and $$z\\approx 21.5$$, with a scatter of 0.4 mag, in our difference images. Given the two-day delay, we search this area for a rapidly declining optical counterpart with $$\\gtrsim 3\\sigma $$ significance steady decline between the first and final observations. We recover four sources that pass our selection criteria, of which three are cataloged active galactic nuclei. The fourth source is offset by 5.8 arcsec from the center of a galaxy at a distance of 187 Mpc, exhibits a rapid decline by 0.5 mag over 4 days, and has a red color of $$i-z\\approx 0.3$$ mag. These properties could satisfy a set of cuts designed to identify kilonovae. However, this source was detected several times, starting 94 days prior to GW151226, in the Pan-STARRS Survey for Transients (dubbed as PS15cdi) and is therefore unrelated to the GW event. Given its long-term behavior, PS15cdi is likely a Type IIP supernova that transitioned out of its plateau phase during our observations, mimicking a kilonova-like behavior. We comment on the implications of this detection for contamination in future optical follow-up observations.« less

  20. A DECam Search for an Optical Counterpart to the LIGO Gravitational Wave Event GW151226

    SciTech Connect

    Cowperthwaite, P.S.; et al.

    2016-07-29

    We report the results of a Dark Energy Camera optical follow-up of the gravitational-wave (GW) event GW151226, discovered by the Advanced Laser Interferometer Gravitational-wave Observatory detectors. Our observations cover 28.8 deg(2) of the localization region in the i and z bands (containing 3% of the BAYESTAR localization probability), starting 10 hr after the event was announced and spanning four epochs at 2–24 days after the GW detection. We achieve $5\\sigma $ point-source limiting magnitudes of $i\\approx 21.7$ and $z\\approx 21.5$, with a scatter of 0.4 mag, in our difference images. Given the two-day delay, we search this area for a rapidly declining optical counterpart with $\\gtrsim 3\\sigma $ significance steady decline between the first and final observations. We recover four sources that pass our selection criteria, of which three are cataloged active galactic nuclei. The fourth source is offset by 5.8 arcsec from the center of a galaxy at a distance of 187 Mpc, exhibits a rapid decline by 0.5 mag over 4 days, and has a red color of $i-z\\approx 0.3$ mag. These properties could satisfy a set of cuts designed to identify kilonovae. However, this source was detected several times, starting 94 days prior to GW151226, in the Pan-STARRS Survey for Transients (dubbed as PS15cdi) and is therefore unrelated to the GW event. Given its long-term behavior, PS15cdi is likely a Type IIP supernova that transitioned out of its plateau phase during our observations, mimicking a kilonova-like behavior. We comment on the implications of this detection for contamination in future optical follow-up observations.

  1. A DECam Search for an Optical Counterpart to the LIGO Gravitational-wave Event GW151226

    NASA Astrophysics Data System (ADS)

    Cowperthwaite, P. S.; Berger, E.; Soares-Santos, M.; Annis, J.; Brout, D.; Brown, D. A.; Buckley-Geer, E.; Cenko, S. B.; Chen, H. Y.; Chornock, R.; Diehl, H. T.; Doctor, Z.; Drlica-Wagner, A.; Drout, M. R.; Farr, B.; Finley, D. A.; Foley, R. J.; Fong, W.; Fox, D. B.; Frieman, J.; Garcia-Bellido, J.; Gill, M. S. S.; Gruendl, R. A.; Herner, K.; Holz, D. E.; Kasen, D.; Kessler, R.; Lin, H.; Margutti, R.; Marriner, J.; Matheson, T.; Metzger, B. D.; Neilsen, E. H., Jr.; Quataert, E.; Rest, A.; Sako, M.; Scolnic, D.; Smith, N.; Sobreira, F.; Strampelli, G. M.; Villar, V. A.; Walker, A. R.; Wester, W.; Williams, P. K. G.; Yanny, B.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Armstrong, R.; Bechtol, K.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Burke, D. L.; Carnero Rosell, A.; Carrasco Kind, M.; Carretero, J.; Castander, F. J.; Cunha, C. E.; D'Andrea, C. B.; da Costa, L. N.; Desai, S.; Dietrich, J. P.; Evrard, A. E.; Fausti Neto, A.; Fosalba, P.; Gerdes, D. W.; Giannantonio, T.; Goldstein, D. A.; Gruen, D.; Gutierrez, G.; Honscheid, K.; James, D. J.; Johnson, M. W. G.; Johnson, M. D.; Krause, E.; Kuehn, K.; Kuropatkin, N.; Lima, M.; Maia, M. A. G.; Marshall, J. L.; Menanteau, F.; Miquel, R.; Mohr, J. J.; Nichol, R. C.; Nord, B.; Ogando, R.; Plazas, A. A.; Reil, K.; Romer, A. K.; Sanchez, E.; Scarpine, V.; Sevilla-Noarbe, I.; Smith, R. C.; Suchyta, E.; Tarle, G.; Thomas, D.; Thomas, R. C.; Tucker, D. L.; Weller, J.; DES Collaboration

    2016-08-01

    We report the results of a Dark Energy Camera optical follow-up of the gravitational-wave (GW) event GW151226, discovered by the Advanced Laser Interferometer Gravitational-wave Observatory detectors. Our observations cover 28.8 deg2 of the localization region in the i and z bands (containing 3% of the BAYESTAR localization probability), starting 10 hr after the event was announced and spanning four epochs at 2-24 days after the GW detection. We achieve 5σ point-source limiting magnitudes of i≈ 21.7 and z≈ 21.5, with a scatter of 0.4 mag, in our difference images. Given the two-day delay, we search this area for a rapidly declining optical counterpart with ≳ 3σ significance steady decline between the first and final observations. We recover four sources that pass our selection criteria, of which three are cataloged active galactic nuclei. The fourth source is offset by 5.8 arcsec from the center of a galaxy at a distance of 187 Mpc, exhibits a rapid decline by 0.5 mag over 4 days, and has a red color of i-z≈ 0.3 mag. These properties could satisfy a set of cuts designed to identify kilonovae. However, this source was detected several times, starting 94 days prior to GW151226, in the Pan-STARRS Survey for Transients (dubbed as PS15cdi) and is therefore unrelated to the GW event. Given its long-term behavior, PS15cdi is likely a Type IIP supernova that transitioned out of its plateau phase during our observations, mimicking a kilonova-like behavior. We comment on the implications of this detection for contamination in future optical follow-up observations.

  2. Thermodynamics and kinetics for base pair opening in the DNA decamer duplexes containing cyclobutane pyrimidine dimer.

    PubMed

    Bang, Jongchul; Kang, Young-Min; Park, Chin-Ju; Lee, Joon-Hwa; Choi, Byong-Seok

    2009-06-18

    The cyclobutane pyrimidine dimer (CPD) is one of the major classes of cytotoxic and carcinogenic DNA photoproducts induced by UV light. Hydrogen exchange rates of the imino protons were measured for various CPD-containing DNA duplexes to better understand the mechanism for CPD recognition by XPC-hHR23B. The results here revealed that double T.G mismatches in a CPD lesion significantly destabilized six consecutive base pairs compared to other DNA duplexes. This flexibility in a DNA duplex caused at the CPD lesions with double T.G mismatches might be the key factor for damage recognition by XPC-hHR23B.

  3. A DECam Search for an Optical Counterpart to the LIGO Gravitational Wave Event GW151226

    SciTech Connect

    Cowperthwaite, P. S.

    2016-07-29

    We report the results of a Dark Energy Camera optical follow-up of the gravitational-wave (GW) event GW151226, discovered by the Advanced Laser Interferometer Gravitational-wave Observatory detectors. Our observations cover 28.8 deg(2) of the localization region in the i and z bands (containing 3% of the BAYESTAR localization probability), starting 10 hr after the event was announced and spanning four epochs at 2–24 days after the GW detection. We achieve $5\\sigma $ point-source limiting magnitudes of $i\\approx 21.7$ and $z\\approx 21.5$, with a scatter of 0.4 mag, in our difference images. Given the two-day delay, we search this area for a rapidly declining optical counterpart with $\\gtrsim 3\\sigma $ significance steady decline between the first and final observations. We recover four sources that pass our selection criteria, of which three are cataloged active galactic nuclei. The fourth source is offset by 5.8 arcsec from the center of a galaxy at a distance of 187 Mpc, exhibits a rapid decline by 0.5 mag over 4 days, and has a red color of $i-z\\approx 0.3$ mag. These properties could satisfy a set of cuts designed to identify kilonovae. However, this source was detected several times, starting 94 days prior to GW151226, in the Pan-STARRS Survey for Transients (dubbed as PS15cdi) and is therefore unrelated to the GW event. Given its long-term behavior, PS15cdi is likely a Type IIP supernova that transitioned out of its plateau phase during our observations, mimicking a kilonova-like behavior. We comment on the implications of this detection for contamination in future optical follow-up observations.

  4. A DECam Search for an Optical Counterpart to the LIGO Gravitational Wave Event GW151226

    DOE PAGES

    Cowperthwaite, P. S.

    2016-07-29

    We report the results of a Dark Energy Camera optical follow-up of the gravitational-wave (GW) event GW151226, discovered by the Advanced Laser Interferometer Gravitational-wave Observatory detectors. Our observations cover 28.8 deg(2) of the localization region in the i and z bands (containing 3% of the BAYESTAR localization probability), starting 10 hr after the event was announced and spanning four epochs at 2–24 days after the GW detection. We achievemore » $$5\\sigma $$ point-source limiting magnitudes of $$i\\approx 21.7$$ and $$z\\approx 21.5$$, with a scatter of 0.4 mag, in our difference images. Given the two-day delay, we search this area for a rapidly declining optical counterpart with $$\\gtrsim 3\\sigma $$ significance steady decline between the first and final observations. We recover four sources that pass our selection criteria, of which three are cataloged active galactic nuclei. The fourth source is offset by 5.8 arcsec from the center of a galaxy at a distance of 187 Mpc, exhibits a rapid decline by 0.5 mag over 4 days, and has a red color of $$i-z\\approx 0.3$$ mag. These properties could satisfy a set of cuts designed to identify kilonovae. However, this source was detected several times, starting 94 days prior to GW151226, in the Pan-STARRS Survey for Transients (dubbed as PS15cdi) and is therefore unrelated to the GW event. Given its long-term behavior, PS15cdi is likely a Type IIP supernova that transitioned out of its plateau phase during our observations, mimicking a kilonova-like behavior. We comment on the implications of this detection for contamination in future optical follow-up observations.« less

  5. Role of monomer arrangement in the amyloid self-assembly

    PubMed Central

    Portillo, Alexander; Hashemi, Mohtadin; Zhang, Yuliang; Breydo, Leonid; Uversky, Vladimir N.; Lyubchenko, Yuri L.

    2015-01-01

    Assembly of amyloid proteins into aggregates requires the ordering of the monomers in oligomers and especially in such highly organized structures as fibrils. This ordering is accompanied by structural transitions leading to the formation of ordered β-structural motifs in proteins and peptides lacking secondary structures. To characterize the effect of the monomers arrangements on the aggregation process at various stages, we performed comparative studies of the yeast prion protein Sup35 heptapeptide (GNNQQNY) along with its dimeric form CGNNQQNY-(d-Pro)-G-GNNQQNY. The (d-Pro)-G linker in this construct is capable of adopting a β-turn, facilitating the assembly of the dimer into the dimeric antiparallel hairpin structure (AP-hairpin). We applied Atomic Force Microscopy (AFM) techniques to follow peptide-peptide interactions at the single molecule level, to visualize the morphology of aggregates formed by both constructs, thioflavin T (ThT) fluorescence to follow the aggregation kinetics, and circular dichroism (CD) spectroscopy to characterize the secondary structure of the constructs. The ThT fluorescence data showed that the AP-hairpin aggregation kinetics is insensitive to the external environment such as ionic strength and pH contrary to the monomers the kinetics of which depends dramatically on the ionic strength and pH. The AFM topographic imaging revealed that AP--hairpins primarily assemble into globular aggregates, whereas linear fibrils are primary assemblies of the monomers suggesting that both constructs follow different aggregation pathways during the self-assembly. These morphological differences are in line with the AFM force spectroscopy experiments and CD spectroscopy measurements, suggesting that the AP-hairpin is structurally rigid regardless of changes of environmental factors. PMID:25542374

  6. Polymeric nanoparticles conjugate a novel heptapeptide as an epidermal growth factor receptor-active targeting ligand for doxorubicin

    PubMed Central

    Liu, Chia Wen; Lin, Wen Jen

    2012-01-01

    Background This study was performed to develop a functional poly(D,L-lactide-co-glycolide)- poly(ethylene glycol) (PLGA-PEG)-bearing amino-active end group for peptide conjugation. Methods and results PLGA was preactivated following by copolymerization with PEG diamine. The resulting amphiphilic PLGA-PEG copolymer bearing 97.0% of amino end groups had a critical micelle concentration of 3.0 × 10−8 mol/L, and the half-effective inhibition concentration (IC50) of the prepared PLGA-PEG nanoparticles was >100 mg/mL, which was much higher than that of PLGA nanoparticles (1.02 ± 0.37 mg/mL). The amphiphilic properties of PLGA-PEG spontaneously formed a core-shell conformation in the aqueous environment, and this special feature provided the amino group on the PEG chain scattered on the surface of PLGA-PEG nanoparticles for efficient peptide conjugation. The peptide-conjugated PLGA-PEG nanoparticles showed three-fold higher uptake than peptide-free PLGA-PEG nanoparticles in a SKOV3 cell line with high expression of epidermal growth factor receptor. Both peptide-conjugated and peptide-free PLGA-PEG nanoparticles were used as nanocarriers for delivery of doxorubicin. Although the rate of release of doxorubicin from both nanoparticles was similar, drug release at pH 4.0 (500 U lipase) was faster than at pH 7.4. The IC50 of doxorubicin-loaded peptide-conjugated PLGA-PEG nanoparticles in SKOV3 cells (0.05 ± 0.03 μg/mL) was much lower (by 62.4-fold) than that of peptide-free PLGA-PEG nanoparticles (3.12 ± 1.44 μg/mL). Conclusion This in vivo biodistribution study in SKOV3 tumor-bearing mice was further promising in that accumulation of doxorubicin in tumor tissue was in the order of peptide-conjugated PLGA-PEG nanoparticles > peptide-free PLGA-PEG nanoparticles > doxorubicin solution. PMID:22973097

  7. Talarolide A, a Cyclic Heptapeptide Hydroxamate from an Australian Marine Tunicate-Associated Fungus, Talaromyces sp. (CMB-TU011).

    PubMed

    Dewapriya, Pradeep; Prasad, Pritesh; Damodar, Rakesh; Salim, Angela A; Capon, Robert J

    2017-04-06

    A miniaturized 24-well plate microbioreactor approach was used to explore secondary metabolite media dependence in an Australian marine tunicate-associated fungus, Talaromyces sp. (CMB TU011). Detailed chemical investigations of an antifungal M1-saline cultivation yielded talarolide A (1), only the second reported natural cyclic peptide hydroxamate, and the first from a fungus. The antifungal properties of the M1-saline extract were attributed to the known diterpene glycoside sordarin (2). Structure elucidation of 1 and 2 was achieved by detailed spectroscopic analysis, with amino acid configurations in 1 assigned by the C3 and C18 Marfey's methods, and l-Ala and d-Ala regiochemistry by the recently reported 2D C3 Marfey's method.

  8. Structure, stability, thermodynamic properties, and IR spectra of the protonated water decamer H+(H2O)10.

    PubMed

    Karthikeyan, S; Kim, Kwang S

    2009-08-13

    Protonated water clusters H+(H2O)n favor two-dimensional (2D) structures for n < or = 7 at low temperatures. At 0 K, the 2D and three-dimensional (3D) structures for n = 8 are almost isoenergetic, and the 3D structures for n > 9 tend to be more stable. However, for n = 9, the netlike structures are likely to be more stable above 150 K. In this regard, we investigate the case of n = 10 to find which structure is more stable between the 3D structure and the netlike structure around 150 and 250 K. We use density functional theory, Møller-Plesset second-order perturbation theory, and coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)). At the complete basis set limit for the CCSD(T) level of theory, three isomers of 3D cage structure are much more stable in zero point energy corrected binding energy and in free binding energies at 150 K than the lowest energy netlike structures, while the netlike structure would be more stable around approximately 250 K. The predicted vibrational spectra are in good agreement with the experiment. One of the three isomers explains the experimental IR observation of an acceptor (A) type peak of a dangling hydrogen atom.

  9. The effect of glycine replacement with flexible ω-amino acids on the antimicrobial and haemolytic activity of an amphipathic cyclic heptapeptide.

    PubMed

    Oddo, Alberto; Nyberg, Nils T; Frimodt-Møller, Niels; Thulstrup, Peter W; Hansen, Paul R

    2015-09-18

    Although cyclic peptide structures are usually investigated as highly constrained scaffolds, cyclic antimicrobial peptides of natural origin often feature flexible residues. Hereby we report our findings concerning a structure-activity study conducted on a model sequence by replacing a glycine residue with a variety of flexible residues (i.e. ω-amino and α,ω-diamino acids). The resulting library has been tested for antimicrobial activity against a wide range of clinically relevant pathogens as well as for toxicity to red blood cells. Circular dichroism and molecular modelling have been used to study changes in conformation. Increments as high as 16-fold in antimicrobial activity (as effective as lipidation) and >2-fold in haemolytic EC50 values were observed. Interestingly, secondary structures can be stabilized by increasing, rather than decreasing, ring flexibility. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  10. Reaction Path Optimization with Holonomic Constraints and Kinetic Energy Potentials

    SciTech Connect

    Brokaw, Jason B.; Haas, Kevin R.; Chu, Jhih-wei

    2009-08-11

    Two methods are developed to enhance the stability, efficiency, and robustness of reaction path optimization using a chain of replicas. First, distances between replicas are kept equal during path optimization via holonomic constraints. Finding a reaction path is, thus, transformed into a constrained optimization problem. This approach avoids force projections for finding minimum energy paths (MEPs), and fast-converging schemes such as quasi-Newton methods can be readily applied. Second, we define a new objective function - the total Hamiltonian - for reaction path optimization, by combining the kinetic energy potential of each replica with its potential energy function. Minimizing the total Hamiltonian of a chain determines a minimum Hamiltonian path (MHP). If the distances between replicas are kept equal and a consistent force constant is used, then the kinetic energy potentials of all replicas have the same value. The MHP in this case is the most probable isokinetic path. Our results indicate that low-temperature kinetic energy potentials (<5 K) can be used to prevent the development of kinks during path optimization and can significantly reduce the required steps of minimization by 2-3 times without causing noticeable differences between a MHP and MEP. These methods are applied to three test cases, the C₇eq-to-Cax isomerization of an alanine dipeptide, the ⁴C₁- to-¹C₄ transition of an α-D-glucopyranose, and the helix-to-sheet transition of a GNNQQNY heptapeptide. By applying the methods developed in this work, convergence of reaction path optimization can be achieved for these complex transitions, involving full atomic details and a large number of replicas (>100). For the case of helix-to-sheet transition, we identify pathways whose energy barriers are consistent with experimental measurements. Further, we develop a method based on the work energy theorem to quantify the accuracy of reaction paths and to determine whether the atoms used to define a

  11. Reaction Path Optimization with Holonomic Constraints and Kinetic Energy Potentials.

    PubMed

    Brokaw, Jason B; Haas, Kevin R; Chu, Jhih-Wei

    2009-08-11

    Two methods are developed to enhance the stability, efficiency, and robustness of reaction path optimization using a chain of replicas. First, distances between replicas are kept equal during path optimization via holonomic constraints. Finding a reaction path is, thus, transformed into a constrained optimization problem. This approach avoids force projections for finding minimum energy paths (MEPs), and fast-converging schemes such as quasi-Newton methods can be readily applied. Second, we define a new objective function - the total Hamiltonian - for reaction path optimization, by combining the kinetic energy potential of each replica with its potential energy function. Minimizing the total Hamiltonian of a chain determines a minimum Hamiltonian path (MHP). If the distances between replicas are kept equal and a consistent force constant is used, then the kinetic energy potentials of all replicas have the same value. The MHP in this case is the most probable isokinetic path. Our results indicate that low-temperature kinetic energy potentials (<5 K) can be used to prevent the development of kinks during path optimization and can significantly reduce the required steps of minimization by 2-3 times without causing noticeable differences between a MHP and MEP. These methods are applied to three test cases, the C7eq-to-Cax isomerization of an alanine dipeptide, the (4)C1-to-(1)C4 transition of an α-d-glucopyranose, and the helix-to-sheet transition of a GNNQQNY heptapeptide. By applying the methods developed in this work, convergence of reaction path optimization can be achieved for these complex transitions, involving full atomic details and a large number of replicas (>100). For the case of helix-to-sheet transition, we identify pathways whose energy barriers are consistent with experimental measurements. Further, we develop a method based on the work energy theorem to quantify the accuracy of reaction paths and to determine whether the atoms used to define a path

  12. Crystal Structure of Reduced and of Oxidized Peroxiredoxin IV Enzyme Reveals a Stable Oxidized Decamer and a Non-disulfide-bonded Intermediate in the Catalytic Cycle*

    PubMed Central

    Cao, Zhenbo; Tavender, Timothy J.; Roszak, Aleksander W.; Cogdell, Richard J.; Bulleid, Neil J.

    2011-01-01

    Peroxiredoxin IV (PrxIV) is an endoplasmic reticulum-localized enzyme that metabolizes the hydrogen peroxide produced by endoplasmic reticulum oxidase 1 (Ero1). It has been shown to play a role in de novo disulfide formation, oxidizing members of the protein disulfide isomerase family of enzymes, and is a member of the typical 2-Cys peroxiredoxin family. We have determined the crystal structure of both reduced and disulfide-bonded, as well as a resolving cysteine mutant of human PrxIV. We show that PrxIV has a similar structure to other typical 2-Cys peroxiredoxins and undergoes a conformational change from a fully folded to a locally unfolded form following the formation of a disulfide between the peroxidatic and resolving cysteine residues. Unlike other mammalian typical 2-Cys peroxiredoxins, we show that human PrxIV forms a stable decameric structure even in its disulfide-bonded state. In addition, the structure of a resolving cysteine mutant reveals an intermediate in the reaction cycle that adopts the locally unfolded conformation. Interestingly the peroxidatic cysteine in the crystal structure is sulfenylated rather than sulfinylated or sulfonylated. In addition, the peroxidatic cysteine in the resolving cysteine mutant is resistant to hyper-oxidation following incubation with high concentrations of hydrogen peroxide. These results highlight some unique properties of PrxIV and suggest that the equilibrium between the fully folded and locally unfolded forms favors the locally unfolded conformation upon sulfenylation of the peroxidatic cysteine residue. PMID:21994946

  13. A peptide study of the relationship between the collagen triple-helix and amyloid.

    PubMed

    Parmar, Avanish S; Nunes, Ana Monica; Baum, Jean; Brodsky, Barbara

    2012-10-01

    Type XXV collagen, or collagen-like amyloidogenic component, is a component of amyloid plaques, and recent studies suggest this collagen affects amyloid fibril elongation and has a genetic association with Alzheimer's disease. The relationship between the collagen triple helix and amyloid fibrils was investigated by studying peptide models, including a very stable triple helical peptide (Pro-Hyp-Gly)₁₀ , an amyloidogenic peptide GNNQQNY, and a hybrid peptide where the GNNQQNY sequence was incorporated between (GPO)(n) domains. Circular dichroism and nuclear magnetic resonance (NMR) spectroscopy showed the GNNQQNY peptide formed a random coil structure, whereas the hybrid peptide contained a central disordered GNNQQNY region transitioning to triple-helical ends. Light scattering confirmed the GNNQQNY peptide had a high propensity to form amyloid fibrils, whereas amyloidogenesis was delayed in the hybrid peptide. NMR data suggested the triple-helix constraints on the GNNQQNY sequence within the hybrid peptide may disfavor the conformational change necessary for aggregation. Independent addition of a triple-helical peptide to the GNNQQNY peptide under aggregating conditions delayed nucleation and amyloid fibril growth. The inhibition of amyloid nucleation depended on the Gly-Xaa-Yaa sequence and required the triple-helix conformation. The inhibitory effect of the collagen triple-helix on an amyloidogenic sequence, when in the same molecule or when added separately, suggests Type XXV collagen, and possibly other collagens, may play a role in regulating amyloid fibril formation.

  14. Antitumor Trans Platinum DNA Adducts: NMR and HPLC Study of the Interaction Between a trans-Pt Iminoether Complex and the Deoxy Decamer d(CCTCGCTCTC)·d(GAGAGCGAGG)

    PubMed Central

    Andersen, Bjørn; Margiotta, Nicola; Coluccia, Mauro; Natile, Giovanni

    2000-01-01

    The single-stranded oligonucleotide 5′-d(CCTCGCTCTC) (I) was reacted with the antitumor trans platinum iminoderivative trans-[PtCl2{E-HN = C(OMe)Me}2] (trans-EE) and subsequently annealed with its complementary strand 5′-d(GAGAGCGAGG) (II). The platinated duplex was characterized by 1D and 2D proton NMR spectroscopy at 600 MHz. In agreement with previous studies by different techniques trans-EE was found to form a monofunctional adduct with the duplex involving the guanine residue. The modification by trans-EE has been found to induce only minor local distortion in the duplex geometry. Two key crosspeaks observed in the NOESY map corresponding to a close contact between G5-H8 and the methoxy and the methyl group, respectively, enabled us to dock the trans-EE complex with the duplex by geometry optimization. The results support the idea that the antitumor activity of trans-EE is related to lesion of DNA fundamentally different from that of cisplatin. Unexpectedly, the NOESY spectra indicated that at the high NaCl concentration used (0.2 M) the duplex was found to undergo slow deplatination. This was subsequently proved by HPLC. In a separate experiment on platination of the single strand in a salt free environment the HPLC analysis showed that the monofunctional adduct was not deplatinated, however, after 24 hours, additidnal minor isomers were detected. PMID:18475920

  15. Thermodynamics of Protein Aggregation

    NASA Astrophysics Data System (ADS)

    Osborne, Kenneth L.; Barz, Bogdan; Bachmann, Michael; Strodel, Birgit

    Amyloid protein aggregation characterizes many neurodegenerative disorders, including Alzheimer's, Parkinson's, and Creutz- feldt-Jakob disease. Evidence suggests that amyloid aggregates may share similar aggregation pathways, implying simulation of full-length amyloid proteins is not necessary for understanding amyloid formation. In this study we simulate GNNQQNY, the N-terminal prion-determining domain of the yeast protein Sup35 to investigate the thermodynamics of structural transitions during aggregation. We use a coarse-grained model with replica-exchange molecular dynamics to investigate the association of 3-, 6-, and 12-chain GNNQQNY systems and we determine the aggregation pathway by studying aggregation states of GN- NQQNY. We find that the aggregation of the hydrophilic GNNQQNY sequence is mainly driven by H-bond formation, leading to the formation of /3-sheets from the very beginning of the assembly process. Condensation (aggregation) and ordering take place simultaneously, which is underpinned by the occurrence of a single heat capacity peak only.

  16. Polyanionic Carboxyethyl Peptide Nucleic Acids (ce-PNAs): Synthesis and DNA Binding

    PubMed Central

    Kirillova, Yuliya; Boyarskaya, Nataliya; Dezhenkov, Andrey; Tankevich, Mariya; Prokhorov, Ivan; Varizhuk, Anna; Eremin, Sergei; Esipov, Dmitry; Smirnov, Igor; Pozmogova, Galina

    2015-01-01

    New polyanionic modifications of polyamide nucleic acid mimics were obtained. Thymine decamers were synthesized from respective chiral α- and γ-monomers, and their enantiomeric purity was assessed. Here, we present the decamer synthesis, purification and characterization by MALDI-TOF mass spectrometry and an investigation of the hybridization properties of the decamers. We show that the modified γ-S-carboxyethyl-T10 PNA forms a stable triplex with polyadenine DNA. PMID:26469337

  17. The stabilizing influence of divalent ions and Na+ on the di-decameric structure of Yoldia limatula hemocyanin.

    PubMed

    Herskovits, T T; Cousins, C J; Hamilton, M G

    1991-01-08

    The stabilizing influence of Ca2+, Mg2+, Ba2+ and Na+ on the di-decameric structure of the hemocyanin of the bivalve, Yoldia limatula has been investigated by light-scattering molecular weight measurements and by analytical ultracentrifugation. The molecular weight (Mw) data, examined as a function of decreasing divalent ion and sodium ion concentrations at pH 8.0 and at a constant hemocyanin concentration of 0.10 g.l-1, show biphasic transition profiles, with a sharp initial decline in Mw as the concentration of the stabilizing cations is reduced. The analysis of the molecular weight data is best described in terms of the four-species, di-decamer-decamer-dimer-monomer scheme of association-dissociation equilibria. About 25 to 35 bound divalent ions and about 10 bound Na+ ions per half-molecule or decamer are required in order to account for the initial step of the observed transitions. The subsequent transitions representing the decamer to dimer and the dimer to monomer steps of the reaction account for the additional binding of three to four and two to four cations per dimer and per monomer, respectively. The relatively large number of divalent ions per decamer suggests strong ionic stabilization of the decamer to decamer contacts within the parent di-decameric assembly of Yoldia hemocyanin. This is consistent with earlier observations showing relatively few hydrophobic groups at the decamer to decamer contact areas.

  18. Evaluation of a High-Throughput Peptide Reactivity Format Assay for Assessment of the Skin Sensitization Potential of Chemicals.

    PubMed

    Wong, Chin Lin; Lam, Ai-Leen; Smith, Maree T; Ghassabian, Sussan

    2016-01-01

    The direct peptide reactivity assay (DPRA) is a validated method for in vitro assessment of the skin sensitization potential of chemicals. In the present work, we describe a peptide reactivity assay using 96-well plate format and systematically identified the optimal assay conditions for accurate and reproducible classification of chemicals with known sensitizing capacity. The aim of the research is to ensure that the analytical component of the peptide reactivity assay is robust, accurate, and reproducible in accordance with criteria that are used for the validation of bioanalytical methods. Analytical performance was evaluated using quality control samples (QCs; heptapeptides at low, medium, and high concentrations) and incubation of control chemicals (chemicals with known sensitization capacity, weak, moderate, strong, extreme, and non-sensitizers) with each of three synthetic heptapeptides, viz Cor1-C420 (Ac-NKKCDLF), cysteine- (Ac-RFAACAA), and lysine- (Ac-RFAAKAA) containing heptapeptides. The optimal incubation temperature for all three heptapeptides was 25°C. Apparent heptapeptide depletion was affected by vial material composition. Incubation of test chemicals with Cor1-C420, showed that peptide depletion was unchanged in polypropylene vials over 3-days storage in an autosampler but this was not the case for borosilicate glass vials. For cysteine-containing heptapeptide, the concentration was not stable by day 3 post-incubation in borosilicate glass vials. Although the lysine-containing heptapeptide concentration was unchanged in both polypropylene and borosilicate glass vials, the apparent extent of lysine-containing heptapeptide depletion by ethyl acrylate, differed between polypropylene (24.7%) and glass (47.3%) vials. Additionally, the peptide-chemical complexes for Cor1-C420-cinnamaldehyde and cysteine-containing heptapeptide-2, 4-dinitrochlorobenzene were partially reversible during 3-days of autosampler storage. These observations further highlight

  19. Evaluation of a High-Throughput Peptide Reactivity Format Assay for Assessment of the Skin Sensitization Potential of Chemicals

    PubMed Central

    Wong, Chin Lin; Lam, Ai-Leen; Smith, Maree T.; Ghassabian, Sussan

    2016-01-01

    The direct peptide reactivity assay (DPRA) is a validated method for in vitro assessment of the skin sensitization potential of chemicals. In the present work, we describe a peptide reactivity assay using 96-well plate format and systematically identified the optimal assay conditions for accurate and reproducible classification of chemicals with known sensitizing capacity. The aim of the research is to ensure that the analytical component of the peptide reactivity assay is robust, accurate, and reproducible in accordance with criteria that are used for the validation of bioanalytical methods. Analytical performance was evaluated using quality control samples (QCs; heptapeptides at low, medium, and high concentrations) and incubation of control chemicals (chemicals with known sensitization capacity, weak, moderate, strong, extreme, and non-sensitizers) with each of three synthetic heptapeptides, viz Cor1-C420 (Ac-NKKCDLF), cysteine- (Ac-RFAACAA), and lysine- (Ac-RFAAKAA) containing heptapeptides. The optimal incubation temperature for all three heptapeptides was 25°C. Apparent heptapeptide depletion was affected by vial material composition. Incubation of test chemicals with Cor1-C420, showed that peptide depletion was unchanged in polypropylene vials over 3-days storage in an autosampler but this was not the case for borosilicate glass vials. For cysteine-containing heptapeptide, the concentration was not stable by day 3 post-incubation in borosilicate glass vials. Although the lysine-containing heptapeptide concentration was unchanged in both polypropylene and borosilicate glass vials, the apparent extent of lysine-containing heptapeptide depletion by ethyl acrylate, differed between polypropylene (24.7%) and glass (47.3%) vials. Additionally, the peptide-chemical complexes for Cor1-C420-cinnamaldehyde and cysteine-containing heptapeptide-2, 4-dinitrochlorobenzene were partially reversible during 3-days of autosampler storage. These observations further highlight

  20. Binding modes of thioflavin T molecules to prion peptide assemblies identified by using scanning tunneling microscopy.

    PubMed

    Mao, Xiaobo; Guo, Yuanyuan; Wang, Chenxuan; Zhang, Min; Ma, Xiaojing; Liu, Lei; Niu, Lin; Zeng, Qingdao; Yang, Yanlian; Wang, Chen

    2011-06-15

    The widely used method to monitor the aggregation process of amyloid peptide is thioflavin T (ThT) assay, while the detailed molecular mechanism is still not clear. In this work, we report here the direct identification of the binding modes of ThT molecules with the prion peptide GNNQQNY by using scanning tunneling microscopy (STM). The assembly structures of GNNQQNY were first observed by STM on a graphite surface, and the introduction of ThT molecules to the surface facilitated the STM observations of the adsorption conformations of ThT with peptide strands. ThT molecules are apt to adsorb on the peptide assembly with β-sheet structure and oriented parallel with the peptide strands adopting four different binding modes. This effort could benefit the understanding of the mechanisms of the interactions between labeling species or inhibitory ligands and amyloid peptides, which is keenly needed for developing diagnostic and therapeutic approaches.

  1. Structural complexity of a composite amyloid fibril.

    PubMed

    Lewandowski, Józef R; van der Wel, Patrick C A; Rigney, Mike; Grigorieff, Nikolaus; Griffin, Robert G

    2011-09-21

    The molecular structure of amyloid fibrils and the mechanism of their formation are of substantial medical and biological importance, but present an ongoing experimental and computational challenge. An early high-resolution view of amyloid-like structure was obtained on amyloid-like crystals of a small fragment of the yeast prion protein Sup35p: the peptide GNNQQNY. As GNNQQNY also forms amyloid-like fibrils under similar conditions, it has been theorized that the crystal's structural features are shared by the fibrils. Here we apply magic-angle-spinning (MAS) NMR to examine the structure and dynamics of these fibrils. Previously multiple NMR signals were observed for such samples, seemingly consistent with the presence of polymorphic fibrils. Here we demonstrate that peptides with these three distinct conformations instead assemble together into composite protofilaments. Electron microscopy (EM) of the ribbon-like fibrils indicates that these protofilaments combine in differing ways to form striations of variable widths, presenting another level of structural complexity. Structural and dynamic NMR data reveal the presence of highly restricted side-chain conformations involved in interfaces between differently structured peptides, likely comprising interdigitated steric zippers. We outline molecular interfaces that are consistent with the observed EM and NMR data. The rigid and uniform structure of the GNNQQNY crystals is found to contrast distinctly with the more complex structural and dynamic nature of these "composite" amyloid fibrils. These results provide insight into the fibril-crystal distinction and also indicate a necessary caution with respect to the extrapolation of crystal structures to the study of fibril structure and formation.

  2. Fibronectin tetrapeptide is target for syphilis spirochete cytadherence

    SciTech Connect

    Thomas, D.D.; Baseman, J.B.; Alderete, J.F.

    1985-11-01

    The syphilis bacterium, Treponema pallidum, parasitizes host cells through recognition of fibronectin (Fn) on cell surfaces. The active site of the Fn molecule has been identified as a four-amino acid sequence, arg-gly-asp-ser (RGDS), located on each monomer of the cell-binding domain. The synthetic heptapeptide gly-arg-gly-asp-ser-pro-cys (GRGDSPC), with the active site sequence RGDS, specifically competed with SVI-labeled cell-binding domain acquisition by T. pallidum. Additionally, the same heptapeptide with the RGDS sequence diminished treponemal attachment to HEp-2 and HT1080 cell monolayers. Related heptapeptides altered in one key amino acid within the RGDS sequence failed to inhibit Fn cell-binding domain acquisition or parasitism of host cells by T. pallidum. The data support the view that T. pallidum cytadherence of host cells is through recognition of the RGDS sequence also important for eukaryotic cell-Fn binding.

  3. A Scalable and High-Yield Strategy for the Synthesis of Sequence-Defined Macromolecules.

    PubMed

    Solleder, Susanne C; Zengel, Deniz; Wetzel, Katharina S; Meier, Michael A R

    2016-01-18

    The efficient synthesis of a sequence-defined decamer, its characterization, and its straightforward dimerization through self-metathesis are described. For this purpose, a monoprotected AB monomer was designed and used to synthesize a decamer bearing ten different and selectable side chains by iterative Passerini three-component reaction (P-3CR) and subsequent deprotection. The highly efficient procedure provided excellent yields and allows for the multigram-scale synthesis of such perfectly defined macromolecules. An olefin was introduced at the end of the synthesis, allowing the self-metathesis reaction of the resulting decamer to provide a sequence-defined 20-mer with a molecular weight of 7046.40 g mol(-1). The obtained oligomers were carefully characterized by NMR and IR spectroscopy, GPC and GPC coupled to ESI-MS, and mass spectrometry (FAB and orbitrap ESI-MS). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. System Architecture of the Dark Energy Survey Camera Readout Electronics

    SciTech Connect

    Shaw, Theresa; Ballester, Otger; Cardiel-Sas, Laia; Castilla, Javier; Chappa, Steve; de Vicente, Juan; Holm, Scott; Huffman, Dave; Kozlovsky, Mark; Martinez, Gustavo; Moore, Todd; /Madrid, CIEMAT /Fermilab /Illinois U., Urbana /Fermilab

    2010-05-27

    The Dark Energy Survey makes use of a new camera, the Dark Energy Camera (DECam). DECam will be installed in the Blanco 4M telescope at Cerro Tololo Inter-American Observatory (CTIO). DECam is presently under construction and is expected to be ready for observations in the fall of 2011. The focal plane will make use of 62 2Kx4K and 12 2kx2k fully depleted Charge-Coupled Devices (CCDs) for guiding, alignment and focus. This paper will describe design considerations of the system; including, the entire signal path used to read out the CCDs, the development of a custom crate and backplane, the overall grounding scheme and early results of system tests.

  5. IDENTIFICATION OF MICROCYSTIN TOXINS FROM A STRAIN OF MICROCYSTIS AERUGINOSA

    EPA Science Inventory

    Microcystin toxins are cyclic heptapeptides produced by several genera and species of cyanobacteria that are responsible for the "green scum" frequently observed on eutrophic surface waters. These toxins, which are a million times more toxic than cyanide ion, have caused deaths o...

  6. IDENTIFICATION OF MICROCYSTIN TOXINS FROM A STRAIN OF MICROCYSTIS AERUGINOSA BY LIQUID CHROMATOGRAPHY INTRODUCTION INTO A HYBRID LINEAR ION TRAP-FOURIER TRANSFORM ION CYCLOTRON RESONANCE MASS SPECTROMETER

    EPA Science Inventory

    The cyclic heptapeptide microcystin toxins produced by a strain of Microcystis aeruginosa that has not been investigated previously were separated by liquid chromatography and identified by high-accuracy m/z measurements of their [M + H]+ ions and the fragment i...

  7. Influence of long-term treatment with tuftsin analogue TP-7 on the anxiety-phobic states and body weight.

    PubMed

    Czabak-Garbacz, Róza; Cygan, Beata; Wolański, Lukasz; Kozlovsky, Igor

    2006-01-01

    TP-7 is a synthetic analogue of tuftsin. It has a structure of tuftsin, to which three natural L-amino-acids Pro-Gly-Pro are attached. This heptapeptide improves learning and memorization and causes antidepressant and anxiolytic effect. It is possible to use TP-7 in the future to optimize cognitive functions and as a potential new anxioselective, fast-acting and easy-dosed drug. Therefore, it was purposeful to study such properties of the heptapeptide as its influence on anxiety-fear and body weight under a long-term treatment regimen. The experiment was performed on 24 preselected Wistar rats with the use of Rodina's method. There were three experimental groups of animals with high initial emotional reactivity: passive control group (P), active control group (A, receiving distilled water) and group treated with TP-7 at the dose of 0.3 mg/kg (T). The rats of A and T groups received intraperitoneal injections every day. The experiments were conducted 15 min after the administration of the drug, one and two days after initial testing day, then 1, 2, 3 and 4 weeks after that. The heptapeptide reduced the anxiety-phobic states significantly starting from the second day of drug application. The observed effects persisted throughout four weeks of the experiment, which confirmed effective long-term anxiolytic properties of the heptapeptide. TP-7 did not cause any changes in the body mass by itself.

  8. High affinity RGD-binding sites at the plasma membrane of Arabidopsis thaliana links the cell wall.

    PubMed

    Canut, H; Carrasco, A; Galaud, J P; Cassan, C; Bouyssou, H; Vita, N; Ferrara, P; Pont-Lezica, R

    1998-10-01

    The heptapeptide Tyr-Gly-Arg-Gly-Asp-Ser-Pro containing the sequence Arg-Gly-Asp (RGD--the essential structure recognised by animal cells in substrate adhesion molecules) was tested on epidermal cells of onion and cultured cells of Arabidopsis upon plasmolysis. Dramatic changes were observed on both types of cells following treatment: on onion cells, Hechtian strands linking the cell wall to the membrane were lost, while Arabidopsis cells changed from concave to convex plasmolysis. A control heptapeptide Tyr-Gly-Asp-Gly-Arg-Ser-Pro had no effect on the shape of plasmolysed cells. Protoplasts isolated from Arabidopsis cells agglutinate in the presence of ProNectinF, a genetically engineered protein of 72 kDa containing 13 RGD sequences: several protoplasts may adhere to a single molecule of ProNectinF. The addition of the RGD-heptapeptide disrupted the adhesion between the protoplasts. Purified plasma membrane from Arabidopsis cells exhibits specific binding sites for the iodinated RGD-heptapeptide. The binding is saturable, reversible, and two types of high affinity sites (Kd1 approximately 1 nM, and Kd2 approximately 40 nM) can be discerned. Competitive inhibition by several structurally related peptides and proteins noted the specific requirement for the RGD sequence. Thus, the RGD-binding activity of Arabidopsis fulfils the adhesion features of integrins, i.e. peptide specificity, subcellular location, and involvement in plasma membrane-cell wall attachments.

  9. IDENTIFICATION OF MICROCYSTIN TOXINS FROM A STRAIN OF MICROCYSTIS AERUGINOSA BY LIQUID CHROMATOGRAPHY INTRODUCTION INTO A HYBRID LINEAR ION TRAP-FOURIER TRANSFORM ION CYCLOTRON RESONANCE MASS SPECTROMETER

    EPA Science Inventory

    The cyclic heptapeptide microcystin toxins produced by a strain of Microcystis aeruginosa that has not been investigated previously were separated by liquid chromatography and identified by high-accuracy m/z measurements of their [M + H]+ ions and the fragment i...

  10. Sulfakinins

    USDA-ARS?s Scientific Manuscript database

    Sulfakinins constitute a family of arthropod neuropeptides that typically contain the C-terminal heptapeptide Y(SO3H)GHMRFamide. They display structural and functional similarities to the vertebrate gastrin-cholecystokinin family of peptides. Sulfakinins are synthesized by a limited number of neuros...

  11. IDENTIFICATION OF MICROCYSTIN TOXINS FROM A STRAIN OF MICROCYSTIS AERUGINOSA

    EPA Science Inventory

    Microcystin toxins are cyclic heptapeptides produced by several genera and species of cyanobacteria that are responsible for the "green scum" frequently observed on eutrophic surface waters. These toxins, which are a million times more toxic than cyanide ion, have caused deaths o...

  12. An Experimental and Computational Evolution-Based Method to Study a Mode of Co-evolution of Overlapping Open Reading Frames in the AAV2 Viral Genome

    PubMed Central

    Kawano, Yasuhiro; Neeley, Shane; Adachi, Kei; Nakai, Hiroyuki

    2013-01-01

    Overlapping open reading frames (ORFs) in viral genomes undergo co-evolution; however, how individual amino acids coded by overlapping ORFs are structurally, functionally, and co-evolutionarily constrained remains difficult to address by conventional homologous sequence alignment approaches. We report here a new experimental and computational evolution-based methodology to address this question and report its preliminary application to elucidating a mode of co-evolution of the frame-shifted overlapping ORFs in the adeno-associated virus (AAV) serotype 2 viral genome. These ORFs encode both capsid VP protein and non-structural assembly-activating protein (AAP). To show proof of principle of the new method, we focused on the evolutionarily conserved QVKEVTQ and KSKRSRR motifs, a pair of overlapping heptapeptides in VP and AAP, respectively. In the new method, we first identified a large number of capsid-forming VP3 mutants and functionally competent AAP mutants of these motifs from mutant libraries by experimental directed evolution under no co-evolutionary constraints. We used Illumina sequencing to obtain a large dataset and then statistically assessed the viability of VP and AAP heptapeptide mutants. The obtained heptapeptide information was then integrated into an evolutionary algorithm, with which VP and AAP were co-evolved from random or native nucleotide sequences in silico. As a result, we demonstrate that these two heptapeptide motifs could exhibit high degeneracy if coded by separate nucleotide sequences, and elucidate how overlap-evoked co-evolutionary constraints play a role in making the VP and AAP heptapeptide sequences into the present shape. Specifically, we demonstrate that two valine (V) residues and β-strand propensity in QVKEVTQ are structurally important, the strongly negative and hydrophilic nature of KSKRSRR is functionally important, and overlap-evoked co-evolution imposes strong constraints on serine (S) residues in KSKRSRR, despite high

  13. Macrocyclic beta-sheet peptides that mimic protein quaternary structure through intermolecular beta-sheet interactions.

    PubMed

    Khakshoor, Omid; Demeler, Borries; Nowick, James S

    2007-05-02

    This paper reports the design, synthesis, and characterization of a family of cyclic peptides that mimic protein quaternary structure through beta-sheet interactions. These peptides are 54-membered-ring macrocycles comprising an extended heptapeptide beta-strand, two Hao beta-strand mimics [JACS 2000, 122, 7654] joined by one additional alpha-amino acid, and two delta-linked ornithine beta-turn mimics [JACS 2003, 125, 876]. Peptide 3a, as the representative of these cyclic peptides, contains a heptapeptide sequence (TSFTYTS) adapted from the dimerization interface of protein NuG2 [PDB ID: 1mio]. 1H NMR studies of aqueous solutions of peptide 3a show a partially folded monomer in slow exchange with a strongly folded oligomer. NOE studies clearly show that the peptide self-associates through edge-to-edge beta-sheet dimerization. Pulsed-field gradient (PFG) NMR diffusion coefficient measurements and analytical ultracentrifugation (AUC) studies establish that the oligomer is a tetramer. Collectively, these experiments suggest a model in which cyclic peptide 3a oligomerizes to form a dimer of beta-sheet dimers. In this tetrameric beta-sheet sandwich, the macrocyclic peptide 3a is folded to form a beta-sheet, the beta-sheet is dimerized through edge-to-edge interactions, and this dimer is further dimerized through hydrophobic face-to-face interactions involving the Phe and Tyr groups. Further studies of peptides 3b-3n, which are homologues of peptide 3a with 1-6 variations in the heptapeptide sequence, elucidate the importance of the heptapeptide sequence in the folding and oligomerization of this family of cyclic peptides. Studies of peptides 3b-3g show that aromatic residues across from Hao improve folding of the peptide, while studies of peptides 3h-3n indicate that hydrophobic residues at positions R3 and R5 of the heptapeptide sequence are important in oligomerization.

  14. Confirmation with the SALT telescope of a young Type Ia supernova at z=0.046 discovered during the "Deeper Wider Faster" program

    NASA Astrophysics Data System (ADS)

    Andreoni, I.; Cooke, J.; Pritchard, T. A.; Kotze, M.; Miszalski, B.; Shara, M.; Mestric, U.; Tucker, B.; Plant, K.; Spiewak, R.; Ryder, S.; Abbott, T.; Allen, Rebecca; Anderson, G.; Asher, A.; Baglio, M. C.; Bannister, K.; Bell, M.; Bernard, S.; Bhandari, S.; Caleb, M.; Campana, S.; Coward, D.; Curtin, C.; D'Avanzo, P.; Deller, A.; Devlin, J. F.; Farah, W.; Fluke, C.; Flynn, C.; Foran, G.; Fugazza, D.; Gawin, B.; Hegarty, S.; Hodgson, R.; Hodgson, S.; Horst, J.; Howell, E.; Hussaini, I.; Jacobs, C.; Ko, M.; Lien, A.; Meade, B.; Melandri, A.; Moller, A.; Murphy, M. T.; Nanayakkara, T.; O'Neill, M.; Oslowski, S.; Peng, B.; Petroff, E.; Rest, A.; Robert, F.; Valdes, F.; Vohl, D.

    2017-02-01

    Further to ATel #10072, we report an additional discovery of a young Type Ia supernova from imaging on February 03.5, 2017 UT with the Dark Energy Camera (DECam) at CTIO during the recent & ldquo;Deeper, Wider, Faster & rdquo; program observations.

  15. Development of an RAPD-based SCAR marker for smut disease resistance in commercial sugarcane cultivars of Pakistan

    USDA-ARS?s Scientific Manuscript database

    Development of RAPD-derived Sequence Characterized Amplified Region (SCAR) marker in order to select Sporisorium scitamineum resistant and susceptible commercial cultivars of sugarcane from Pakistan was achieved. Bulked segregant and RAPD-analysis were conducted using 480 random decamers in initial ...

  16. Association Equilibrium for Cross-Associating Chains in a Good Solvent: Crowding and Other Nonideality Effects.

    PubMed

    Gotlib, Igor Yu; Malov, Ivan K; Victorov, Alexey I; Voznesenskiy, Mikhail A

    2016-07-28

    Association equilibrium has been studied by molecular dynamics (MD) for mixtures of cross-associating molecules (n-decamer+p-dimer and n-decamer+p-decamer) in a good solvent. Each monomer of n-decamers carries an associative site (n-sticker); each molecule of the second component contains two terminal associative sites (p-stickers). To model the univalent association between the n-sticker and the p-sticker, a technique based on introduction of dummy atoms has been used. We report MD data on the effects of temperature, chain flexibility, and location of the sticker within the chain on the association equilibrium. We find that the presence of nonassociating monomer units of p-chain has a substantial effect on the association equilibrium. This effect is similar to "crowding" in reactive mixtures known to be caused by the presence of inert molecules. Widely used mean field theories of associating chains (e.g., SAFT or Semenov-Rubinstein theory) do not account for the effect of crowding caused by the inert fragments of reactive chains. We introduce simple empirical corrections for crowding that describe association equilibrium in the presence of nonassociating fragment in a chain-like molecule.

  17. A population 'consensus', partial linkage map of Picea abies Karst. based on RAPD markers

    Treesearch

    G. Bucci; Thomas L. Kubisiak; W.L. Nance; P. Menozzi

    1997-01-01

    The authors built a "consensus" partial linkage map based on RAPD markers using 48 sibships of eight megagametophytes each from a natural population of Norway spruce. A RAPD linkage map for a single individual from the same population had previously been constructed. Using 30 random decamers that had yielded 83 RAPD markers in the single-tree map, eight...

  18. RAPD markers linked to eastern filbert blight resistance in Corylus avellana

    Treesearch

    S.A. Mehlenbacher; R.N. Brown; J.W. Davis; H. Chen; N.V. Bassil; D.C. Smith; Thomas L. Kubisiak

    2004-01-01

    A total of 1,110 decamer primers were screened for RAPD markers linked to a dominant allele in hazelnut (Corylus avellana) that confers resistance to eastern filbert blight caused by Anisogramma anomnala. Twenty RAPD markers linked in coupling, and five markers linked in repulsion, were found. A seedling population was used to...

  19. Personality dependent effects of the ACTH 4--10 fragment on test performances and on concomitant autonomic reactions.

    PubMed

    Breier, C; Kain, H; Konzett, H

    1979-11-01

    The effect of the ACTH-fragment 4--10 (30 mg SC) on a mental performance test and on some concomitant cardiovascular changes was investigated in comparison with a placebo in a double blind cross-over study. The subjects were either mainly extraverted or mainly introverted according to Eysenck's 'Maudsley Personality Inventory'. Under the influence of the heptapeptide extraverted subjects achieved a higher total score in the mental task performance with a smaller increase of forearm blood flow and of heart rate than under the influence of the placebo. In contrast, under the influence of the placebo introverted subjects achieved a higher total score in the mental task performance with a smaller increase of forearm blood flow and of heart rate than under the influence of the ACTH-fragment. Personality, therefore, determines to some degree how this centrally acting heptapeptide influences efficiency in the mental task performance and the concomitant cardiovascular changes.

  20. DEVD-Based Hydrogelator Minimizes Cellular Apoptosis Induction

    PubMed Central

    Tang, An-Ming; Wang, Wei-Juan; Mei, Bin; Hu, Wang-Lai; Wu, Mian; Liang, Gao-Lin

    2013-01-01

    Herein, we report the rational design of a DEVD-based heptapeptide hydrogelator 1 which is susceptible to caspase-3 (CASP3), and its isomeric control hydrogelator 2 with a DEDV-based heptapeptide sequence. Self-assembly of 1 in water results in flexuous, long nanofibers to form supramolecular hydrogel I with higher mechanical strength than that of hydrogel II which is composed of rigid, short nanofibers of 2. In vitro enzymatic analysis indicated that 1 is susceptive to CASP3 while 2 is not. 3-(4,5-dimethylthiazol-2-yl) 2,5 diphenyl tetrazolium bromide (MTT) and Western blot analyses indicated that DEDV-based hydrogelator 2 induces cell death via apoptotic pathway while the DEVD-based hydrogelator 1 minimizes cellular apoptosis induction. PMID:23673405

  1. [Semax and selank inhibit the enkephalin-degrading enzymes from human serum

    PubMed

    Kost, N V; Sokolov, O Iu; Gabaeva, M V; Grivennikov, I A; Andreeva, L A; Miasoedov, N F; Zozulia, A A

    2001-01-01

    A dose-dependent effect of synthetic heptapeptides Semax (Met-Glu-His-Phe-Pro-Gly-Pro) and Selank (Thr-Lys-Pro-Arg-Pro-Gly-Pro) on the enkephalin-degrading enzymes of human serum was demonstrated. The inhibitory effects of Semax (IC50 10 microM) and Selank (IC50 20 microM) are more pronounced than those of puromycin (IC50 10 mM), bacitracin, and some other inhibitors of peptidases. Beside the heptapeptides, their pentapeptide fragments also possessed an inhibitory effect; tri-, tetra-, and hexapeptide fragments did not display such an effect. As the above enzymes take part in degradation of not only enkephalins but also other regulatory peptides, it can be assumed that one of the mechanisms of biological activity of Semax and Selank is related to this inhibitory activity of theirs.

  2. DEVD-Based Hydrogelator Minimizes Cellular Apoptosis Induction

    NASA Astrophysics Data System (ADS)

    Tang, An-Ming; Wang, Wei-Juan; Mei, Bin; Hu, Wang-Lai; Wu, Mian; Liang, Gao-Lin

    2013-05-01

    Herein, we report the rational design of a DEVD-based heptapeptide hydrogelator 1 which is susceptible to caspase-3 (CASP3), and its isomeric control hydrogelator 2 with a DEDV-based heptapeptide sequence. Self-assembly of 1 in water results in flexuous, long nanofibers to form supramolecular hydrogel I with higher mechanical strength than that of hydrogel II which is composed of rigid, short nanofibers of 2. In vitro enzymatic analysis indicated that 1 is susceptive to CASP3 while 2 is not. 3-(4,5-dimethylthiazol-2-yl) 2,5 diphenyl tetrazolium bromide (MTT) and Western blot analyses indicated that DEDV-based hydrogelator 2 induces cell death via apoptotic pathway while the DEVD-based hydrogelator 1 minimizes cellular apoptosis induction.

  3. A novel self-assembling peptide with UV-responsive properties.

    PubMed

    Wei, Ran; Jin, Cheng-Cheng; Quan, Jing; Nie, Hua-li; Zhu, Li-Min

    2014-03-01

    A novel heptapeptide comprising Ile-Gln-Ser-Pro-His-Phe-Phe (IQSPHFF) identified and found to undergo self-assembly into microparticles in solution. To understand the effects of ultraviolet (UV) irradiation on the self-assembly process, IQSPHFF solutions were exposed to the UV light of 365 nm at room temperature. This exposure was found to have a profound effect on the morphology of the self-assembled aggregates, converting the microparticles to nanorod shapes. Circular dichroism and FTIR studies indicated distinct structural differences in the arrangements of the peptide moieties before and after UV irradiation. However, Mass spectrum analysis and high performance liquid chromatography of the peptide molecules before and after UV irradiation demonstrated that the chemical structure of IQSPHFF was not changed. UV-visible spectroscopy and fluorescence spectroscopy studies showed that the absorption peak both increased after UV irradiation. Overall, our data show that the heptapeptide with UV-responsive properties. Copyright © 2013 Wiley Periodicals, Inc.

  4. Duck-billed platypus venom peptides induce Ca2+ influx in neuroblastoma cells.

    PubMed

    Kita, Masaki; Black, David StC; Ohno, Osamu; Yamada, Kaoru; Kigoshi, Hideo; Uemura, Daisuke

    2009-12-23

    The duck-billed platypus (Ornithorhynchus anatinus) is one of the few venomous Australian mammals. We previously found that its crude venom potently induces Ca(2+) influx in human neuroblastoma IMR-32 cells. Guided by this bioassay, we identified 11 novel peptides, including the heptapeptide H-His-Asp-His-Pro-Asn-Pro-Arg-OH (1). Compounds 1-4 and 5-11 coincided with the 6-9 N-terminal residues of Ornithorhynchus venom C-type natriuretic peptide (OvCNP) and the 132-150 part of OvCNP precursor peptide, respectively. Heptapeptide 1, which is one of the primary components of the venom fluid (approximately 200 ng/microL), induced a significant increase in [Ca(2+)](i) in IMR-32 cells at 75 microM. To the best of our knowledge, this is the first example of the isolation of the N-terminal linear fragments of CNPs in any mammal.

  5. Mammalian neuronal actions of FMRFamide and the structurally related opioid Met-enkephalin-Arg6-Phe7.

    PubMed

    Gayton, R J

    1982-07-15

    Since the enkephalins were first isolated a number of opioid peptides have been discovered, including a heptapeptide with the sequence Tyr-Gly-Gly-Phe-Met-Arg-Phe (Met-enkephalin-Arg6-Phe7). The heptapeptide was first isolated from chromaffin granules in bovine adrenal medulla, but using immunochemical techniques it has now been identified in human, rat and bovine brains. The C-terminal tetrapeptide of this molecule (Phe-Met-Arg-Phe) occurs in amidated form as the molluscan peptide FMRFamide. Antisera raised against FMRFamide have revealed immunoreactive material in the brains of several vertebrate species, including the rat where it occurs in nerve cell bodies and terminals. I now report that ionophoretically applied FMRFamide has an excitatory effect on rat medullary neurones which is unaffected by the opiate antagonist naloxone. In contrast, Met-enkephalin-Arg6-Phe7 and leucine-enkephalin (Leu-enkephalin) have predominantly depressant effects, which suggests that FMRFamide acts at a separate receptor.

  6. Coprisamides A and B, new branched cyclic peptides from a gut bacterium of the dung beetle Copris tripartitus.

    PubMed

    Um, Soohyun; Park, So Hyun; Kim, Jihye; Park, Hyen Joo; Ko, Keebeom; Bang, Hea-Son; Lee, Sang Kook; Shin, Jongheon; Oh, Dong-Chan

    2015-03-06

    Coprisamides A and B (1 and 2) were isolated from a bacterium in the gut of the dung beetle Copris tripartitus. Spectroscopic analysis revealed that the planar structures of 1 and 2 are novel cyclic heptapeptides bearing unusual units, such as β-methylaspartic acid and 2,3-diaminopropanoic acid branched to valine and 2-heptatrienyl cinnamic acid. Absolute configurations were established by chemical derivatization and chiroptical spectroscopy. The coprisamides displayed significant activity for induction of quinone reductase.

  7. Simulations of Peptide Models in a Solvent

    NASA Astrophysics Data System (ADS)

    Arkin, Handan

    The three-dimensional structures of the heptapeptide deltorphin (H-Tyr1-D-Met2-Phe3-His4-Leu5-Met6-Asp7-NH2) are studied in aqueous solution using Energy Landscape Paving (ELP) method. The effect of a solvation energy term on the conformations are determined by analyzing Ramachandran plots. The structures are compared with experimental NMR data. By minimizing the energy structures, the low-energy microstates of the molecule in aqueous solution are determined.

  8. Identification of a Peptide from Mammal Albumins Responsible for Enhanced Pigment Production by Group B Streptococci

    PubMed Central

    Rosa-Fraile, Manuel; Sampedro, Antonio; Varela, Javier; Garcia-Peña, Marisa; Gimenez-Gallego, Guillermo

    1999-01-01

    The peptide from peptones responsible for enhanced pigment production by Streptococcus agalactiae in culture media has been isolated from a peptic digest of human albumin and has been identified as Ile-Ala-Arg-Arg-His-Pro-Tyr-Phe. The related heptapeptide lacking the N-terminal Ile also had pigment-enhancing activity. A sequence similarity search showed that these sequences are present only in mammal albumins. PMID:10225848

  9. Interaction of Microcystin-LR with SuperChar: Water Decontamination and Therapy

    DTIC Science & Technology

    1989-01-01

    latest developments and findings in this rapidly changing field. CLINICAL TOXICOLOGY, 27(4&5), 271-280 (1989) INTERACTION OF MICROCYSTIN -LR WITH...therapeutic use against poisoning by several toxic agents, but it has not been tested against microcystin -LR toxicosis. Microcystin - LR, a cyclic heptapeptide...degree of in vitro adsorption of microcystin -LR to SuperChar and to assess the efficacy of SuperChar as a therapeutic agent against microcystin -LR in

  10. Are Reactive Oxygen Species Involved in Microcystin-LR Intoxication?

    DTIC Science & Technology

    1988-05-12

    peroxidation in paracetamol intoxication, did not alter the effect of BHA pretreatment., -- 2-A 4" 4 2 - INTRODUCTION The toxic cyclic heptapeptide...changes, we hypothesized that compounds that alter the concentration N of reactive oxygen species would alter the toxic effects of the peptide...reactive oxygen species would alter the toxic effects of the peptide-hepatotoxin produced by Microcystis aeruginosa. We show here that pretreatment with a

  11. Structure and mode of action of microcin 7, an antibacterial peptide produced by Escherichia coli.

    PubMed Central

    Garcia-Bustos, J F; Pezzi, N; Mendez, E

    1985-01-01

    Microcin 7 is a small peptide produced and excreted to the culture medium by stationary-phase Escherichia coli cells harboring the pMccC7 plasmid (formerly named pRYC7). This peptide inhibited the growth of the enterobacteria phylogenetically closer to E. coli, apparently by blocking protein biosynthesis. The molecule was degraded with trypsin, and the resulting fragments were purified and sequenced. The results show that microcin 7 is a linear heptapeptide blocked at both ends. PMID:2861788

  12. beta-Hydroxyaspartic acid in vitamin K-dependent protein C.

    PubMed

    Drakenberg, T; Fernlund, P; Roepstorff, P; Stenflo, J

    1983-04-01

    Previous work has shown that the light chain of protein C, an anticoagulant plasma protein, contains an unusual amino acid [Fernlund, P. & Stenflo, J. (1982) J. Biol. Chem. 257, 12170-12179]. To determine the structure of this amino acid a heptapeptide, CMCys-Ile-X-Gly-Leu-Gly-Gly (residues 69-75 in the light chain), was isolated from enzymatic digests of the light chain. According to automatic Edman sequence analysis, 1H NMR spectroscopy, and mass spectrometry the heptapeptide had beta-hydroxyaspartic acid in its third position, which corresponds to position 71 in the light chain of protein C. Analysis of acid and aminopeptidase M hydrolysates of the heptapeptide showed the beta-hydroxyaspartic acid to be the erythro form. Acid hydrolysis of protein C released approximately equal to 1 mol of beta-hydroxyaspartic acid per mol of protein. The function of this amino acid, which, to the best of our knowledge, has not been found previously in proteins, is unknown.

  13. Molecular modeling of various peptide sequences of gliadins and low-molecular-weight glutenin subunits.

    PubMed

    Yaşar, Fatih; Celik, Süeda; Köksel, Hamit

    2003-08-01

    The contribution of the three-dimensional structures of one heptapeptide (PQPQPFP) sequence and one pentapeptide (PQQPY) repeat sequence of alpha/beta-gliadins, one heptapeptide (PQQPFPQ) repeat sequence of gamma-gliadins, two heptapeptide (PQQPPFS and QQQQPVL) repeat motifs of low-molecular-weight (LMW) subunits and a tetrapeptide sequence in polyQ region of S-rich prolamins to their conformations are investigated by using the recently developed multicanonical simulation procedure. Ramachandran plots were prepared and analysed to predict the relative occurrence probabilities of gamma-tutn, gamma-turn, and helical structures. The probability of inverse 7-turn was generally higher than that of beta-turns in all sequences investigated. Occurrence probability of helical structure in the repetitive domain of gliadins was low. Structural predictions of QQQQPVL sequence of LMW-glutenin subunits and QQQQ sequence in the polyQ region of S-rich prolamins indicate the presence of helical structures with the probability of >20%. The probability of helical structure significantly decreased around 100 degrees C.

  14. Systematic identification and analysis of exonic splicing silencers.

    PubMed

    Wang, Zefeng; Rolish, Michael E; Yeo, Gene; Tung, Vivian; Mawson, Matthew; Burge, Christopher B

    2004-12-17

    Exonic splicing silencers (ESSs) are cis-regulatory elements that inhibit the use of adjacent splice sites, often contributing to alternative splicing (AS). To systematically identify ESSs, an in vivo splicing reporter system was developed to screen a library of random decanucleotides. The screen yielded 141 ESS decamers, 133 of which were unique. The silencer activity of over a dozen of these sequences was also confirmed in a heterologous exon/intron context and in a second cell type. Of the unique ESS decamers, most could be clustered into groups to yield seven putative ESS motifs, some resembling known motifs bound by hnRNPs H and A1. Potential roles of ESSs in constitutive splicing were explored using an algorithm, ExonScan, which simulates splicing based on known or putative splicing-related motifs. ExonScan and related bioinformatic analyses suggest that these ESS motifs play important roles in suppression of pseudoexons, in splice site definition, and in AS.

  15. Dark Energy Camera for Blanco

    SciTech Connect

    Binder, Gary A.; /Caltech /SLAC

    2010-08-25

    In order to make accurate measurements of dark energy, a system is needed to monitor the focus and alignment of the Dark Energy Camera (DECam) to be located on the Blanco 4m Telescope for the upcoming Dark Energy Survey. One new approach under development is to fit out-of-focus star images to a point spread function from which information about the focus and tilt of the camera can be obtained. As a first test of a new algorithm using this idea, simulated star images produced from a model of DECam in the optics software Zemax were fitted. Then, real images from the Mosaic II imager currently installed on the Blanco telescope were used to investigate the algorithm's capabilities. A number of problems with the algorithm were found, and more work is needed to understand its limitations and improve its capabilities so it can reliably predict camera alignment and focus.

  16. Cross-linking analysis reveals the putative dimer structure of the cyanobacterial BLUF photoreceptor PixD.

    PubMed

    Ren, Shukun; Sugimoto, Yuki; Kobayashi, Taichi; Masuda, Shinji

    2015-07-08

    PixD is a blue light using flavin (BLUF)-type blue-light photoreceptor controlling phototaxis in the cyanobacterium Synechocystis sp. PCC6803. The crystal structure of PixD shows a decamer, although in solution an equilibrium is maintained between the dimer and decamer. Because the ratio of these two conformers is altered by illumination, the equilibrium state determines photosensitivity. However, no structural information is available for the PixD dimer. Here, we report a predicted structure for the dimer based on docking simulation, mutagenesis, and mass spectrometry-based cross-linking analyses. The results indicate the importance of the PixD C-terminus for dimer preference and photosensitivity. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  17. Global optimization of cholic acid aggregates

    NASA Astrophysics Data System (ADS)

    Jójárt, Balázs; Viskolcz, Béla; Poša, Mihalj; Fejer, Szilard N.

    2014-04-01

    In spite of recent investigations into the potential pharmaceutical importance of bile acids as drug carriers, the structure of bile acid aggregates is largely unknown. Here, we used global optimization techniques to find the lowest energy configurations for clusters composed between 2 and 10 cholate molecules, and evaluated the relative stabilities of the global minima. We found that the energetically most preferred geometries for small aggregates are in fact reverse micellar arrangements, and the classical micellar behaviour (efficient burial of hydrophobic parts) is achieved only in systems containing more than five cholate units. Hydrogen bonding plays a very important part in keeping together the monomers, and among the size range considered, the most stable structure was found to be the decamer, having 17 hydrogen bonds. Molecular dynamics simulations showed that the decamer has the lowest dissociation propensity among the studied aggregation numbers.

  18. Toyz: A framework for scientific analysis of large datasets and astronomical images

    NASA Astrophysics Data System (ADS)

    Moolekamp, F.; Mamajek, E.

    2015-11-01

    As the size of images and data products derived from astronomical data continues to increase, new tools are needed to visualize and interact with that data in a meaningful way. Motivated by our own astronomical images taken with the Dark Energy Camera (DECam) we present Toyz, an open source Python package for viewing and analyzing images and data stored on a remote server or cluster. Users connect to the Toyz web application via a web browser, making it ​a convenient tool for students to visualize and interact with astronomical data without having to install any software on their local machines. In addition it provides researchers with an easy-to-use tool that allows them to browse the files on a server and quickly view very large images (>2 Gb) taken with DECam and other cameras with a large FOV and create their own visualization tools that can be added on as extensions to the default Toyz framework.

  19. The B----Z transition in two synthetic oligonucleotides: d(C-2-amino-ACGTG) and d(m5CGCAm5CGTGCG) studied by IR, NMR and CD spectroscopies.

    PubMed Central

    Taboury, J A; Adam, S; Taillandier, E; Neumann, J M; Tran-Dinh, S; Huynh-Dinh, T; Langlois d'Estaintot, B; Conti, M; Igolen, J

    1984-01-01

    The sequences CA'CGTG (where A' = 2-aminodeoxyadenosine) and m5CGCAm5CGTGCG are prepared and studied by IR, CD and 1H-NMR. Infrared spectra demonstrate the capacity of the modified hexamer and decamer to adopt a Z conformation. The influence of the NH2 substitution on the adenine or of the methylated terminal part of the decamer acting with the increase of the DNA concentration stabilizes the Z conformation at room temperature in low humidity films. Very weak proportion of Z conformation is detected in UV dilute solutions. In more concentrated NMR solutions, the Z proportion induced by high salt content is only 20-25%. The effects of the concentration and of the covalent modification of the bases are discussed. PMID:6332307

  20. The role of poly-M and poly-GM sequences in the metal-mediated assembly of alginate gels.

    PubMed

    Stewart, Matthew B; Gray, Stephen R; Vasiljevic, Todor; Orbell, John D

    2014-11-04

    Whilst the involvement of poly-G sequences in the formation of metal-mediated alginate gels has been previously studied in some detail, investigations into the role of poly-M and poly-GM sequences has been relatively neglected. In this regard, the binding of sodium and calcium ions to poly-M and poly-GM decamers, and their influence on chain aggregation, has been modelled by conducting a series of molecular dynamics simulations. This work complements a previous analogous study carried out for the poly-G decamer, whereby up to three strands are systematically introduced into each simulation. As in the previous study, this method allows intrinsic binding modes and interchain structural motifs to be revealed, that are consistent with those observed in available AFM images of consolidated 3-D networks. It is apparent from these studies that different sequences have different structural implications for metal-mediated chain association. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Short peptides allowing preferential detection of Candida albicans hyphae.

    PubMed

    Kaba, Hani E J; Pölderl, Antonia; Bilitewski, Ursula

    2015-09-01

    Whereas the detection of pathogens via recognition of surface structures by specific antibodies and various types of antibody mimics is frequently described, the applicability of short linear peptides as sensor molecules or diagnostic tools is less well-known. We selected peptides which were previously reported to bind to recombinant S. cerevisiae cells, expressing members of the C. albicans Agglutinin-Like-Sequence (ALS) cell wall protein family. We slightly modified amino acid sequences to evaluate peptide sequence properties influencing binding to C. albicans cells. Among the selected peptides, decamer peptides with an "AP"-N-terminus were superior to shorter peptides. The new decamer peptide FBP4 stained viable C. albicans cells more efficiently in their mature hyphal form than in their yeast form. Moreover, it allowed distinction of C. albicans from other related Candida spp. and could thus be the basis for the development of a useful tool for the diagnosis of invasive candidiasis.

  2. Cooling the dark energy camera CCD array using a closed-loop two-phase liquid nitrogen system

    NASA Astrophysics Data System (ADS)

    Cease, H.; DePoy, D.; Derylo, G.; Diehl, H. T.; Estrada, J.; Flaugher, B.; Kuk, K.; Kuhlmann, S.; Lathrop, A.; Schultz, K.; Reinert, R. J.; Schmitt, R. L.; Stefanik, A.; Zhao, A.

    2010-07-01

    The Dark Energy Camera (DECam) is the new wide field prime-focus imager for the Blanco 4m telescope at CTIO. This instrument is a 3 sq. deg. camera with a 45 cm diameter focal plane consisting of 62 2k × 4k CCDs and 12 2k × 2k CCDs and was developed for the Dark Energy Survey that will start operations at CTIO in 2011. The DECam CCD array is inside the imager vessel. The focal plate is cooled using a closed loop liquid nitrogen system. As part of the development of the mechanical and cooling design, a full scale prototype imager vessel has been constructed and is now being used for Multi-CCD readout tests. The cryogenic cooling system and thermal controls are described along with cooling results from the prototype camera. The cooling system layout on the Blanco telescope in Chile is described.

  3. Presentation of Ligands on Hydroxylapatite

    NASA Technical Reports Server (NTRS)

    Chu, Barbara C. F.; Orgel, Leslie E.

    1997-01-01

    Conjugates of biotin with the decamer of glutamic acid (glu(sub 10)) and the trimer of D,L-2-amino-5-phosphonovaleric acid (I) have been synthesized, and it has been shown that they mediate the binding of avidin to hydroxylapatite. In a similar way a conjugate of methotrexate with glu(sub 10) mediates the binding of dihydrofolate reductase to the mineral. The presentation of ligands on the hydroxylapatite component of bone may find applications in clinical medicine.

  4. Mass and galaxy distributions of four massive galaxy clusters from Dark Energy Survey Science Verification data

    SciTech Connect

    Melchior, P.; Suchyta, E.; Huff, E.; Hirsch, M.; Kacprzak, T.; Rykoff, E.; Gruen, D.; Armstrong, R.; Bacon, D.; Bechtol, K.; Bernstein, G. M.; Bridle, S.; Clampitt, J.; Honscheid, K.; Jain, B.; Jouvel, S.; Krause, E.; Lin, H.; MacCrann, N.; Patton, K.; Plazas, A.; Rowe, B.; Vikram, V.; Wilcox, H.; Young, J.; Zuntz, J.; Abbott, T.; Abdalla, F. B.; Allam, S. S.; Banerji, M.; Bernstein, J. P.; Bernstein, R. A.; Bertin, E.; Buckley-Geer, E.; Burke, D. L.; Castander, F. J.; da Costa, L. N.; Cunha, C. E.; Depoy, D. L.; Desai, S.; Diehl, H. T.; Doel, P.; Estrada, J.; Evrard, A. E.; Neto, A. F.; Fernandez, E.; Finley, D. A.; Flaugher, B.; Frieman, J. A.; Gaztanaga, E.; Gerdes, D.; Gruendl, R. A.; Gutierrez, G. R.; Jarvis, M.; Karliner, I.; Kent, S.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Maia, M. A. G.; Makler, M.; Marriner, J.; Marshall, J. L.; Merritt, K. W.; Miller, C. J.; Miquel, R.; Mohr, J.; Neilsen, E.; Nichol, R. C.; Nord, B. D.; Reil, K.; Roe, N. A.; Roodman, A.; Sako, M.; Sanchez, E.; Santiago, B. X.; Schindler, R.; Schubnell, M.; Sevilla-Noarbe, I.; Sheldon, E.; Smith, C.; Soares-Santos, M.; Swanson, M. E. C.; Sypniewski, A. J.; Tarle, G.; Thaler, J.; Thomas, D.; Tucker, D. L.; Walker, A.; Wechsler, R.; Weller, J.; Wester, W.

    2015-03-31

    We measure the weak-lensing masses and galaxy distributions of four massive galaxy clusters observed during the Science Verification phase of the Dark Energy Survey. This pathfinder study is meant to 1) validate the DECam imager for the task of measuring weak-lensing shapes, and 2) utilize DECam's large field of view to map out the clusters and their environments over 90 arcmin. We conduct a series of rigorous tests on astrometry, photometry, image quality, PSF modelling, and shear measurement accuracy to single out flaws in the data and also to identify the optimal data processing steps and parameters. We find Science Verification data from DECam to be suitable for the lensing analysis described in this paper. The PSF is generally well-behaved, but the modelling is rendered difficult by a flux-dependent PSF width and ellipticity. We employ photometric redshifts to distinguish between foreground and background galaxies, and a red-sequence cluster finder to provide cluster richness estimates and cluster-galaxy distributions. By fitting NFW profiles to the clusters in this study, we determine weak-lensing masses that are in agreement with previous work. For Abell 3261, we provide the first estimates of redshift, weak-lensing mass, and richness. Additionally, the cluster-galaxy distributions indicate the presence of filamentary structures attached to 1E 0657-56 and RXC J2248.7-4431, stretching out as far as 1degree (approximately 20 Mpc), showcasing the potential of DECam and DES for detailed studies of degree-scale features on the sky.

  5. Mass and galaxy distributions of four massive galaxy clusters from Dark Energy Survey Science Verification data

    SciTech Connect

    Melchior, P.; Suchyta, E.; Huff, E.; Hirsch, M.; Kacprzak, T.; Rykoff, E.; Gruen, D.; Armstrong, R.; Bacon, D.; Bechtol, K.; Bernstein, G. M.; Bridle, S.; Clampitt, J.; Honscheid, K.; Jain, B.; Jouvel, S.; Krause, E.; Lin, H.; MacCrann, N.; Patton, K.; Plazas, A.; Rowe, B.; Vikram, V.; Wilcox, H.; Young, J.; Zuntz, J.; Abbott, T.; Abdalla, F. B.; Allam, S. S.; Banerji, M.; Bernstein, J. P.; Bernstein, R. A.; Bertin, E.; Buckley-Geer, E.; Burke, D. L.; Castander, F. J.; da Costa, L. N.; Cunha, C. E.; Depoy, D. L.; Desai, S.; Diehl, H. T.; Doel, P.; Estrada, J.; Evrard, A. E.; Neto, A. F.; Fernandez, E.; Finley, D. A.; Flaugher, B.; Frieman, J. A.; Gaztanaga, E.; Gerdes, D.; Gruendl, R. A.; Gutierrez, G. R.; Jarvis, M.; Karliner, I.; Kent, S.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Maia, M. A. G.; Makler, M.; Marriner, J.; Marshall, J. L.; Merritt, K. W.; Miller, C. J.; Miquel, R.; Mohr, J.; Neilsen, E.; Nichol, R. C.; Nord, B. D.; Reil, K.; Roe, N. A.; Roodman, A.; Sako, M.; Sanchez, E.; Santiago, B. X.; Schindler, R.; Schubnell, M.; Sevilla-Noarbe, I.; Sheldon, E.; Smith, C.; Soares-Santos, M.; Swanson, M. E. C.; Sypniewski, A. J.; Tarle, G.; Thaler, J.; Thomas, D.; Tucker, D. L.; Walker, A.; Wechsler, R.; Weller, J.; Wester, W.

    2015-03-31

    We measure the weak-lensing masses and galaxy distributions of four massive galaxy clusters observed during the Science Verification phase of the Dark Energy Survey. This pathfinder study is meant to 1) validate the DECam imager for the task of measuring weak-lensing shapes, and 2) utilize DECam's large field of view to map out the clusters and their environments over 90 arcmin. We conduct a series of rigorous tests on astrometry, photometry, image quality, PSF modeling, and shear measurement accuracy to single out flaws in the data and also to identify the optimal data processing steps and parameters. We find Science Verification data from DECam to be suitable for the lensing analysis described in this paper. The PSF is generally well-behaved, but the modeling is rendered difficult by a flux-dependent PSF width and ellipticity. We employ photometric redshifts to distinguish between foreground and background galaxies, and a red-sequence cluster finder to provide cluster richness estimates and cluster-galaxy distributions. By fitting NFW profiles to the clusters in this study, we determine weak-lensing masses that are in agreement with previous work. For Abell 3261, we provide the first estimates of redshift, weak-lensing mass, and richness. In addition, the cluster-galaxy distributions indicate the presence of filamentary structures attached to 1E 0657-56 and RXC J2248.7-4431, stretching out as far as 1 degree (approximately 20 Mpc), showcasing the potential of DECam and DES for detailed studies of degree-scale features on the sky.

  6. Mass and galaxy distributions of four massive galaxy clusters from Dark Energy Survey Science Verification data

    SciTech Connect

    Melchior, P.; Suchyta, E.; Huff, E.; Hirsch, M.; Kacprzak, T.; Rykoff, E.; Gruen, D.; Armstrong, R.; Bacon, D.; Bechtol, K.; Bernstein, G. M.; Bridle, S.; Clampitt, J.; Honscheid, K.; Jain, B.; Jouvel, S.; Krause, E.; Lin, H.; MacCrann, N.; Patton, K.; Plazas, A.; Rowe, B.; Vikram, V.; Wilcox, H.; Young, J.; Zuntz, J.; Abbott, T.; Abdalla, F. B.; Allam, S. S.; Banerji, M.; Bernstein, J. P.; Bernstein, R. A.; Bertin, E.; Buckley-Geer, E.; Burke, D. L.; Castander, F. J.; da Costa, L. N.; Cunha, C. E.; Depoy, D. L.; Desai, S.; Diehl, H. T.; Doel, P.; Estrada, J.; Evrard, A. E.; Neto, A. F.; Fernandez, E.; Finley, D. A.; Flaugher, B.; Frieman, J. A.; Gaztanaga, E.; Gerdes, D.; Gruendl, R. A.; Gutierrez, G. R.; Jarvis, M.; Karliner, I.; Kent, S.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Maia, M. A. G.; Makler, M.; Marriner, J.; Marshall, J. L.; Merritt, K. W.; Miller, C. J.; Miquel, R.; Mohr, J.; Neilsen, E.; Nichol, R. C.; Nord, B. D.; Reil, K.; Roe, N. A.; Roodman, A.; Sako, M.; Sanchez, E.; Santiago, B. X.; Schindler, R.; Schubnell, M.; Sevilla-Noarbe, I.; Sheldon, E.; Smith, C.; Soares-Santos, M.; Swanson, M. E. C.; Sypniewski, A. J.; Tarle, G.; Thaler, J.; Thomas, D.; Tucker, D. L.; Walker, A.; Wechsler, R.; Weller, J.; Wester, W.

    2015-03-31

    We measure the weak lensing masses and galaxy distributions of four massive galaxy clusters observed during the Science Verification phase of the Dark Energy Survey (DES). This pathfinder study is meant to (1) validate the Dark Energy Camera (DECam) imager for the task of measuring weak lensing shapes, and (2) utilize DECam's large field of view to map out the clusters and their environments over 90 arcmin. We conduct a series of rigorous tests on astrometry, photometry, image quality, point spread function (PSF) modelling, and shear measurement accuracy to single out flaws in the data and also to identify the optimal data processing steps and parameters. We find Science Verification data from DECam to be suitable for the lensing analysis described in this paper. The PSF is generally well behaved, but the modelling is rendered difficult by a flux-dependent PSF width and ellipticity. We employ photometric redshifts to distinguish between foreground and background galaxies, and a red-sequence cluster finder to provide cluster richness estimates and cluster-galaxy distributions. By fitting Navarro-Frenk-White profiles to the clusters in this study, we determine weak lensing masses that are in agreement with previous work. For Abell 3261, we provide the first estimates of redshift, weak lensing mass, and richness. In addition, the cluster-galaxy distributions indicate the presence of filamentary structures attached to 1E 0657-56 and RXC J2248.7-4431, stretching out as far as 1. (approximately 20 Mpc), showcasing the potential of DECam and DES for detailed studies of degree-scale features on the sky.

  7. Mass and galaxy distributions of four massive galaxy clusters from Dark Energy Survey Science Verification data

    DOE PAGES

    Melchior, P.; Suchyta, E.; Huff, E.; ...

    2015-03-31

    We measure the weak-lensing masses and galaxy distributions of four massive galaxy clusters observed during the Science Verification phase of the Dark Energy Survey. This pathfinder study is meant to 1) validate the DECam imager for the task of measuring weak-lensing shapes, and 2) utilize DECam's large field of view to map out the clusters and their environments over 90 arcmin. We conduct a series of rigorous tests on astrometry, photometry, image quality, PSF modelling, and shear measurement accuracy to single out flaws in the data and also to identify the optimal data processing steps and parameters. We find Sciencemore » Verification data from DECam to be suitable for the lensing analysis described in this paper. The PSF is generally well-behaved, but the modelling is rendered difficult by a flux-dependent PSF width and ellipticity. We employ photometric redshifts to distinguish between foreground and background galaxies, and a red-sequence cluster finder to provide cluster richness estimates and cluster-galaxy distributions. By fitting NFW profiles to the clusters in this study, we determine weak-lensing masses that are in agreement with previous work. For Abell 3261, we provide the first estimates of redshift, weak-lensing mass, and richness. Additionally, the cluster-galaxy distributions indicate the presence of filamentary structures attached to 1E 0657-56 and RXC J2248.7-4431, stretching out as far as 1degree (approximately 20 Mpc), showcasing the potential of DECam and DES for detailed studies of degree-scale features on the sky.« less

  8. Quality Control Review of the Defense Commissary Agency Internal Audit Function

    DTIC Science & Technology

    2012-09-10

    Mark Center Drive Alexandria, VA 22350-1500 Acronyms and Abbreviations DeCA Defense Commissary Agency DeCAM Defense...We have reviewed the Defense Commissary Agency ( DeCA ) Office of Internal Audit system of quality control in effect for the period ended July 31...GAGAS). The DeCA Office of Internal Audit is responsible for designing a system of quality control and complying with its system to provide DeCA

  9. Characterization of human TCR Vbeta gene promoter. Role of the dodecamer motif in promoter activity.

    PubMed

    Deng, X; Sun, G R; Zheng, Q; Li, Y

    1998-09-11

    During T-lymphocyte development, the T-cell antigen receptor (TCR) gene expression is controlled by its promoter and enhancer elements and regulated in tissue- and development stage-specific manner. To uncover the promoter function and to define positive and negative regulatory elements in TCR gene promoters, the promoter activities from 13 human TCR Vbeta genes were determined by the transient transfection system and luciferase reporter assay. Although most of the TCR Vbeta gene promoters that we tested are inactive by themselves, some promoters were found to be constitutively strong. Among them, Vbeta6.7 is the strongest. 5'-Deletion and fragmentation experiments have narrowed the full promoter activity of Vbeta6.7 to a fragment of 147 base pairs immediately 5' to the transcription initiation site. A decanucleotide motif with the consensus sequence AGTGAYRTCA has been found to be conserved in most TCR Vbeta gene promoters. There are three such decamer motifs in the promoter region of Vbeta6.7, and the contribution of each such motif to the promoter activity has been examined. Further site-directed mutagenesis analyses showed that: 1) when two Ts in the decamer were mutated, the promoter activity was totally abolished; 2) when two additional nucleotides 3' to the end of decamer were mutated, the promoter activity was decreased to two-thirds of the full level; and 3) when the element with the sequence AGTGATGTCACT was inserted into other promoters, the original weak promoters become very strong. Taken together, our data suggest that the positive regulatory element in Vbeta6.7 should be considered a dodecamer rather than a decamer and that it confers strong basal transcriptional activity on TCR Vbeta genes.

  10. Anomalous pressure effects on the photoreaction of a light-sensor protein from Synechocystis, PixD (Slr1694), and the compressibility change of its intermediates.

    PubMed

    Nakajima, Tsubasa; Kuroi, Kunisato; Nakasone, Yusuke; Okajima, Koji; Ikeuchi, Masahiko; Tokutomi, Satoru; Terazima, Masahide

    2016-09-21

    SyPixD (Slr1694) is a blue-light receptor that contains a BLUF (blue-light sensor using a flavin chromophore) domain for the function of phototaxis. The key reaction of this protein is a light-induced conformational change and subsequent dissociation reaction from the decamer to the dimer. In this study, anomalous effects of pressure on this reaction were discovered, and changes in the compressibility of its short-lived intermediates were investigated. While the absorption spectra of the dark and light states are not sensitive to pressure, the formation yield of the first intermediate decreases with pressure to about 40% at 150 MPa. Upon blue-light illumination with a sufficiently strong intensity, the transient grating signal, which represents the dissociation of the SyPixD decamer, was observed at 0.1 MPa, and the signal intensity significantly decreased with increasing pressure. This behavior shows that the dissociation of the decamer from the second intermediate state is suppressed by pressure. However, while the decamer undergoes no dissociation upon excitation of one monomer unit at 0.1 MPa, dissociation is gradually induced with increasing pressure. For solving this strange behavior, the compressibility changes of the intermediates were measured as a function of pressure at weak light intensity. Interestingly, the compressibility change was negative at low pressure, but became positive with increasing pressure. Because the compressibility is related to the volume fluctuation, this observation suggests that the driving force for this reaction is fluctuation of the protein. The relationship between the cavities at the interfaces of the monomer units and the reactivity was also discussed.

  11. Light-induced conformational change and transient dissociation reaction of the BLUF photoreceptor Synechocystis PixD (Slr1694).

    PubMed

    Tanaka, Keisuke; Nakasone, Yusuke; Okajima, Koji; Ikeuchi, Masahiko; Tokutomi, Satoru; Terazima, Masahide

    2011-06-24

    The light-induced reaction of the BLUF (blue light photoreceptor using flavin adenine dinucleotide) photoreceptor PixD from Synechocystis sp. PCC6803 (Slr1694) was investigated using the time-resolved transient grating method. A conformational change coupled with a volume contraction of 13 mL mol(-1) was observed with a time constant of 45 ms following photoexcitation. At a weak excitation light intensity, there were no further changes in volume and diffusion coefficient (D). The determined D-value (3.7×10(-11) m(2) s(-1)) suggests that PixD exists as a decamer in solution, and this oligomeric state was confirmed by size-exclusion chromatography and blue native polyacrylamide gel electrophoresis. Surprisingly, by increasing the excitation laser power, we observed a large increase in D with a time constant of 350 ms following the volume contraction reaction. The D-value of this photoproduct species (7.5×10(-11) m(2) s(-1)) is close to that of the PixD dimer. Combined with transient grating and size-exclusion chromatography measurements under light-illuminated conditions, the light-induced increase in D was attributed to a transient dissociation reaction of the PixD decamer to a dimer. For the M93A-mutated PixD, no volume or D-change was observed. Furthermore, we showed that the M93A mutant did not form the decamer but only the dimer in the dark state. These results indicate that the formation of the decamer and the conformational change around the Met residue are important factors that control the regulation of the downstream signal transduction by the PixD photoreceptor. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. Physical investigations of the hemocyanin of the chiton, Cryptochiton stelleri (Middendorff).

    PubMed

    Herskovits, T T; Hamilton, M G

    1987-01-01

    The hemocyanin of the giant Pacific chiton, Cryptochiton stelleri has a molecular weight of 4.2 +/- 0.3 X 10(6), determined by light-scattering, and a sedimentation coefficient of 60S. The fully dissociated subunits in nondenaturing solvents, at pH 10.6, 1 X 10(-2)M EDTA and in 8.0 M urea, pH 7.4 have molecular weights of 4.10 X 10(5) and 4.35 X 10(5), close to one-tenth of the molecular mass of the parent hemocyanin decamers. In the pH region from about 3.5 to 11 the molecular weight (Mw), determined at constant protein concentration of 0.10 g1(-1) exhibits a bell-shaped molecular weight profile centering about the physiological pH of the hemolymph of 7.2. The pH-Mw profile is best accounted for in terms of a three state, decamer-dimer-monomer dissociation scheme. Analysis of the Mg2+ and Ca2+ effects on the molecular weight transitions suggest stabilization of the hemocyanin decamers through one bound divalent ion per hemocyanin monomer or dimer. Urea, GdmCl, and the higher members of the chaotropic salt series are effective dissociating agents for Cryptochiton stelleri hemocyanin. The dissociation profile obtained with urea at pH 8.5, 0.01 M Mg2+, 0.01 M Ca2+ has been analyzed in terms of both the two- and three-species schemes of subunit-dissociation. Hydrophobic stabilization of the subunit contacts is suggested by the large number of apparent amino acid groups (Napp), of the order of 30 between dimers stabilizing the decamers, and 120 apparent amino acid groups between each monomer forming the constituent dimers.

  13. Direct Observation of a Cytosine Analogue that Forms Five Hydrogen Bonds to Guanosine: Guanyl G-Clamp

    SciTech Connect

    Wilds, C.J.; Maier, M.A.; Tereshko, V.; Manoharan, M.; Egli, M.

    2010-03-08

    A novel heterocyclic base modification, the guanidino G-clamp, is designed to allow two Hoogsteen-type hydrogen bonds to form between the amino and imino nitrogen atoms of a tethered guanidinium group to O6 and N7 of guanosine, which results in a total of five hydrogen bonds (broken lines, see picture). Details of a crystal structure at 1.0-{angstrom} resolution of a modified DNA decamer containing this guanidino G-clamp analogue demonstrate its mechanism of binding.

  14. Mass and galaxy distributions of four massive galaxy clusters from Dark Energy Survey Science Verification data

    NASA Astrophysics Data System (ADS)

    Melchior, P.; Suchyta, E.; Huff, E.; Hirsch, M.; Kacprzak, T.; Rykoff, E.; Gruen, D.; Armstrong, R.; Bacon, D.; Bechtol, K.; Bernstein, G. M.; Bridle, S.; Clampitt, J.; Honscheid, K.; Jain, B.; Jouvel, S.; Krause, E.; Lin, H.; MacCrann, N.; Patton, K.; Plazas, A.; Rowe, B.; Vikram, V.; Wilcox, H.; Young, J.; Zuntz, J.; Abbott, T.; Abdalla, F. B.; Allam, S. S.; Banerji, M.; Bernstein, J. P.; Bernstein, R. A.; Bertin, E.; Buckley-Geer, E.; Burke, D. L.; Castander, F. J.; da Costa, L. N.; Cunha, C. E.; Depoy, D. L.; Desai, S.; Diehl, H. T.; Doel, P.; Estrada, J.; Evrard, A. E.; Neto, A. Fausti; Fernandez, E.; Finley, D. A.; Flaugher, B.; Frieman, J. A.; Gaztanaga, E.; Gerdes, D.; Gruendl, R. A.; Gutierrez, G. R.; Jarvis, M.; Karliner, I.; Kent, S.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Maia, M. A. G.; Makler, M.; Marriner, J.; Marshall, J. L.; Merritt, K. W.; Miller, C. J.; Miquel, R.; Mohr, J.; Neilsen, E.; Nichol, R. C.; Nord, B. D.; Reil, K.; Roe, N. A.; Roodman, A.; Sako, M.; Sanchez, E.; Santiago, B. X.; Schindler, R.; Schubnell, M.; Sevilla-Noarbe, I.; Sheldon, E.; Smith, C.; Soares-Santos, M.; Swanson, M. E. C.; Sypniewski, A. J.; Tarle, G.; Thaler, J.; Thomas, D.; Tucker, D. L.; Walker, A.; Wechsler, R.; Weller, J.; Wester, W.

    2015-05-01

    We measure the weak lensing masses and galaxy distributions of four massive galaxy clusters observed during the Science Verification phase of the Dark Energy Survey (DES). This pathfinder study is meant to (1) validate the Dark Energy Camera (DECam) imager for the task of measuring weak lensing shapes, and (2) utilize DECam's large field of view to map out the clusters and their environments over 90 arcmin. We conduct a series of rigorous tests on astrometry, photometry, image quality, point spread function (PSF) modelling, and shear measurement accuracy to single out flaws in the data and also to identify the optimal data processing steps and parameters. We find Science Verification data from DECam to be suitable for the lensing analysis described in this paper. The PSF is generally well behaved, but the modelling is rendered difficult by a flux-dependent PSF width and ellipticity. We employ photometric redshifts to distinguish between foreground and background galaxies, and a red-sequence cluster finder to provide cluster richness estimates and cluster-galaxy distributions. By fitting Navarro-Frenk-White profiles to the clusters in this study, we determine weak lensing masses that are in agreement with previous work. For Abell 3261, we provide the first estimates of redshift, weak lensing mass, and richness. In addition, the cluster-galaxy distributions indicate the presence of filamentary structures attached to 1E 0657-56 and RXC J2248.7-4431, stretching out as far as 1°(approximately 20 Mpc), showcasing the potential of DECam and DES for detailed studies of degree-scale features on the sky.

  15. Surface cleaning of CCD imagers using an electrostatic dissipative formulation of First Contact polymer

    NASA Astrophysics Data System (ADS)

    Derylo, G.; Estrada, J.; Flaugher, B.; Hamilton, J.; Kubik, D.; Kuk, K.; Scarpine, V.

    2008-07-01

    We describe the results obtained cleaning the surface of DECam CCD detectors with a new electrostatic dissipative formulation of First ContactTM polymer from Photonic Cleaning Technologies. We demonstrate that cleaning with this new product is possible without ESD damage to the sensors and without degradation of the antireflective coating used to optimize the optical performance of the detector. We show that First ContactTM is more effective for cleaning a CCD than the commonly used acetone swab.

  16. Conformational studies of the robust 2-Cys peroxiredoxin Salmonella typhimurium AhpC by solution phase hydrogen/deuterium (H/D) exchange monitored by electrospray ionization mass spectrometry

    PubMed Central

    Nirudodhi, Sasidhar; Parsonage, Derek; Karplus, P. Andrew; Poole, Leslie B.; Maier, Claudia S.

    2010-01-01

    This is the first comprehensive HX-MS study of a “robust” 2-Cys peroxiredoxin (Prx), namely Salmonella typhimurium AhpC (StAhpC). Prx proteins control intracellular peroxide levels and are abundant antioxidant proteins in eukaryotes, archaea and bacteria. Crystal structural analyses and structure/activity studies of several bacterial and mammalian 2-Cys Prxs have revealed that the activity of 2-Cys Prxs is regulated by redox-dependent oligmerization and a sensitivity of the active site cysteine residue to overoxidation. The propensity to overoxidation is linked to the conformational flexibility of the peroxidatic active site loop. The HX-MS results emphasize the modulation of the conformational motility of the active site loop by disulfide formation. To obtain information on the conformational impact of decamer formation on the active site loop motility, mutants with Thr77 substituted by Ile, a decamer-disrupting mutation or by Val, a decamer-stabilizing mutation, were studied. For the isoleucine mutant, enhanced mobility was observed for regions encompassing the α4 helix located in the dimer-dimer interface and regions surrounding the peroxidatic loop. In contrast, the T77V mutation resulted in an increase in conformational stability in most regions of the protein except for the active site loop and the region encompassing the resolving cysteine. PMID:21516234

  17. A Dark Energy Camera Search for an Optical Counterpart to the First Advanced LIGO Gravitational Wave Event GW150914

    DOE PAGES

    Soares-Santos, M.

    2016-05-27

    We report the results of a deep search for an optical counterpart to the gravitational wave (GW) event GW150914, the first trigger from the Advanced LIGO GW detectors. We used the Dark Energy Camera (DECam) to image a 102 deg2 area, corresponding to 38% of the initial trigger high-probability sky region and to 11% of the revised high-probability region. We observed in the i and z bands at 4–5, 7, and 24 days after the trigger. The median 5σ point-source limiting magnitudes of our search images are i = 22.5 and z = 21.8 mag. We processed the images throughmore » a difference-imaging pipeline using templates from pre-existing Dark Energy Survey data and publicly available DECam data. Due to missing template observations and other losses, our effective search area subtends 40 deg2, corresponding to a 12% total probability in the initial map and 3% in the final map. In this area, we search for objects that decline significantly between days 4–5 and day 7, and are undetectable by day 24, finding none to typical magnitude limits of i = 21.5, 21.1, 20.1 for object colors (i – z) = 1, 0, –1, respectively. Lastly, our search demonstrates the feasibility of a dedicated search program with DECam and bodes well for future research in this emerging field.« less

  18. Evolution of molluscan hemocyanin structures.

    PubMed

    Markl, Jürgen

    2013-09-01

    Hemocyanin transports oxygen in the hemolymph of many molluscs and arthropods and is therefore a central physiological factor in these animals. Molluscan hemocyanin molecules are oligomers composed of many protein subunits that in turn encompass subsets of distinct functional units. The structure and evolution of molluscan hemocyanin have been studied for decades, but it required the recent progress in DNA sequencing, X-ray crystallography and 3D electron microscopy to produce a detailed view of their structure and evolution. The basic quaternary structure is a cylindrical decamer 35nm in diameter, consisting of wall and collar (typically at one end of the cylinder). Depending on the animal species, decamers, didecamers and multidecamers occur in the hemolymph. Whereas the wall architecture of the decamer seems to be invariant, four different types of collar have been identified in different molluscan taxa. Correspondingly, there exist four subunit types that differ in their collar functional units and range from 350 to 550kDa. Thus, molluscan hemocyanin subunits are among the largest polypeptides in nature. In this report, recent 3D reconstructions are used to explain and visualize the different functional units, subunits and quaternary structures of molluscan hemocyanins. Moreover, on the basis of DNA analyses and structural considerations, their possible evolution is traced. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins. Copyright © 2013 Elsevier B.V. All rights reserved.

  19. A Dark Energy Camera Search for an Optical Counterpart to the First Advanced LIGO Gravitational Wave Event GW150914

    NASA Astrophysics Data System (ADS)

    Soares-Santos, M.; Kessler, R.; Berger, E.; Annis, J.; Brout, D.; Buckley-Geer, E.; Chen, H.; Cowperthwaite, P. S.; Diehl, H. T.; Doctor, Z.; Drlica-Wagner, A.; Farr, B.; Finley, D. A.; Flaugher, B.; Foley, R. J.; Frieman, J.; Gruendl, R. A.; Herner, K.; Holz, D.; Lin, H.; Marriner, J.; Neilsen, E.; Rest, A.; Sako, M.; Scolnic, D.; Sobreira, F.; Walker, A. R.; Wester, W.; Yanny, B.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Armstrong, R.; Banerji, M.; Benoit-Lévy, A.; Bernstein, R. A.; Bertin, E.; Brown, D. A.; Burke, D. L.; Capozzi, D.; Carnero Rosell, A.; Carrasco Kind, M.; Carretero, J.; Castander, F. J.; Cenko, S. B.; Chornock, R.; Crocce, M.; D'Andrea, C. B.; da Costa, L. N.; Desai, S.; Dietrich, J. P.; Drout, M. R.; Eifler, T. F.; Estrada, J.; Evrard, A. E.; Fairhurst, S.; Fernandez, E.; Fischer, J.; Fong, W.; Fosalba, P.; Fox, D. B.; Fryer, C. L.; Garcia-Bellido, J.; Gaztanaga, E.; Gerdes, D. W.; Goldstein, D. A.; Gruen, D.; Gutierrez, G.; Honscheid, K.; James, D. J.; Karliner, I.; Kasen, D.; Kent, S.; Kuropatkin, N.; Kuehn, K.; Lahav, O.; Li, T. S.; Lima, M.; Maia, M. A. G.; Margutti, R.; Martini, P.; Matheson, T.; McMahon, R. G.; Metzger, B. D.; Miller, C. J.; Miquel, R.; Mohr, J. J.; Nichol, R. C.; Nord, B.; Ogando, R.; Peoples, J.; Plazas, A. A.; Quataert, E.; Romer, A. K.; Roodman, A.; Rykoff, E. S.; Sanchez, E.; Scarpine, V.; Schindler, R.; Schubnell, M.; Sevilla-Noarbe, I.; Sheldon, E.; Smith, M.; Smith, N.; Smith, R. C.; Stebbins, A.; Sutton, P. J.; Swanson, M. E. C.; Tarle, G.; Thaler, J.; Thomas, R. C.; Tucker, D. L.; Vikram, V.; Wechsler, R. H.; Weller, J.; DES Collaboration

    2016-06-01

    We report the results of a deep search for an optical counterpart to the gravitational wave (GW) event GW150914, the first trigger from the Advanced LIGO GW detectors. We used the Dark Energy Camera (DECam) to image a 102 deg2 area, corresponding to 38% of the initial trigger high-probability sky region and to 11% of the revised high-probability region. We observed in the i and z bands at 4-5, 7, and 24 days after the trigger. The median 5σ point-source limiting magnitudes of our search images are i = 22.5 and z = 21.8 mag. We processed the images through a difference-imaging pipeline using templates from pre-existing Dark Energy Survey data and publicly available DECam data. Due to missing template observations and other losses, our effective search area subtends 40 deg2, corresponding to a 12% total probability in the initial map and 3% in the final map. In this area, we search for objects that decline significantly between days 4-5 and day 7, and are undetectable by day 24, finding none to typical magnitude limits of i = 21.5, 21.1, 20.1 for object colors (i - z) = 1, 0, -1, respectively. Our search demonstrates the feasibility of a dedicated search program with DECam and bodes well for future research in this emerging field.

  20. Selective dispersion of single-walled carbon nanotubes with specific chiral indices by poly(N-decyl-2,7-carbazole).

    PubMed

    Lemasson, Fabien A; Strunk, Timo; Gerstel, Peter; Hennrich, Frank; Lebedkin, Sergei; Barner-Kowollik, Christopher; Wenzel, Wolfgang; Kappes, Manfred M; Mayor, Marcel

    2011-02-02

    Physico-chemical methods to sort single-walled carbon nanotubes (SWNTs) by chiral index are presently lacking but are required for in-depth experimental analysis and also for potential future applications of specific species. Here we report the unexpected selectivity of poly(N-decyl-2,7-carbazole) to almost exclusively disperse semiconducting SWNTs with differences of their chiral indices (n - m) ≥ 2 in toluene. The observed selectivity complements perfectly the dispersing features of the fluorene analogue poly(9,9-dialkyl-2,7-fluorene), which disperses semiconducting SWNTs with (n - m) ≤ 2 in toluene. The dispersed samples are further purified by density gradient centrifugation and analyzed by photoluminescence excitation spectroscopy. All-atom molecular modeling with decamer model compounds of the polymers and (10,2) and (7,6) SWNTs suggests differences in the π-π stacking interaction as origin of the selectivity. We observe energetically favored complexes between the (10,2) SWNT and the carbazole decamer and between the (7,6) SWNT and the fluorene decamer, respectively. These findings demonstrate that subtle structural changes of polymers lead to selective solvation of different families of carbon nanotubes. Furthermore, chemical screening of closely related polymers may pave the way toward simple, low-cost, and index-specific isolation of SWNTs.

  1. A Dark Energy Camera Search for an Optical Counterpart to the First Advanced LIGO Gravitational Wave Event GW150914

    SciTech Connect

    Soares-Santos, M.

    2016-05-27

    We report initial results of a deep search for an optical counterpart to the gravitational wave event GW150914, the first trigger from the Advanced LIGO gravitational wave detectors. We used the Dark Energy Camera (DECam) to image a 102 deg$^2$ area, corresponding to 38% of the initial trigger high-probability sky region and to 11% of the revised high-probability region. We observed in i and z bands at 4-5, 7, and 24 days after the trigger. The median $5\\sigma$ point-source limiting magnitudes of our search images are i=22.5 and z=21.8 mag. We processed the images through a difference-imaging pipeline using templates from pre-existing Dark Energy Survey data and publicly available DECam data. Due to missing template observations and other losses, our effective search area subtends 40 deg$^{2}$, corresponding to 12% total probability in the initial map and 3% of the final map. In this area, we search for objects that decline significantly between days 4-5 and day 7, and are undetectable by day 24, finding none to typical magnitude limits of i= 21.5,21.1,20.1 for object colors (i-z)=1,0,-1, respectively. Our search demonstrates the feasibility of a dedicated search program with DECam and bodes well for future research in this emerging field.

  2. A Dark Energy Camera Search for an Optical Counterpart to the First Advanced LIGO Gravitational Wave Event GW150914

    SciTech Connect

    Soares-Santos, M.; Kessler, R.; Berger, E.; Annis, J.; Brout, D.; Buckley-Geer, E.; Chen, H.; Cowperthwaite, P. S.; Diehl, H. T.; Doctor, Z.; Drlica-Wagner, A.; Farr, B.; Finley, D. A.; Flaugher, B.; Foley, R. J.; Frieman, J.; Gruendl, R. A.; Herner, K.; Holz, D.; Lin, H.; Marriner, J.; Neilsen, E.; Rest, A.; Sako, M.; Scolnic, D.; Sobreira, F.; Walker, A. R.; Wester, W.; Yanny, B.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Armstrong, R.; Banerji, M.; Benoit-Lévy, A.; Bernstein, R. A.; Bertin, E.; Brown, D. A.; Burke, D. L.; Capozzi, D.; Rosell, A. Carnero; Kind, M. Carrasco; Carretero, J.; Castander, F. J.; Cenko, S. B.; Chornock, R.; Crocce, M.; D’Andrea, C. B.; da Costa, L. N.; Desai, S.; Dietrich, J. P.; Drout, M. R.; Eifler, T. F.; Estrada, J.; Evrard, A. E.; Fairhurst, S.; Fernandez, E.; Fischer, J.; Fong, W.; Fosalba, P.; Fox, D. B.; Fryer, C. L.; Garcia-Bellido, J.; Gaztanaga, E.; Gerdes, D. W.; Goldstein, D. A.; Gruen, D.; Gutierrez, G.; Honscheid, K.; James, D. J.; Karliner, I.; Kasen, D.; Kent, S.; Kuropatkin, N.; Kuehn, K.; Lahav, O.; Li, T. S.; Lima, M.; Maia, M. A. G.; Margutti, R.; Martini, P.; Matheson, T.; McMahon, R. G.; Metzger, B. D.; Miller, C. J.; Miquel, R.; Mohr, J. J.; Nichol, R. C.; Nord, B.; Ogando, R.; Peoples, J.; Plazas, A. A.; Quataert, E.; Romer, A. K.; Roodman, A.; Rykoff, E. S.; Sanchez, E.; Scarpine, V.; Schindler, R.; Schubnell, M.; Sevilla-Noarbe, I.; Sheldon, E.; Smith, M.; Smith, N.; Smith, R. C.; Stebbins, A.; Sutton, P. J.; Swanson, M. E. C.; Tarle, G.; Thaler, J.; Thomas, R. C.; Tucker, D. L.; Vikram, V.; Wechsler, R. H.; Weller, J.

    2016-05-27

    We report initial results of a deep search for an optical counterpart to the gravitational wave event GW150914, the first trigger from the Advanced LIGO gravitational wave detectors. We used the Dark Energy Camera (DECam) to image a 102 deg$^2$ area, corresponding to 38% of the initial trigger high-probability sky region and to 11% of the revised high-probability region. We observed in i and z bands at 4-5, 7, and 24 days after the trigger. The median $5\\sigma$ point-source limiting magnitudes of our search images are i=22.5 and z=21.8 mag. We processed the images through a difference-imaging pipeline using templates from pre-existing Dark Energy Survey data and publicly available DECam data. Due to missing template observations and other losses, our effective search area subtends 40 deg$^{2}$, corresponding to 12% total probability in the initial map and 3% of the final map. In this area, we search for objects that decline significantly between days 4-5 and day 7, and are undetectable by day 24, finding none to typical magnitude limits of i= 21.5,21.1,20.1 for object colors (i-z)=1,0,-1, respectively. Our search demonstrates the feasibility of a dedicated search program with DECam and bodes well for future research in this emerging field.

  3. A Dark Energy Camera Search for an Optical Counterpart to the First Advanced LIGO Gravitational Wave Event GW150914

    NASA Technical Reports Server (NTRS)

    Soares-Santos, M.; Kessler, R.; Burger, E.; Annis, J.; Brout, D.; Buckley-Geer, E.; Chen, H.; Cowperthwaite, P. S.; Diehl, H.T.; Doctor, Z.; hide

    2016-01-01

    We report the results of a deep search for an optical counterpart to the gravitational wave (GW) event GW150914, the first trigger from the Advanced LIGO GW detectors. We used the Dark Energy Camera (DECam) to image a 102 deg(exp 2) area, corresponding to 38% of the initial trigger high-probability sky region and to 11% of the revised high-probability region. We observed in the i and z bands at 4-5, 7, and 24 days after the trigger. The median 5(sigma) point-source limiting magnitudes of our search images are i = 22.5 and z = 21.8 mag. We processed the images through a difference-imaging pipeline using templates from pre-existing Dark Energy Survey data and publicly available DECam data. Due to missing template observations and other losses, our effective search area subtends 40 deg(exp 2), corresponding to a 12% total probability in the initial map and 3% in the final map. In this area, we search for objects that decline significantly between days 4-5 and day 7, and are undetectable by day 24, finding none to typical magnitude limits of i = 21.5, 21.1, 20.1 for object colors (i-z)= 1, 0, -1, respectively. Our search demonstrates the feasibility of a dedicated search program with DECam and bodes well for future research in this emerging field.

  4. The Dark Energy Survey instrument design

    SciTech Connect

    Flaugher, B.; /Fermilab

    2006-05-01

    We describe a new project, the Dark Energy Survey (DES), aimed at measuring the dark energy equation of state parameter, w, to a statistical precision of {approx}5%, with four complementary techniques. The survey will use a new 3 sq. deg. mosaic camera (DECam) mounted at the prime focus of the Blanco 4m telescope at the Cerro-Tololo International Observatory (CTIO). DECam includes a large mosaic camera, a five element optical corrector, four filters (g,r,i,z), and the associated infrastructure for operation in the prime focus cage. The focal plane consists of 62 2K x 4K CCD modules (0.27''/pixel) arranged in a hexagon inscribed within the 2.2 deg. diameter field of view. We plan to use the 250 micron thick fully-depleted CCDs that have been developed at the Lawrence Berkeley National Laboratory (LBNL). At Fermilab, we will establish a packaging factory to produce four-side buttable modules for the LBNL devices, as well as to test and grade the CCDs. R&D is underway and delivery of DECam to CTIO is scheduled for 2009.

  5. Embrace the Dark Side: Advancing the Dark Energy Survey

    NASA Astrophysics Data System (ADS)

    Suchyta, Eric

    The Dark Energy Survey (DES) is an ongoing cosmological survey intended to study the properties of the accelerated expansion of the Universe. In this dissertation, I present work of mine that has advanced the progress of DES. First is an introduction, which explores the physics of the cosmos, as well as how DES intends to probe it. Attention is given to developing the theoretical framework cosmologists use to describe the Universe, and to explaining observational evidence which has furnished our current conception of the cosmos. Emphasis is placed on the dark sector - dark matter and dark energy - the content of the Universe not explained by the Standard Model of particle physics. As its name suggests, the Dark Energy Survey has been specially designed to measure the properties of dark energy. DES will use a combination of galaxy cluster, weak gravitational lensing, angular clustering, and supernovae measurements to derive its state of the art constraints, each of which is discussed in the text. The work described in this dissertation includes science measurements directly related to the first three of these probes. The dissertation presents my contributions to the readout and control system of the Dark Energy Camera (DECam); the name of this software is SISPI. SISPI uses client-server and publish-subscribe communication patterns to coordinate and command actions among the many hardware components of DECam - the survey instrument for DES, a 570 megapixel CCD camera, mounted at prime focus of the Blanco 4-m Telescope. The SISPI work I discuss includes coding applications for DECam's filter changer mechanism and hexapod, as well as developing the Scripts Editor, a GUI application for DECam users to edit and export observing sequence SISPI can load and execute. Next, the dissertation describes the processing of early DES data, which I contributed. This furnished the data products used in the first-completed DES science analysis, and contributed to improving the

  6. Structural and functional characterization of microcin C resistance peptidase MccF from Bacillus anthracis

    PubMed Central

    Nocek, Boguslaw; Tikhonov, Anton; Babnigg, Gyorgy; Gu, Minyi; Zhou, Min; Makarova, Kira S.; Vondenhoff, Gaston; Van Aerschot, Arthur; Kwon, Keehwan; Anderson, Wayne F.; Severinov, Konstantin; Joachimiak, Andrzej

    2012-01-01

    Microcin C (McC) is heptapeptide-adenylate antibiotic produced by Escherichia coli strains carrying the mccABCDEF gene cluster encoding enzymes, in addition to the heptapeptide structural gene mccA, necessary for McC biosynthesis and self-immunity of the producing cell. The heptapeptide facilitates McC transport into susceptible cells, where it is processed releasing a non-hydrolyzable aminoacyl adenylate that inhibits an essential aminoacyl-tRNA synthetase. The self-immunity gene mccF encodes a specialized serine-peptidase that cleaves an amide bond connecting the peptidyl or aminoacyl moieties of, respectively, intact and processed McC with the nucleotidyl moiety. Most mccF orthologs from organisms other than E. coli are not linked to the McC biosynthesis gene cluster. Here, we show that a protein product of one such gene, MccF from Bacillus anthracis (BaMccF), is able to cleave intact and processed McC and we present a series of structures of this protein. Structural analysis of apo-BaMccF and its AMP-complex reveal specific features of MccF-like peptidases that allow them to interact with substrates containing nucleotidyl moieties. Sequence analyses and phylogenetic reconstructions suggest that several distinct subfamilies form the MccF clade of the large S66 family of bacterial serine peptidases. We show that various representatives of the MccF clade can specifically detoxify non-hydrolyzable aminoacyl adenylates differing in their aminoacyl moieties. We hypothesize that bacterial mccF genes serve as a source of bacterial antibiotic resistance. PMID:22516613

  7. Synthesis and biological activity of some partially modified retro-inverso analogues of cholecystokinin.

    PubMed

    Rodriguez, M; Galas, M C; Lignon, M F; Mendre, C; Laur, J; Aumelas, A; Martinez, J

    1989-10-01

    Syntheses of some partially modified retro-inverso analogues of the C-terminal octa- or heptapeptide of cholecystokinin are described. These analogues (in which the C-terminal carboxamide was deleted or not) were obtained by reverting one or several peptide bonds in the parent molecule. All these compounds were able to inhibit binding of labeled CCK-8 to rat pancreatic acini and guinea pig brain membranes and to stimulate amylase release from rat pancreatic acini with various potencies. Some of these derivatives reproduce only part of the biological response of CCK on amylase release.

  8. 2-Phenylethyl ester and 2-phenylethyl amide derivative analogues of the C-terminal hepta- and octapeptide of cholecystokinin.

    PubMed

    Fulcrand, P; Rodriguez, M; Galas, M C; Lignon, M F; Laur, J; Aumelas, A; Martinez, J

    1988-11-01

    Syntheses of analogues of the C-terminal octa- and heptapeptide of cholecystokinin are described. These analogues were obtained by replacing the C-terminal phenylalanine residue by 2-phenylethyl alcohol or by 2-phenylethylamine derivatives and by replacing the tryptophan residue by a D-tryptophan. The CCK-derivatives were tested for their ability to inhibit binding of labeled CCK-8 to rat pancreatic acini and to guinea pig brain membranes, and for their action on stimulation of amylase release from rat pancreatic acini. Some of these derivatives appeared to exhibit only part of the CCK-activity on amylase release, the D-Trp analogues behaving as CCK-antagonists.

  9. Synthesis and biological activities of some cholecystokinin analogues substituted in position 29 by a beta-alanine.

    PubMed

    Rodriguez, M; Rolland, M; Lignon, M F; Galas, M C; Laur, J; Aumelas, A; Martinez, J

    1989-11-01

    Syntheses of analogues of the C-terminal heptapeptide of cholecystokinin are described. These analogues were obtained by replacing glycine 29 by a beta-alanine. The C-terminal phenylalanine amide was in some cases substituted by 2-phenylethyl alcohol and/or residues of the C-terminal tetrapeptide by their D-enantiomers. These compounds were tested for their action on stimulation of amylase release from rat pancreatic acini and for their ability to inhibit binding of labeled CCK to rat pancreatic acini and guinea pig brain membranes. Some of these derivatives behaved as CCK receptor antagonists.

  10. Measurement of intrinsic properties of amyloid fibrils by the peak force QNM method

    NASA Astrophysics Data System (ADS)

    Adamcik, Jozef; Lara, Cecile; Usov, Ivan; Jeong, Jae Sun; Ruggeri, Francesco S.; Dietler, Giovanni; Lashuel, Hilal A.; Hamley, Ian W.; Mezzenga, Raffaele

    2012-07-01

    We report the investigation of the mechanical properties of different types of amyloid fibrils by the peak force quantitative nanomechanical (PF-QNM) technique. We demonstrate that this technique correctly measures the Young's modulus independent of the polymorphic state and the cross-sectional structural details of the fibrils, and we show that values for amyloid fibrils assembled from heptapeptides, α-synuclein, Aβ(1-42), insulin, β-lactoglobulin, lysozyme, ovalbumin, Tau protein and bovine serum albumin all fall in the range of 2-4 GPa.

  11. Toxins produced in cyanobacterial water blooms – toxicity and risks

    PubMed Central

    Bláha, Luděk; Babica, Pavel; Maršálek, Blahoslav

    2009-01-01

    Cyanobacterial blooms in freshwaters represent a major ecological and human health problem worldwide. This paper briefly summarizes information on major cyanobacterial toxins (hepatotoxins, neurotoxins etc.) with special attention to microcystins-cyclic heptapeptides with high acute and chronic toxicities. Besides discussion of human health risks, microcystin ecotoxicology and consequent ecological risks are also highlighted. Although significant research attention has been paid to microcystins, cyanobacteria produce a wide range of currently unknown toxins, which will require research attention. Further research should also address possible additive, synergistic or antagonistic effects among different classes of cyanobacterial metabolites, as well as interactions with other toxic stressors such as metals or persistent organic pollutants. PMID:21217843

  12. Biodiscovery of Aluminum Binding Peptides

    DTIC Science & Technology

    2013-08-01

    for an additional 35-45 min. After induction, 5 µL cells were added to 25µL 250 nM YPet-Mona for 45 min. on ice. Cells were then pelleted and...binding mechanism of phage particles displaying a constrained heptapeptide with specific affinity to SiO2 and TiO2 ," Anal. Chem. 78(14), 4872-4879 (2006...hydroxyapatite crystals," Langmuir 27(12), 7620-7628 (2011). [15] Dickerson, M. B. A., et al., Peptide-induced room temperature formation of nanostructured TiO2

  13. Investigating the Mechanism of Peptide Aggregation: Insights from Mixed Monte Carlo-Molecular Dynamics Simulations

    PubMed Central

    Meli, Massimiliano; Morra, Giulia; Colombo, Giorgio

    2008-01-01

    The early stages of peptide aggregation are currently not accessible by experimental techniques at atomic resolution. In this article, we address this problem through the application of a mixed simulation scheme in which a preliminary coarse-grained Monte Carlo analysis of the free-energy landscape is used to identify representative conformations of the aggregates and subsequent all-atom molecular dynamics simulations are used to analyze in detail possible pathways for the stabilization of oligomers. This protocol was applied to systems consisting of multiple copies of the model peptide GNNQQNY, whose detailed structures in the aggregated state have been recently solved in another study. The analysis of the various trajectories provides dynamical and structural insight into the details of aggregation. In particular, the simulations suggest a hierarchical mechanism characterized by the initial formation of stable parallel β-sheet dimers and identify the formation of the polar zipper motif as a fundamental feature for the stabilization of initial oligomers. Simulation results are consistent with experimentally derived observations and provide an atomically detailed view of the putative initial stages of fibril formation. PMID:18263661

  14. Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns

    PubMed Central

    Brewster, Aaron S.; Sawaya, Michael R.; Rodriguez, Jose; Hattne, Johan; Echols, Nathaniel; McFarlane, Heather T.; Cascio, Duilio; Adams, Paul D.; Eisenberg, David S.; Sauter, Nicholas K.

    2015-01-01

    Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of the Computational Crystallography Toolbox (cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented. PMID:25664747

  15. Defining and quantifying frustration in the energy landscape: Applications to atomic and molecular clusters, biomolecules, jammed and glassy systems

    NASA Astrophysics Data System (ADS)

    de Souza, V. K.; Stevenson, J. D.; Niblett, S. P.; Farrell, J. D.; Wales, D. J.

    2017-03-01

    The emergence of observable properties from the organisation of the underlying potential energy landscape is analysed, spanning a full range of complexity from self-organising to glassy and jammed systems. The examples include atomic and molecular clusters, a β-barrel protein, the GNNQQNY peptide dimer, and models of condensed matter that exhibit structural glass formation and jamming. We have considered measures based on several different properties, namely, the Shannon entropy, an equilibrium thermodynamic measure that uses a sample of local minima, and indices that require additional information about the connections between local minima in the form of transition states. A frustration index is defined that correlates directly with key properties that distinguish relaxation behaviour within this diverse set. The index uses the ratio of the energy barrier to the energy difference with reference to the global minimum. The contributions for each local minimum are weighted by the equilibrium occupation probabilities. Hence we obtain fundamental insight into the connections and distinctions between systems that cover the continuum from efficient structure-seekers to landscapes that exhibit broken ergodicity and rare event dynamics.

  16. Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns

    SciTech Connect

    Brewster, Aaron S.; Sawaya, Michael R.; Rodriguez, Jose; Hattne, Johan; Echols, Nathaniel; McFarlane, Heather T.; Cascio, Duilio; Adams, Paul D.; Eisenberg, David S.; Sauter, Nicholas K.

    2015-02-01

    Special methods are required to interpret sparse diffraction patterns collected from peptide crystals at X-ray free-electron lasers. Bragg spots can be indexed from composite-image powder rings, with crystal orientations then deduced from a very limited number of spot positions. Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of the Computational Crystallography Toolbox (cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.

  17. Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42.

    PubMed

    Zheng, Jie; Jang, Hyunbum; Ma, Buyong; Nussinov, Ruth

    2008-06-05

    We report all-atom molecular dynamics simulations of annular beta-amyloid (17-42) structures, single- and double-layered, in solution. We assess the structural stability and association force of Abeta annular oligomers associated through different interfaces, with a mutated sequence (M35A), and with the oxidation state (M35O). Simulation results show that single-layered annular models display inherent structural instability: one is broken down into linear-like oligomers, and the other collapses. On the other hand, a double-layered annular structure where the two layers interact through their C-termini to form an NC-CN interface (where N and C are the N and C termini, respectively) exhibits high structural stability over the simulation time due to strong hydrophobic interactions and geometrical constraints induced by the closed circular shape. The observed dimensions and molecular weight of the oligomers from atomic force microscopy (AFM) experiments are found to correspond well to our stable double-layered model with the NC-CN interface. Comparison with K3 annular structures derived from the beta 2-microglobulin suggests that the driving force for amyloid formation is sequence specific, strongly dependent on side-chain packing arrangements, structural morphologies, sequence composition, and residue positions. Combined with our previous simulations of linear-like Abeta, K3 peptide, and sup35-derived GNNQQNY peptide, the annular structures provide useful insight into oligomeric structures and driving forces that are critical in amyloid fibril formation.

  18. Indexing amyloid peptide diffraction from serial femtosecond crystallography: New algorithms for sparse patterns

    SciTech Connect

    Brewster, Aaron S.; Sawaya, Michael R.; Rodriguez, Jose; Hattne, Johan; Echols, Nathaniel; McFarlane, Heather T.; Cascio, Duilio; Adams, Paul D.; Eisenberg, David S.; Sauter, Nicholas K.

    2015-01-23

    Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of theComputational Crystallography Toolbox(cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.

  19. The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy

    SciTech Connect

    Langkilde, Annette E.; Morris, Kyle L.; Serpell, Louise C.; Svergun, Dmitri I.; Vestergaard, Bente

    2015-04-01

    The aggregation process and the fibril state of an amyloidogenic peptide suggest monomer addition to be the prevailing mechanism of elongation and a model of the peptide packing in the fibrils has been obtained. Structural analysis of protein fibrillation is inherently challenging. Given the crucial role of fibrils in amyloid diseases, method advancement is urgently needed. A hybrid modelling approach is presented enabling detailed analysis of a highly ordered and hierarchically organized fibril of the GNNQQNY peptide fragment of a yeast prion protein. Data from small-angle X-ray solution scattering, fibre diffraction and electron microscopy are combined with existing high-resolution X-ray crystallographic structures to investigate the fibrillation process and the hierarchical fibril structure of the peptide fragment. The elongation of these fibrils proceeds without the accumulation of any detectable amount of intermediate oligomeric species, as is otherwise reported for, for example, glucagon, insulin and α-synuclein. Ribbons constituted of linearly arranged protofilaments are formed. An additional hierarchical layer is generated via the pairing of ribbons during fibril maturation. Based on the complementary data, a quasi-atomic resolution model of the protofilament peptide arrangement is suggested. The peptide structure appears in a β-sheet arrangement reminiscent of the β-zipper structures evident from high-resolution crystal structures, with specific differences in the relative peptide orientation. The complexity of protein fibrillation and structure emphasizes the need to use multiple complementary methods.

  20. Indexing amyloid peptide diffraction from serial femtosecond crystallography: New algorithms for sparse patterns

    DOE PAGES

    Brewster, Aaron S.; Sawaya, Michael R.; Rodriguez, Jose; ...

    2015-01-23

    Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of theComputational Crystallography Toolbox(cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patternsmore » with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.« less

  1. Astrometric Calibration and Performance of the Dark Energy Camera

    DOE PAGES

    Bernstein, G. M.; Armstrong, R.; Plazas, A. A.; ...

    2017-05-30

    We characterize the ability of the Dark Energy Camera (DECam) to perform relative astrometry across its 500 Mpix, 3more » $deg^2$ science field of view, and across 4 years of operation. This is done using internal comparisons of $~ 4 x 10^7$ measurements of high-S/N stellar images obtained in repeat visits to fields of moderate stellar density, with the telescope dithered to move the sources around the array. An empirical astrometric model includes terms for: optical distortions; stray electric fields in the CCD detectors; chromatic terms in the instrumental and atmospheric optics; shifts in CCD relative positions of up to $$\\approx 10 \\mu m$$ when the DECam temperature cycles; and low-order distortions to each exposure from changes in atmospheric refraction and telescope alignment. Errors in this astrometric model are dominated by stochastic variations with typical amplitudes of 10-30 mas (in a 30 s exposure) and $$5^{\\prime}-10^{\\prime}$$ arcmin coherence length, plausibly attributed to Kolmogorov-spectrum atmospheric turbulence. The size of these atmospheric distortions is not closely related to the seeing. Given an astrometric reference catalog at density $$\\approx 0.7$$ $$arcmin^{-2}$$, e.g. from Gaia, the typical atmospheric distortions can be interpolated to $$\\approx$$ 7 mas RMS accuracy (for 30 s exposures) with $$1^{\\prime}$$ arcmin coherence length for residual errors. Remaining detectable error contributors are 2-4 mas RMS from unmodelled stray electric fields in the devices, and another 2-4 mas RMS from focal plane shifts between camera thermal cycles. Thus the astrometric solution for a single DECam exposure is accurate to 3-6 mas ( $$\\approx$$ 0.02 pixels, or $$\\approx$$ 300 nm) on the focal plane, plus the stochastic atmospheric distortion.« less

  2. Astrometric Calibration and Performance of the Dark Energy Camera

    NASA Astrophysics Data System (ADS)

    Bernstein, G. M.; Armstrong, R.; Plazas, A. A.; Walker, A. R.; Abbott, T. M. C.; Allam, S.; Bechtol, K.; Benoit-Lévy, A.; Brooks, D.; Burke, D. L.; Carnero Rosell, A.; Carrasco Kind, M.; Carretero, J.; Cunha, C. E.; da Costa, L. N.; DePoy, D. L.; Desai, S.; Diehl, H. T.; Eifler, T. F.; Fernandez, E.; Fosalba, P.; Frieman, J.; García-Bellido, J.; Gerdes, D. W.; Gruen, D.; Gruendl, R. A.; Gschwend, J.; Gutierrez, G.; Honscheid, K.; James, D. J.; Kent, S.; Krause, E.; Kuehn, K.; Kuropatkin, N.; Li, T. S.; Maia, M. A. G.; March, M.; Marshall, J. L.; Menanteau, F.; Miquel, R.; Ogando, R. L. C.; Reil, K.; Roodman, A.; Rykoff, E. S.; Sanchez, E.; Scarpine, V.; Schindler, R.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, M.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; DES Collaboration

    2017-07-01

    We characterize the ability of the Dark Energy Camera (DECam) to perform relative astrometry across its 500 Mpix, 3-deg2 science field of view and across four years of operation. This is done using internal comparisons of ˜4 × 107 measurements of high signal-to-noise ratio stellar images obtained in repeat visits to fields of moderate stellar density, with the telescope dithered to move the sources around the array. An empirical astrometric model includes terms for optical distortions; stray electric fields in the CCD detectors; chromatic terms in the instrumental and atmospheric optics; shifts in CCD relative positions of up to ≈10 μm when the DECam temperature cycles; and low-order distortions to each exposure from changes in atmospheric refraction and telescope alignment. Errors in this astrometric model are dominated by stochastic variations with typical amplitudes of 10-30 mas (in a 30 s exposure) and 5‧-10‧ coherence length, plausibly attributed to Kolmogorov-spectrum atmospheric turbulence. The size of these atmospheric distortions is not closely related to the seeing. Given an astrometric reference catalog at density ≈ 0.7 {{arcmin}}-2, e.g., from Gaia, the typical atmospheric distortions can be interpolated to ≈7 mas rms accuracy (for 30 s exposures) with 1\\prime coherence length in residual errors. Remaining detectable error contributors are 2-4 mas rms from unmodelled stray electric fields in the devices, and another 2-4 mas rms from focal plane shifts between camera thermal cycles. Thus the astrometric solution for a single DECam exposure is accurate to 3-6 mas (≈0.02 pixels, or ≈300 nm) on the focal plane, plus the stochastic atmospheric distortion.

  3. VizieR Online Data Catalog: New extreme trans-Neptunian objects (Sheppard+, 2016)

    NASA Astrophysics Data System (ADS)

    Sheppard, S. S.; Trujillo, C.

    2017-02-01

    The majority of the area surveyed was with the Cerro Tololo Inter-American Observatory (CTIO) 4m Blanco telescope in Chile with the 2.7 square degree Dark Energy Camera (DECam). DECam has 62 2048*4096 pixel CCD chips from Lawrence Livermore Berkeley Labs with a scale of 0.26arcsec per pixel. The r-band filter was used during the early observing runs (2012 November and December and 2013 March, May, and November) and the ultra-wide VR filter was used in the later observations (2014 March and September and 2015 April). Before DECam became operational, the initial IOC survey was begun using the 0.255 square degree SuprimeCam on the 8m Subaru telescope, the 0.16 square degree IMACS on the 6.5m Magellan telescope, and the 0.36 square degree Mosaic-1.1 on the Kitt Peak National Observatory (KPNO) 4m Mayall telescope. The observing nights and conditions of the survey fields are shown in Table1. Usable survey data required no significant extinction from clouds and seeing less than 1.5 arcsec at the CTIO 4m and KPNO 4m. In general, the exposure times were set to reach the 24th magnitude with the r-band filter and 24.5 magnitude with the VR filter during the night. In the best seeing of 0.8 arcsec, integration times were around 330s, while in the worst seeing exposure times were up to 700s. This allowed our survey to obtain a similar depth regardless of the seeing conditions. The Subaru and Magellan observations went deeper, with the target depth of around 25.5 magnitudes in the r-band and useful seeing being less than 1.0 arcsec. (4 data files).

  4. Sedna, 2012 VP113 and the Inner Oort Cloud Population

    NASA Astrophysics Data System (ADS)

    Trujillo, Chadwick A.; Sheppard, Scott S.

    2014-11-01

    The Inner Oort Cloud objects are the most distant solar system population observed. Sedna and our recent discovery 2012 VP113 are defining members of this class both with perihelia greater than 75 Astronomical Units (AU). It is not clear how the Inner Oort Cloud objects formed, however all formation scenarios invoke the action of significant mass in the formation stages of our solar system. We are conducting an ongoing survey for Inner Oort Cloud objects using the Dark Energy Camera (DECam) on the Cerro Tololo 4-m telescope. The goal of our survey is to find more Inner Oort Cloud objects so that fundamental constraints can be placed on the Inner Oort Cloud formation scenarios, and thus the events that took place in our early solar system.With its 3 square degree field of view, DECam has the largest sky coverage of any 4-m class telescope or greater. The DECam/CTIO 4-m instrument combination is uniquely suited to detect Inner Oort Cloud objects which are both faint due to their extreme distance and rare in the sky. In the first data from our survey we discovered Inner Oort Cloud Object 2012 VP113 with a perihelion of 80 AU, the first solar system object found with a perihelion well beyond 50 AU since Sedna's discovery about a decade ago. We find the following about the Inner Oort Cloud objects: (1) there appears to be a paucity of Inner Oort Cloud objects with perihelia less than 75 AU, (2) the total number and mass of the Inner Oort Cloud could exceed that of the Kuiper Belt, and (3) there is a clustering of the argument of perihelion of the Inner Oort Cloud objects and extreme Kuiper Belt Objects which is consistent with the action of a super earth mass body at hundreds of AU. We present the latest results from our ongoing survey of the outer solar system.

  5. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides.

    PubMed

    Tran, Thanh Thuy; Nguyen, Phuong H; Derreumaux, Philippe

    2016-05-28

    Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ16-22 and Aβ37-42 of the full length Aβ1-42 Alzheimer's peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ16-22 dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ16-22 and the dimer and trimer of Aβ37-42. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ16-22 decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ37-42 decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.

  6. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides

    NASA Astrophysics Data System (ADS)

    Tran, Thanh Thuy; Nguyen, Phuong H.; Derreumaux, Philippe

    2016-05-01

    Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ16-22 and Aβ37-42 of the full length Aβ1-42 Alzheimer's peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ16-22 dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ16-22 and the dimer and trimer of Aβ37-42. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ16-22 decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ37-42 decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.

  7. Hemocyanin of the chiton, Stenoplax conspicua (Dall).

    PubMed

    Herskovits, T T; Hamilton, M G

    1987-01-01

    1. The hemocyanin of the chiton, Stenoplax conspicua, has a molecular weight determined by light-scattering of 4.2 X 10(6) daltons, (dt) and a sedimentation coefficient of 60 S. 2. The fully dissociated subunits in 6.0 and 8.0 M urea, and at pH 8.9-10 in the absence of divalent ions, have molecular weights of 4.15-4.30 x 10(5) and 4.17-4.75 x 10(5) dt, which is close to one-tenth of the molecular weight of the parent hemocyanin assembly. 3. The pH dependence of the molecular weights from pH 4.5 to 11 exhibit bell-shaped transition profiles, best accounted for by a three-species, decamer to dimer to monomer scheme of subunit dissociation, with one acidic and one basic ionizing group per dimer and 5-8 acidic and basic groups per monomer. 4. In the absence of stabilizing divalent ions S. conspicua hemocyanin is relatively unstable. At pH 7.4 in the presence of 0.01 M EDTA, it is predominantly in the dimeric state, characterized by a sedimentation constant of 18 S. It is also more readily dissociated to monomers at high pHs (8-9 and above) than are the C. stelleri and A. granulata hemocyanins. 5. Urea and GdmCl are effective dissociating agents of S. conspicua hemocyanin. The urea dissociation profile obtained at pH 8.5, 0.01 M Mg2+, 0.01 M Ca2+, and analyzed by means of the decamer-dimer-monomer scheme of subunit dissociation gave estimates of about 30 amino acid groups (Napp) at the dimer contacts within the hemocyanin decamers and about 120 groups per monomer within each dimer, suggesting hydrophobic stabilization of hemocyanin assembly.

  8. Nautilus pompilius hemocyanin: 9 A cryo-EM structure and molecular model reveal the subunit pathway and the interfaces between the 70 functional units.

    PubMed

    Gatsogiannis, Christos; Moeller, Arne; Depoix, Frank; Meissner, Ulrich; Markl, Jürgen

    2007-11-23

    Hemocyanins are giant extracellular oxygen carriers in the hemolymph of many molluscs. Nautilus pompilius (Cephalopoda) hemocyanin is a cylindrical decamer of a 350 kDa polypeptide subunit that in turn is a "pearl-chain" of seven different functional units (FU-a to FU-g). Each globular FU has a binuclear copper centre that reversibly binds one O(2) molecule, and the 70-FU decamer is a highly allosteric protein. Its primary structure and an 11 A cryo-electron microscopy (cryo-EM) structure have recently been determined, and the crystal structures of two related FU types are available in the databanks. However, in molluscan hemocyanin, the precise subunit pathway within the decamer, the inter-FU interfaces, and the allosteric unit are still obscure, but this knowledge is crucial to understand assembly and allosterism of these proteins. Here we present the cryo-EM structure of Nautilus hemocyanin at 9.1 A resolution (FSC(1/2-bit) criterion), and its molecular model obtained by rigid-body fitting of the individual FUs. In this model we identified the subunit dimer, the subunit pathway, and 15 types of inter-FU interface. Four interface types correspond to the association mode of the two protomers in the published Octopus FU-g crystal. Other interfaces explain previously described morphological structures such as the fenestrated wall (which shows D5 symmetry), the three horizontal wall tiers, the major and minor grooves, the anchor structure and the internal collar (which unexpectedly has C5 symmetry). Moreover, the potential calcium/magnesium and N-glycan binding sites have emerged. Many interfaces have amino acid constellations that might transfer allosteric interaction between FUs. From their topologies we propose that the prime allosteric unit is the oblique segment between major and minor groove, consisting of seven FUs from two different subunits. Thus, the 9 A structure of Nautilus hemocyanin provides fundamentally new insight into the architecture and function

  9. Cooperativity in beryllium bonds.

    PubMed

    Alkorta, Ibon; Elguero, José; Yáñez, Manuel; Mó, Otilia

    2014-03-07

    A theoretical study of the beryllium bonded clusters of the (iminomethyl)beryllium hydride and (iminomethyl)beryllium fluoride [HC(BeX)=NH, X = H, F] molecules has been carried out at the B3LYP/6-311++G(3df,2p) level of theory. Linear and cyclic clusters have been characterized up to the decamer. The geometric, energetic, electronic and NMR properties of the clusters clearly indicate positive cooperativity. The evolution of the molecular properties, as the size of the cluster increases, is similar to those reported in polymers held together by hydrogen bonds.

  10. Crystallizations of human serum amyloid P component (SAP)

    NASA Astrophysics Data System (ADS)

    O'Hara, B. P.; Wood, S. P.; Oliva, G.; White, H. E.; Pepys, M. B.

    1988-07-01

    Human serum amyloid P component (SAP) crystallizes readily by batch methods at its isoelectric pH of 5.5 in the presence of calcium ions and small quantities of PEG 6000. Gel filtration under similar conditions shows the protein to be pentameric while under more physiological conditions of pH and ionic strength it is known to exist as stable decamers. The protein exhibits a calcium dependent affinity for the β-D-galactopyranoside pyruvate acetal moiety of agarose. The isolated sugar has been successfully employed as a crystallization additive to modify growth rate and crystal habit.

  11. DNA oligonucleotide duplexes containing intramolecular platinated cross-links: energetics, hydration, sequence, and ionic effects.

    PubMed

    Kankia, Besik I; Soto, Ana Maria; Burns, Nicole; Shikiya, Ronald; Tung, Chang-Shung; Marky, Luis A

    2002-11-05

    The anticancer activity of cisplatin arises from its ability to bind covalently to DNA, forming primarily intrastrand cross-links to adjacent purine residues; the most common adducts involve d(GpG) (65%) and d(ApG) (25%) intrastrand cross-links. The incorporation of these platinum adducts in a B-DNA helix induces local distortions, causing bending and unwinding of the DNA. In this work, we used temperature-dependent UV spectroscopy to investigate the unfolding thermodynamics, and associated ionic effects, of two sets of DNA decamer duplexes containing either cis-[Pt(NH(3))(2)[d(GpG

  12. VizieR Online Data Catalog: Galaxies in X-ray clusters with DES. I. Stellar mass (Zhang+, 2016)

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; Miller, C.; McKay, T.; Rooney, P.; Evrard, A. E.; Romer, A. K.; Perfecto, R.; Song, J.; Desai, S.; Mohr, J.; Wilcox, H.; Bermeo-Hernandez, A.; Jeltema, T.; Hollowood, D.; Bacon, D.; Capozzi, D.; Collins, C.; Das, R.; Gerdes, D.; Hennig, C.; Hilton, M.; Hoyle, B.; Kay, S.; Liddle, A.; Mann, R. G.; Mehrtens, N.; Nichol, R. C.; Papovich, C.; Sahlen, M.; Soares-Santos, M.; Stott, J.; Viana, P. T.; Abbott, T.; Abdalla, F. B.; Banerji, M.; Bauer, A. H.; Benoit-Levy, A.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Carnero Rosell, A.; Castander, F. J.; Diehl, H. T.; Doel, P.; Cunha, C. E.; Eifler, T. F.; Fausti Neto, A.; Fernandez, E.; Flaugher, B.; Fosalba, P.; Frieman, J.; Gaztanaga, E.; Gruen, D.; Gruendl, R. A.; Honscheid, K.; James, D.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Maia, M. A. G.; Makler, M.; Marshall, J. L.; Martini, P.; Miquel, R.; Ogando, R.; Plazas, A. A.; Roodman, A.; Rykoff, E. S.; Sako, M.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sevilla, I.; Smith, R. C.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thaler, J.; Tucker, D.; Vikram, V.; da Costa, L. N.

    2016-03-01

    The Dark Energy Survey (DES) is a ground-based optical survey that uses the wide-field DECam camera mounted on the 4m Blanco telescope to image 5000deg2 of the southern hemisphere sky (Sanchez et al. 2010JPhCS.259a2080S). The paper is based on 200deg2 DES Science Verification (SV) data. This data set was taken during the 2012B observing season before the main survey (Diehl et al. 2014SPIE.9149E..0VD) began. (1 data file).

  13. Crystal structure of the stimulatory complex of GTP cyclohydrolase I and its feedback regulatory protein GFRP.

    PubMed

    Maita, Nobuo; Okada, Kengo; Hatakeyama, Kazuyuki; Hakoshima, Toshio

    2002-02-05

    In the presence of phenylalanine, GTP cyclohydrolase I feedback regulatory protein (GFRP) forms a stimulatory 360-kDa complex with GTP cyclohydrolase I (GTPCHI), which is the rate-limiting enzyme in the biosynthesis of tetrahydrobiopterin. The crystal structure of the stimulatory complex reveals that the GTPCHI decamer is sandwiched by two GFRP homopentamers. Each GFRP pentamer forms a symmetrical five-membered ring similar to beta-propeller. Five phenylalanine molecules are buried inside each interface between GFRP and GTPCHI, thus enhancing the binding of these proteins. The complex structure suggests that phenylalanine-induced GTPCHI x GFRP complex formation enhances GTPCHI activity by locking the enzyme in the active state.

  14. Nuclear magnetic resonance spectroscopy of mussel adhesive protein repeating peptide segment.

    PubMed

    Olivieri, M P; Wollman, R M; Alderfer, J L

    1997-12-01

    Mussel adhesive protein (MAP) is the adhesive agent used by the common blue sea mussel (Mytilus edulis) to attach the animal to various underwater surfaces. It is generally composed of 75 to 85 repeating decameric units with the reported primary sequence NH2-Ala(1)-Lyst(2)-Pro(3)-Ser(4)-Tyr(5)-Hyp(6)-Hyp(7)-Thr(8)-DOPA( 9)- Lys(10)-COOH. This study examines this peptide's solution-state conformation using proton nuclear magnetic resonance (NMR) spectroscopy. NMR and molecular modeling of the decamer before and after molecular dynamics calculations in water suggests a conformation that retains an overall bent helix.

  15. RAPD based genetic variability among cultivated varieties of Aonla (Indian Gooseberry, Phyllanthus emblica L.).

    PubMed

    Chaurasia, A K; Subramaniam, V R; Krishna, Bal; Sane, P V

    2009-04-01

    Aonla, the Indian Gooseberry (Phyllanthus emblica) is widely grown in India due to its neutraceutical properties. Investigations on the use of RAPD markers enabled us to estimate genetic variability among commercially cultivated varieties. This study also enabled us to distinguish these varieties using a set of four decamer primers, which was otherwise difficult by using morphological markers. Cluster analysis revealed three different groups of varieties directly associated to their place of origin. RAPD markers were also able to differentiate varieties of same origin or even selection from same parents. This information can be used for identification of varieties and further crop improvement programme.

  16. Protein interactions between the C-terminus of Aβ-peptide and phospholipase A2--a structure biology based approach to identify novel Alzheimer's therapeutics.

    PubMed

    Mirza, Zeenat; Pillai, Vikram G; Kamal, Mohammad A

    2014-01-01

    Amyloid β (Aβ) polypeptide plays a key role in determining the state of protein aggregation in Alzheimer's disease. The hydrophobic C-terminal part of the Aβ peptide is critical in triggering the transformation from α-helical to β- sheet structure. We hypothesized that phospholipase A2 (PLA2) may inhibit the aggregation of Aβ peptide by interacting with the peptide and keeping the two peptide chains apart. In order to examine the nature of interactions between PLA2 and Aβ peptide, we prepared and crystallized complex of Naja naja sagittifera PLA2 with the C-terminal hepta-peptide Val-Gly-Gly-Val-Val-Ile-Ala. The X-ray intensity data were collected to 2.04 A resolution and the structure was determined by molecular replacement and refined to the crystallographic R factor of 0.186. The structural analysis revealed that the peptide binds to PLA2 at the hydrophobic substrate binding cavity forming at least eight hydrogen bonds and approximately a two dozen Van der Waals interactions. The number and nature of interactions indicate that the affinity between PLA2 and the hepta-peptide is greater than the affinity between two Aβ peptide chains. Therefore, PLA2 is proposed as a probable ligand to prevent the aggregation of Aβ peptides.

  17. How the MccB bacterial ancestor of ubiquitin E1 initiates biosynthesis of the microcin C7 antibiotic

    SciTech Connect

    Regni, Catherine A.; Roush, Rebecca F.; Miller, Darcie J.; Nourse, Amanda; Walsh, Christopher T.; Schulman, Brenda A.

    2009-09-11

    The 39-kDa Escherichia coli enzyme MccB catalyses a remarkable posttranslational modification of the MccA heptapeptide during the biosynthesis of microcin C7 (MccC7), a 'Trojan horse' antibiotic. The approximately 260-residue C-terminal region of MccB is homologous to ubiquitin-like protein (UBL) activating enzyme (E1) adenylation domains. Accordingly, MccB-catalysed C-terminal MccA-acyl-adenylation is reminiscent of the E1-catalysed activation reaction. However, unlike E1 substrates, which are UBLs with a C-terminal di-glycine sequence, MccB's substrate, MccA, is a short peptide with an essential C-terminal Asn. Furthermore, after an intramolecular rearrangement of MccA-acyl-adenylate, MccB catalyses a second, unique reaction, producing a stable phosphoramidate-linked analogue of acyl-adenylated aspartic acid. We report six-crystal structures of MccB in apo, substrate-, intermediate-, and inhibitor-bound forms. Structural and kinetic analyses reveal a novel-peptide clamping mechanism for MccB binding to heptapeptide substrates and a dynamic-active site for catalysing dual adenosine triphosphate-consuming reactions. The results provide insight into how a distinctive member of the E1 superfamily carries out two-step activation for generating the peptidyl-antibiotic MccC7.

  18. Redirecting intracellular trafficking and the secretion pattern of FSH dramatically enhances ovarian function in mice

    PubMed Central

    Wang, Huizhen; Larson, Melissa; Jablonka-Shariff, Albina; Pearl, Christopher A.; Miller, William L.; Conn, P. Michael; Boime, Irving; Kumar, T. Rajendra

    2014-01-01

    FSH and luteinizing hormone (LH) are secreted constitutively or in pulses, respectively, from pituitary gonadotropes in many vertebrates, and regulate ovarian function. The molecular basis for this evolutionarily conserved gonadotropin-specific secretion pattern is not understood. Here, we show that the carboxyterminal heptapeptide in LH is a gonadotropin-sorting determinant in vivo that directs pulsatile secretion. FSH containing this heptapeptide enters the regulated pathway in gonadotropes of transgenic mice, and is released in response to gonadotropin-releasing hormone, similar to LH. FSH released from the LH secretory pathway rescued ovarian defects in Fshb-null mice as efficiently as constitutively secreted FSH. Interestingly, the rerouted FSH enhanced ovarian follicle survival, caused a dramatic increase in number of ovulations, and prolonged female reproductive lifespan. Furthermore, the rerouted FSH vastly improved the in vivo fertilization competency of eggs, their subsequent development in vitro and when transplanted, the ability to produce offspring. Our study demonstrates the feasibility to fine-tune the target tissue responses by modifying the intracellular trafficking and secretory fate of a pituitary trophic hormone. The approach to interconvert the secretory fate of proteins in vivo has pathophysiological significance, and could explain the etiology of several hormone hyperstimulation and resistance syndromes. PMID:24706813

  19. Targeted binding of the M13 bacteriophage to thiamethoxam organic crystals.

    PubMed

    Cho, Whirang; Fowler, Jeffrey D; Furst, Eric M

    2012-04-10

    Phage display screening with a combinatorial library was used to identify M13-type bacteriophages that express peptides with selective binding to organic crystals of thiamethoxam. The six most strongly binding phages exhibit at least 1000 times the binding affinity of wild-type M13 and express heptapeptide sequences that are rich in hydrophobic, hydrogen-bonding amino acids and proline. Among the peptide sequences identified, M13 displaying the pIII domain heptapeptide ASTLPKA exhibits the strongest binding to thiamethoxam in competitive binding assays. Electron and confocal microscopy confirm the specific binding affinity of ASTLPKA to thiamethoxam. Using atomic force microscope (AFM) probes functionalized with ASTLPKA expressing phage, we found that the average adhesion force between the bacteriophage and a thiamethoxam surface is 1.47 ± 0.80 nN whereas the adhesion force of wild-type M13KE phage is 0.18 ± 0.07 nN. Such a strongly binding bacteriophage could be used to modify the surface chemistry of thiamethoxam crystals and other organic solids with a high degree of specificity.

  20. Hepatotoxic Seafood Poisoning (HSP) Due to Microcystins: A Threat from the Ocean?

    PubMed Central

    Vareli, Katerina; Jaeger, Walter; Touka, Anastasia; Frillingos, Stathis; Briasoulis, Evangelos; Sainis, Ioannis

    2013-01-01

    Cyanobacterial blooms are a major and growing problem for freshwater ecosystems worldwide that increasingly concerns public health, with an average of 60% of blooms known to be toxic. The most studied cyanobacterial toxins belong to a family of cyclic heptapeptide hepatotoxins, called microcystins. The microcystins are stable hydrophilic cyclic heptapeptides with a potential to cause cell damage following cellular uptake via organic anion-transporting proteins (OATP). Their intracellular biologic effects presumably involve inhibition of catalytic subunits of protein phosphatases (PP1 and PP2A) and glutathione depletion. The microcystins produced by cyanobacteria pose a serious problem to human health, if they contaminate drinking water or food. These toxins are collectively responsible for human fatalities, as well as continued and widespread poisoning of wild and domestic animals. Although intoxications of aquatic organisms by microcystins have been widely documented for freshwater ecosystems, such poisonings in marine environments have only occasionally been reported. Moreover, these poisonings have been attributed to freshwater cyanobacterial species invading seas of lower salinity (e.g., the Baltic) or to the discharge of freshwater microcystins into the ocean. However, recent data suggest that microcystins are also being produced in the oceans by a number of cosmopolitan marine species, so that Hepatotoxic Seafood Poisoning (HSP) is increasingly recognized as a major health risk that follows consumption of contaminated seafood. PMID:23921721

  1. Identification of a Ubiquinone-binding Site That Affects Autophosphorylation of the Sensor Kinase RegB*S

    PubMed Central

    Swem, Lee R.; Gong, Xing; Yu, Chang-An; Bauer, Carl E.

    2009-01-01

    Rhodobacter capsulatus regulates many metabolic processes in response to the level of environmental oxygen and the energy state of the cell. One of the key global redox regulators of the cell’s metabolic physiology is the sensor kinase RegB that controls the synthesis of numerous energy generation and utilization processes. In this study, we have succeeded in purifying full-length RegB containing six transmembrane-spanning elements. Exogenous addition of excess oxidized coenzyme Q1 is capable of inhibiting RegB autophosphorylation ~6-fold. However, the addition of reduced coenzyme Q1 exhibits no inhibitory effect on kinase activity. A ubiquinone-binding site, as defined by azidoquinone photo affinity cross-linking, was determined to lie within a periplasmic loop between transmembrane helices 3 and 4 that contains a fully conserved heptapeptide sequence of GGXXNPF. Mutation of the phenylalanine in this heptapeptide renders RegB constitutively active in vivo, indicating that this domain is responsible for sensing the redox state of the ubiquinone pool and subsequently controlling RegB autophosphorylation. PMID:16407278

  2. Angiotensin-(1-7) Decreases Cell Growth and Angiogenesis of Human Nasopharyngeal Carcinoma Xenografts.

    PubMed

    Pei, Nana; Wan, Renqiang; Chen, Xinglu; Li, Andrew; Zhang, Yanling; Li, Jinlong; Du, Hongyan; Chen, Baihong; Wei, Wenjin; Qi, Yanfei; Zhang, Yi; Katovich, Michael J; Sumners, Colin; Zheng, Haifa; Li, Hongwei

    2016-01-01

    Angiotensin-(1-7) [Ang-(1-7)] is an endogenous, heptapeptide hormone acting through the Mas receptor (MasR), with antiproliferative and antiangiogenic properties. Recent studies have shown that Ang-(1-7) has an antiproliferative action on lung adenocarcinoma cells and prostate cancer cells. In this study, we report that MasR levels were significantly upregulated in nasopharyngeal carcinoma (NPC) specimens and NPC cell lines. Viral vector-mediated expression of Ang-(1-7) dramatically suppressed NPC cell proliferation and migration in vitro. These effects were completely blocked by the specific Ang-(1-7) receptor antagonist A-779, suggesting that they are mediated by the Ang-(1-7) receptor Mas. In this study, Ang-(1-7) not only caused a significant reduction in the growth of human nasopharyngeal xenografts, but also markedly decreased vessel density, suggesting that the heptapeptide inhibits angiogenesis to reduce tumor size. Mechanistic investigations revealed that Ang-(1-7) inhibited the expression of the proangiogenic factors VEGF and PlGF. Taken together, the data suggest that upregulation of MasR could be used as a diagnostic marker of NPC and Ang-(1-7) may be a novel therapeutic agent for nasopharyngeal cancer therapy because it exerts significant antiangiogenic activity.

  3. Spectroscopic and biological activity studies of the chromium-binding peptide EEEEGDD.

    PubMed

    Arakawa, Hirohumi; Kandadi, Machender R; Panzhinskiy, Evgeniy; Belmore, Kenneth; Deng, Ge; Love, Ebony; Robertson, Preshus M; Commodore, Juliette J; Cassady, Carolyn J; Nair, Sreejayan; Vincent, John B

    2016-06-01

    While trivalent chromium has been shown at high doses to have pharmacological effects improving insulin resistance in rodent models of insulin resistance, the mechanism of action of chromium at a molecular level is not known. The chromium-binding and transport agent low-molecular-weight chromium-binding substance (LMWCr) has been proposed to be the biologically active form of chromium. LMWCr has recently been shown to be comprised of a heptapeptide of the sequence EEEEDGG. The binding of Cr(3+) to this heptapeptide has been examined. Mass spectrometric and a variety of spectroscopic studies have shown that multiple chromic ions bind to the peptide in an octahedral fashion through carboxylate groups and potentially small anionic ligands such as oxide and hydroxide. A complex of Cr and the peptide when administered intravenously to mice is able to decrease area under the curve in intravenous glucose tolerance tests. It can also restore insulin-stimulated glucose uptake in myotubes rendered insulin resistant by treating them with a high-glucose media.

  4. Crystal structure of OxyB, a cytochrome P450 implicated in an oxidative phenol coupling reaction during vancomycin biosynthesis.

    PubMed

    Zerbe, Katja; Pylypenko, Olena; Vitali, Francesca; Zhang, Weiwen; Rouset, Severine; Heck, Markus; Vrijbloed, Jan W; Bischoff, Daniel; Bister, Bojan; Süssmuth, Roderich D; Pelzer, Stefan; Wohlleben, Wolfgang; Robinson, John A; Schlichting, Ilme

    2002-12-06

    Gene-inactivation studies point to the involvement of OxyB in catalyzing the first oxidative phenol coupling reaction during glycopeptide antibiotic biosynthesis. The oxyB gene has been cloned and sequenced from the vancomycin producer Amycolatopsis orientalis, and the hemoprotein has been produced in Escherichia coli, crystallized, and its structure determined to 1.7-A resolution. OxyB gave UV-visible spectra characteristic of a P450-like hemoprotein in the low spin ferric state. After reduction to the ferrous state by dithionite or by spinach ferredoxin and ferredoxin reductase, the CO-ligated form gave a 450-nm peak in a UV-difference spectrum. Addition of putative heptapeptide substrates to resting OxyB produced type I changes to the UV spectrum, but no turnover was observed in the presence of ferredoxin and ferredoxin reductase, showing that either the peptides or the reduction system, or both, are insufficient to support a full catalytic cycle. OxyB exhibits the typical P450-fold, with helix L containing the signature sequence FGHGXHXCLG and Cys(347) being the proximal axial thiolate ligand of the heme iron. The structural similarity of OxyB is highest to P450nor, P450terp, CYP119, and P450eryF. In OxyB, the F and G helices are rotated out of the active site compared with P450nor, resulting in a much more open active site, consistent with the larger size of the presumed heptapeptide substrate.

  5. Crystal structure of OxyC, a cytochrome P450 implicated in an oxidative C-C coupling reaction during vancomycin biosynthesis.

    PubMed

    Pylypenko, Olena; Vitali, Francesca; Zerbe, Katja; Robinson, John A; Schlichting, Ilme

    2003-11-21

    Gene inactivation studies point to the involvement of OxyC in catalyzing the last oxidative phenol coupling reaction during glycopeptide antibiotic biosynthesis. Presently, the substrate and exact timing of the OxyC reaction are unknown. The substrate might be the bicyclic heptapeptide or a thioester derivative bound to a protein carrier domain. OxyC from the vancomycin producer Amycolatopsis orientalis was produced in Escherichia coli and crystallized, and its structure was determined to 1.9 A resolution. OxyC gave UV-visible spectra characteristic of a P450-like hemoprotein in the low spin ferric state. After reduction to the ferrous state by dithionite the CO-ligated form gave a 450-nm peak in a UV-difference spectrum. The addition of vancomycin aglycone to OxyC produced type I changes to the UV spectrum. OxyC exhibits the typical P450-fold, with the Cys ligand loop containing the signature sequence FGHGX-HXCLG and Cys-356 being the proximal axial thiolate ligand of the heme iron. The observation of a water molecule bound to the heme iron is consistent with the UV-visible spectra of OxyC indicating a low spin heme. A polyethylene glycol molecule occupying the active site might mimic the bicyclic heptapeptide substrate. Analysis of the structure of Oxy-proteins and other P450s indicates regions that might be involved in binding of the redox partner and possibly the protein carrier domain.

  6. Enkephalin-related peptides: direct action on the octopus heart.

    PubMed

    Voigt, K H; Kiehling, C; Frösch, D; Schiebe, M; Martin, R

    1981-11-18

    Immunocytochemical evidence for the occurrence of "vertebrate" peptides in the neuropil of the vena cava [12, 13] and the structural similarity between enkephalin precursor peptides and the molluscan cardioexcitatory peptide [16], lead us to study the action of enkephalin-related peptides on the octopus heart. Systemic hearts of Octopus vulgaris were perfused with sea wate and test substances and a crude extract of vena cave were added for 1 min; frequency and pressure were monitored continuously. The heptapeptide Leu5-enkephalin-Arg6-Phe7 and the Met5-analogue, both in the amidized form, displayed dose-response relationship with a sensitivity of about 10 nmol. The C-terminal tetrapeptide amides, Phe-Leu/Met-Arg-Phe-NH2, were active at the same doses. Opiate receptors do not seem to be involved in this action on the octopus heart, as naloxone treatment had no effect. Whereas the N-terminal portion of the heptapeptide is known to be crucial for activity as an opioid, the C-terminal NH2 group is essential for cardioexcitatory activity.

  7. A few atoms make the difference: synthetic, CD, NMR and computational studies on antiviral and antibacterial activities of glycopeptide antibiotic aglycon derivatives.

    PubMed

    Bereczki, Ilona; Mándi, Attila; Rőth, Erzsébet; Borbás, Anikó; Fizil, Ádám; Komáromi, István; Sipos, Attila; Kurtán, Tibor; Batta, Gyula; Ostorházi, Eszter; Rozgonyi, Ferenc; Vanderlinden, Evelien; Naesens, Lieve; Sztaricskai, Ferenc; Herczegh, Pál

    2015-04-13

    Despite the close structural similarity between the heptapeptide cores of the glycopeptide antibiotics teicoplanin and ristocetin, synthetically modified derivatives of their aglycons show significantly different antibacterial and antiviral properties. The teicoplanin aglycon derivatives with one exception proved to be potent antibacterials but they did not exhibit anti-influenza virus activity. In contrast, the aglycoristocetin derivatives generally showed high anti-influenza virus activity and possessed moderate antibacterial activity. A systematic structure-activity relationship study has been carried out on ristocetin and teicoplanin aglycon derivatives, to explore which structural differences are responsible for these markedly different biological activities. According to electronic circular dichroism and in silico conformational studies, it was found that the differences in anti-influenza virus activity are mainly determined by the conformation of the heptapeptide core of the antibiotics controlled by the presence or absence of chloro substituents. Knowledge of the bioactive conformation will help to design new analogs with improved anti-influenza virus activity. For the teicoplanin derivatives, it was shown that derivatization to improve the antiviral efficacy was accompanied by a significant decrease in antibacterial activity. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  8. Stabilization of Angiotensin-(1-7) by key substitution with a cyclic non-natural amino acid.

    PubMed

    Wester, Anita; Devocelle, Marc; Tallant, E Ann; Chappell, Mark C; Gallagher, Patricia E; Paradisi, Francesca

    2017-07-25

    Angiotensin-(1-7) [Ang-(1-7)], a heptapeptide hormone of the renin-angiotensin-aldosterone system, is a promising candidate as a treatment for cancer that reflects its anti-proliferative and anti-angiogenic properties. However, the peptide's therapeutic potential is limited by the short half-life and low bioavailability resulting from rapid enzymatic metabolism by peptidases including angiotensin-converting enzyme (ACE) and dipeptidyl peptidase 3 (DPP 3). We report the facile assembly of three novel Ang-(1-7) analogues by solid-phase peptide synthesis which incorporates the cyclic non-natural δ-amino acid ACCA. The analogues containing the ACCA substitution at the site of ACE cleavage exhibit complete resistance to human ACE, while substitution at the DDP 3 cleavage site provided stability against DPP 3 hydrolysis. Furthermore, the analogues retain the anti-proliferative properties of Ang-(1-7) against the 4T1 and HT-1080 cancer cell lines. These results suggest that ACCA-substituted Ang-(1-7) analogues which show resistance against proteolytic degradation by peptidases known to hydrolyze the native heptapeptide may be novel therapeutics in the treatment of cancer.

  9. Biomimetic design of platelet adhesion inhibitors to block integrin α2β1-collagen interactions: II. Inhibitor library, screening, and experimental validation.

    PubMed

    Zhang, Lin; Zhang, Chao; Sun, Yan

    2014-04-29

    Platelet adhesion on collagen mediated by integrin α2β1 has been proven important in arterial thrombus formation, leading to an exigent demand on development of potent inhibitors for the integrin α2β1-collagen binding. In the present study, a biomimetic design strategy of platelet adhesion inhibitors was established, based on the affinity binding model of integrin proposed in part I. First, a heptapeptide library containing 8000 candidates was designed to functionally mimic the binding motif of integrin α2β1. Then, each heptapeptide in the library was docked onto a collagen molecule for the assessment of its affinity, followed by a screening based on its structure similarity to the original structure in the affinity binding model. Eight candidates were then selected for further screening by molecular dynamics (MD) simulations. Thereafter, three candidates chosen from MD simulations were separately added into the physiological saline containing separated integrin and collagen, to check their abilities for blocking the integrin-collagen interaction using MD simulations. Of these three candidates, significant inhibition was observed in the presence of LWWNSYY. Finally, the binding affinity of LWWNSYY for collagen was demonstrated by isothermal titration calorimetry. Moreover, significant inhibition of platelet adhesion in the presence of LWWNSYY has been experimentally validated. This work has thus developed an effective strategy for the biomimetic design of peptide-based platelet adhesion inhibitors.

  10. A Hero's Little Horse: Discovery of a Dissolving Star Cluster in Pegasus

    NASA Astrophysics Data System (ADS)

    Kim, Dongwon; Jerjen, Helmut

    2015-01-01

    We report the discovery of an ultra-faint stellar system in the constellation of Pegasus. This concentration of stars was detected by applying our overdensity detection algorithm to the Sloan Digital Sky Survey Data Release 10 and confirmed with deeper photometry from the Dark Energy Camera (DECam) at the 4 m Blanco telescope. The best-fitting model isochrone indicates that this stellar system, Kim 1, features an old (12 Gyr) and metal-poor ([Fe/H] ~ -1.7) stellar population at a heliocentric distance of 19.8 ± 0.9 kpc. We measure a half-light radius of 6.9 ± 0.6 pc using a Plummer profile. The small physical size and the extremely low luminosity are comparable to the faintest known star clusters Segue 3, Koposov 1 and 2, and Muñoz 1. However, Kim 1 exhibits a lower star concentration and is lacking a well-defined center. It also has an unusually high ellipticity and irregular outer isophotes, which suggests that we are seeing an intermediate mass star cluster being stripped by the Galactic tidal field. An extended search for evidence of an associated stellar stream within the 3 \\deg 2 DECam field remains inconclusive. The finding of Kim 1 is consistent with current overdensity detection limits and supports the hypothesis that there are still a substantial number of extreme low-luminosity star clusters undetected in the wider Milky Way halo.

  11. Highly oligomeric procyanidins from areca nut induce lymphocyte apoptosis via the depletion of intracellular thiols.

    PubMed

    Wang, Chia-Chi; Huang, Pei-Ling; Liu, Tsung-Yun; Jan, Tong-Rong

    2009-10-01

    Procyanidins are plant-derived polyphenolic compounds possessing a variety of biological activities, such as immunomodulation, and induction of tumor cell apoptosis. We previously reported that total extract of areca nut exhibited a suppressive effect on the metabolic activity and cytokine expression in normal splenic lymphocytes. As areca nut contains a rich amount of polyphenols, the objective of the present study was to investigate the pro-apoptotic effect of polyphenol-enriched areca nut extract (PANE) and its fractionated oligomeric procyanidins in splenic lymphocytes. Our data showed that PANE markedly induced lymphocyte apoptosis in a concentration- and time-dependent manner. Notably, the fractionated oligomeric procyanidins from pentamers to decamers were active in inducing the apoptosis, whereas monomers to tetramers were inactive. In addition, a marked diminishment in the level of intracellular thiols was revealed in lymphocytes treated with pentamers to decamers. Pretreatment with N-acetyl-L-cysteine, a precursor of glutathione, resulted in significant attenuation of both apoptosis and thiol diminishment induced by areca procyanidins. Taken together, our results indicated that highly oligomeric procyanidins derived from areca nut exhibited a chain length-dependent pro-apoptotic effect in primary lymphocytes, which is mediated, at least in part, by the diminishment of intracellular thiols.

  12. Automated Detection of Dwarf Galaxies and Star Clusters in SMASH through the NOAO Data Lab

    NASA Astrophysics Data System (ADS)

    Olsen, Knut A.; Nidever, David L.; Fitzpatrick, Michael J.; Mighell, Kenneth J.; SMASH Collaboration; NOAO Data Lab Team

    2017-01-01

    We present an automated method, using the NOAO Data Lab environment, for the detection of dwarf galaxy-scale objects in catalog data from the Survey of the Magellanic Stellar History (SMASH). SMASH has imaged ~480 square degrees of the southern sky, over a partially filled area of 2400 square degrees, to 24th mag in gri (uz~23) using the Dark Energy Camera (DECam). The NOAO Data Lab (http://datalab.noao.edu) is being developed to support community research of the massive data sets now being derived from NOAO’s wide-field telescopes, in particular DECam. A key feature of the Data Lab is the ability to perform efficient automated analysis of catalog and imaging data. Our method, which is an example of this feature, allows for the rapid search of candidate dwarf galaxies and stellar clusters in deep catalog data. Using SMASH as the catalog data source, we easily recover the previously discovered Hydra II dwarf galaxy and SMASH-I LMC globular cluster, as well as a number of other potentially interesting candidate stellar systems.

  13. The effect of cocoa procyanidins on the transcription and secretion of interleukin 1 beta in peripheral blood mononuclear cells.

    PubMed

    Mao, T K; Powell, J; Van de Water, J; Keen, C L; Schmitz, H H; Hammerstone, J F; Gershwin, M E

    2000-03-03

    Recent data has demonstrated that cacao liquor polyphenols (procyanidins) have antioxidant activity, inhibit mRNA expression of interleukin-2 and are potent inhibitors of acute inflammation. Given the widespread ingestion of cocoa in many cultures, we investigated whether cocoa, in its isolated procyanidin fractions (monomer through decamer), would modulate synthesis of the pro-inflammatory cytokine, interleukin-1 beta. Both resting and phytohemagglutinin (PHA)-stimulated peripheral blood mononuclear cells (PBMC) were investigated at the levels of transcription and protein secretion. Individual cocoa fractions were shown to augment constitutive IL-1 beta gene expression, although values varied between subjects. Interestingly, the smaller fractions of cocoa (monomer-tetramer) consistently reduced IL-1 beta expression of PHA-stimulated cells by 1-15%, while the larger oligomers (pentamer-decamer) increased expression by 4-52%. These data, observed at the transcription level, were reflected in protein levels in PHA-induced PBMC. The presence or absence of PHA did not alter the effects of the cocoa procyanidins with the exception of the pentamer. This study offers additional data for the consideration of the health-benefits of dietary polyphenols from a wide variety of foods, including those benefits associated specifically with cocoa and chocolate consumption.

  14. Inhibition of Key Digestive Enzymes by Cocoa Extracts 1 and Procyanidins

    PubMed Central

    Gu, Yeyi; Hurst, William J.; Stuart, David A.; Lambert, Joshua D.

    2011-01-01

    We determined the in vitro inhibitory effects of cocoa extracts and procyanidins against pancreatic α-amylase (PA), pancreatic lipase (PL) and secreted phospholipase A2 (PLA2), and characterized the kinetics of such inhibition. Lavado, regular and Dutch-processed cocoa extracts as well as cocoa procyanidins (degree of polymerization (DP) = 2 to 10) were examined. Cocoa extracts and procyanidins dose-dependently inhibited PA, PL and PLA2. Lavado cocoa extract was the most potent inhibitor (IC50 = 8.5 – 47 μg/mL). An inverse correlation between Log IC50 and DP (R2 > 0.93) was observed. Kinetic analysis suggested that regular cocoa extract, the pentamer and decamer inhibited PL activity in a mixed mode. The pentamer and decamer non-competitively inhibited PLA2 activity, whereas regular cocoa extract inhibited PLA2 competitively. Our study demonstrates that cocoa polyphenols can inhibit digestive enzymes in vitro, and may, in conjunction with a low calorie diet, play a role in body weight management. PMID:21495725

  15. Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site.

    PubMed

    Walsh, M A; Otwinowski, Z; Perrakis, A; Anderson, P M; Joachimiak, A

    2000-05-15

    Cyanase is an enzyme found in bacteria and plants that catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. In Escherichia coli, cyanase is induced from the cyn operon in response to extracellular cyanate. The enzyme is functionally active as a homodecamer of 17 kDa subunits, and displays half-site binding of substrates or substrate analogs. The enzyme shows no significant amino acid sequence homology with other proteins. We have determined the crystal structure of cyanase at 1.65 A resolution using the multiwavelength anomalous diffraction (MAD) method. Cyanase crystals are triclinic and contain one homodecamer in the asymmetric unit. Selenomethionine-labeled protein offers 40 selenium atoms for use in phasing. Structures of cyanase with bound chloride or oxalate anions, inhibitors of the enzyme, allowed identification of the active site. The cyanase monomer is composed of two domains. The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. The C-terminal domain has an 'open fold' with no structural homology to other proteins. The subunits of cyanase are arranged in a novel manner both at the dimer and decamer level. The dimer structure reveals the C-terminal domains to be intertwined, and the decamer is formed by a pentamer of these dimers. The active site of the enzyme is located between dimers and is comprised of residues from four adjacent subunits of the homodecamer. The structural data allow a conceivable reaction mechanism to be proposed.

  16. Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA

    PubMed Central

    Kandiah, Eaazhisai; Carriel, Diego; Perard, Julien; Malet, Hélène; Bacia, Maria; Liu, Kaiyin; Chan, Sze W. S.; Houry, Walid A.; Ollagnier de Choudens, Sandrine; Elsen, Sylvie; Gutsche, Irina

    2016-01-01

    The inducible lysine decarboxylase LdcI is an important enterobacterial acid stress response enzyme whereas LdcC is its close paralogue thought to play mainly a metabolic role. A unique macromolecular cage formed by two decamers of the Escherichia coli LdcI and five hexamers of the AAA+ ATPase RavA was shown to counteract acid stress under starvation. Previously, we proposed a pseudoatomic model of the LdcI-RavA cage based on its cryo-electron microscopy map and crystal structures of an inactive LdcI decamer and a RavA monomer. We now present cryo-electron microscopy 3D reconstructions of the E. coli LdcI and LdcC, and an improved map of the LdcI bound to the LARA domain of RavA, at pH optimal for their enzymatic activity. Comparison with each other and with available structures uncovers differences between LdcI and LdcC explaining why only the acid stress response enzyme is capable of binding RavA. We identify interdomain movements associated with the pH-dependent enzyme activation and with the RavA binding. Multiple sequence alignment coupled to a phylogenetic analysis reveals that certain enterobacteria exert evolutionary pressure on the lysine decarboxylase towards the cage-like assembly with RavA, implying that this complex may have an important function under particular stress conditions. PMID:27080013

  17. MASS SUBSTRUCTURE IN ABELL 3128

    SciTech Connect

    McCleary, J.; Dell’Antonio, I.; Huwe, P.

    2015-05-20

    We perform a detailed two-dimensional weak gravitational lensing analysis of the nearby (z = 0.058) galaxy cluster Abell 3128 using deep ugrz imaging from the Dark Energy Camera (DECam). We have designed a pipeline to remove instrumental artifacts from DECam images and stack multiple dithered observations without inducing a spurious ellipticity signal. We develop a new technique to characterize the spatial variation of the point-spread function that enables us to circularize the field to better than 0.5% and thereby extract the intrinsic galaxy ellipticities. By fitting photometric redshifts to sources in the observation, we are able to select a sample of background galaxies for weak-lensing analysis free from low-redshift contaminants. Photometric redshifts are also used to select a high-redshift galaxy subsample with which we successfully isolate the signal from an interloping z = 0.44 cluster. We estimate the total mass of Abell 3128 by fitting the tangential ellipticity of background galaxies with the weak-lensing shear profile of a Navarro–Frenk–White (NFW) halo and also perform NFW fits to substructures detected in the 2D mass maps of the cluster. This study yields one of the highest resolution mass maps of a low-z cluster to date and is the first step in a larger effort to characterize the redshift evolution of mass substructures in clusters.

  18. Crystal Structure and Function of Human Nucleoplasmin (Npm2): A Histone Chaperone in Oocytes and Embryos

    SciTech Connect

    O Platonova; I Akey; J Head; C Akey

    2011-12-31

    Human Npm2 is an ortholog of Xenopus nucleoplasmin (Np), a chaperone that binds histones. We have determined the crystal structure of a truncated Npm2-core at 1.9 {angstrom} resolution and show that the N-terminal domains of Npm2 and Np form similar pentamers. This allowed us to model an Npm2 decamer which may be formed by hydrogen bonds between quasi-conserved residues in the interface between two pentamers. Interestingly, the Npm2 pentamer lacks a prototypical A1-acidic tract in each of its subunits. This feature may be responsible for the inability of Npm2-core to bind histones. However, Npm2 with a large acidic tract in its C-terminal tail (Npm2-A2) is able to bind histones and form large complexes. Fluorescence resonance energy transfer experiments and biochemical analysis of loop mutations support the premise that nucleoplasmins form decamers when they bind H2A-H2B dimers and H3-H4 tetramers simultaneously. In the absence of histone tetramers, these chaperones bind H2A-H2B dimers with a single pentamer forming the central hub. When taken together, our data provide insights into the mechanism of histone binding by nucleoplasmins.

  19. The novel double-folded structure of d(GCATGCATGC): a possible model for triplet-repeat sequences.

    PubMed

    Thirugnanasambandam, Arunachalam; Karthik, Selvam; Mandal, Pradeep Kumar; Gautham, Namasivayam

    2015-10-01

    The structure of the decadeoxyribonucleotide d(GCATGCATGC) is presented at a resolution of 1.8 Å. The decamer adopts a novel double-folded structure in which the direction of progression of the backbone changes at the two thymine residues. Intra-strand stacking interactions (including an interaction between the endocylic O atom of a ribose moiety and the adjacent purine base), hydrogen bonds and cobalt-ion interactions stabilize the double-folded structure of the single strand. Two such double-folded strands come together in the crystal to form a dimer. Inter-strand Watson-Crick hydrogen bonds form four base pairs. This portion of the decamer structure is similar to that observed in other previously reported oligonucleotide structures and has been dubbed a `bi-loop'. Both the double-folded single-strand structure, as well as the dimeric bi-loop structure, serve as starting points to construct models for triplet-repeat DNA sequences, which have been implicated in many human diseases.

  20. Influence of packing interactions on the average conformation of B-DNA in crystalline structures.

    PubMed

    Tereshko, V; Subirana, J A

    1999-04-01

    The molecular interactions in crystals of oligonucleotides in the B form have been analysed and in particular the end-to-end interactions. Phosphate-phosphate interactions in dodecamers are also reviewed. A strong influence of packing constraints on the average conformation of the double helix is found. There is a strong relationship between the space group, the end-to-end interactions and the average conformation of DNA. Dodecamers must have a B-form average conformation with 10 +/- 0.1 base pairs per turn in order to crystallize in the P212121 and related space groups usually found. Decamers show a wider range of conformational variation, with 9.7-10. 6 base pairs per turn, depending on the terminal sequence and the space group. The influence of the space group in decamers is quite striking and remains unexplained. Only small variations are allowed in each case. Thus, crystal packing is strongly related to the average DNA conformation in the crystals and deviations from the average are rather limited. The constraints imposed by the crystal lattice explain why the average twist of the DNA in solution (10.6 base pairs per turn) is seldom found in oligonucleotides crystallized in the B form.

  1. Crystallization and preliminary X-ray crystallographic study of a 3.8-MDa respiratory supermolecule hemocyanin.

    PubMed

    Matsuno, Asuka; Gai, Zuoqi; Tanaka, Miyuki; Kato, Koji; Kato, Sanae; Katoh, Tsuyoshi; Shimizu, Takeshi; Yoshioka, Takeya; Kishimura, Hideki; Tanaka, Yoshikazu; Yao, Min

    2015-06-01

    Many molluscs transport oxygen using a very large cylindrical multimeric copper-containing protein named hemocyanin. The molluscan hemocyanin forms a decamer (cephalopods) or multidecamer (gastropods) of approximately 330-450kDa subunits, resulting in a molecular mass >3.3MDa. Therefore, molluscan hemocyanin is one of the largest proteins. The reason why these organisms use such a large supermolecule for oxygen transport remains unclear. Atomic-resolution X-ray crystallographic analysis is necessary to unveil the detailed molecular structure of this mysterious large molecule. However, its propensity to dissociate in solution has hampered the crystallization of its intact form. In the present study, we successfully obtained the first crystals of an intact decameric molluscan hemocyanin. The diffraction dataset at 3.0-Å resolution was collected by merging the datasets of two isomorphic crystals. Electron microscopy analysis of the dissolved crystals revealed cylindrical particles. Furthermore, self-rotation function analysis clearly showed the presence of a fivefold symmetry with several twofold symmetries perpendicular to the fivefold axis. The absorption spectrum of the crystals showed an absorption peak around 345nm. These results indicated that the crystals contain intact hemocyanin decamers in the oxygen-bound form.

  2. Light Echoes of Galactic Explosions and Eruptions

    NASA Astrophysics Data System (ADS)

    Rest, Armin; Bianco, Federica; Chornock, Ryan; Foley, Ryan; Matheson, Thomas; Narayan, Gautham; Olsen, Knut; Prieto, Jose Luis; Smith, Chris; Smith, Nathan; Suntzeff, Nick; Welch, Doug; Zenteno, Alfredo

    2014-02-01

    We propose to continue our search for the first light echoes (LEs) associated with historical Galactic supernovae and LBV outbursts: SN 1006, Kepler's SN, RCW 86, Crab Nebula, and P Cygni. In previously granted NOAO time, we have discovered LEs of three ancient SNe in the LMC as well as from the historic SN events of Cas A and Tycho [2, 3], which allowed their spectroscopic classification [6, 7, 10] and 3D spectroscopy [8, 9]. Most recently, we discovered light echoes of the mid-19th-century Great Eruption of η Carinae using CTIO 4m Mosaic images [11]. Subsequent spectroscopic follow-up of Eta Carinae revealed that its outburst spectral type was most similar to those of G-type supergiants, rather than reported LBV outburst spectral types of F-type (or earlier) [11]. We propose to continue our search for light echoes of the remaining historical events. With DECam, we have a 10-15 fold improvement in efficiency over the retired CTIO-Mosaic camera, which allows us to cover the bigger search areas of most of the remaining targets. With the KPNO 4-m, we will observe fields too far north for CTIO/DECam. The study of scattered-light echoes from these Galactic supernovae and eruptions will give us the opportunity to directly compare the original outburst and its current remnant, and in favorable cases (like Eta Carinae), it provides a three-dimensional view of the event and/or a spectral time series.

  3. The peroxidase and peroxynitrite reductase activity of human erythrocyte peroxiredoxin 2.

    PubMed

    Manta, Bruno; Hugo, Martín; Ortiz, Cecilia; Ferrer-Sueta, Gerardo; Trujillo, Madia; Denicola, Ana

    2009-04-15

    Peroxiredoxin 2 (Prx2) is a 2-Cys peroxiredoxin extremely abundant in the erythrocyte. The peroxidase activity was studied in a steady-state approach yielding an apparent K(M) of 2.4 microM for human thioredoxin and a very low K(M) for H2O2 (0.7 microM). Rate constants for the reaction of peroxidatic cysteine with the peroxide substrate, H2O2 or peroxynitrite, were determined by competition kinetics, k(2) = 1.0 x 10(8) and 1.4 x 10(7) M(-1) s(-1) at 25 degrees C and pH 7.4, respectively. Excess of both oxidants inactivated the enzyme by overoxidation and also tyrosine nitration and dityrosine were observed with peroxynitrite treatment. Prx2 associates into decamers (5 homodimers) and we estimated a dissociation constant K(d) < 10(-23) M(4) which confirms the enzyme exists as a decamer in vivo. Our kinetic results indicate Prx2 is a key antioxidant enzyme for the erythrocyte and reveal red blood cells as active oxidant scrubbers in the bloodstream.

  4. Catalytic Thr or Ser Residue Modulates Structural Switches in 2-Cys Peroxiredoxin by Distinct Mechanisms

    PubMed Central

    Tairum, Carlos A.; Santos, Melina Cardoso; Breyer, Carlos A.; Geyer, R. Ryan; Nieves, Cecilia J.; Portillo-Ledesma, Stephanie; Ferrer-Sueta, Gerardo; Toledo, José Carlos; Toyama, Marcos H.; Augusto, Ohara; Netto, Luis E. S.; de Oliveira, Marcos A.

    2016-01-01

    Typical 2-Cys Peroxiredoxins (2-Cys Prxs) reduce hydroperoxides with extraordinary rates due to an active site composed of a catalytic triad, containing a peroxidatic cysteine (CP), an Arg, and a Thr (or Ser). 2-Cys Prx are involved in processes such as cancer; neurodegeneration and host-pathogen interactions. During catalysis, 2-Cys Prxs switch between decamers and dimers. Analysis of 2-Cys Prx structures in the fully folded (but not locally unfolded) form revealed a highly conserved, non-conventional hydrogen bond (CH-π) between the catalytic triad Thr of a dimer with an aromatic residue of an adjacent dimer. In contrast, structures of 2-Cys Prxs with a Ser in place of the Thr do not display this CH-π bond. Chromatographic and structural data indicate that the Thr (but not Ser) destabilizes the decamer structure in the oxidized state probably through steric hindrance. As a general trend, mutations in a yeast 2-Cys Prx (Tsa1) favoring the dimeric state also displayed a decreased catalytic activity. Remarkably, yeast naturally contains Thr-Ser variants (Tsa1 and Tsa2, respectively) with distinct oligomeric stabilities in their disulfide states. PMID:27629822

  5. Replica-exchange molecular dynamics simulations of cellulose solvated in water and in the ionic liquid 1-butyl-3-methylimidazolium chloride

    SciTech Connect

    Mostofian, Barmak; Cheng, Xiaolin; Smith, Jeremy C.

    2014-09-02

    Ionic liquids have become a popular solvent for cellulose pretreatment in biorefineries due to their efficiency in dissolution and their reusability. Understanding the interactions between cations, anions, and cellulose is key to the development of better solvents and the improvement of pretreatment conditions. While previous studies described the interactions between ionic liquids and cellulose fibers, shedding light on the initial stages of the cellulose dissolution process, we study the end state of that process by exploring the structure and dynamics of a single cellulose decamer solvated in 1-butyl-3-methyl-imidazolium chloride (BmimCl) and in water using replica-exchange molecular dynamics. In both solvents, global structural features of the cellulose chain are similar. However, analyses of local structural properties show that cellulose explores greater conformational variability in the ionic liquid than in water. For instance, in BmimCl the cellulose intramolecular hydrogen bond O3H'••• O5 is disrupted more often resulting in greater flexibility of the solute. Our results indicate that the cellulose chain is more dynamic in BmimCl than in water, which may play a role in the favorable dissolution of cellulose in the ionic liquid. Here, the calculation of the configurational entropy of the cellulose decamer confirms its higher conformational flexibility in BmimCl than in water at elevated temperatures.

  6. Protein Self-Association Induced by Macromolecular Crowding: A Quantitative Analysis by Magnetic Relaxation Dispersion

    PubMed Central

    Snoussi, Karim; Halle, Bertil

    2005-01-01

    In the presence of high concentrations of inert macromolecules, the self-association of proteins is strongly enhanced through an entropic, excluded-volume effect variously called macromolecular crowding or depletion attraction. Despite the predicted large magnitude of this universal effect and its far-reaching biological implications, few experimental studies of macromolecular crowding have been reported. Here, we introduce a powerful new technique, fast field-cycling magnetic relaxation dispersion, for investigating crowding effects on protein self-association equilibria. By recording the solvent proton spin relaxation rate over a wide range of magnetic field strengths, we determine the populations of coexisting monomers and decamers of bovine pancreatic trypsin inhibitor in the presence of dextran up to a macromolecular volume fraction of 27%. Already at a dextran volume fraction of 14%, we find a 30-fold increase of the decamer population and 5105-fold increase of the association constant. The analysis of these results, in terms of a statistical-mechanical model that incorporates polymer flexibility as well as the excluded volume of the protein, shows that the dramatic enhancement of bovine pancreatic trypsin inhibitor self-association can be quantitatively rationalized in terms of hard repulsive interactions. PMID:15665132

  7. The development of a cryogenic over-pressure pump

    NASA Astrophysics Data System (ADS)

    Alvarez, M.; Cease, H.; Flaugher, B.; Flores, R.; Garcia, J.; Lathrop, A.; Ruiz, F.

    2014-01-01

    A cryogenic over-pressure pump (OPP) was tested in the prototype telescope liquid nitrogen (LN2) cooling system for the Dark Energy Survey (DES) Project. This OPP consists of a process cylinder (PC), gas generator, and solenoid operated valves (SOVs). It is a positive displacement pump that provided intermittent liquid nitrogen (LN2) flow to an array of charge couple devices (CCDs) for the prototype Dark Energy Camera (DECam). In theory, a heater submerged in liquid would generate the drive gas in a closed loop cooling system. The drive gas would be injected into the PC to displace that liquid volume. However, due to limitations of the prototype closed loop nitrogen system (CCD cooling system) for DECam, a quasiclosed-loop nitrogen system was created. During the test of the OPP, the CCD array was cooled to its designed set point temperature of 173K. It was maintained at that temperature via electrical heaters. The performance of the OPP was captured in pressure, temperature, and flow rate in the CCD LN2 cooling system at Fermi National Accelerator Laboratory (FNAL).

  8. Is it possible to study the kinetic parameters of interaction between PNA and parallel and antiparallel DNA by stopped-flow fluorescence?

    PubMed

    Barbero, N; Cauteruccio, S; Thakare, P; Licandro, E; Viscardi, G; Visentin, S

    2016-10-01

    Peptide nucleic acids (PNAs) are among the most interesting and versatile artificial structural mimics of nucleic acids and exhibit peculiar and important properties (i.e. high chemical stability, and a high resistance to cellular enzymes and nucleases). Despite their unnatural structure, they are able to recognize and bind DNA and RNA in a very high, specific and selective manner. One of the most popular, easy and reliable method to measure the stability of PNA-DNA hybrid systems is the melting temperature but the thermodynamic data are obtained using a big quantity of materials failing to provide information on the kinetics of the interaction. In the present work, the PNA decamer 6, with the TCACTAGATG sequence of nucleobases, and the corresponding fluorescent PNA-FITU (fluorescein isothiourea) decamer 8 were synthesized with standard manual Boc-based chemistry. The interaction of the PNA-FITU with parallel and antiparallel DNA has been studied by stopped-flow fluorescence, which is proposed as an alternative technique to obtain the kinetic parameters of the binding. The great advantage of using the stopped-flow technique is the possibility of studying the kinetics of the PNA-DNA duplex formation in a physiological environment. In particular, fluorescence stopped-flow technique has been exploited to compare the affinity of two PNA-DNA duplexes since it can discriminate between parallel and antiparallel DNA binding.

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

    PubMed Central

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

    2012-01-01

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

  10. In vivo parameters influencing 2-Cys Prx oligomerization: The role of enzyme sulfinylation.

    PubMed

    Noichri, Y; Palais, G; Ruby, V; D'Autreaux, B; Delaunay-Moisan, A; Nyström, T; Molin, M; Toledano, M B

    2015-12-01

    2-Cys Prxs are H2O2-specific antioxidants that become inactivated by enzyme hyperoxidation at elevated H2O2 levels. Although hyperoxidation restricts the antioxidant physiological role of these enzymes, it also allows the enzyme to become an efficient chaperone holdase. The critical molecular event allowing the peroxidase to chaperone switch is thought to be the enzyme assembly into high molecular weight (HMW) structures brought about by enzyme hyperoxidation. How hyperoxidation promotes HMW assembly is not well understood and Prx mutants allowing disentangling its peroxidase and chaperone functions are lacking. To begin addressing the link between enzyme hyperoxidation and HMW structures formation, we have evaluated the in vivo 2-Cys Prxs quaternary structure changes induced by H2O2 by size exclusion chromatography (SEC) on crude lysates, using wild type (Wt) untagged and Myc-tagged S. cerevisiae 2-Cys Prx Tsa1 and derivative Tsa1 mutants or genetic conditions known to inactivate peroxidase or chaperone activity or altering the enzyme sensitivity to hyperoxidation. Our data confirm the strict causative link between H2O2-induced hyperoxidation and HMW formation/stabilization, also raising the question of whether CP hyperoxidation triggers the assembly of HMW structures by the stacking of decamers, which is the prevalent view of the literature, or rather, the stabilization of preassembled stacked decamers.

  11. Genetic variation among populations of Pla-mong fish (Pangasuis bocourti Sauvage 1880) of the Mae Kong River in Northeast Thailand.

    PubMed

    Champasri, T; Jiwyam, W; Budriang, Ch; Charoenwattanasak, S

    2010-04-15

    This study was carried out at the Department of Fisheries, Faculty of Agriculture, Khon Kaen University, Khon Kaen, Thailand during April to September 2007 to determine DNA patterns of Pla-mong fish (Pangasuis bocourti Sauvage 1880) with the use of RAPD-PCR amplification. One hundred twenty individual fish samples were harvested from four locations along the Mae Kong River, i.e., Nongkhai, Nakornphanom, Mukdaharn and Ubon Ratchatani provinces, each location has thirty individual fish samples and the four locations were used as treatments and thirty individual fish of each location were used as replications. Sixteen RAPD decamer primers from three kits of Operon Technologies were subjected to a preliminary test and only seven decamer primers were suited most for PCR amplification. The results on both similarity correlation coefficients and genetic distances revealed that the fish of Pla-mong of the Mae Kong River could be divided into two groups, i.e., the first group included the fish harvested from Nongkhai and Nakornphanom provinces with their genetic values ranged from 0.20 to 0.36 and the second group included the harvested fish from Mukdaharn and Nakornphanom provinces with their genetic values ranged from 0.20 to 0.44.

  12. The readout and control system of the Dark Energy Camera

    NASA Astrophysics Data System (ADS)

    Honscheid, Klaus; Elliott, Ann; Annis, James; Bonati, Marco; Buckley-Geer, Elizabeth; Castander, Francisco; daCosta, Luiz; Fausti, Angelo; Karliner, Inga; Kuhlmann, Steve; Neilsen, Eric; Patton, Kenneth; Reil, Kevin; Roodman, Aaron; Thaler, Jon; Serrano, Santiago; Soares Santos, Marcelle; Suchyta, Eric

    2012-09-01

    The Dark Energy Camera (DECam) is a new 520 Mega Pixel CCD camera with a 3 square degree field of view designed for the Dark Energy Survey (DES). DES is a high precision, multi-bandpass, photometric survey of 5000 square degrees of the southern sky. DECam is currently being installed at the prime focus of the Blanco 4-m telescope at the Cerro- Tololo International Observatory (CTIO). In this paper we describe SISPI, the data acquisition and control system of the Dark Energy Camera. SISPI is implemented as a distributed multi-processor system with a software architecture based on the Client-Server and Publish-Subscribe design patterns. The underlying message passing protocol is based on PYRO, a powerful distributed object technology system written entirely in Python. A distributed shared variable system was added to support exchange of telemetry data and other information between different components of the system. We discuss the SISPI infrastructure software, the image pipeline, the observer console and user interface architecture, image quality monitoring, the instrument control system, and the observation strategy tool.

  13. Geographic Variations and Genetic Distance of Three Geographic Cyclina Clam (Cyclina sinensis Gmelin) Populations from the Yellow Sea.

    PubMed

    Yoon, Jong-Man

    2012-12-01

    The gDNA isolated from Cyclina sinensis from Gochang (GOCHANG), Incheon (INCHEON) and a Chinese site (CHINESE), were amplified by PCR. Here, the seven oligonucleotide decamer primers (BION-66, BION-68, BION-72, BION-73, BION-74, BION-76, and BION-80) were used to generate the unique shared loci to each population and shared loci by the three cyclina clam populations. As regards multiple comparisons of average bandsharing value results, cyclina clam population from Chinese (0.763) exhibited higher bandsharing values than did clam from Incheon (0.681). In this study, the dendrogram obtained by the seven decamer primers indicates three genetic clusters: cluster 1 (GOCHANG 01~ GOCHANG 07), cluster 2 (INCHEON 08~INCHEON 14), cluster 3 (CHINESE 15~CHINESE 21). The shortest genetic distance that displayed significant molecular differences was between individuals 15 and 17 from the Chinese cyclina clam (0.049), while the longest genetic distance among the twenty-one cyclina clams that displayed significant molecular differences was between individuals GOCHANG no. 03 and INCHEON no. 12 (0.575). Individuals of Incheon cyclina clam population was somewhat closely related to that of Chinese cyclina clam population. In conclusion, our PCR analysis revealed a significant genetic distance among the three cyclina clam populations.

  14. Alternative packing modes leading to amyloid polymorphism in five fragments studied with molecular dynamics.

    PubMed

    Berhanu, Workalemahu M; Masunov, Artëm E

    2012-01-01

    Amyloid aggregates have been implicated in the pathogenesis of diseases such as type 2 diabetes, Alzheimer's, Parkinson's, and prion disease. Recently determined microcrystal structures of several short peptide segments derived from fibril-forming proteins revealed coexistence of alternative aggregation modes (amyloid polymorphism) formed by the same segment. This polymorphism may help in understanding the influence of the side chain packing on the amyloid stability. Here we use molecular dynamics (MD) simulation to analyze the stability of five pairs of polar and nonpolar polymorphic oligomers. MD simulation shows polymorphs with steric zipper interface containing large polar and/or aromatic side chains (GNNQQNY, and NNQNTF) are more stable than steric zipper interfaces made of small or hydrophobic residues (SSTNGVG, VQIVYK, and MVGGVV). Several geometric analyses revealed that larger sheet to sheet interface of the dry steric zipper through polar Q/N rich side chains holds the sheets together. Mutant simulations (Q/N→G) show substitutions with glycine disrupt the steric zipper, leading to unstable oligomers. Stability of Q/N rich oligomers was found to result from the large average number of hydrogen bonds. The molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method reports the nonpolar component of free energy to be favorable, while electrostatic solvation is unfavorable for β-sheet association. Knowledge of structural properties of these fibrils might be useful for developing therapeutic agents against amyloidoses as well as for developing biomaterials. © 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 98: 131-144, 2012. Copyright © 2011 Wiley Periodicals, Inc.

  15. Thermodynamic selection of steric zipper patterns in the amyloid cross-beta spine.

    PubMed

    Park, Jiyong; Kahng, Byungnam; Hwang, Wonmuk

    2009-09-01

    At the core of amyloid fibrils is the cross-beta spine, a long tape of beta-sheets formed by the constituent proteins. Recent high-resolution x-ray studies show that the unit of this filamentous structure is a beta-sheet bilayer with side chains within the bilayer forming a tightly interdigitating "steric zipper" interface. However, for a given peptide, different bilayer patterns are possible, and no quantitative explanation exists regarding which pattern is selected or under what condition there can be more than one pattern observed, exhibiting molecular polymorphism. We address the structural selection mechanism by performing molecular dynamics simulations to calculate the free energy of incorporating a peptide monomer into a beta-sheet bilayer. We test filaments formed by several types of peptides including GNNQQNY, NNQQ, VEALYL, KLVFFAE and STVIIE, and find that the patterns with the lowest binding free energy correspond to available atomistic structures with high accuracy. Molecular polymorphism, as exhibited by NNQQ, is likely because there are more than one most stable structures whose binding free energies differ by less than the thermal energy. Detailed analysis of individual energy terms reveals that these short peptides are not strained nor do they lose much conformational entropy upon incorporating into a beta-sheet bilayer. The selection of a bilayer pattern is determined mainly by the van der Waals and hydrophobic forces as a quantitative measure of shape complementarity among side chains between the beta-sheets. The requirement for self-complementary steric zipper formation supports that amyloid fibrils form more easily among similar or same sequences, and it also makes parallel beta-sheets generally preferred over anti-parallel ones. But the presence of charged side chains appears to kinetically drive anti-parallel beta-sheets to form at early stages of assembly, after which the bilayer formation is likely driven by energetics.

  16. Degradation of the ACTH(4-10) analog Semax in the presence of rat basal forebrain cell cultures and plasma membranes.

    PubMed

    Zolotarev, Yu A; Dolotov, O V; Inozemtseva, L S; Dadayan, A K; Dorokhova, E M; Andreeva, L A; Alfeeva, L Yu; Grivennikov, I A; Myasoedov, N F

    2006-06-01

    Here a new approach of the elucidation of paths of proteolytic biodegradation of physiologically active peptides, based on the use of a peptide with isotopic label at all amino acid residues and the enrichment of HPLC samples with unlabeled peptide fragments in UV-detectable concentration, has been proposed. The method has been applied for the investigation of degradation dynamics of the neuroactive heptapeptide MEHFPGP (Semax) in the presence of plasma membranes, and cultures of glial and neuronal cells obtained from the rat basal forebrain. The splitting away of ME and GP, and formation of pentapeptides are the predominant processes in the presence of all tested objects, whereas the difference in patterns of resulting peptide products for glial and neuronal cells has been detected. In conclusion, the approach applied allows analyzing physiologically active peptide concentrations in biological tissues and degradation pathways of peptides in the presence of targets of their action.

  17. [Effect of modification of the N-terminal region of molecule on the expression of neotropic effect of semax analogues].

    PubMed

    Glazova, N Iu; Sebentsova, E A; Levitskaia, N G; Andreeva, L A; Alfeeva, L Iu; Kamenskiĭ, A A; Miasoedov, N F

    2005-01-01

    A comparative study of neotropic activity of semax (MEHFPGP), an analogue of the ACTH(4-10), and some of its derivatives in which the N-terminal methionine was modified or substituted with other amino acid residues was performed. The effect of these peptides on learning of albino rats in tests with positive (alimentary) and negative (pain) reinforcement was studied. In the case of modification of methionine by attachment of the gluconic-acid residue or substitution of methionine with lysine, the neotropic effect of the peptide was retained. The substitution of methionine with tryptophan or serine resulted in a decrease in the neotropic activity. The substitution of methionine with glycine, threonine, or alanine caused a complete loss of the neotropic activity of the peptide. Therefore, the amino acid residue located at position 1 of the heptapeptide analogue semax, plays a key role in retaining the neotropic effects of the peptide and determines the degree of their expression.

  18. Semax, an analog of ACTH(4-10) with cognitive effects, regulates BDNF and trkB expression in the rat hippocampus.

    PubMed

    Dolotov, Oleg V; Karpenko, Ekaterina A; Inozemtseva, Lyudmila S; Seredenina, Tamara S; Levitskaya, Natalia G; Rozyczka, Joanna; Dubynina, Elena V; Novosadova, Ekaterina V; Andreeva, Lyudmila A; Alfeeva, Lyudmila Yu; Kamensky, Andrey A; Grivennikov, Igor A; Myasoedov, Nikolay F; Engele, Jürgen

    2006-10-30

    The heptapeptide Semax (Met-Glu-His-Phe-Pro-Gly-Pro) is an analog of the adrenocorticotropin fragment (4-10) which after intranasal application has profound effects on learning and exerts marked neuroprotective activities. Here, we found that a single application of Semax (50 microg/kg body weight) results in a maximal 1.4-fold increase of BDNF protein levels accompanying with 1.6-fold increase of trkB tyrosine phosporylation levels, and a 3-fold and a 2-fold increase of exon III BDNF and trkB mRNA levels, respectively, in the rat hippocampus. Semax-treated animals showed a distinct increase in the number of conditioned avoidance reactions. We suggest that Semax affects cognitive brain functions by modulating the expression and the activation of the hippocampal BDNF/trkB system.

  19. First Total Synthesis and Biological Screening of a Proline-Rich Cyclopeptide from a Caribbean Marine Sponge.

    PubMed

    Dahiya, Rajiv; Singh, Sunil; Sharma, Ajay; Chennupati, Suresh V; Maharaj, Sandeep

    2016-12-15

    A natural heptacyclopeptide, stylissamide G (7), previously isolated from the Bahamian marine sponge Stylissa caribica from the Caribbean Sea, was synthesized via coupling of the tetrapeptide l-phenylalanyl-l-prolyl-l-phenylalanyl-l-proline methyl ester with the tripeptide Boc-l-leucyl-l-isoleucyl-l-proline, followed by cyclization of the linear heptapeptide fragment. The structure of the synthesized cyclooligopeptide was confirmed using quantitative elemental analysis, FT-IR, ¹H NMR, (13)C NMR and mass spectrometry. Results of pharmacological activity studies indicated that the newly synthesized cycloheptapeptide displayed good anthelmintic potential against Megascoplex konkanensis, Pontoscotex corethruses and Eudrilus eugeniea at 2 mg/mL and in addition, potent antifungal activity against pathogenic Candida albicans and dermatophytes Trichophyton mentagrophytes and Microsporum audouinii at a concentration of 6 μg/mL.

  20. Harnessing the synthetic capabilities of glycopeptide antibiotic tailoring enzymes: characterization of the UK-68,597 biosynthetic cluster.

    PubMed

    Yim, Grace; Kalan, Lindsay; Koteva, Kalinka; Thaker, Maulik N; Waglechner, Nicholas; Tang, Irene; Wright, Gerard D

    2014-11-24

    In this study, a draft genome sequence of Actinoplanes sp. ATCC 53533 was assembled, and an 81-kb biosynthetic cluster for the unusual sulfated glycopeptide UK-68,597 was identified. Glycopeptide antibiotics are important in the treatment of infections caused by Gram-positive bacteria. Glycopeptides contain heptapeptide backbones that are modified by many tailoring enzymes, including glycosyltransferases, sulfotransferases, methyltransferases, and halogenases, generating extensive chemical and functional diversity. Several tailoring enzymes in the cluster were examined in vitro for their ability to modify glycopeptides, resulting in the synthesis of novel molecules. Tailoring enzymes were also expressed in the producer of the glycopeptide aglycone A47934, generating additional chemical diversity. This work characterizes the biosynthetic program of UK-68,597 and demonstrates the capacity to expand glycopeptide chemical diversity by harnessing the unique chemistry of tailoring enzymes.

  1. Identification of Bacterial Surface Antigens by Screening Peptide Phage Libraries Using Whole Bacteria Cell-Purified Antisera.

    PubMed

    Hu, Yun-Fei; Zhao, Dun; Yu, Xing-Long; Hu, Yu-Li; Li, Run-Cheng; Ge, Meng; Xu, Tian-Qi; Liu, Xiao-Bo; Liao, Hua-Yuan

    2017-01-01

    Bacterial surface proteins can be good vaccine candidates. In the present study, we used polyclonal antibodies purified with intact Erysipelothrix rhusiopthiae to screen phage-displayed random dodecapeptide and loop-constrained heptapeptide libraries, which led to the identification of mimotopes. Homology search of the mimotope sequences against E. rhusiopthiae-encoded ORF sequences revealed 14 new antigens that may localize on the surface of E. rhusiopthiae. When these putative surface proteins were used to immunize mice, 9/11 antigens induced protective immunity. Thus, we have demonstrated that a combination of using the whole bacterial cells to purify antibodies and using the phage-displayed peptide libraries to determine the antigen specificities of the antibodies can lead to the discovery of novel bacterial surface antigens. This can be a general approach for identifying surface antigens for other bacterial species.

  2. Synthesis of a Cytotoxic Amanitin for Biorthogonal Conjugation.

    PubMed

    Zhao, Liang; May, Jonathan P; Blanc, Antoine; Dietrich, David J; Loonchanta, Anastak; Matinkhoo, Kaveh; Pryyma, Alla; Perrin, David M

    2015-07-06

    Alpha-amanitin is an exceedingly toxic, naturally occurring, bicyclic octapeptide that inhibits RNA polymerase and results in cellular and organismal death. Here we report the straightforward synthesis of an amanitin analogue that exhibited near-native toxicity. A pendant alkyne was readily installed to enable copper-catalyzed alkyne-azide cycloaddition (CuAAC) to azido-rhodamine and two azide-bearing versions of the RGD peptide. The fluorescent toxin analogue entered cells and provoked morphological changes consistent with cell death. The latter two conjugates are as toxic as the parent alkyne precursor, which demonstrates that conjugation does not diminish toxicity. In addition, we showed that toxicity depends on a single diastereomer of the unnatural amino acid, dihydroxyisoleucine (DHIle), at position 3. The convenient synthesis of a heptapeptide precursor now provides access to bioactive amanitin analogues that may be readily conjugated to biomolecules of interest. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Peptide inhibitor modified magnetic particles for pepsin separation.

    PubMed

    Filuszová, Michaela; Kucerová, Zdenka; Tichá, Marie

    2009-06-01

    Synthetic heptapeptide containing D-amino acid residues (Val-D-Leu-Pro-Phe-Phe-Val-D-Leu) was coupled to glyoxal-activated magnetic agarose particles via the free peptide amino group. The peptide-modified magnetic particles were used for the separation of pepsins. Porcine pepsin A and human pepsin A were adsorbed to the magnetic peptide-modified affinity carrier, while the rat pepsin C and human pepsin C did not interact with the immobilized ligand. Conditions of pepsin adsorption to peptide-modified magnetic particles, as well as elution buffers were optimized. Porcine pepsin A did not interact with the immobilized peptide in the presence of pepsin inhibitor pepstatin A, indicating that the enzyme binding site is involved in the studied interaction. The elaborated method represents a rapid and simple technique not only for the separation of pepsins but also, in combination with MS, for the enzyme detection and determination.

  4. Chromopeptides from phycoerythrocyanin. Structure and linkage of the three bilin groups. [Mastigocladus laminosus; Anabaena variabilis

    SciTech Connect

    Bishop, J.E.; Rapoport, H.; Klotz, A.V.; Chan, C.F.; Glazer, A.N.; Fueglistaller, P.; Zuber, H.

    1987-01-01

    Phycoerythrocyanin carries two covalently attached phycocyanobilin (PCB) groups on the ..beta.. subunit and a phycobiliviolinoid (PXB) group on the ..cap alpha.. subunit. Three distinct bilipeptides were obtained by proteolytic digestion of this protein: Asn-Gln-Ala-Ala-Cys(PCB)-Ile-Arg, Gly-Asp-Cys(PCB)-Ser-Gln, and Cys(PXB)-Val-Arg. Correlation 500-MHz /sup 1/H NMR analyses showed that the heptapeptide and pentapeptide were attached by cysteinyl thioether linkage to the A ring of the PCB moiety. /sup 1/H NMR and mass spectrometry determinations led to structural assignment for the hitherto uncharacterized PXB moiety, with peptide-thioether bonding possible to either ring A or D. Amino acid sequence homologies strongly favor A-ring linkage.

  5. The role of PP2A-associated proteins and signal pathways in microcystin-LR toxicity.

    PubMed

    Liu, Jing; Sun, Yu

    2015-07-02

    Microcystins are a family of monocyclic heptapeptides produced by cyanobacteria during water blooms. Microcystin-LR (MC-LR) is the most common member of this family. Microcystins induce a variety of toxic cellular effects, including oxidative damage, apoptosis, cytoskeletal destabilization, and cancer cell invasion. Recent studies have examined the molecular mechanism of their toxicity. Protein phosphatase 2A (PP2A) is emerging as a critical regulator of the microcystin-induced molecular network. Furthermore, it has been shown that several molecules or signal pathways associated with PP2A play important roles in microcystin-induced toxic effects. This review summarizes the recent research progress of the molecular mechanism and focuses on the role of PP2A in MC-LR toxicity, which will contribute to a better understanding of the mechanism of microcystin toxicity, and will provide biomarkers for toxicity assessment and control.

  6. Regulation of RNA polymerase II activity by CTD phosphorylation and cell cycle control.

    PubMed

    Oelgeschläger, Thomas

    2002-02-01

    The carboxyl-terminal domain (CTD) of the largest subunit of mammalian RNA polymerase II (RNAP II) consists of 52 repeats of a consensus heptapeptide and is subject to phosphorylation and dephosphorylation events during each round of transcription. RNAP II activity is regulated during the cell cycle and cell cycle-dependend changes in RNAP II activity correlate well with CTD phosphorylation. In addition, global changes in the CTD phosphorylation status are observed in response to mitogenic or cytostatic signals such as growth factors, mitogens and DNA-damaging agents. Several CTD kinases are members of the cyclin-dependent kinase (CDK) superfamily and associate with transcription initiation complexes. Other CTD kinases implicated in cell cycle regulation include the mitogen-activated protein kinases ERK-1/2 and the c-Abl tyrosine kinase. These observations suggest that reversible RNAP II CTD phosphorylation may play a key role in linking cell cycle regulatory events to coordinated changes in transcription.

  7. [Nootropic and analgesic effects of Semax following different routes of administration].

    PubMed

    Manchenko, D M; Glazova, N Iu; Levitskaia, N G; Andreeva, L A; Kamenskiĭ, A A; Miasoedov, N F

    2010-10-01

    Heptapeptide Semax (MEHFPGP) is the fragment of ACTH(4-10) analogue with prolonged neurotropic activity. The aim of the present work was to study the Semax effects on learning capability and pain sensitivity in white rats following intraperitoneal and intranasal administration in different doses. Semax nootropic effects were studied in the test of acquisition of passive avoidance task. Pain sensitivity was estimated in Randall-Selitto paw-withdrawal test. It was shown that Semax exerts nootropic and analgesic activities following intraperitoneal administration. Analysis of dependence of these effects on dose resulted in different dose-response curves. Following intranasal administration, Semax was more potent in learning improvement compared to intraperitoneal administration. The peptide failed to affect the animal pain sensitivity following intranasal administration as opposed to intraperitoneal administration. The data obtained suggest different mechanisms and brain structures involved in realization of the nootropic and analgesic effects of Semax.

  8. Sub-lethal cadmium exposure increases phytochelatin concentrations in the aquatic snail Lymnaea stagnalis.

    PubMed

    Sf, Gonçalves; Sk, Davies; Bennett, M; Raab, A; Feldmann, J; Kille, P; Loureiro, S; Dj, Spurgeon; Jg, Bundy

    2016-10-15

    Phytochelatins are metal-binding metabolites found in almost all plant species and some animal groups, including nematodes and annelids, where they can play an important role in detoxifying metals such as cadmium. Species from several other taxa contain a phytochelatin synthase (PCS) gene orthologue, including molluscs, indicating they may have the potential to synthesize phytochelatins. However, the presence of a gene alone does not demonstrate that it plays a functional role in metal detoxification. In the present study, we show that the aquatic snail Lymnaea stagnalis produced both penta- and heptapeptide phytochelatins (i.e. phytochelatin-2 and phytochelatin-3), and their levels increased in response to sub-lethal levels of cadmium. Copyright © 2016. Published by Elsevier B.V.

  9. The primary structure of the aridicin aglycon as revealed by long-range J values

    NASA Astrophysics Data System (ADS)

    Mueller, Luciano; Jeffs, Peter W.

    The aglycon of aridicin, which is a member of the vancomycin class of antibiotics, was analyzed by utilizing J spin-spin interactions in two-dimensional NMR experiments.This unusual heptapeptide with the molecular formula C 59H 45N 7O 19Cl 4 (MW 1296.160) has a large number of quateernary carbons in aromatic side chains. For that reason most information was obtained from delayed COSY and COLOC spectra which reveal homo- and heteronuclear connectivities via long-range J couplings. The carbon-13 spectrum was assigned completely. In addition, the primary structure of the aridicin aglycon could be deduced, with the exception of the ether linkages between the side chains A, B, and C, by solely relying on J-connectivity maps.

  10. [Synthesis of [1,6-bis(L-alpha, beta-diaminopropionic acid) oxytocin].

    PubMed

    Wu, Kaiqun; Weng, Lingling; Zheng, Hu

    2006-08-01

    A novel derivative of oxytocin containing nonprotein amino acid L-alpha, beta-diaminopropionic acid (L-Dap) was synthesized by 7+2 fragment combination in solution. N beta of all the amino acid necessary was protected by carbobenzoxy (Z) and N beta of L-Dap was protected by tert. -butoxycarbonyl (Boc) . The important intermediate, heptapeptide, was synthesized by the stepwise elongation method using carbobenzoxy amino acid p-nitrophenyl esters in solution. Azide synthesis was used to get the nonapeptide. Z group was removed by treatment with 5% Pd/C and Boc with CF3COOH. Eight new compounds incorporating L-Dap were obtained and confirmed by the amino acid analysis and mass spectral detection.

  11. Identification of Bacterial Surface Antigens by Screening Peptide Phage Libraries Using Whole Bacteria Cell-Purified Antisera

    PubMed Central

    Hu, Yun-Fei; Zhao, Dun; Yu, Xing-Long; Hu, Yu-Li; Li, Run-Cheng; Ge, Meng; Xu, Tian-Qi; Liu, Xiao-Bo; Liao, Hua-Yuan

    2017-01-01

    Bacterial surface proteins can be good vaccine candidates. In the present study, we used polyclonal antibodies purified with intact Erysipelothrix rhusiopthiae to screen phage-displayed random dodecapeptide and loop-constrained heptapeptide libraries, which led to the identification of mimotopes. Homology search of the mimotope sequences against E. rhusiopthiae-encoded ORF sequences revealed 14 new antigens that may localize on the surface of E. rhusiopthiae. When these putative surface proteins were used to immunize mice, 9/11 antigens induced protective immunity. Thus, we have demonstrated that a combination of using the whole bacterial cells to purify antibodies and using the phage-displayed peptide libraries to determine the antigen specificities of the antibodies can lead to the discovery of novel bacterial surface antigens. This can be a general approach for identifying surface antigens for other bacterial species. PMID:28184219

  12. Antibiotics GE23077, novel inhibitors of bacterial RNA polymerase. Part 3: Chemical derivatization.

    PubMed

    Mariani, Riccardo; Granata, Giorgio; Maffioli, Sonia I; Serina, Stefania; Brunati, Cristina; Sosio, Margherita; Marazzi, Alessandra; Vannini, Alfredo; Patel, Dinesh; White, Richard; Ciabatti, Romeo

    2005-08-15

    GE23077 is a novel RNA polymerase inhibitor that is isolated from the fermentation broth of an Actinomadura sp. It is a cyclic heptapeptide complex made up of four factors, differing in the structure of acyl group connected to the side chain of an alpha,beta-diaminopropanoic acid moiety and in the configuration of the stereocenter of an alpha-amino-malonic acid residue. Although GE23077 shows strong inhibitory activity on both Rifampicin-sensitive and -resistant polymerases, it exhibits poor antimicrobial activity. The most reasonable explanation for this property has been based on the lack of penetration of the molecule across the bacterial membrane, owing to its strong hydrophilic character. To improve penetration, several parts of the molecule were accordingly modified with the aim of altering the physico-chemical properties of GE23077. The current SAR study has identified moieties important for RNA polymerase activity.

  13. First Total Synthesis and Biological Screening of a Proline-Rich Cyclopeptide from a Caribbean Marine Sponge

    PubMed Central

    Dahiya, Rajiv; Singh, Sunil; Sharma, Ajay; Chennupati, Suresh V.; Maharaj, Sandeep

    2016-01-01

    A natural heptacyclopeptide, stylissamide G (7), previously isolated from the Bahamian marine sponge Stylissa caribica from the Caribbean Sea, was synthesized via coupling of the tetrapeptide l-phenylalanyl-l-prolyl-l-phenylalanyl-l-proline methyl ester with the tripeptide Boc-l-leucyl-l-isoleucyl-l-proline, followed by cyclization of the linear heptapeptide fragment. The structure of the synthesized cyclooligopeptide was confirmed using quantitative elemental analysis, FT-IR, 1H NMR, 13C NMR and mass spectrometry. Results of pharmacological activity studies indicated that the newly synthesized cycloheptapeptide displayed good anthelmintic potential against Megascoplex konkanensis, Pontoscotex corethruses and Eudrilus eugeniea at 2 mg/mL and in addition, potent antifungal activity against pathogenic Candida albicans and dermatophytes Trichophyton mentagrophytes and Microsporum audouinii at a concentration of 6 μg/mL. PMID:27983681

  14. Isolation of a highly specific ligand for the alpha 5 beta 1 integrin from a phage display library

    PubMed Central

    1994-01-01

    Our previous studies showed that the alpha 5 beta 1 integrin selects cysteine pair-containing RGD peptides from a phage display library based on a random hexapeptide. We have therefore searched for more selective peptides for this integrin using a larger phage display library, where heptapeptides are flanked by cysteine residues, thus making the inserts potentially cyclic. Most of the phage sequences that bound to alpha 5 beta 1 (69 of 125) contained the RGD motif. Some of the heptapeptides contained an NGR motif. As the NGR sequence occurs in the cell-binding region of the fibronectin molecule, this sequence could contribute to the specific recognition of fibronectin by alpha 5 beta 1. Selection for high affinity peptides for alpha 5 beta 1 surprisingly yielded a sequence RRETAWA that does not bear obvious resemblance to known integrin ligand sequences. The synthetic cyclic peptide GACRRETAWACGA (*CRRETAWAC*) was a potent inhibitor of alpha 5 beta 1-mediated cell attachment to fibronectin. This peptide is nearly specific for the alpha 5 beta 1 integrin, because much higher concentrations were needed to inhibit the alpha v beta 1 integrin, and there was no effect on alpha v beta 3- and alpha v beta 5-mediated cell attachment to vitronectin. The peptide also did not bind to the alpha IIb beta 3 integrin. *CRRETAWAC* appears to interact with the same or an overlapping binding site in alpha 5 beta 1 as RGD, because cell attachment to *CRRETAWAC* coated on plastic was divalent cation dependent and could be blocked by an RGD-containing peptide. These results reveal a novel binding specificity in the alpha 5 beta 1 integrin. PMID:7507494

  15. Systemic co-delivery of doxorubicin and siRNA using nanoparticles conjugated with EGFR-specific targeting peptide to enhance chemotherapy in ovarian tumor bearing mice

    NASA Astrophysics Data System (ADS)

    Liu, C. W.; Lin, W. J.

    2013-10-01

    This aim of this study was to develop peptide-conjugated nanoparticles (NPs) for systemic co-delivery of siRNA and doxorubicin to enhance chemotherapy in epidermal growth factor receptor (EGFR) high-expressed ovarian tumor bearing mice. The active targeting NPs were prepared using heptapeptide-conjugated poly( d, l-lactic-co-glycolic acid)-poly(ethylene glycol). The particle sizes of peptide-free and peptide-conjugated NPs were 159.3 ± 32.5 and 184.0 ± 52.9 nm, respectively, with zeta potential -21.3 ± 3.8 and -15.3 ± 2.8 mV. The peptide-conjugated NPs uptake were more efficient in EGFR high-expressed SKOV3 cells than in EGFR low-expressed HepG2 cells due to heptapeptide specificity. The NPs were used to deliver small molecule anticancer drug (e.g., doxorubicin) and large molecule genetic agent (e.g., siRNA). The IC50 of doxorubicin-loaded peptide-conjugated NPs (0.09 ± 0.06 μM) was significantly lower than peptide-free NPs (5.72 ± 2.64 μM). The similar result was observed in siRNA-loaded NPs. The peptide-conjugated NPs not only served as a nanocarrier to efficiently deliver doxorubicin and siRNA to EGFR high-expressed ovarian cancer cells but also increased the intracellular accumulation of the therapeutic agents to induce assured anti-tumor growth effect in vivo.

  16. NMR studies of the stable mismatch purine-thymine in the self-complementary d(CGPuAATTTCG) duplex in solution

    SciTech Connect

    Ikuta, S.; Eritja, R.; Kaplan, B.E.; Itakura, K.

    1987-09-08

    One- and two-dimensional nuclear Overhauser effect experiments demonstrate that a single hydrogen bond between a T imino proton and purine N3 is sufficient to hold the base pair dPu-dT in d(CGPuAATTTCG) by a Watson-Crick fashion rather than a Hoogsteen type. In addition, the dPu-dT base pair is well stacked with neighboring base pairs. The spin-lattice relaxation measurements at 30 and 35/sup 0/C of two decamers, d(CGPuAATTTCG) and d(CGAAATTTCG), reveal that the elimination of two single hydrogen bonds of dA-dT base pairs (due to the substitution of adenine for purine) in the sequence results in an increase in the overall imino proton exchange rate from 7 to 36 s/sup -1/ at the site of mismatch.

  17. Glutamine synthetase isoforms in nitrogen-fixing soybean nodules: distinct oligomeric structures and thiol-based regulation.

    PubMed

    Masalkar, Pintu D; Roberts, Daniel M

    2015-01-16

    Legume root nodule glutamine synthetase (GS) catalyzes the assimilation of ammonia produced by nitrogen fixation. Two GS isoform subtypes (GS1β and GS1γ) are present in soybean nodules. GS1γ isoforms differ from GS1β isoforms in terms of their susceptibility to reversible inhibition by intersubunit disulfide bond formation between C159 and C92 at the shared active site at subunit interfaces. Although nodule GS enzymes share 86% amino acid sequence identity, analytical ultracentrifugation experiments showed that GS1γ is a dodecamer, whereas the GS1β is a decamer. It is proposed that this difference contributes to the differential thiol sensitivity of each isoform, and that GS1γ1 may be a target of thiol-based regulation.

  18. Genome relationship among nine species of Millettieae (Leguminosae: Papilionoideae) based on random amplified polymorphic DNA (RAPD).

    PubMed

    Acharya, Laxmikanta; Mukherjee, Arup Kumar; Panda, Pratap Chandra

    2004-01-01

    Random amplified polymorphic DNA (RAPD) marker was used to establish intergeneric classification and phylogeny of the tribe Millettieae sensu Geesink (1984) (Leguminosae: Papilionoideae) and to assess genetic relationship between 9 constituent species belonging to 5 traditionally recognized genera under the tribe. DNA from pooled leaf samples was isolated and RAPD analysis performed using 25 decamer primers. The genetic similarities were derived from the dendrogram constructed by the pooled RAPD data using a similarity index, which supported clear grouping of species under their respective genera, inter- and intra-generic classification and phylogeny and also merger of Pongamia with Millettia. Elevation of Tephrosia purpurea var. pumila to the rank of a species (T. pumila) based on morphological characteristics is also supported through this study of molecular markers.

  19. Observation of two new L4 Neptune Trojans in the Dark Energy Survey supernova fields

    SciTech Connect

    Gerdes, D. W.

    2016-01-28

    We report the discovery of the eighth and ninth known Trojans in stable orbits around Neptune's leading Lagrange point, L4. The objects 2014 QO441 and 2014 QP441 were detected in data obtained during the 2013-14 and 2014-15 observing seasons by the Dark Energy Survey, using the Dark Energy Camera (DECam) on the 4-meter Blanco telescope at Cerro Tololo Inter- American Observatory. Both are in high-inclination orbits (18.8° and 19.4° respectively). Furthermore, with an eccentricity of 0.104, 2014 QO441 has the most eccentric orbit of the eleven known stable Neptune Trojans. We describe the search procedure and investigate the objects' long-term dynamical stability and physical properties.

  20. The Crystal Structure of the Escherichia coli Autoinducer-2 Processing Protein LsrF

    SciTech Connect

    Diaz, Z.; Xavier, K; Miller, S

    2009-01-01

    Many bacteria produce and respond to the quorum sensing signal autoinducer-2 (AI-2). Escherichia coli and Salmonella typhimurium are among the species with the lsr operon, an operon containing AI-2 transport and processing genes that are up regulated in response to AI-2. One of the Lsr proteins, LsrF, has been implicated in processing the phosphorylated form of AI-2. Here, we present the structure of LsrF, unliganded and in complex with two phospho-AI-2 analogues, ribose-5-phosphate and ribulose-5-phosphate. The crystal structure shows that LsrF is a decamer of (??)8-barrels that exhibit a previously unseen N-terminal domain swap and have high structural homology with aldolases that process phosphorylated sugars. Ligand binding sites and key catalytic residues are structurally conserved, strongly implicating LsrF as a class I aldolase.

  1. Observation of two new L4 Neptune Trojans in the Dark Energy Survey supernova fields

    DOE PAGES

    Gerdes, D. W.

    2016-01-28

    We report the discovery of the eighth and ninth known Trojans in stable orbits around Neptune's leading Lagrange point, L4. The objects 2014 QO441 and 2014 QP441 were detected in data obtained during the 2013-14 and 2014-15 observing seasons by the Dark Energy Survey, using the Dark Energy Camera (DECam) on the 4-meter Blanco telescope at Cerro Tololo Inter- American Observatory. Both are in high-inclination orbits (18.8° and 19.4° respectively). Furthermore, with an eccentricity of 0.104, 2014 QO441 has the most eccentric orbit of the eleven known stable Neptune Trojans. We describe the search procedure and investigate the objects' long-termmore » dynamical stability and physical properties.« less

  2. DNA binding studies of Vinca alkaloids: experimental and computational evidence.

    PubMed

    Pandya, Prateek; Gupta, Surendra P; Pandav, Kumud; Barthwal, Ritu; Jayaram, B; Kumar, Surat

    2012-03-01

    Fluorescence studies on the indole alkaloids vinblastine sulfate, vincristine sulfate, vincamine and catharanthine have demonstrated the DNA binding ability of these molecules. The binding mode of these molecules in the minor groove of DNA is non-specific. A new parameter of the purine-pyrimidine base sequence specificty was observed in order to define the non-specific DNA binding of ligands. Catharanthine had shown 'same' pattern of 'Pu-Py' specificity while evaluating its DNA binding profile. The proton resonances of a DNA decamer duplex were assigned. The models of the drug:DNA complexes were analyzed for DNA binding features. The effect of temperature on the DNA binding was also evaluated.

  3. Tidal Tails around the Outer Halo Globular Clusters Eridanus and Palomar 15

    NASA Astrophysics Data System (ADS)

    Myeong, G. C.; Jerjen, Helmut; Mackey, Dougal; Da Costa, Gary S.

    2017-05-01

    We report the discovery of tidal tails around the two outer halo globular clusters, Eridanus and Palomar 15, based on gi-band images obtained with DECam at the CTIO 4 m Blanco Telescope. The tidal tails are among the most remote stellar streams currently known in the Milky Way halo. Cluster members have been determined from the color-magnitude diagrams and used to establish the radial density profiles, which show, in both cases, a strong departure in the outer regions from the best-fit King profile. Spatial density maps reveal tidal tails stretching out on opposite sides of both clusters, extending over a length of ˜760 pc for Eridanus and ˜1160 pc for Palomar 15. The great circle projected from the Palomar 15 tidal tails encompasses the Galactic Center, while that for Eridanus passes close to four dwarf satellite galaxies, one of which (Sculptor) is at a comparable distance to that of Eridanus.

  4. Variable Stars in the Field of the Hydra II Ultra-Faint Dwarf Galaxy

    NASA Astrophysics Data System (ADS)

    Vivas, Anna Katherina; Olsen, Knut A.; Blum, Robert D.; Nidever, David L.; Walker, Alistair R.; Martin, Nicolas; Besla, Gurtina; Gallart, Carme; Van Der Marel, Roeland P.; Majewski, Steven R.; Munoz, Ricardo; Kaleida, Catherine C.; Saha, Abhijit; Conn, Blair; Jin, Shoko

    2016-06-01

    We searched for variable stars in Hydra II, one of the recently discovered ultra-faint dwarf satellites of the Milky Way, using gri time-series obtained with the Dark Energy Camera (DECam) at Cerro Tololo Inter-American Observatory, Chile. We discovered one RR Lyrae star in the galaxy which was used to derive a distance of 154±8 kpc to this system and to re-calculate its absolute magnitude and half-light radius.A comparison with other RR Lyrae stars in ultra-faint systems indicates similar pulsational properties among them, which are different to those found among halo field stars and those in the largest of the Milky Way satellites. We also report the discovery of 31 additional short period variables in the field of view (RR Lyrae, SX Phe, eclipsing binaries, and a likely anomalous cepheid) which are likely not related with Hydra II.

  5. Crystal Structure of the 3.8-MDa Respiratory Supermolecule Hemocyanin at 3.0 Å Resolution.

    PubMed

    Gai, Zuoqi; Matsuno, Asuka; Kato, Koji; Kato, Sanae; Khan, Md Rafiqul Islam; Shimizu, Takeshi; Yoshioka, Takeya; Kato, Yuki; Kishimura, Hideki; Kanno, Gaku; Miyabe, Yoshikatsu; Terada, Tohru; Tanaka, Yoshikazu; Yao, Min

    2015-12-01

    Molluscan hemocyanin, a copper-containing oxygen transporter, is one of the largest known proteins. Although molluscan hemocyanins are currently applied as immunotherapeutic agents, their precise structure has not been determined because of their enormous size. Here, we have determined the first X-ray crystal structure of intact molluscan hemocyanin. The structure unveiled the architecture of the 3.8-MDa supermolecule composed of homologous functional units (FUs), wherein the dimers of FUs hierarchically associated to form the entire cylindrical decamer. Most of the specific inter-FU interactions were localized at narrow regions in the FU dimers, suggesting that rigid FU dimers formed by specific interactions assemble with flexibility. Furthermore, the roles of carbohydrates in assembly and allosteric effect, and conserved sulfur-containing residues in copper incorporation, were revealed. The precise structural information obtained in this study will accelerate our understanding of the molecular basis of hemocyanin and its future applications.

  6. The Blanco Telescope and its instruments: a status report

    NASA Astrophysics Data System (ADS)

    Abbott, Timothy M. C.; Walker, Alistair R.; Points, Sean D.; James, David J.; Gregory, Brooke; Tighe, Roberto; David, Nicole; Parkes, Esteban; Cantarutti, Rolando; Warner, Michael; Estay, Omar; Martínez, Manuel; Bonati, Marco; Bustos, Edison; Montané, Andrés.; Muñoz, Freddy; Schurter, Patricio

    2016-07-01

    In recent years the V. M. Blanco 4-m telescope at Cerro Tololo Inter-American Observatory (CTIO) has been renovated for use as a platform for a completely new suite of instruments: DECam, a 520-megapixel optical imager, COSMOS, a multi-object optical imaging spectrograph, and ARCoIRIS, a near-infrared imaging spectrograph. This has had considerable impact, both internally to CTIO and for its wider community of observers. In this paper, we report on the performance of the renovated facility, ongoing improvements, lessons learned during the deployment of the new instruments, how practical operations have adapted to them, unexpected phenomena and subsequent responses. We conclude by discussing the role for the Blanco telescope in the era of LSST and the new generation of extremely large telescopes.

  7. Method for high-volume sequencing of nucleic acids: random and directed priming with libraries of oligonucleotides

    DOEpatents

    Studier, F. William

    1995-04-18

    Random and directed priming methods for determining nucleotide sequences by enzymatic sequencing techniques, using libraries of primers of lengths 8, 9 or 10 bases, are disclosed. These methods permit direct sequencing of nucleic acids as large as 45,000 base pairs or larger without the necessity for subcloning. Individual primers are used repeatedly to prime sequence reactions in many different nucleic acid molecules. Libraries containing as few as 10,000 octamers, 14,200 nonamers, or 44,000 decamers would have the capacity to determine the sequence of almost any cosmid DNA. Random priming with a fixed set of primers from a smaller library can also be used to initiate the sequencing of individual nucleic acid molecules, with the sequence being completed by directed priming with primers from the library. In contrast to random cloning techniques, a combined random and directed priming strategy is far more efficient.

  8. Genomic relations among 31 species of Mammillaria haworth (Cactaceae) using random amplified polymorphic DNA.

    PubMed

    Mattagajasingh, Ilwola; Mukherjee, Arup Kumar; Das, Premananda

    2006-01-01

    Thirty-one species of Mammillaria were selected to study the molecular phylogeny using random amplified polymorphic DNA (RAPD) markers. High amount of mucilage (gelling polysaccharides) present in Mammillaria was a major obstacle in isolating good quality genomic DNA. The CTAB (cetyl trimethyl ammonium bromide) method was modified to obtain good quality genomic DNA. Twenty-two random decamer primers resulted in 621 bands, all of which were polymorphic. The similarity matrix value varied from 0.109 to 0.622 indicating wide variability among the studied species. The dendrogram obtained from the unweighted pair group method using arithmetic averages (UPGMA) analysis revealed that some of the species did not follow the conventional classification. The present work shows the usefulness of RAPD markers for genetic characterization to establish phylogenetic relations among Mammillaria species.

  9. A Radiometric All-Sky Infrared Camera (RASICAM) for DES/CTIO

    SciTech Connect

    Lewis, Peter M.; Rogers, Howard; Schindler, Rafe H.; /SLAC

    2010-08-25

    A novel radiometric all-sky infrared camera [RASICAM] has been constructed to allow automated real-time quantitative assessment of night sky conditions for the Dark Energy Camera [DECam] located on the Blanco Telescope at the Cerro Tololo Inter-American Observatory in Chile. The camera is optimized to detect the position, motion and optical depth of thin, high (8-10km) cirrus clouds and contrails by measuring their apparent temperature above the night sky background. The camera system utilizes a novel wide-field equiresolution catadioptic mirror system that provides sky coverage of 2{pi} azimuth and 14-90{sup o} from zenith. Several new technological and design innovations allow the RASICAM system to provide unprecedented cloud detection and IR-based photometricity quantification. The design of the RASICAM system is presented.

  10. Investigation of Reddening in Fields of the SMASH Survey

    NASA Astrophysics Data System (ADS)

    Juelfs, Elizabeth A.; Olsen, Knut A.; SMASH Team

    2016-01-01

    We present dust extinction maps derived from eight fields in the Survey of the MAgellanic Stellar History (SMASH), a survey that is imaging 480 deg^2 of the southern sky in DES-ugriz with the CTIO 4-m Blanco telescope and the Dark Energy Camera (DECam). We derive the extinction due to dust using fits to the stellar locus of stars brighter than g=21 in color-color diagrams, and explore the spatial distribution of the extinction within each of the fields. We compare our results to the extinction map of Schlegel, Finkbeiner, & Davis (1998), and find generally good agreement. We describe plans to measure the three-dimensional distribution of extinction in these fields using fainter stars and background galaxies as tracers. Juelfs was supported by the NOAO/KPNO Research Experiences for Undergraduates (REU) Program which is funded by the National Science Foundation Research Experiences for Undergraduates Program (AST-1262829).

  11. Sampling saddle points on the free energy surface

    NASA Astrophysics Data System (ADS)

    Samanta, Amit

    2014-03-01

    We develop an algorithm for finding the saddle points on the free energy surface ``on-the-fly'' without having to find the free energy function itself. This is done by using the general strategy of the heterogeneous multi-scale method, applying a macro-scale solver, here the gentlest ascent dynamics algorithm, with the needed force and Hessian values computed on-the-fly using a micro-scale model such as molecular dynamics. The algorithm is capable of dealing with problems involving many coarse-grained variables. The utility of the algorithm is illustrated by studying the saddle points associated with (a) the isomerization transition of the alanine dipeptide using two coarse-grained variables, specifically the Ramachandran dihedral angles, and (b) the beta-hairpin structure of the alanine decamer using twenty coarse-grained variables, specifically the full set of Ramachandran angle pairs associated with each residue.

  12. The DES Science Verification Weak Lensing Shear Catalogs

    SciTech Connect

    Jarvis, M.

    2016-05-01

    We present weak lensing shear catalogs for 139 square degrees of data taken during the Science Verification (SV) time for the new Dark Energy Camera (DECam) being used for the Dark Energy Survey (DES). We describe our object selection, point spread function estimation and shear measurement procedures using two independent shear pipelines, IM3SHAPE and NGMIX, which produce catalogs of 2.12 million and 3.44 million galaxies respectively. We also detail a set of null tests for the shear measurements and find that they pass the requirements for systematic errors at the level necessary for weak lensing science applications using the SV data. Furthermore, we discuss some of the planned algorithmic improvements that will be necessary to produce sufficiently accurate shear catalogs for the full 5-year DES, which is expected to cover 5000 square degrees.

  13. The DES Science Verification Weak Lensing Shear Catalogs

    DOE PAGES

    Jarvis, M.

    2016-05-01

    We present weak lensing shear catalogs for 139 square degrees of data taken during the Science Verification (SV) time for the new Dark Energy Camera (DECam) being used for the Dark Energy Survey (DES). We describe our object selection, point spread function estimation and shear measurement procedures using two independent shear pipelines, IM3SHAPE and NGMIX, which produce catalogs of 2.12 million and 3.44 million galaxies respectively. We also detail a set of null tests for the shear measurements and find that they pass the requirements for systematic errors at the level necessary for weak lensing science applications using the SVmore » data. Furthermore, we discuss some of the planned algorithmic improvements that will be necessary to produce sufficiently accurate shear catalogs for the full 5-year DES, which is expected to cover 5000 square degrees.« less

  14. Genomic fingerprinting of "Haemophilus somnus" isolates by using a random-amplified polymorphic DNA assay.

    PubMed Central

    Myers, L E; Silva, S V; Procunier, J D; Little, P B

    1993-01-01

    The random-amplified polymorphic DNA (RAPD) assay was used to generate DNA fingerprints for 16 isolates of "Haemophilus somnus," and one isolate each of "Haemophilus agni," "Histophilus ovis," "Actinobacillus seminis," Pasteurella haemolytica, and Escherichia coli. The RAPD assay differentiated among "H. somnus" isolates, which shared similarity coefficients of 0.46 to 1.00 on the basis of pairwise comparisons of RAPD markers produced with nine random decamer primers. Three virulent encephalitic "H. somnus" isolates exhibited identical banding patterns, suggesting a common clonal ancestry. The RAPD assay clearly distinguished between the "H. somnus"-"H. agni"-"H. ovis" group and the other bacterial species tested. The results of the present study suggest that DNA fingerprinting of "H. somnus" isolates by the RAPD assay could be valuable in revealing subspecific divisions within this largely unexplored species. Images PMID:8458944

  15. The DES Science Verification weak lensing shear catalogues

    NASA Astrophysics Data System (ADS)

    Jarvis, M.; Sheldon, E.; Zuntz, J.; Kacprzak, T.; Bridle, S. L.; Amara, A.; Armstrong, R.; Becker, M. R.; Bernstein, G. M.; Bonnett, C.; Chang, C.; Das, R.; Dietrich, J. P.; Drlica-Wagner, A.; Eifler, T. F.; Gangkofner, C.; Gruen, D.; Hirsch, M.; Huff, E. M.; Jain, B.; Kent, S.; Kirk, D.; MacCrann, N.; Melchior, P.; Plazas, A. A.; Refregier, A.; Rowe, B.; Rykoff, E. S.; Samuroff, S.; Sánchez, C.; Suchyta, E.; Troxel, M. A.; Vikram, V.; Abbott, T.; Abdalla, F. B.; Allam, S.; Annis, J.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Capozzi, D.; Carnero Rosell, A.; Carrasco Kind, M.; Carretero, J.; Castander, F. J.; Clampitt, J.; Crocce, M.; Cunha, C. E.; D'Andrea, C. B.; da Costa, L. N.; DePoy, D. L.; Desai, S.; Diehl, H. T.; Doel, P.; Fausti Neto, A.; Flaugher, B.; Fosalba, P.; Frieman, J.; Gaztanaga, E.; Gerdes, D. W.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; James, D. J.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Li, T. S.; Lima, M.; March, M.; Martini, P.; Miquel, R.; Mohr, J. J.; Neilsen, E.; Nord, B.; Ogando, R.; Reil, K.; Romer, A. K.; Roodman, A.; Sako, M.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Swanson, M. E. C.; Tarle, G.; Thaler, J.; Thomas, D.; Walker, A. R.; Wechsler, R. H.

    2016-08-01

    We present weak lensing shear catalogues for 139 square degrees of data taken during the Science Verification (SV) time for the new Dark Energy Camera (DECam) being used for the Dark Energy Survey (DES). We describe our object selection, point spread function estimation and shear measurement procedures using two independent shear pipelines, IM3SHAPE and NGMIX, which produce catalogues of 2.12 million and 3.44 million galaxies, respectively. We detail a set of null tests for the shear measurements and find that they pass the requirements for systematic errors at the level necessary for weak lensing science applications using the SV data. We also discuss some of the planned algorithmic improvements that will be necessary to produce sufficiently accurate shear catalogues for the full 5-yr DES, which is expected to cover 5000 square degrees.

  16. Observation of Two New L4 Neptune Trojans in the Dark Energy Survey Supernova Fields

    NASA Astrophysics Data System (ADS)

    Gerdes, D. W.; Jennings, R. J.; Bernstein, G. M.; Sako, M.; Adams, F.; Goldstein, D.; Kessler, R.; Hamilton, S.; Abbott, T.; Abdalla, F. B.; Allam, S.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Capozzi, D.; Carnero Rosell, A.; Carrasco Kind, M.; Carretero, J.; Cunha, C. E.; D'Andrea, C. B.; da Costa, L. N.; DePoy, D. L.; Desai, S.; Dietrich, J. P.; Doel, P.; Eifler, T. F.; Fausti Neto, A.; Flaugher, B.; Frieman, J.; Gaztanaga, E.; Gruen, D.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; James, D. J.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Li, T. S.; Maia, M. A. G.; March, M.; Martini, P.; Miller, C. J.; Miquel, R.; Nichol, R. C.; Nord, B.; Ogando, R.; Plazas, A. A.; Romer, A. K.; Roodman, A.; Sanchez, E.; Santiago, B.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarlé, G.; Thaler, J.; Walker, A. R.; Wester, W.; Zhang, Y.; DES Collaboration

    2016-02-01

    We report the discovery of the eighth and ninth known Trojans in stable orbits around Neptune’s leading Lagrange point, L4. The objects 2014 QO441 and 2014 QP441 were detected in data obtained during the 2013-14 and 2014-15 observing seasons by the Dark Energy Survey, using the Dark Energy Camera (DECam) on the 4-m Blanco telescope at Cerro Tololo Inter-American Observatory. Both are in high-inclination orbits (18.°8 and 19.°4, respectively). With an eccentricity of 0.104, 2014 QO441 has the most eccentric orbit of the 11 known stable Neptune Trojans. Here we describe the search procedure and investigate the objects’ long-term dynamical stability and physical properties.

  17. High-Molecular-Weight Proanthocyanidins in Foods: Overcoming Analytical Challenges in Pursuit of Novel Dietary Bioactive Components.

    PubMed

    Neilson, Andrew P; O'Keefe, Sean F; Bolling, Bradley W

    2016-01-01

    Proanthocyanidins (PACs) are an abundant but complex class of polyphenols found in foods and botanicals. PACs are polymeric flavanols with a variety of linkages and subunits. Connectivity and degree of polymerization (DP) determine PAC bioavailability and bioactivity. Current quantitative and qualitative methods may ignore a large percentage of dietary PACs. Subsequent correlations between intake and activity are hindered by a lack of understanding of the true PAC complexity in many foods. Additionally, estimates of dietary intakes are likely inaccurate, as nutrient databank values are largely based on standards from cocoa (monomers to decamers) and blueberries (mean DP of 36). Improved analytical methodologies are needed to increase our understanding of the biological roles of these complex compounds.

  18. Detection of a possible superluminous supernova in the epoch of reionization

    NASA Astrophysics Data System (ADS)

    Mould, Jeremy; Abbott, Tim; Cooke, Jeff; Curtin, Chris; Katsiani, Antonios; Koekemoer, Anton; Tescari, Edoardo; Uddin, Syed; Wang, Lifan; Wyithe, Stuaet

    2017-04-01

    An interesting transient has been detected in one of our three Dark Energy Camera deep fields. Observations of these deep fields take advantage of the high red sensitivity of DECam on the Cerro Tololo Interamerican Observatory Blanco telescope. The survey includes the Y band with rest wavelength 1430{Å} at z = 6. Survey fields (the Prime field 0555-6130, the 16hr field 1600-75 and the SUDSS New Southern Field) are deeper in Y than other infrared surveys. They are circumpolar, allowing all night to be used efficiently, exploiting the moon tolerance of 1 micron observations to minimize conflict with the Dark Energy Survey. As an i-band dropout (meaning that the flux decrement shortward of Lyman alpha is in the i bandpass), the transient we report here is a supernova candidate with z 6, with a luminosity comparable to the brightest known current epoch superluminous supernova (i.e., 2 x 10^11 solar luminosities).

  19. Automated three-dimensional reconstruction of keyhole limpet hemocyanin type 1.

    PubMed

    Mouche, Fabrice; Zhu, Yuanxin; Pulokas, James; Potter, Clinton S; Carragher, Bridget

    2003-12-01

    We have reconstructed a three-dimensional map of keyhole limpet hemocyanin isoform 1 (KLH1), using our automated data collection software, Leginon, integrated with particle selection algorithms, and the SPIDER reconstruction package. KLH1, a 7.9 MDa macromolecule, is an extracellular respiratory pigment composed of two asymmetric decamers, and presents an overall D(5) point-group symmetry. The reconstruction is in agreement with previous data published on molluscan hemocyanins. The reconstructed map (11.3A resolution, 3sigma criterion) was used to fit an available X-ray crystallography structure of Octopus dofleini Odg, solved at 2.3A [J. Mol. Biol. 278 (4) (1998) 855], with satisfactory results. The results validate the approach of automating the cryoEM process and demonstrate that the quality of the images acquired and the particles selected is comparable to those obtained using manual methods. Several problems remain to be solved however before these results can be generalized.

  20. Estimation of genetic diversity Among Turkish kale populations (Brassica oleracea var. acephala L.) using RAPD markers.

    PubMed

    Okumus, A; Balkaya, A

    2007-04-01

    20 populations of kale (B. oleracea var. acephala L.) selected from 127 populations for fresh consumption terms of yield and leaf quality characteristics as superior types using weight-based ranking method from the Black Sea Region of Turkey were evaluated at the DNA level using randomly amplified polymorphic DNA (RAPD) markers compared to some morphological characters. The 7 primers selected from 100 decamers used generated 110 bands, of which 60 (54.5%) were polymorphic. Jaccard's genetic distances were calculated and dendogram was generated using the UPGMA algorithm. The dendogram obtained were classified into three main groups and four subgroups. The accessions showed a limited clustering in compare to morphological characters such as the number of leaf, leaf intentation of the margin, leaf and midrib color and thickness of midrib than geographical characteristics. Leaf color and midrib thickness characters clustered in the same group as OR49 and G18 accessions; S20, G6 and OR37 accessions, respectively.

  1. The Canarias Einstein ring: a newly discovered optical Einstein ring

    NASA Astrophysics Data System (ADS)

    Bettinelli, M.; Simioni, M.; Aparicio, A.; Hidalgo, S. L.; Cassisi, S.; Walker, A. R.; Piotto, G.; Valdes, F.

    2016-09-01

    We report the discovery of an optical Einstein ring in the Sculptor constellation, IAC J010127-334319, in the vicinity of the Sculptor dwarf spheroidal galaxy. It is an almost complete ring (˜300°) with a diameter of ˜4.5 arcsec. The discovery was made serendipitously from inspecting Dark Energy Camera (DECam) archive imaging data. Confirmation of the object nature has been obtained by deriving spectroscopic redshifts for both components, lens and source, from observations at the 10.4 m Gran Telescopio CANARIAS (GTC) with the spectrograph OSIRIS. The lens, a massive early-type galaxy, has a redshift of z = 0.581, while the source is a starburst galaxy with redshift of z = 1.165. The total enclosed mass that produces the lensing effect has been estimated to be Mtot = (1.86 ± 0.23) × 1012 M⊙.

  2. Collaborative Workspaces to Accelerate Discovery

    NASA Astrophysics Data System (ADS)

    Meade, Bernard; Fluke, Christopher; Cooke, Jeff; Andreoni, Igor; Pritchard, Tyler; Curtin, Christopher; Bernard, Stephanie R.; Asher, Albany; Mack, Katherine J.; Murphy, Michael T.; Vohl, Dany; Codoreanu, Alex; Kotuš, Srđan M.; Rumokoy, Fanuel; Horst, Chuck; Reynolds, Tristan

    2017-05-01

    By applying a display ecology to the Deeper, Wider, Faster proactive, simultaneous telescope observing campaign, we have shown a dramatic reduction in the time taken to inspect DECam CCD images for potential transient candidates and to produce time-critical triggers to standby telescopes. We also show how facilitating rapid corroboration of potential candidates and the exclusion of non-candidates improves the accuracy of detection; and establish that a practical and enjoyable workspace can improve the experience of an otherwise taxing task for astronomers. We provide a critical road test of two advanced displays in a research context-a rare opportunity to demonstrate how they can be used rather than simply discuss how they might be used to accelerate discovery.

  3. Efficacy of random primer-pair arrays in plant genome analysis: a case study of Cucumis (Cucurbitaceae) for identification of wild and cultivated species.

    PubMed

    Gatphoh, E M; Sharma, S K; Rajkumari, K; Rama Rao, S

    2011-01-01

    The efficacy of random primer-pair arrays compared to conventional RAPD method with a single decamer primer was evaluated using DNA from two species of Cucumis. The banding patterns of amplicons revealed enhanced utility of primer-pair arrays over conventional RAPDs, producing more bands and a higher degree of polymorphism, both at intra- and inter-specific levels. Amplification produced by both methods clearly distinguished a wild from a cultivated species of the genus Cucumis. The main advantage of the primer-pair RAPD over single-primer-based RAPD is the increase in the number of reactions and amplification products in the form of novel/unique bands with a limited number of primers. It also enables the generation of reliable amplicons with a large number of polymorphic bands, which can be linked to gene-governing traits, allowing sequence-characterized partial genome analysis.

  4. The Inner Oort Cloud Population

    NASA Astrophysics Data System (ADS)

    Sheppard, Scott; Trujillo, Chad

    2014-08-01

    The Kuiper Belt population has an outer edge at about 50 AU. Sedna and our recent discovery, 2012 VP113, are the only known objects with perihelion significantly beyond this edge at about 80 AU. These inner Oort cloud objects obtained their orbits when the solar system was vastly different from now. There are several theories as to the origin of these objects that can only be tested by finding several more. This population is likely larger than the Kuiper Belt but previous surveys did not go faint enough, did not have the required long cadence, or covered too small of sky area to find them. The dynamical and physical properties of objects in this region offer key constraints on the formation and evolution of our solar system. We propose to continue our survey with DECam in order to find several more inner Oort cloud objects to further constrain formation theories and thus learn about our Sun's formation environment and evolution.

  5. Genetic population structure of the prosobranch snail Potamopyrgus antipodarum (Gray) in Denmark using PCR-RAPD fingerprints.

    PubMed

    Jacobsen, R; Forbes, V E; Skovgaard, O

    1996-08-22

    Parthenogenetic species are often more widely distributed geographically than their sexual relatives. This success in colonizing can be explained either by dispersal of one or a few clones of wide physiological tolerance or by the distribution of many locally adapted clones. Here we test the hypothesis that successfully invading clones of Potamopyrgus antipodarum (Gray) are composed of a few broadly adapted genotypes by using polymerase chain reaction random amplified polymorphic DNA (PCR-RAPD) fingerprinting on six different populations of P. antipodarum from Denmark and three morphotypes of P. antipodarum from Britain. We detected two genotypes of P. antipodarum in six populations examined across Denmark using four decamer primers. The two genotypes were found to be morphologically and genetically indistinguishable from British P. antipodarum. In five of the six Danish populations only one genotype was found; at the remaining site, the two genotypes occurred sympatrically. The present study suggests that P. antipodarum successfully invaded Europe by the proliferation of very few clones.

  6. 2-O-[2-(Methylthio)ethyl]-Modified Oligonucleotide: An Analog of 2-O-[2-(Methoxy)ethyl]-Modified Oligonucleotide with Improved Protein Binding Properties and High Binding Affinity to Target RNA

    SciTech Connect

    Prakash, T.P.; Manoharan, M.; Fraser, A.S.; Kawasaki, A.M.; Lesnik, E.; Sioufi, N.; Leeds, J.M.; Teplova, M.; Egli, M.

    2010-03-08

    A novel 2'-modification, 2'-O-[2-(methylthio)ethyl] or 2'-O-MTE, has been incorporated into oligonucleotides and evaluated for properties relevant to antisense activity. The results were compared with the previously characterized 2'-O-[2-(methoxy)ethyl] 2'-O-MOE modification. As expected, the 2'-O-MTE modified oligonucleotides exhibited improved binding to human serum albumin compared to the 2'-O-MOE modified oligonucleotides. The 2'-O-MTE oligonucleotides maintained high binding affinity to target RNA. Nuclease digestion of 2'-O-MTE oligonucleotides showed that they have limited resistance to exonuclease degradation. We analyzed the crystal structure of a decamer DNA duplex containing the 2'-O-MTE modifcation. Analysis of the crystal structure provides insight into the improved RNA binding affinity, protein binding affinity and limited resistance of 2'-O-MTE modified oligonucleotides to exonuclease degradation.

  7. Goodpasture Antigen-binding Protein/Ceramide Transporter Binds to Human Serum Amyloid P-Component and Is Present in Brain Amyloid Plaques*

    PubMed Central

    Mencarelli, Chiara; Bode, Gerard H.; Losen, Mario; Kulharia, Mahesh; Molenaar, Peter C.; Veerhuis, Robert; Steinbusch, Harry W. M.; De Baets, Marc H.; Nicolaes, Gerry A. F.; Martinez-Martinez, Pilar

    2012-01-01

    Serum amyloid P component (SAP) is a non-fibrillar glycoprotein belonging to the pentraxin family of the innate immune system. SAP is present in plasma, basement membranes, and amyloid deposits. This study demonstrates, for the first time, that the Goodpasture antigen-binding protein (GPBP) binds to human SAP. GPBP is a nonconventional Ser/Thr kinase for basement membrane type IV collagen. Also GPBP is found in plasma and in the extracellular matrix. In the present study, we demonstrate that GPBP specifically binds SAP in its physiological conformations, pentamers and decamers. The START domain in GPBP is important for this interaction. SAP and GPBP form complexes in blood and partly colocalize in amyloid plaques from Alzheimer disease patients. These data suggest the existence of complexes of SAP and GPBP under physiological and pathological conditions. These complexes are important for understanding basement membrane, blood physiology, and plaque formation in Alzheimer disease. PMID:22396542

  8. Method for high-volume sequencing of nucleic acids: random and directed priming with libraries of oligonucleotides

    DOEpatents

    Studier, F.W.

    1995-04-18

    Random and directed priming methods for determining nucleotide sequences by enzymatic sequencing techniques, using libraries of primers of lengths 8, 9 or 10 bases, are disclosed. These methods permit direct sequencing of nucleic acids as large as 45,000 base pairs or larger without the necessity for subcloning. Individual primers are used repeatedly to prime sequence reactions in many different nucleic acid molecules. Libraries containing as few as 10,000 octamers, 14,200 nonamers, or 44,000 decamers would have the capacity to determine the sequence of almost any cosmid DNA. Random priming with a fixed set of primers from a smaller library can also be used to initiate the sequencing of individual nucleic acid molecules, with the sequence being completed by directed priming with primers from the library. In contrast to random cloning techniques, a combined random and directed priming strategy is far more efficient. 2 figs.

  9. Identical linkage and cooperativity of oxygen and carbon monoxide binding to Octopus dofleini hemocyanin

    SciTech Connect

    Connelly, P.R.; Gill, S.J.; Miller, K.I.; Zhou, G.; van Holde, K.E. )

    1989-02-21

    Employment of high-precision thin-layer methods has enabled detailed functional characterization of oxygen and carbon monoxide binding for (1) the fully assembled form with 70 binding sites and (2) the isolated chains with 7 binding sites of octopus dofleini hemocyanin. The striking difference in the cooperativities of the two ligands for the assembled decamer is revealed through an examination of the binding capacities and the partition coefficient, determined as functions of the activities of both ligands. A global analysis of the data sets supported by a two-state allosteric model assuming an allosteric unit of 7. Higher level allosteric interactions were not indicated. This contrasts to results obtained for arthropod hemocyanins. Oxygen and carbon monoxide experiments performed on the isolated subunit chain confirmed the presence of functional heterogeneity reported previously. The analysis shows two types of binding sites in the ratio of 4:3.

  10. The DES Science Verification Weak Lensing Shear Catalogs

    SciTech Connect

    Jarvis, M.

    2016-05-01

    We present weak lensing shear catalogs for 139 square degrees of data taken during the Science Verification (SV) time for the new Dark Energy Camera (DECam) being used for the Dark Energy Survey (DES). We describe our object selection, point spread function estimation and shear measurement procedures using two independent shear pipelines, IM3SHAPE and NGMIX, which produce catalogs of 2.12 million and 3.44 million galaxies respectively. We also detail a set of null tests for the shear measurements and find that they pass the requirements for systematic errors at the level necessary for weak lensing science applications using the SV data. Furthermore, we discuss some of the planned algorithmic improvements that will be necessary to produce sufficiently accurate shear catalogs for the full 5-year DES, which is expected to cover 5000 square degrees.

  11. Introducing the All-sky NOAO Source Catalog

    NASA Astrophysics Data System (ADS)

    Nidever, David L.; NOAO DataLab

    2017-06-01

    Most of the sky has been imaged with NOAO's telescopes from both hemispheres. While the large majority of these data were obtained for PI-led projects only a small fraction have been released to the community via well-calibrated and easily accessible catalogs. We are remedying this by created a catalog of sources from most of the public data taken on CTIO-4m+DECam as well as KPNO-4m+Mosaic3. This catalog, called the NOAO Source Catalog (NSC), already contains 2.3 billion unique objects, 19 billion source measurements, covers ~25,000 square degrees of the sky, has 10-sigma depths of ~23rd magnitude in most broadband filters, and astrometric accuracy of ~20 mas. We plan to release the catalog via the new NOAO Data Lab service in the near future.

  12. The Size Distribution of Near-Earth Objects Larger Than 10 m

    NASA Astrophysics Data System (ADS)

    Trilling, D. E.; Valdes, F.; Allen, L.; James, D.; Fuentes, C.; Herrera, D.; Axelrod, T.; Rajagopal, J.

    2017-10-01

    We analyzed data from the first year of a survey for Near-Earth Objects (NEOs) that we are carrying out with the Dark Energy Camera (DECam) on the 4 m Blanco telescope at the Cerro Tololo Inter-American Observatory. We implanted synthetic NEOs into the data stream to derive our nightly detection efficiency as a function of magnitude and rate of motion. Using these measured efficiencies and the solar system absolute magnitudes derived by the Minor Planet Center for the 1377 measurements of 235 unique NEOs detected, we directly derive, for the first time from a single observational data set, the NEO size distribution from 1 km down to 10 m. We find that there are {10}6.6 NEOs larger than 10 m. This result implies a factor of 10 fewer small NEOs than some previous results, though our derived size distribution is in good agreement with several other estimates.

  13. Coding and decoding libraries of sequence-defined functional copolymers synthesized via photoligation.

    PubMed

    Zydziak, Nicolas; Konrad, Waldemar; Feist, Florian; Afonin, Sergii; Weidner, Steffen; Barner-Kowollik, Christopher

    2016-11-30

    Designing artificial macromolecules with absolute sequence order represents a considerable challenge. Here we report an advanced light-induced avenue to monodisperse sequence-defined functional linear macromolecules up to decamers via a unique photochemical approach. The versatility of the synthetic strategy-combining sequential and modular concepts-enables the synthesis of perfect macromolecules varying in chemical constitution and topology. Specific functions are placed at arbitrary positions along the chain via the successive addition of monomer units and blocks, leading to a library of functional homopolymers, alternating copolymers and block copolymers. The in-depth characterization of each sequence-defined chain confirms the precision nature of the macromolecules. Decoding of the functional information contained in the molecular structure is achieved via tandem mass spectrometry without recourse to their synthetic history, showing that the sequence information can be read. We submit that the presented photochemical strategy is a viable and advanced concept for coding individual monomer units along a macromolecular chain.

  14. Characterization of primary standards for use in the HPLC analysis of the procyanidin content of cocoa and chocolate containing products.

    PubMed

    Hurst, William J; Stanley, Bruce; Glinski, Jan A; Davey, Matthew; Payne, Mark J; Stuart, David A

    2009-10-15

    This report describes the characterization of a series of commercially available procyanidin standards ranging from dimers DP = 2 to decamers DP = 10 for the determination of procyanidins from cocoa and chocolate. Using a combination of HPLC with fluorescence detection and MALDI-TOF mass spectrometry, the purity of each standard was determined and these data were used to determine relative response factors. These response factors were compared with other response factors obtained from published methods. Data comparing the procyanidin analysis of a commercially available US dark chocolate calculated using each of the calibration methods indicates divergent results and demonstrate that previous methods may significantly underreport the procyanidins in cocoa-containing products. These results have far reaching implications because the previous calibration methods have been used to develop data for a variety of scientific reports, including food databases and clinical studies.

  15. HPLC method for the quantification of procyanidins in cocoa and chocolate samples and correlation to total antioxidant capacity.

    PubMed

    Adamson, G E; Lazarus, S A; Mitchell, A E; Prior, R L; Cao, G; Jacobs, P H; Kremers, B G; Hammerstone, J F; Rucker, R B; Ritter, K A; Schmitz, H H

    1999-10-01

    Monomeric and oligomeric procyanidins present in cocoa liquors and chocolates were separated and quantified in four different laboratories using a normal-phase high-performance liquid chromatography (HPLC) method with fluorescence detection. Procyanidin standards through decamers were obtained by extraction from cocoa beans, enrichment by Sephadex LH-20 gel permeation chromatography, and final purification by preparative normal-phase HPLC. The purity of each oligomeric fraction was assessed using HPLC coupled to mass spectrometry. A composite standard was then prepared, and calibration curves were generated for each oligomeric class using a quadratic fit of area sum versus concentration. Results obtained by each of the laboratories were in close agreement, which suggests this method is reliable and reproducible for quantification of procyanidins. Furthermore, the procyanidin content of the samples was correlated to the antioxidant capacity measured using the ORAC assay as an indicator for potential biological activity.

  16. PreCam: A Step Towards the Photometric Calibration of the Dark Energy Survey

    NASA Astrophysics Data System (ADS)

    Allam, S. S.; Tucker, D. L.; PreCam Team; DES Collaboration

    2016-05-01

    The Dark Energy Survey (DES) will be taking the next step in probing the properties of Dark Energy and in understanding the physics of cosmic acceleration. A step towards the photometric calibration of DES is to have a quick, bright survey in the DES footprint (PreCam), using a pre-production set of the Dark Energy Camera (DECam) CCDs and a set of 100 mm×100 mm DES filters. The objective of the PreCam Survey is to create a network of calibrated DES grizY standard stars that will be used for DES nightly calibrations and to improve the DES global relative calibrations. Here, we describe the first year of PreCam observation, results, and photometric calibrations.

  17. Classifying X-ray Sources from the Chandra Galactic Bulge Survey

    NASA Astrophysics Data System (ADS)

    Hynes, Robert

    2012-09-01

    The completion of the Galactic Bulge Survey (GBS) by Chandra in AO-13 identified 400 new X-ray sources (on top of the 1200 already known), many of which are expected to have accessible optical counterparts. Wide-field variability studies can be an extremely powerful tool to classify these sources. In two nights with the new NOAO DECam we can obtain lightcurves of ALL of the optically accessible objects, together with another 400 GBS sources from earlier AOs, and about 1700 additional fainter objects from the Chandra Source Catalog. We therefore propose a joint Archival-NOAO study to obtain these lightcurves, use them to classify the X-ray sources, and pick out ellipsoidal variations and eclipses from the many quiescent low-mass X-ray binaries predicted to be accessible.

  18. Decameric uracil complexes around Li+.

    PubMed

    Zins, Emilie-Laure; Pepe, Claude; Schröder, Detlef

    2010-07-01

    Electrospray ionization (ESI) in combination with mass spectrometry (MS) experiments were carried out to study decameric uracil complexes cationized with Li(+) ion. A previous study has shown that, under specific experimental conditions, a particularly intense peak of the decamer U(10)Li(+) is formed, which was referred to as an indication for so-called 'magic number' cluster. In order to gain more insight on the structure of this decameric complex, here, we report experimental studies concerning the kinetics of the fragmentation. In accordance with the new experimental data, structural models were constructed and fully optimized using ab initio and density functional theory quantum chemistry calculations. The theoretical study allowed us to propose a stable gas-phase structure which is compatible with all experimental findings. 2010 John Wiley & Sons, Ltd.

  19. The use of random amplified polymorphic DNA (RAPD) analysis for studies of genetic variation in populations of Coccinella septempunctata in Belgium.

    PubMed

    Haubruge, Eric; Vanlerberghe-Masutti, Flavie; Collignon, Pierre; Francis, Frédéric

    2002-01-01

    The movement and dispersion of Coccinella septempunctata and its efficacy as aphid control agent over large areas is not really understood because of the difficulty in identifying the origins of predators. To quantify the genetic diversity within the species and monitor the spatial foraging, populations were sampled from Belgium and analysed for RAPD DNA variation. Twenty decamer primers generated more than hundred polymorphic RAPD bands and pairwise distances were calculated between populations according to Nei and Li, then used to construct a radial neighbour-joining dendrogram and examine intra- and inter-population variance coefficients, by analysis of molecular variation (AMOVA). This study shows that while a number of factors can complicate the use and interpretation of RAPD fragments as genetic markers, RAPD analysis can be a valuable technique for studies of intra-specific genetic variation in C. septempunctata.

  20. Assembly of Octopus dofleini hemocyanin. A study of the kinetics by sedimentation, light scattering and electron microscopy.

    PubMed

    van Holde, K E; Miller, K; Schabtach, E; Libertini, L

    1991-01-20

    The kinetics of association of Octopus dofleini hemocyanin subunits to form the native decameric molecule have been studied with a combination of sedimentation, light scattering and electron microscopy. The reaction, initiated by addition of magnesium, is relatively slow, requiring hours to reach completion, with monomer and decamer as predominant molecular species throughout. Analysis of the light-scattering data, including stopped-flow studies, reveals an initial lag period in the reaction, followed by a second-order process that is rate limiting. The lag period depends on both protein and magnesium ion concentration. Electron microscope studies reveal intermediates in the process, and support a model of assembly in which nucleation begins at the dimer level. Theoretical models for the process are compared.

  1. Low density shear viscosity of Lennard-Jones chains of variable rigidities.

    PubMed

    Santacreu, S Delage; Galliero, G; Odunlami, M; Boned, C

    2012-11-28

    The zero-density shear viscosity of different types of short Lennard-Jones chains, up to the hexa-decamer, has been evaluated using a non-equilibrium molecular dynamics scheme. Simulations have been performed on chains of variable rigidities going from the fully flexible to the fully rigid chains. Very interestingly, it is found that there exists a universal relation (a power law) between the zero-density viscosity of the Lennard-Jones chains and their radius of gyration whatever the rigidity of the chain and for all tested temperatures (ranging from 2.5 to 6 in reduced units). Furthermore, for the studied range of temperature, it is shown that the zero-density viscosity of both fully flexible chains and fully rigid chains models can be obtained with an accuracy of a few percents knowing only the dimer viscosity and the length of the chain.

  2. Caterpillar Track Complexes in Template-Directed Synthesis and Correlated Molecular Motion.

    PubMed

    Liu, Shiqi; Kondratuk, Dmitry V; Rousseaux, Sophie A L; Gil-Ramírez, Guzmán; O'Sullivan, Melanie C; Cremers, Jonathan; Claridge, Tim D W; Anderson, Harry L

    2015-04-27

    Small alterations to the structure of a star-shaped template totally change its mode of operation. The hexapyridyl template directs the conversion of a porphyrin dimer to the cyclic hexamer, but deleting one pyridine site changes the product to the cyclic decamer, while deleting two binding sites changes the product to the cyclic octamer. This surprising switch in selectivity is explained by the formation of 2:1 caterpillar track complexes, in which two template wheels bind inside the nanoring. Caterpillar track complexes can also be prepared by binding the hexapyridyl template inside the 8- and 10-porphyrin nanorings. NMR exchange spectroscopy (EXSY) experiments show that these complexes exhibit correlated motion, in which the conrotatory rotation of the two template wheels is coupled to rotation of the nanoring track. In the case of the 10-porphyrin system, the correlated motion can be locked by binding palladium(II) dichloride between the two templates.

  3. Coding and decoding libraries of sequence-defined functional copolymers synthesized via photoligation

    NASA Astrophysics Data System (ADS)

    Zydziak, Nicolas; Konrad, Waldemar; Feist, Florian; Afonin, Sergii; Weidner, Steffen; Barner-Kowollik, Christopher

    2016-11-01

    Designing artificial macromolecules with absolute sequence order represents a considerable challenge. Here we report an advanced light-induced avenue to monodisperse sequence-defined functional linear macromolecules up to decamers via a unique photochemical approach. The versatility of the synthetic strategy--combining sequential and modular concepts--enables the synthesis of perfect macromolecules varying in chemical constitution and topology. Specific functions are placed at arbitrary positions along the chain via the successive addition of monomer units and blocks, leading to a library of functional homopolymers, alternating copolymers and block copolymers. The in-depth characterization of each sequence-defined chain confirms the precision nature of the macromolecules. Decoding of the functional information contained in the molecular structure is achieved via tandem mass spectrometry without recourse to their synthetic history, showing that the sequence information can be read. We submit that the presented photochemical strategy is a viable and advanced concept for coding individual monomer units along a macromolecular chain.

  4. Green fluorescent protein nanopolygons as monodisperse supramolecular assemblies of functional proteins with defined valency

    NASA Astrophysics Data System (ADS)

    Kim, Young Eun; Kim, Yu-Na; Kim, Jung A.; Kim, Ho Min; Jung, Yongwon

    2015-05-01

    Supramolecular protein assemblies offer novel nanoscale architectures with molecular precision and unparalleled functional diversity. A key challenge, however, is to create precise nano-assemblies of functional proteins with both defined structures and a controlled number of protein-building blocks. Here we report a series of supramolecular green fluorescent protein oligomers that are assembled in precise polygonal geometries and prepared in a monodisperse population. Green fluorescent protein is engineered to be self-assembled in cells into oligomeric assemblies that are natively separated in a single-protein resolution by surface charge manipulation, affording monodisperse protein (nano)polygons from dimer to decamer. Several functional proteins are multivalently displayed on the oligomers with controlled orientations. Spatial arrangements of protein oligomers and displayed functional proteins are directly visualized by a transmission electron microscope. By employing our functional protein assemblies, we provide experimental insight into multivalent protein-protein interactions and tools to manipulate receptor clustering on live cell surfaces.

  5. PreCam

    SciTech Connect

    Allam, Sahar S.; Tucker, Douglas L.

    2015-01-01

    The Dark Energy Survey (DES) will be taking the next step in probing the properties of Dark Energy and in understanding the physics of cosmic acceleration. A step towards the photometric calibration of DES is to have a quick, bright survey in the DES footprint (PreCam), using a pre-production set of the Dark Energy Camera (DECam) CCDs and a set of 100 mm×100 mm DES filters. The objective of the PreCam Survey is to create a network of calibrated DES grizY standard stars that will be used for DES nightly calibrations and to improve the DES global relative calibrations. Here, we describe the first year of PreCam observation, results, and photometric calibrations.

  6. Ultrafiltration as alternative purification procedure for the characterization of low and high molecular-mass phenolics from almond skins.

    PubMed

    Prodanov, Marin; Garrido, Ignacio; Vacas, Visitación; Lebrón-Aguilar, Rosa; Dueñas, Montserrat; Gómez-Cordovés, Carmen; Bartolomé, Begoña

    2008-02-25

    A combination of sample preparation (ultrafiltration) and analysis techniques is proposed for the characterization of complex phenolic mixtures such as extracts from almond (Prunus dulcis (Mill.) D.A. Webb) skins. LC/ESI-MS analysis of the permeates obtained after ultrafiltration on semipermeable membranes (low molecular-mass phenolic fractions) allowed the identification of several benzoic acids and aldehydes, flavan-3-ol monomers and oligomers, and flavonol and flavanone glycosides in almond skins. MALDI-TOF and ESI-MS/MS analysis of the diafiltered concentrates (high molecular-mass phenolic fractions) demonstrated the presence of proanthocyanidin oligomers up to decamers, composed of (epi)afzelechin, (epi)catechin and (epi)gallocatechin units linked by C-C bonds (type B) and by both C-C and C-O bonds (type A). This analytical protocol can be of utility in the study of low and high molecular-mass phenolic compounds in natural products.

  7. Genotyping by RAPD-PCR analyses of Malassezia furfur strains from pityriasis versicolor and seborrhoeic dermatitis patients.

    PubMed

    Gandra, Rinaldo F; Simão, Rita C G; Matsumoto, Flávia E; da Silva, Bosco C M; Ruiz, Luciana S; da Silva, Eriques G; Gambale, Walderez; Paula, Claudete R

    2006-10-01

    Malassezia furfur is lypophilic yeast commonly associate with dermatological disorders. In the present work, we described the isolation of 47 M. furfur strains from three groups of patients: pityriasis versicolor (21 isolates), seborrhoeic dermatitis (15 isolates) and seborrhoeic dermatitis of the HIV positive patients (11 isolates). To investigate the identity of the strains at molecular level, DNA genomic of M. furfur strains were prepared and used to RAPD-PCR analyses. RAPD assay were carried out using two decamer primers and bands pattern generated were analyzed by an Unweighted Pair-Group Method (UPGMA). Dendrogram established a distinct differentiation between M. furfur isolates from pityriasis versicolor and seborrhoeic dermatitis patients with or without AIDS. We concluded that RAPD typing presented a high discriminatory power between strains studied in this work and can be applied in epidemiological investigation of skin disease causing by M. furfur.

  8. The Crystal Structure of the Escherichia coli Autoinducer-2 Processing Protein LsrF

    PubMed Central

    Diaz, Zamia; Xavier, Karina B.; Miller, Stephen T.

    2009-01-01

    Many bacteria produce and respond to the quorum sensing signal autoinducer-2 (AI-2). Escherichia coli and Salmonella typhimurium are among the species with the lsr operon, an operon containing AI-2 transport and processing genes that are up regulated in response to AI-2. One of the Lsr proteins, LsrF, has been implicated in processing the phosphorylated form of AI-2. Here, we present the structure of LsrF, unliganded and in complex with two phospho-AI-2 analogues, ribose-5-phosphate and ribulose-5-phosphate. The crystal structure shows that LsrF is a decamer of (αβ)8-barrels that exhibit a previously unseen N-terminal domain swap and have high structural homology with aldolases that process phosphorylated sugars. Ligand binding sites and key catalytic residues are structurally conserved, strongly implicating LsrF as a class I aldolase. PMID:19714241

  9. Kriging atomic properties with a variable number of inputs.

    PubMed

    Davie, Stuart J; Di Pasquale, Nicodemo; Popelier, Paul L A

    2016-09-14

    A new force field called FFLUX uses the machine learning technique kriging to capture the link between the properties (energies and multipole moments) of topological atoms (i.e., output) and the coordinates of the surrounding atoms (i.e., input). Here we present a novel, general method of applying kriging to chemical systems that do not possess a fixed number of (geometrical) inputs. Unlike traditional kriging methods, which require an input system to be of fixed dimensionality, the method presented here can be readily applied to molecular simulation, where an interaction cutoff radius is commonly used and the number of atoms or molecules within the cutoff radius is not constant. The method described here is general and can be applied to any machine learning technique that normally operates under a fixed number of inputs. In particular, the method described here is also useful for interpolating methods other than kriging, which may suffer from difficulties stemming from identical sets of inputs corresponding to different outputs or input biasing. As a demonstration, the new method is used to predict 54 energetic and electrostatic properties of the central water molecule of a set of 5000, 4 Å radius water clusters, with a variable number of water molecules. The results are validated against equivalent models from a set of clusters composed of a fixed number of water molecules (set to ten, i.e., decamers) and against models created by using a naïve method of treating the variable number of inputs problem presented. Results show that the 4 Å water cluster models, utilising the method presented here, return similar or better kriging models than the decamer clusters for all properties considered and perform much better than the truncated models.

  10. Kriging atomic properties with a variable number of inputs

    NASA Astrophysics Data System (ADS)

    Davie, Stuart J.; Di Pasquale, Nicodemo; Popelier, Paul L. A.

    2016-09-01

    A new force field called FFLUX uses the machine learning technique kriging to capture the link between the properties (energies and multipole moments) of topological atoms (i.e., output) and the coordinates of the surrounding atoms (i.e., input). Here we present a novel, general method of applying kriging to chemical systems that do not possess a fixed number of (geometrical) inputs. Unlike traditional kriging methods, which require an input system to be of fixed dimensionality, the method presented here can be readily applied to molecular simulation, where an interaction cutoff radius is commonly used and the number of atoms or molecules within the cutoff radius is not constant. The method described here is general and can be applied to any machine learning technique that normally operates under a fixed number of inputs. In particular, the method described here is also useful for interpolating methods other than kriging, which may suffer from difficulties stemming from identical sets of inputs corresponding to different outputs or input biasing. As a demonstration, the new method is used to predict 54 energetic and electrostatic properties of the central water molecule of a set of 5000, 4 Å radius water clusters, with a variable number of water molecules. The results are validated against equivalent models from a set of clusters composed of a fixed number of water molecules (set to ten, i.e., decamers) and against models created by using a naïve method of treating the variable number of inputs problem presented. Results show that the 4 Å water cluster models, utilising the method presented here, return similar or better kriging models than the decamer clusters for all properties considered and perform much better than the truncated models.

  11. Sampling saddle points on a free energy surface.

    PubMed

    Samanta, Amit; Chen, Ming; Yu, Tang-Qing; Tuckerman, Mark; E, Weinan

    2014-04-28

    Many problems in biology, chemistry, and materials science require knowledge of saddle points on free energy surfaces. These saddle points act as transition states and are the bottlenecks for transitions of the system between different metastable states. For simple systems in which the free energy depends on a few variables, the free energy surface can be precomputed, and saddle points can then be found using existing techniques. For complex systems, where the free energy depends on many degrees of freedom, this is not feasible. In this paper, we develop an algorithm for finding the saddle points on a high-dimensional free energy surface "on-the-fly" without requiring a priori knowledge the free energy function itself. This is done by using the general strategy of the heterogeneous multi-scale method by applying a macro-scale solver, here the gentlest ascent dynamics algorithm, with the needed force and Hessian values computed on-the-fly using a micro-scale model such as molecular dynamics. The algorithm is capable of dealing with problems involving many coarse-grained variables. The utility of the algorithm is illustrated by studying the saddle points associated with (a) the isomerization transition of the alanine dipeptide using two coarse-grained variables, specifically the Ramachandran dihedral angles, and (b) the beta-hairpin structure of the alanine decamer using 20 coarse-grained variables, specifically the full set of Ramachandran angle pairs associated with each residue. For the alanine decamer, we obtain a detailed network showing the connectivity of the minima obtained and the saddle-point structures that connect them, which provides a way to visualize the gross features of the high-dimensional surface.

  12. A HERO'S LITTLE HORSE: DISCOVERY OF A DISSOLVING STAR CLUSTER IN PEGASUS

    SciTech Connect

    Kim, Dongwon; Jerjen, Helmut E-mail: helmut.jerjen@anu.edu.au

    2015-01-20

    We report the discovery of an ultra-faint stellar system in the constellation of Pegasus. This concentration of stars was detected by applying our overdensity detection algorithm to the Sloan Digital Sky Survey Data Release 10 and confirmed with deeper photometry from the Dark Energy Camera (DECam) at the 4 m Blanco telescope. The best-fitting model isochrone indicates that this stellar system, Kim 1, features an old (12 Gyr) and metal-poor ([Fe/H] ∼ -1.7) stellar population at a heliocentric distance of 19.8 ± 0.9 kpc. We measure a half-light radius of 6.9 ± 0.6 pc using a Plummer profile. The small physical size and the extremely low luminosity are comparable to the faintest known star clusters Segue 3, Koposov 1 and 2, and Muñoz 1. However, Kim 1 exhibits a lower star concentration and is lacking a well-defined center. It also has an unusually high ellipticity and irregular outer isophotes, which suggests that we are seeing an intermediate mass star cluster being stripped by the Galactic tidal field. An extended search for evidence of an associated stellar stream within the 3 deg{sup 2} DECam field remains inconclusive. The finding of Kim 1 is consistent with current overdensity detection limits and supports the hypothesis that there are still a substantial number of extreme low-luminosity star clusters undetected in the wider Milky Way halo.

  13. Cocoa procyanidins and human cytokine transcription and secretion.

    PubMed

    Mao, T; Van De Water, J; Keen, C L; Schmitz, H H; Gershwin, M E

    2000-08-01

    We examined whether cocoa, in its isolated procyanidin fractions (monomer through decamer), would modulate cytokine production at the levels of transcription and protein secretion in both resting and phytohemagglutinin (PHA)-stimulated peripheral blood mononuclear cells (PBMC). In resting cells, interleukin (IL)-1beta and IL-4 gene expression from cocoa-treated cells varied markedly among the subjects tested. However, at the protein level, the larger fractions (pentamer through decamer) stimulated a dramatic increase in IL-1beta concentration (up to ninefold) with increasing degree of polymerization. Similarly, these larger fractions augmented IL-4 concentration by as much as 2 pg/ml, whereas the control displayed levels nearly undetectable. In the presence of PHA, gene expression also seemed to be most affected by the larger procyanidin fractions. The pentameric through decameric fractions increased IL-1 beta expression by 7-19% compared with PHA control, whereas the hexameric through decameric fractions significantly inhibited PHA-induced IL-4 transcription in the range of 71-86%. This observation at the transcription level for IL-1 beta was reflected at the protein level in PHA-stimulated PBMC. Significant reductions in mitogen-induced IL-4 production were also seen at the protein level with the hexamer, heptamer and octamer. Individual oligomeric cocoa fractions were unstimulatory for IL-2 in resting PBMC. However, when induced with PHA, the pentamer, hexamer and heptamer fractions caused a 61-73% inhibition in IL-2 gene expression. This study offers additional data for the consideration of the health benefits of dietary polyphenols from a wide variety of foods, including those benefits associated specifically with cocoa and chocolate consumption.

  14. Genetic relatedness of artichoke (Cynara scolymus L.) hybrids using random amplified polymorphic DNA (RAPD) fingerprinting.

    PubMed

    Sharaf-Eldin, M A; Al-Tamimi, A; Alam, P; Elkholy, S F; Jordan, J R

    2015-12-28

    The artichoke (Cynara scolymus L.) is an important food and medicinal crop that is cultivated in Mediterranean countries. Morphological characteristics, such as head shape and diameter, leaf shape, and bract shape, are mainly affected by environmental conditions. A molecular marker approach was used to analyze the degree of polymorphism between artichoke hybrid lines. The degree of genetic difference among three artichoke hybrids was evaluated using random amplified polymorphic DNA-PCR (RAPD-PCR). In this study, the DNA fingerprints of three artichoke lines (A13-010, A11-018, and A12-179) were generated, and a total of 10 decamer primers were applied for RAPD-PCR analyses. Polymorphism  (16.66 to 62.50%) was identified using eight arbitrary decamers and total genomic DNA extracted from the hybrids. Of the 59 loci detected, there were 25 polymorphic and 34 monomorphic loci. Jaccard's similarity index (JSI) ranged between 1.0 and 0.84. Based on the unweighted pair group method with arithmetic mean (UPGMA) similarity matrix and dendrogram, the results indicated that two hybrids (A13-010 and A11-018) were closely related to each other, and the A12-179 line showed more divergence. When identifying correct accessions, consideration of the genetic variation and genetic relationships among the genotypes are required. The RAPD-PCR fingerprinting of artichoke lines clearly showed that it is possible to analyze the RAPD patterns for correlation between genetic means and differences or resemblance between close accessions (A13-010 and A11- 018) at the genomic level.

  15. Sampling saddle points on a free energy surface

    NASA Astrophysics Data System (ADS)

    Samanta, Amit; Chen, Ming; Yu, Tang-Qing; Tuckerman, Mark; E, Weinan

    2014-04-01

    Many problems in biology, chemistry, and materials science require knowledge of saddle points on free energy surfaces. These saddle points act as transition states and are the bottlenecks for transitions of the system between different metastable states. For simple systems in which the free energy depends on a few variables, the free energy surface can be precomputed, and saddle points can then be found using existing techniques. For complex systems, where the free energy depends on many degrees of freedom, this is not feasible. In this paper, we develop an algorithm for finding the saddle points on a high-dimensional free energy surface "on-the-fly" without requiring a priori knowledge the free energy function itself. This is done by using the general strategy of the heterogeneous multi-scale method by applying a macro-scale solver, here the gentlest ascent dynamics algorithm, with the needed force and Hessian values computed on-the-fly using a micro-scale model such as molecular dynamics. The algorithm is capable of dealing with problems involving many coarse-grained variables. The utility of the algorithm is illustrated by studying the saddle points associated with (a) the isomerization transition of the alanine dipeptide using two coarse-grained variables, specifically the Ramachandran dihedral angles, and (b) the beta-hairpin structure of the alanine decamer using 20 coarse-grained variables, specifically the full set of Ramachandran angle pairs associated with each residue. For the alanine decamer, we obtain a detailed network showing the connectivity of the minima obtained and the saddle-point structures that connect them, which provides a way to visualize the gross features of the high-dimensional surface.

  16. A modern approach to upgrading the telescope control system of the CTIO Blanco 4-m telescope

    NASA Astrophysics Data System (ADS)

    Warner, Michael; Cantarutti, Rolando; Schumacher, German; Mondaca, Eduardo; Estay, Omar; Martinez, Manuel; Aguirre, Victor; Alvarez, Rodrigo; Leiva, Rodrigo; Abbott, Timothy M. C.; van der Bliek, Nicole S.

    2012-09-01

    In preparation for the arrival of the Dark Energy Camera (DECam) at the CTIO Blanco 4-m telescope, both the hardware and the software of the Telescope Control System (TCS) have been upgraded in order to meet the more stringent requirements on cadence and tracking required for efficient execution of the Dark Energy Survey1. This upgrade was also driven by the need to replace obsolete hardware, some of it now over half a century old. In this paper we describe the architecture of the new mount control system, and in particular the method used to develop and implement the servo-driver portion of the new TCS. This portion of the system had to be completely rethought, when an initial approach, based on commercial off the shelf components, lacked the flexibility needed to cope with the complex behavior of the telescope. Central to our design approach was the early implementation of extensive telemetry, which allowed us to fully characterize the real dynamics of the telescope. These results then served as input to extensive simulations of the proposed new servo system allowing us to iteratively refine the control model. This flexibility will be important later when DECam is installed, since this will significantly increase the moving mass and inertia of the telescope. Based on these results, a fully digital solution was chosen and implemented. The core of this new servo hardware is modern cRIO hardware, which combines an embedded processor with a high-performance FPGA, allowing the execution of LabVIEW applications in real time.

  17. First Results from the Lyman Alpha Galaxies in the Epoch of Reionization (LAGER) Survey: Cosmological Reionization at z ˜ 7

    NASA Astrophysics Data System (ADS)

    Zheng, Zhen-Ya; Wang, Junxian; Rhoads, James; Infante, Leopoldo; Malhotra, Sangeeta; Hu, Weida; Walker, Alistair R.; Jiang, Linhua; Jiang, Chunyan; Hibon, Pascale; Gonzalez, Alicia; Kong, Xu; Zheng, XianZhong; Galaz, Gaspar; Barrientos, L. Felipe

    2017-06-01

    We present the first results from the ongoing Lyman Alpha Galaxies in the Epoch of Reionization (LAGER) project, which is the largest narrowband survey for z ˜ 7 galaxies to date. Using a specially built narrowband filter NB964 for the superb large-area Dark Energy Camera (DECam) on the NOAO/CTIO 4 m Blanco telescope, LAGER has collected 34 hr NB964 narrowband imaging data in the 3 deg2 COSMOS field. We have identified 23 Lyα Emitter candidates at z = 6.9 in the central 2-deg2 region, where DECam and public COSMOS multi-band images exist. The resulting luminosity function (LF) can be described as a Schechter function modified by a significant excess at the bright end (four galaxies with L Lyα ˜ 1043.4±0.2 erg s-1). The number density at L Lyα ˜ 1043.4±0.2 erg s-1 is little changed from z = 6.6, while at fainter L Lyα it is substantially reduced. Overall, we see a fourfold reduction in Lyα luminosity density from z = 5.7 to z = 6.9. Combined with a more modest evolution of the continuum UV luminosity density, this suggests a factor of ˜3 suppression of Lyα by radiative transfer through the z ˜ 7 intergalactic medium (IGM). It indicates an IGM neutral fraction of x H i ˜ 0.4-0.6 (assuming Lyα velocity offsets of 100-200 km s-1). The changing shape of the Lyα LF between z ≲ 6.6 and z = 6.9 supports the hypothesis of ionized bubbles in a patchy reionization at z ˜ 7.

  18. Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography.

    PubMed

    Peters, Justin P; Kowal, Ewa A; Pallan, Pradeep S; Egli, Martin; Maher, L James

    2017-09-04

    Leveraging structural biology tools, we report the results of experiments seeking to determine if the different mechanical properties of DNA polymers with base analog substitutions can be attributed, at least in part, to induced changes from classical B-form DNA. The underlying hypothesis is that different inherent bending and twisting flexibilities may characterize non-canonical B-DNA, so that it is inappropriate to interpret mechanical changes caused by base analog substitution as resulting simply from 'electrostatic' or 'base stacking' influences without considering the larger context of altered helical geometry. Circular dichroism spectra of inosine-substituted oligonucleotides and longer base-substituted DNAs in solution indicated non-canonical helical conformations, with the degree of deviation from a standard B-form geometry depending on the number of I⋅C pairs. X-ray diffraction of a highly inosine-substituted DNA decamer crystal (eight I⋅C and two A⋅T pairs) revealed an A-tract-like conformation with a uniformly narrow minor groove, reduced helical rise, and the majority of sugars adopting a C1'-exo (southeastern) conformation. This contrasts with the standard B-DNA geometry with C2'-endo sugar puckers (south conformation). In contrast, the crystal structure of a decamer with only four I⋅C pairs has a geometry similar to that of the reference duplex with eight G⋅C and two A⋅T pairs. The unique crystal geometry of the inosine-rich duplex is noteworthy given its unusual CD signature in solution and the altered mechanical properties of some inosine-containing DNAs.

  19. Deep Surveys for Inner Oort Cloud Objects

    NASA Astrophysics Data System (ADS)

    Trujillo, Chadwick A.; Tholen, David J.; Sheppard, Scott S.

    2015-11-01

    We are undertaking two deep wide-field surveys to discover extremely distant solar system objects. While our target solar system population is the Inner Oort Cloud objects such as 2012 VP113 and Sedna, we are also sensitive to other populations with high perihelia such as the Scattered Kuiper Belt Objects and the highest perihelion Kuiper Belt Objects which have similar arguments of perihelion to the Inner Oort Cloud Objects. These unusual populations are thought to consist primarily of highly eccentric objects which spend most of their orbits hundreds or thousands of AU from the sun. Large aperture telescopes are needed to reach the faintness limits, red magnitudes of 23.5 to 25, required for detection of even the large members of the population. In addition, wide fields of view are also needed since the sky density of the detectable members of the populations approach 1 in 100 square degrees even with large telescopes.Our primary discovery instruments are the Dark Energy Camera (DECam) on the 4 meter Blanco Telescope at the Cerro Tololo Inter-American Observatory and Hyper Suprime-Cam (HSC) on Subaru Telescope at Maunakea. Each of these instruments has a tremendously wide field of view considering the size of the telescope they are mounted on. DECam has a field of view of about 3 square degrees and HSC has a field of view of about 1.75 square degrees. We will present our survey progress in terms of sky area covered and new objects discovered and highlight some of our more interesting findings.

  20. Noncanonical DNA Motifs as Transactivation Targets by Wild Type and Mutant p53

    PubMed Central

    Jordan, Jennifer J.; Menendez, Daniel; Inga, Alberto; Nourredine, Maher; Bell, Douglas; Resnick, Michael A.

    2008-01-01

    Sequence-specific binding by the human p53 master regulator is critical to its tumor suppressor activity in response to environmental stresses. p53 binds as a tetramer to two decameric half-sites separated by 0–13 nucleotides (nt), originally defined by the consensus RRRCWWGYYY (n = 0–13) RRRCWWGYYY. To better understand the role of sequence, organization, and level of p53 on transactivation at target response elements (REs) by wild type (WT) and mutant p53, we deconstructed the functional p53 canonical consensus sequence using budding yeast and human cell systems. Contrary to early reports on binding in vitro, small increases in distance between decamer half-sites greatly reduces p53 transactivation, as demonstrated for the natural TIGER RE. This was confirmed with human cell extracts using a newly developed, semi–in vitro microsphere binding assay. These results contrast with the synergistic increase in transactivation from a pair of weak, full-site REs in the MDM2 promoter that are separated by an evolutionary conserved 17 bp spacer. Surprisingly, there can be substantial transactivation at noncanonical ½-(a single decamer) and ¾-sites, some of which were originally classified as biologically relevant canonical consensus sequences including PIDD and Apaf-1. p53 family members p63 and p73 yielded similar results. Efficient transactivation from noncanonical elements requires tetrameric p53, and the presence of the carboxy terminal, non-specific DNA binding domain enhanced transactivation from noncanonical sequences. Our findings demonstrate that RE sequence, organization, and level of p53 can strongly impact p53-mediated transactivation, thereby changing the view of what constitutes a functional p53 target. Importantly, inclusion of ½- and ¾-site REs greatly expands the p53 master regulatory network. PMID:18714371

  1. The Mayall z-band Legacy Survey

    NASA Astrophysics Data System (ADS)

    Silva, David R.; Blum, Robert D.; Allen, Lori; Dey, Arjun; Schlegel, David J.; Lang, Dustin; Moustakas, John; Meisner, Aaron M.; Valdes, Francisco; Patej, Anna; Myers, Adam D.; Sprayberry, David; Saha, Abi; Olsen, Knut A.; Safonova, Sasha; Yang, Qian; Burleigh, Kaylan J.; MzLS Team

    2016-06-01

    The Mayall z-band Legacy Survey (MzLS) is conducting a deep z-band imaging survey covering 5000 square degrees in the north Galactic cap as part of the Legacy Survey, which is associated with the Dark Energy Spectroscopic Instrument (DESI) redshift survey. The Legacy Survey covers 14000 square degrees in the g, r, and z bands and is being executed on the Blanco 4-m, Mayall 4-m, and Bok 2.3-m telescopes. The MzLS footprint will be observed in the g and r bands using the Bok 2.3-m telescope also on Kitt Peak. The Beijing Arizona Sky Survey (BASS) is being conducted by a parallel team from Beijing and the University of Arizona. MzLS will cover the sky north of declination 30 degrees and reach a depth of z=23.0. The survey began in January 2016 and will run through June 2017 comprising approximately 230 nights on the Mayall telescope. The data are being obtained with an upgraded Mosaic camera that deploys with newred-sensitive CCDs from Lawrence Berkeley Lab (LBL) whose throughput is in excess of 80% at 8000 to approximately 9800 Angstrom. The upgrade project was a collaboration of Yale, LBL, and NOAO. MzLS images are public as soon as they are taken and delivered to the NOAO archive. Catalogs based on Tractor photometry for all available Legacy Survey images are released soon after they are constructed and MzLS sources will be included in next release planned for summer 2016. The Dark Energy Spectroscopic Instrument (DESI) will observe 30+ million galaxies and quasars in a 14,000 square degree extragalactic footprint. The targeting in that footprint will be provided by a combination of these MzLS data, DECam data from the DECam Legacy Survey, and data from the BASS survey.

  2. Hydrophobic stabilization of chiton hemocyanins: effects of ureas, Hofmeister salts and pH on their dissociation.

    PubMed

    Herskovits, T T; Hamilton, M G

    1987-09-24

    The subunit dissociation of the hemocyanins from five members of the Polyplacophora families, Acanthochitonidae, Callistoplacidae, Chitonidae, Ischnochitonidae and Mopalidae, represented by the chitons Cryptochiton stelleri, Nutallina fluxa, Acanthopleura granulata, Stenoplax conspicua and Mopalia mucosa, respectively, have been investigated by light-scattering molecular-weight and ultracentrifugation methods, using the hydrophobic reagents of the urea series and the Hofmeister salt series as probes of the contact areas of the hemocyanin subunits. The polyplacophoran hemocyanins are decamers with molecular weights of (4.2-4.6) X 10(6). The effectiveness of dissociation by the ureas follows the order of increasing hydrophobicity of the reagent, i.e., urea, methyl-, ethyl-, propyl- and butylurea, as expected of hydrophobically stabilized subunit systems. The urea dissociation is found to be a two-step reaction: the dissociation of parent decamers to dimers followed by dissociation of the dimers to monomers. Analysis of the observed decrease in molecular weight requires the interaction with urea of about 27 to 35 apparent amino-acid groups (Napp) at the contact areas of the dimers, and a much larger number of apparent binding groups ranging from about 100 to 120 per monomer at the contact areas of the monomers. Fitting of the pH dissociation profiles of A. granulata, C. stelleri, M. muscosa and S. conspicua requires the participation of a much smaller number of amino-acid residues in the interaction with the probe-solvent components. The ionization or protonation of one acidic and one basic group per dimer, and five to eight acidic and basic groups per monomer is found to be adequate for the description of the two-step pH dissociation reaction.

  3. Oxygen equilibria of Octopus dofleini hemocyanin.

    PubMed

    Miller, K I

    1985-08-13

    Oxygen binding by Octopus dofleini hemocyanin was examined under very nearly physiological conditions. The effects of pH, ionic composition, temperature, and aggregation were controlled so that the role each plays in modulating oxygen binding can be isolated. There is a very large effect of pH on affinity, the Bohr effect (delta log P50/delta pH = -1.7), which is the same at 10 and 20 degrees C. However, cooperativity is substantially altered over the same range of pHs at the two temperatures. The allosteric properties were examined by comparing the experimental data points to curves generated by use of the Monod-Wyman-Changeux model. A computer-fitting process was developed which allowed the individual allosteric parameters to be varied independently until the best fit could be determined. The relationship between kR and kT is responsible for the effect of pH on cooperativity. A change in the allosteric properties of the T form is primarily responsible for the differences due to temperature. Changing cation concentrations when the molecule is in the fully aggregated 51S form alters affinity without influencing cooperativity. The effect of Mg2+ is much greater than that of Na+. If the 51S decamer is dissociated to 11S monomers by removing divalent cations, oxygen binding is noncooperative. There is evidence for negative cooperativity, indicating heterogeneity of function within the subunit which contains seven oxygen binding domains. Association into decamers generates conformational change which results in a much wider range of allosteric function.

  4. Discovery of two low-luminosity star clusters in the Milky Way halo

    NASA Astrophysics Data System (ADS)

    Kim, Dongwon

    2015-08-01

    Star clusters in the halo of the Milky Way (MW) hold important clues to the formation and structure of their host galaxy. In the talk, I present the discovery of two new low-luminosity star clusters in the inner and outer halo of the Milky Way. These two star clusters, named as Kim 1 and Kim 2, were first detected in the Sloan Digital Sky Survey and our independent 500 sqr degree survey using the Dark Energy Survey camera (DECam) at the 4m Blanco telescope at CTIO repectively. Their true identies were confirmed by deep follow-up imaging using DECam and Gemini-South 8-m telescope. Kim 1 and Kim 2 both exhibit unsual physical properties compared to other classically known star clusters. Kim 1, located at a heliocentric distance of 17 kpc, features extremely low luminosity (Mv~0.3 mag) and low star concentration. Together with the high ellipticity (e ~ 0.4) and irregular isophotes, these properties suggest that we are seeing an intermediate mass star cluster being stripped by the Galactic tidal field. In the case of Kim 2, ~ 104 kpc away from the sun, is the faintest globular cluster ever found in the outer halo of the Milky Way. The globular cluster exhibits evidence of significant mass loss such as extra-tidal stars and mass-segregation. The observed properties of the new star cluster also raise the question about how such a low luminosity star cluster could have survived until today. One possible scenario is that Kim 2 is a star cluster originally located in a satellite dwarf galaxy and was accreted into the Milky Way's halo.

  5. Is Flat fielding Safe for Precision CCD Astronomy?

    NASA Astrophysics Data System (ADS)

    Baumer, Michael; Davis, Christopher P.; Roodman, Aaron

    2017-08-01

    The ambitious goals of precision cosmology with wide-field optical surveys such as the Dark Energy Survey (DES) and the Large Synoptic Survey Telescope (LSST) demand precision CCD astronomy as their foundation. This in turn requires an understanding of previously uncharacterized sources of systematic error in CCD sensors, many of which manifest themselves as static effective variations in pixel area. Such variation renders a critical assumption behind the traditional procedure of flat fielding—that a sensor’s pixels comprise a uniform grid—invalid. In this work, we present a method to infer a curl-free model of a sensor’s underlying pixel grid from flat-field images, incorporating the superposition of all electrostatic sensor effects—both known and unknown—present in flat-field data. We use these pixel grid models to estimate the overall impact of sensor systematics on photometry, astrometry, and PSF shape measurements in a representative sensor from the Dark Energy Camera (DECam) and a prototype LSST sensor. Applying the method to DECam data recovers known significant sensor effects for which corrections are currently being developed within DES. For an LSST prototype CCD with pixel-response non-uniformity (PRNU) of 0.4%, we find the impact of “improper” flat fielding on these observables is negligible in nominal .7″ seeing conditions. These errors scale linearly with the PRNU, so for future LSST production sensors, which may have larger PRNU, our method provides a way to assess whether pixel-level calibration beyond flat fielding will be required.

  6. An identification in fish of the genus Puntius Hamilton 1822 (Cypriniformes: Cyprinidae) of some wetlands in northeast Thailand with the use of random amplified polymorphic DNA technique.

    PubMed

    Champasri, T; Rapley, R; Duangjinda, M; Suksri, A

    2008-02-15

    The experiment was carried out during the 2003 to 2006 at the Department of Fisheries, Khon Kaen University, Khon Kaen, Thailand in collaboration with the Department of Biosciences, the University of Hertfordshire, College Land, Hatfield, Herts, UK. Molecular RAPD technique was used for the determinations of DNA patterns of the fish genus Puntius Hamilton 1822. The fish samples of 1,500 individual fish were collected from fifteen wetlands in Northeast Thailand and they were used for DNA extraction. Before the experiment was carried out the fish samples were morphologically identified and it was found that the collected fish consisted of 9 species i.e., Puntius altus, P. aurotaeniatus, P. binotatus, P. gonionotus, (e) P. leiacanthus, P. orphoides, P. partipentazona, P. schwanenfeldi and P. wetmorei. Genomic DNAs were extracted from 5 mg of muscle tissues (skeleton muscles) with the use of PUREGENE DNA Isolation Kit for Laboratory Use, Gentra Systems, USA. Eighty decamer primers from four kits were subjected to a preliminary test. It was found that only 10 decamer primers were most suited for this PCR amplification. The results showed that genetic distant values being established among and between pairs of the fishes of the 9 fish species ranged from 0.191 to 0.456 for a pair between Puntius gonionotus and Puntius altus and a pair between Puntius schwanenfeldi and Puntius leiacanthus, respectively. Similarity coefficient values within the 9 fish species ranged from 0.109 to 0.231. The results on a Dendrogram of clusters showed that there were 5 minor groups of the 9 fish species but the 9 species could not be split or shifted into other genera of the fish due to small differences found within the values of similarity coefficients.

  7. Activity of purified hepatitis C virus protease NS3 on peptide substrates.

    PubMed Central

    Steinkühler, C; Urbani, A; Tomei, L; Biasiol, G; Sardana, M; Bianchi, E; Pessi, A; De Francesco, R

    1996-01-01

    The protease domain of the hepatitis C virus (HCV) protein NS3 was expressed in Escherichia coli, purified to homogeneity, and shown to be active on peptides derived from the sequence of the NS4A-NS4B junction. Experiments were carried out to optimize protease activity. Buffer requirements included the presence of detergent, glycerol, and dithiothreitol, pH between 7.5 and 8.5, and low ionic strength. C- and N-terminal deletion experiments defined a peptide spanning from the P6 to the P4' residue as a suitable substrate. Cleavage kinetics were subsequently measured by using decamer P6-P4' peptides corresponding to all intermolecular cleavage sites of the HCV polyprotein. The following order of cleavage efficiency, in terms of kcat/Km, was determined: NS5A-NS5B > NS4A-NS4B >> NS4B-NS5A. A 14-mer peptide containing residues 21 to 34 of the protease cofactor NS4A (Pep4A 21-34), when added in stoichiometric amounts, was shown to increase cleavage rates of all peptides, the largest effect (100-fold) being observed on the hydrolysis of the NS4B-NS5A decamer. From the kinetic analysis of cleavage data, we conclude that (i) primary structure is an important determinant of the efficiency with which each site is cleaved during polyprotein processing, (ii) slow cleavage of the NS4B-NS5A site in the absence of NS4A is due to low binding affinity of the enzyme for this site, and (iii) formation of a 1:1 complex between the protease and Pep4A 21-34 is sufficient and required for maximum activation. PMID:8794305

  8. Is flat fielding safe for precision CCD astronomy?

    DOE PAGES

    Baumer, Michael; Davis, Christopher P.; Roodman, Aaron

    2017-07-06

    The ambitious goals of precision cosmology with wide-field optical surveys such as the Dark Energy Survey (DES) and the Large Synoptic Survey Telescope (LSST) demand precision CCD astronomy as their foundation. This in turn requires an understanding of previously uncharacterized sources of systematic error in CCD sensors, many of which manifest themselves as static effective variations in pixel area. Such variation renders a critical assumption behind the traditional procedure of flat fielding—that a sensor's pixels comprise a uniform grid—invalid. In this work, we present a method to infer a curl-free model of a sensor's underlying pixel grid from flat-field images,more » incorporating the superposition of all electrostatic sensor effects—both known and unknown—present in flat-field data. We use these pixel grid models to estimate the overall impact of sensor systematics on photometry, astrometry, and PSF shape measurements in a representative sensor from the Dark Energy Camera (DECam) and a prototype LSST sensor. Applying the method to DECam data recovers known significant sensor effects for which corrections are currently being developed within DES. For an LSST prototype CCD with pixel-response non-uniformity (PRNU) of 0.4%, we find the impact of "improper" flat fielding on these observables is negligible in nominal .7'' seeing conditions. Furthermore, these errors scale linearly with the PRNU, so for future LSST production sensors, which may have larger PRNU, our method provides a way to assess whether pixel-level calibration beyond flat fielding will be required.« less

  9. Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ16−22 and Sup357−13 in AOT reverse micelles

    PubMed Central

    Martinez, Anna Victoria; Małolepsza, Edyta; Rivera, Eva; Lu, Qing; Straub, John E.

    2014-01-01

    Knowledge of how intermolecular interactions of amyloid-forming proteins cause protein aggregation and how those interactions are affected by sequence and solution conditions is essential to our understanding of the onset of many degenerative diseases. Of particular interest is the aggregation of the amyloid-β (Aβ) peptide, linked to Alzheimer's disease, and the aggregation of the Sup35 yeast prion peptide, which resembles the mammalian prion protein linked to spongiform encephalopathies. To facilitate the study of these important peptides, experimentalists have identified small peptide congeners of the full-length proteins that exhibit amyloidogenic behavior, including the KLVFFAE sub-sequence, Aβ16−22, and the GNNQQNY subsequence, Sup357−13. In this study, molecular dynamics simulations were used to examine these peptide fragments encapsulated in reverse micelles (RMs) in order to identify the fundamental principles that govern how sequence and solution environment influence peptide aggregation. Aβ16−22 and Sup357−13 are observed to organize into anti-parallel and parallel β-sheet arrangements. Confinement in the sodium bis(2-ethylhexyl) sulfosuccinate (AOT) reverse micelles is shown to stabilize extended peptide conformations and enhance peptide aggregation. Substantial fluctuations in the reverse micelle shape are observed, in agreement with earlier studies. Shape fluctuations are found to facilitate peptide solvation through interactions between the peptide and AOT surfactant, including direct interaction between non-polar peptide residues and the aliphatic surfactant tails. Computed amide I IR spectra are compared with experimental spectra and found to reflect changes in the peptide structures induced by confinement in the RM environment. Furthermore, examination of the rotational anisotropy decay of water in the RM demonstrates that the water dynamics are sensitive to the presence of peptide as well as the peptide sequence. Overall, our results

  10. Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ16-22 and Sup357-13 in AOT reverse micelles

    NASA Astrophysics Data System (ADS)

    Martinez, Anna Victoria; Małolepsza, Edyta; Rivera, Eva; Lu, Qing; Straub, John E.

    2014-12-01

    Knowledge of how intermolecular interactions of amyloid-forming proteins cause protein aggregation and how those interactions are affected by sequence and solution conditions is essential to our understanding of the onset of many degenerative diseases. Of particular interest is the aggregation of the amyloid-β (Aβ) peptide, linked to Alzheimer's disease, and the aggregation of the Sup35 yeast prion peptide, which resembles the mammalian prion protein linked to spongiform encephalopathies. To facilitate the study of these important peptides, experimentalists have identified small peptide congeners of the full-length proteins that exhibit amyloidogenic behavior, including the KLVFFAE sub-sequence, Aβ16-22, and the GNNQQNY subsequence, Sup357-13. In this study, molecular dynamics simulations were used to examine these peptide fragments encapsulated in reverse micelles (RMs) in order to identify the fundamental principles that govern how sequence and solution environment influence peptide aggregation. Aβ16-22 and Sup357-13 are observed to organize into anti-parallel and parallel β-sheet arrangements. Confinement in the sodium bis(2-ethylhexyl) sulfosuccinate (AOT) reverse micelles is shown to stabilize extended peptide conformations and enhance peptide aggregation. Substantial fluctuations in the reverse micelle shape are observed, in agreement with earlier studies. Shape fluctuations are found to facilitate peptide solvation through interactions between the peptide and AOT surfactant, including direct interaction between non-polar peptide residues and the aliphatic surfactant tails. Computed amide I IR spectra are compared with experimental spectra and found to reflect changes in the peptide structures induced by confinement in the RM environment. Furthermore, examination of the rotational anisotropy decay of water in the RM demonstrates that the water dynamics are sensitive to the presence of peptide as well as the peptide sequence. Overall, our results

  11. Effect of electrostatics on aggregation of prion protein Sup35 peptide

    NASA Astrophysics Data System (ADS)

    Portillo, Alexander M.; Krasnoslobodtsev, Alexey V.; Lyubchenko, Yuri L.

    2012-04-01

    Self-assembly of misfolded proteins into ordered fibrillar structures is a fundamental property of a wide range of proteins and peptides. This property is also linked with the development of various neurodegenerative diseases such as Alzheimer’s and Parkinson’s. Environmental conditions modulate the misfolding and aggregation processes. We used a peptide, CGNNQQNY, from yeast prion protein Sup35, as a model system to address effects of environmental conditions on aggregate formation. The GNNQQNY peptide self-assembles in fibrils with structural features that are similar to amyloidogenic proteins. Atomic force microscopy (AFM) and thioflavin T (ThT) fluorescence assay were employed to follow the aggregation process at various pHs and ionic strengths. We also used single molecule AFM force spectroscopy to probe interactions between the peptides under various conditions. The ThT fluorescence data showed that the peptide aggregates fast at pH values approaching the peptide isoelectric point (pI = 5.3) and the kinetics is 10 times slower at acidic pH (pH 2.0), suggesting that electrostatic interactions contribute to the peptide self-assembly into aggregates. This hypothesis was tested by experiments performed at low (11 mM) and high (150 mM) ionic strengths. Indeed, the aggregation lag time measured at pH 2 at low ionic strength (11 mM) is 195 h, whereas the lag time decreases ˜5 times when the ionic strength is increased to 150 mM. At conditions close to the pI value, pH 5.6, the aggregation lag time is 12 ± 6 h under low ionic strength, and there is minimal change to the lag time at 150 mM NaCl. The ionic strength also influences the morphology of aggregates visualized with AFM. In pH 2.0 and at high ionic strength, the aggregates are twofold taller than those formed at low ionic strength. In parallel, AFM force spectroscopy studies revealed minimal contribution of electrostatics to dissociation of transient peptide dimers.

  12. Ir-Uv Double Resonance Spectroscopy of a Cold Protonated Fibril-Forming Peptide: NNQQNY\\cdotH+

    NASA Astrophysics Data System (ADS)

    DeBlase, Andrew F.; Harrilal, Christopher P.; Walsh, Patrick S.; McLuckey, Scott A.; Zwier, Timothy S.

    2016-06-01

    Protein aggregation to form amyloid-like fibrils is a purported molecular manifestation that leads to Alzheimer's, Huntington's, and other neurodegenerative diseases. The propensity for a protein to aggregate is often driven by the presence of glutamine (Q) and asparagine (N) rich tracts within the primary sequence. For example, Eisenberg and coworkers [Nature 2006, 435, 773] have shown by X-ray crystallography that the peptides NNQQNY and GNNQQNY aggregate into a parallel β-sheet configuration with side chains that intercalate into a "steric zipper". These sequences are commonly found at the N-terminus of the prion-determining domain in the yeast protein Sup35, a typical fibril-forming protein. Herein, we invoke recent advances in cold ion spectroscopy to explore the nascent conformational preferences of the protonated peptides that are generated by electrospray ionization. Towards this aim, we have used UV and IR spectroscopy to record conformation-specific photofragment action spectra of the NNQQNY monomer cryogenically cooled in an octopole ion trap. This short peptide contains 20 hydride stretch oscillators, leading to a rich infrared spectrum with at least 18 resolved transitions in the 2800-3800 cm-1 region. The infrared spectrum suggests the presence of both a free acid OH moiety and an H-bonded tyrosine OH group. We compare our results with resonant ion dip infrared spectra (RIDIRS) of the acyl/NH-benzyl capped neutral glutamine amino acid and its corresponding dipeptide: Ac-Q-NHBn and Ac-QQ-NHBn, respectively. These comparisons bring empirical insight to the NH stretching region of the spectrum, which contains contributions from free and singly H-bonded NH2 side-chain groups, and from peptide backbone amide NH groups. We further compare our spectrum to harmonic calculations at the M05-2X/6-31+G* level of theory, which were performed on low energy structures obtained from Monte Carlo conformational searches using the Amber* and OPLS force fields to assess

  13. Screening a phage display library for a novel FGF8b-binding peptide with anti-tumor effect on prostate cancer

    SciTech Connect

    Wang, Wenhui; Chen, Xilei; Li, Tao; Li, Yanmei; Wang, Ruixue; He, Dan; Luo, Wu; Li, Xiaokun; Wu, Xiaoping

    2013-05-01

    Fibroblast growth factor 8b (FGF8b) is the major isoform of FGF8 expressed in prostate cancer and it correlates with the stage and grade of the disease. FGF8b has been considered as a potential target for prostate cancer therapy. Here we isolated 12 specific FGF8b-binding phage clones by screening a phage display heptapeptide library with FGF8b. The peptide (HSQAAVP, named as P12) corresponding to one of these clones showed high homology to the immunoglobulin-like (Ig-like) domain II(D2) of high-affinity FGF8b receptor (FGFR3c), contained 3 identical amino acids (AVP) to the authentic FGFR3 D2 sequence aa 163–169 (LLAVPAA) directly participating in ligand binding, carried the same charges as its corresponding motif (aa163–169) in FGFR3c, suggesting that P12 may have a greater potential to interrupt FGF8b binding to its receptors than other identified heptapeptides do. Functional analysis indicated that synthetic P12 peptides mediate significant inhibition of FGF8b-induced cell proliferation, arrest cell cycle at the G0/G1 phase via suppression of Cyclin D1 and PCNA, and blockade of the activations of Erk1/2 and Akt cascades in both prostate cancer cells and vascular endothelial cells. The results demonstrated that the P12 peptide acting as an FGF8b antagonist may have therapeutic potential in prostate cancer. - Highlights: ► A novel FGF8b-binding peptide P12 was isolated from a phage display library. ► The mechanisms for P12 peptide inhibiting cell proliferation were proposed. ► P12 caused cell cycle arrest at G0/G1 phase via suppression of Cyclin D1 and PCNA. ► P12 suppressed FGF8b-induced activations of Akt and MAP kinases. ► P12 acting as an FGF8b antagonist may have therapeutic potential in prostate cancer.

  14. Flexibility of Ras Lipid Modifications Studied by 2H Solid-State NMR and Molecular Dynamics Simulations

    PubMed Central

    Vogel, Alexander; Tan, Kui-Thong; Waldmann, Herbert; Feller, Scott E.; Brown, Michael F.; Huster, Daniel

    2007-01-01

    Human posttranslationally modified N-ras oncogenes are known to be implicated in numerous human cancers. Here, we applied a combination of experimental and computational techniques to determine structural and dynamical details of the lipid chain modifications of an N-ras heptapeptide in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) membranes. Experimentally, 2H NMR spectroscopy was used to study oriented membranes that incorporated ras heptapeptides with two covalently attached perdeuterated hexadecyl chains. Atomistic molecular dynamics simulations of the same system were carried out over 100 ns including 60 DMPC and 4 ras molecules. Several structural and dynamical experimental parameters could be directly compared to the simulation. Experimental and simulated 2H NMR order parameters for the methylene groups of the ras lipid chains exhibited a systematic difference attributable to the absence of collective motions in the simulation and to geometrical effects. In contrast, experimental 2H NMR spin-lattice relaxation rates for Zeeman order were well reproduced in the simulation. The lack of slower collective motions in the simulation did not appreciably influence the relaxation rates at a Larmor frequency of 115.1 MHz. The experimental angular dependence of the 2H NMR relaxation rates with respect to the external magnetic field was also relatively well simulated. These relaxation rates showed a weak angular dependence, suggesting that the lipid modifications of ras are very flexible and highly mobile in agreement with the low order parameters. To quantify these results, the angular dependence of the 2H relaxation rates was calculated by an analytical model considering both molecular and collective motions. Peptide dynamics in the membrane could be modeled by an anisotropic diffusion tensor with principal values of D‖ = 2.1 × 109 s−1 and D⊥ = 4.5 × 105 s−1. A viscoelastic fitting parameter describing the membrane elasticity, viscosity, and temperature

  15. Developing bifunctional beta-lactamase molecules with built-in target-recognizing module for prodrug therapy: identification of Enterobacter Cloacae P99 cephalosporinase loops suitable for randomization and phage-display selection.

    PubMed

    Shukla, Girja S; Krag, David N

    2009-01-01

    This study was focused on developing catalytically active beta-lactamase enzyme molecules that have target-recognizing sites built within their scaffold. Using phage-display approach, nine libraries were constructed by inserting the randomized linear or cysteine-constrained heptapeptides in the five different loops on the outer surface of P99 beta-lactamase molecule. The pIII signal peptide of Sec-pathway was employed for a periplasmic translocation of the beta-lactamase fusion protein, which we found more efficient than the DsbA signal peptide of SRP-pathway. The randomized heptapeptide loops replaced native amino acids between positions (34)Y-(37)K, (238)M-(246)A, (275)N-(280)A, (305)A-(311)S, or (329)I-(334)I of the P99 beta-lactamase molecules for generating the loop-1 to -5 libraries, respectively. The diversity of each loop library was judged by counting the primary and beta-lactamase-active clones. The linear peptide inserts in the loop-2 library showed the maximum number of the beta-lactamase-active clones, followed by the loop-5, loop-3, and loop-4. The insertion of the cysteine-constrained loops exhibited a dramatic loss of the enzyme-active beta-lactamase clones. The complexity of the loop-2 linear library, as determined by the frequency and diversity of amino acid distributions in the randomized region, appears consistent with the standards of other types of phage display library systems. The selection of the loop-2 linear library on streptavidin protein as a test target identified several beta-lactamase clones that specifically bound to streptavidin. In conclusion, this study identified the suitability of the loop-2 of P99 beta-lactamase for constructing a phage-display library of the beta-lactamase enzyme-active molecules that can be selected against a target. This is an enabling step in our long-term goal of developing bifunctional beta-lactamase molecules against cancer-specific targets for enzyme prodrug therapy of cancer.

  16. Chemical Synthesis and In Vitro Evaluation of a Phage Display-Derived Peptide Active against Infectious Salmon Anemia Virus

    PubMed Central

    Ojeda, Nicolás; Cárdenas, Constanza; Guzmán, Fanny

    2016-01-01

    ABSTRACT Infectious salmon anemia virus (ISAV) is the etiological agent of the disease by the same name and causes major losses in the salmon industry worldwide. Epizootic ISAV outbreaks have occurred in Norway and, to a lesser degree, in Canada. In 2007, an ISAV outbreak in Chile destroyed most of the seasonal production and endangered the entire Chilean salmon industry. None of the existing prophylactic approaches have demonstrated efficacy in providing absolute protection from or even a palliative effect on ISAV proliferation. Sanitary control measures for ISAV, based on molecular epidemiology data, have proven insufficient, mainly due to high salmon culture densities and a constant presence of a nonpathogenic strain of the virus. This report describes an alternative treatment approach based on interfering peptides selected from a phage display library. The screening of a phage display heptapeptide library resulted in the selection of a novel peptide with significant in vitro antiviral activity against ISAV. This peptide specifically interacted with the viral hemagglutinin-esterase protein, thereby impairing virus binding, with plaque reduction assays showing a significant reduction in viral yields. The identified peptide acts at micromolar concentrations against at least two different pathogenic strains of the virus, without detectable cytotoxic effects on the tested fish cells. Therefore, antiviral peptides represent a novel alternative for controlling ISAV and, potentially, other fish pathogens. IMPORTANCE Identifying novel methods for the efficient control of infectious diseases is imperative for the future of global aquaculture. The present study used a phage display heptapeptide library to identify a peptide with interfering activity against a key protein of the infectious salmon anemia virus (ISAV). A piscine orthomyxovirus, ISAV is a continuous threat to the commercial sustainability of cultured salmon production worldwide. The complex epidemiological

  17. Chemical Synthesis and In Vitro Evaluation of a Phage Display-Derived Peptide Active against Infectious Salmon Anemia Virus.

    PubMed

    Ojeda, Nicolás; Cárdenas, Constanza; Guzmán, Fanny; Marshall, Sergio H

    2016-04-01

    Infectious salmon anemia virus (ISAV) is the etiological agent of the disease by the same name and causes major losses in the salmon industry worldwide. Epizootic ISAV outbreaks have occurred in Norway and, to a lesser degree, in Canada. In 2007, an ISAV outbreak in Chile destroyed most of the seasonal production and endangered the entire Chilean salmon industry. None of the existing prophylactic approaches have demonstrated efficacy in providing absolute protection from or even a palliative effect on ISAV proliferation. Sanitary control measures for ISAV, based on molecular epidemiology data, have proven insufficient, mainly due to high salmon culture densities and a constant presence of a nonpathogenic strain of the virus. This report describes an alternative treatment approach based on interfering peptides selected from a phage display library. The screening of a phage display heptapeptide library resulted in the selection of a novel peptide with significant in vitro antiviral activity against ISAV. This peptide specifically interacted with the viral hemagglutinin-esterase protein, thereby impairing virus binding, with plaque reduction assays showing a significant reduction in viral yields. The identified peptide acts at micromolar concentrations against at least two different pathogenic strains of the virus, without detectable cytotoxic effects on the tested fish cells. Therefore, antiviral peptides represent a novel alternative for controlling ISAV and, potentially, other fish pathogens. Identifying novel methods for the efficient control of infectious diseases is imperative for the future of global aquaculture. The present study used a phage display heptapeptide library to identify a peptide with interfering activity against a key protein of the infectious salmon anemia virus (ISAV). A piscine orthomyxovirus, ISAV is a continuous threat to the commercial sustainability of cultured salmon production worldwide. The complex epidemiological strategy of this

  18. Measuring the Flatness of Focal Plane for Very Large Mosaic CCD Camera

    SciTech Connect

    Hao, Jiangang; Estrada, Juan; Cease, Herman; Diehl, H.Thomas; Flaugher, Brenna L.; Kubik, Donna; Kuk, Keivin; Kuropatkine, Nickolai; Lin, Huan; Montes, Jorge; Scarpine, Vic; /Fermilab

    2010-06-08

    Large mosaic multiCCD camera is the key instrument for modern digital sky survey. DECam is an extremely red sensitive 520 Megapixel camera designed for the incoming Dark Energy Survey (DES). It is consist of sixty two 4k x 2k and twelve 2k x 2k 250-micron thick fully-depleted CCDs, with a focal plane of 44 cm in diameter and a field of view of 2.2 square degree. It will be attached to the Blanco 4-meter telescope at CTIO. The DES will cover 5000 square-degrees of the southern galactic cap in 5 color bands (g, r, i, z, Y) in 5 years starting from 2011. To achieve the science goal of constraining the Dark Energy evolution, stringent requirements are laid down for the design of DECam. Among them, the flatness of the focal plane needs to be controlled within a 60-micron envelope in order to achieve the specified PSF variation limit. It is very challenging to measure the flatness of the focal plane to such precision when it is placed in a high vacuum dewar at 173 K. We developed two image based techniques to measure the flatness of the focal plane. By imaging a regular grid of dots on the focal plane, the CCD offset along the optical axis is converted to the variation the grid spacings at different positions on the focal plane. After extracting the patterns and comparing the change in spacings, we can measure the flatness to high precision. In method 1, the regular dots are kept in high sub micron precision and cover the whole focal plane. In method 2, no high precision for the grid is required. Instead, we use a precise XY stage moves the pattern across the whole focal plane and comparing the variations of the spacing when it is imaged by different CCDs. Simulation and real measurements show that the two methods work very well for our purpose, and are in good agreement with the direct optical measurements.

  19. High performance thin-layer chromatography-mass spectrometry of Japanese knotweed flavan-3-ols and proanthocyanidins on silica gel plates.

    PubMed

    Glavnik, Vesna; Vovk, Irena; Albreht, Alen

    2017-01-27

    On-line elution based TLC-MS is now a well-established technique, but the quality of the data obtained can sometimes be hampered by a severe spectral background or by strong ion suppression, especially when silica gel plates are used in combination with an acidic modifier in the developing solvent. We solved this issue simply and efficiently using two pre-developments of the plates, firstly with methanol-formic acid (10:1, v/v) and secondly with acetonitrile-methanol (2:1, v/v). This solution resulted in significant improvement in the sensitivity of HPTLC-MS methods. The applicability of this approach was proven on analysis of flavan-3-ols and proanthocyanidins in crude extracts of Japanese knotweed (Fallopia japonica Houtt.) rhizomes. Separations on HPTLC silica gel and HPTLC silica gel MS grade plates using developing solvents toluene-acetone-formic acid (3:3:1, 6:6:1, 3:6:1, v/v) and dichloromethane-acetone-formic acid (1:1:0.1, v/v) were followed by post-chromatographic derivatization with 4-dimethylaminocinnamaldehyde (DMACA) detection reagent. Examination of the stability of the analytes on the start confirmed that the plates should be developed immediately after the application of standards and sample test solutions. In a five hours stability testing after development we discovered an unexpected phenomenon of enhanced absorption at 280nm. However, based on an experiment with post-chromatographic derivatization with DMACA detection reagent, the analytes were proven to be sufficiently stable in the time frame of an HPTLC-MS analysis. This was important for development of the first HPTLC-MS and HPTLC-MS(n) methods for identification of flavan-3-ols and B-type proanthocyanidins from monomers up to decamers. For the first time, based on this research methodology, trimers, trimer gallates, tetramer gallates, pentamers, pentamer gallates, hexamers, hexamer gallates, heptamers, octamers, nonamers and decamers were tentatively identified in Japanese knotweed rhizomes

  20. Polymer-peptide delivery platforms: effect of oligopeptide orientation on polymer-based DNA delivery

    PubMed Central

    Parelkar, Sangram S.; Letteri, Rachel; Chan-Seng, Delphine; Zolochevska, Olga; Ellis, Jayne; Figueiredo, Marxa; Emrick, Todd

    2014-01-01

    The success of non-viral transfection using polymers hinges on efficient nuclear uptake of nucleic acid cargo and overcoming intra- and extracellular barriers. By incorporating PKKKRKV heptapeptide pendent groups as nuclear localization signals (NLS) on a polymer backbone, we demonstrate protein expression levels higher than obtained from JetPEI™ and Lipofectamine™ 2000, the latter being notorious for coupling high transfection efficiency with cytotoxicity. The orientation of the NLS peptide grafts markedly affected transfection performance. Polymers with the sequence attached to the backbone from the valine residue achieved higher nuclear translocation relative to those having the NLS groups attached in the opposite orientation. The differences in nuclear localization and DNA complexation strength between the two orientations correlated with a striking difference in protein expression, both in cell culture and in vivo. Polyplexes formed from these comb polymer structures exhibited transfection efficiencies superior to those of Lipofectamine 2000 but with greatly reduced toxicity. Moreover, these novel polymers enabled high reporter gene expression in mice when administered by intramuscular ultrasound-mediated delivery, demonstrating their therapeutic promise in vivo. PMID:24606402

  1. Genetic engineering of the branched fatty acid metabolic pathway of Bacillus subtilis for the overproduction of surfactin C14 isoform.

    PubMed

    Dhali, Debarun; Coutte, François; Arias, Anthony Argüelles; Auger, Sandrine; Bidnenko, Vladimir; Chataigné, Gabrielle; Lalk, Michael; Niehren, Joachim; de Sousa, Joana; Versari, Cristian; Jacques, Philippe

    2017-04-03

    Surfactin, a lipopeptide produced by Bacillus subtilis, is one of the most powerful biosurfactants known. This molecule consists of a cyclic heptapeptide linked to a β-hydroxy fatty acid chain. The isomery and the length of the fatty acid (FA) chain are responsible for the surfactin's activities. In this study, the gene codY, which encode for the global transcriptional regulator and the gene lpdV, located in the bkd operon (lpdV, bkdAA, bkdAB and bkdB genes), which is responsible for the last step of the branched chain amino acid (BCAA) degradation in acyl-CoA were deleted. The influence of these deletions on the quantitative and qualitative surfactin production was analysed. The surfactin production was quantified by RP-HPLC and the surfactin isoforms were characterized using LC-MS-MS and GC-MS analysis. The results obtained in the mutants showed an enhancement of surfactin specific production by a factor of 5.8 for the codY mutant and 1.4 for lpdV mutant. Moreover qualitative analysis of the lpdV mutant reveals that it mainly produced surfactin C14 isoform (2 fold more than the wild type) with linear FA chain. Complete analysis of the extracellular metabolites using (1) H quantitative NMR reveals a reduced production of acetoin in this mutant. This work demonstrates for the first time an original approach to overproduce specifically surfactin with C14 FA chain.

  2. Influence of the enzyme phosphorylation state and the substrate on PKA enzyme dynamics.

    PubMed

    Montenegro, Manuel; Masgrau, Laura; González-Lafont, Angels; Lluch, José M; Garcia-Viloca, Mireia

    2012-02-01

    cAMP-dependent protein kinase (PKA) is one of the simplest and best understood members of the protein kinase family. In a previous study, we have theoretically studied the complex between PKA and the heptapeptide substrate Kemptide by classical molecular dynamics. On the basis of the results obtained for Kemptide, the aim of the present work is to explore how the different conditions, such as phosphorylation state, substrate, and mutations of key residues affect the enzyme dynamics. We have built different models of the complex; particularly we have focused our attention on two crystallographic structures which main difference consists in their phosphorylation state. The first one has the residue Thr197 modified into a phospho-threonine (pThr197); the second one, in addition to the same Thr197, has also the residue Ser338 modified into a phospho-serine (pSer338). In addition, we have analyzed the effect of the choice of the substrate by building a model of the PKA-SP20 Michaelis complex. Finally, we have theoretically studied the effect of the mutation of the highly conserved residue Asp166 that, experimentally, leads to a decrease of the reaction rate. The results of this study give insight into the dynamical states of the enzyme and their relationship with different elements of the model, which correspond to different natural or human guided situations of the active biological system.

  3. Omnipotent decoding potential resides in eukaryotic translation termination factor eRF1 of variant-code organisms and is modulated by the interactions of amino acid sequences within domain 1.

    PubMed

    Ito, Koichi; Frolova, Ludmila; Seit-Nebi, Alim; Karamyshev, Andrey; Kisselev, Lev; Nakamura, Yoshikazu

    2002-06-25

    In eukaryotes, a single translational release factor, eRF1, deciphers three stop codons, although its decoding mechanism remains puzzling. In the ciliate Tetrahymena thermophila, UAA and UAG codons are reassigned to Gln codons. A yeast eRF1-domain swap containing Tetrahymena domain 1 responded only to UGA in vitro and failed to complement a defect in yeast eRF1 in vivo at 37 degrees C. This finding demonstrates that decoding specificity of eRF1 from variant code organisms resides at domain 1. However, the wild-type eRF1 hybrid fully restored the growth of eRF1-deficient yeast at 30 degrees C. Tetrahymena eRF1 contains a variant sequence, KATNIKD, at the tip of domain 1. The TASNIKD variant of hybrid eRF1 rendered the eRF1-nullified yeast viable, although in an in vitro assay, the same hybrid eRF1 responded only to UGA. Nevertheless, the yeast eRF1 bearing the KATNIKD motif instead of the TASNIKS heptapeptide present in higher eukaryotes remains omnipotent in vivo. Collectively, these data suggest that variant genetic code organisms like Tetrahymena have an intrinsic potential to decode three stop codons in vivo, and that interaction within domain 1 between the KAT tripeptide and other sequences modulates the decoding specificity of Tetrahymena eRF1.

  4. 1,4-Disubstituted-[1,2,3]triazolyl-Containing Analogues of MT-II: Design, Synthesis, Conformational Analysis, and Biological Activity

    PubMed Central

    2015-01-01

    Side chain-to-side chain cyclizations represent a strategy to select a family of bioactive conformations by reducing the entropy and enhancing the stabilization of functional ligand-induced receptor conformations. This structural manipulation contributes to increased target specificity, enhanced biological potency, improved pharmacokinetic properties, increased functional potency, and lowered metabolic susceptibility. The CuI-catalyzed azide–alkyne 1,3-dipolar Huisgen’s cycloaddition, the prototypic click reaction, presents a promising opportunity to develop a new paradigm for an orthogonal bioorganic and intramolecular side chain-to-side chain cyclization. In fact, the proteolytic stable 1,4- or 4,1-disubstituted [1,2,3]triazolyl moiety is isosteric with the peptide bond and can function as a surrogate of the classical side chain-to-side chain lactam forming bridge. Herein we report the design, synthesis, conformational analysis, and functional biological activity of a series of i-to-i+5 1,4- and 4,1-disubstituted [1,2,3]triazole-bridged cyclopeptides derived from MT-II, the homodetic Asp5 to Lys10 side chain-to-side chain bridged heptapeptide, an extensively studied agonist of melanocortin receptors. PMID:25347033

  5. A plasmid-borne Rap-Phr system regulates sporulation of Bacillus thuringiensis in insect larvae.

    PubMed

    Fazion, Fernanda; Perchat, Stéphane; Buisson, Christophe; Vilas-Bôas, Gislayne; Lereclus, Didier

    2017-10-02

    The entomopathogen Bacillus thuringiensis specie harbours numerous plasmids essentially studied for their involvement in pathogenicity, as Cry-plasmids. The lifecycle of B. thuringiensis in the insect host is regulated by the sequential activation of quorum sensing systems to kill, survive and sporulate. In this study, we characterize a new quorum sensing system belonging to the Rap-Phr family. The Rap8-Phr8 system is borne by the pHT8_1 plasmid, a small cryptic plasmid from the B. thuringiensis var. kurstaki HD73 strain. Our results demonstrate that the Rap8 protein inhibits sporulation and biofilm formation through the Spo0A pathway. The Rap8 activity is inhibited by the mature Phr8 heptapeptide YAHGKDI. The key residues specific for the Rap phosphatase activity are conserved in Rap8 suggesting a common mode of action. Interestingly, we show that the Rap8-Phr8 system is specifically required for regulating sporulation of B. thuringiensis in insect larvae. This system may allow the bacteria to exert a tight control of the sporulation process in the host cadaver for optimizing the multiplication, the survival and the dissemination of the bacteria. Thus, our results suggest that pHT8_1 provides advantages for adaptation and evolution of B. thuringiensis in its ecological niche. This article is protected by copyright. All rights reserved. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  6. Comparison of the level of residual coagulant activity in different cheese varieties.

    PubMed

    Bansal, Nidhi; Fox, Patrick F; McSweeney, Paul L H

    2009-08-01

    The coagulant retained in cheese curd is a major contributor to proteolysis during ripening. The objective of this study was to quantify residual coagulant in 9 cheese varieties by measuring its activity on a synthetic heptapeptide (Pro-Thr-Glu-Phe-[NO2-Phe]-Arg-Leu) assayed using reversed-phase HPLC. The level of residual coagulant activity was highest in Camembert cheese, probably due to its low pH at whey drainage and the high moisture content of the cheese, followed in order by Feta=Port du Salut=Cheddar>Gouda>Emmental=Parmigiano Reggiano=low-moisture part-skim Mozzarella=Mozzarella di Bufala Campana. The high cooking temperature (50-54 degrees C) used during the manufacture of Emmental and Parmigiano Reggiano cheeses and the cooking and stretching step in hot water during the manufacture of Mozzarella cheese may be the reasons for the lowest residual coagulant activity in these cheeses. The level of residual coagulant activity was higher in Feta cheese made from milk concentrated by ultrafiltration than in conventional Feta.

  7. Molluscan attractins, a family of water-borne protein pheromones with interspecific attractiveness.

    PubMed

    Cummins, Scott F; Schein, Catherine H; Xu, Yuan; Braun, Werner; Nagle, Gregg T

    2005-01-01

    The marine mollusk Aplysia releases the water-borne pheromone attractin during egg laying. This small protein stimulates the formation and maintenance of mating and egg-laying aggregations. Attractin has been characterized from five Aplysia species: A. californica, A. brasiliana, A. fasciata, A. vaccaria, and A. depilans. We describe here the isolation of attractin from Bursatella leachii, and show that it belongs to the same protein family. The pattern of residue conservation, especially the six invariant cysteines, suggests that all of these attractins have a common fold. The nuclear magnetic resonance solution structure of A. californica attractin contains two antiparallel alpha-helices, the second of which contains the heptapeptide sequence IEECKTS that has been implicated in attractin function. Synthetic peptides containing this IEECKTS region are attractive, and mutating surface exposed charged residues within this region of attractin abolishes attractin activity. This suggests that the second helix is an essential part of the receptor-binding interface. In contrast to the peptide pheromonal attractants in amphibians, which are species specific, the attractins are, to our knowledge, the first water-borne peptide or protein pheromone family in invertebrates and vertebrates that are not species specific.

  8. The histone chaperone sNASP binds a conserved peptide motif within the globular core of histone H3 through its TPR repeats

    PubMed Central

    Bowman, Andrew; Lercher, Lukas; Singh, Hari R.; Zinne, Daria; Timinszky, Gyula; Carlomagno, Teresa; Ladurner, Andreas G.

    2016-01-01

    Eukaryotic chromatin is a complex yet dynamic structure, which is regulated in part by the assembly and disassembly of nucleosomes. Key to this process is a group of proteins termed histone chaperones that guide the thermodynamic assembly of nucleosomes by interacting with soluble histones. Here we investigate the interaction between the histone chaperone sNASP and its histone H3 substrate. We find that sNASP binds with nanomolar affinity to a conserved heptapeptide motif in the globular domain of H3, close to the C-terminus. Through functional analysis of sNASP homologues we identified point mutations in surface residues within the TPR domain of sNASP that disrupt H3 peptide interaction, but do not completely disrupt binding to full length H3 in cells, suggesting that sNASP interacts with H3 through additional contacts. Furthermore, chemical shift perturbations from 1H-15N HSQC experiments show that H3 peptide binding maps to the helical groove formed by the stacked TPR motifs of sNASP. Our findings reveal a new mode of interaction between a TPR repeat domain and an evolutionarily conserved peptide motif found in canonical H3 and in all histone H3 variants, including CenpA and have implications for the mechanism of histone chaperoning within the cell. PMID:26673727

  9. Crystal structure of a phenol-coupling P450 monooxygenase involved in teicoplanin biosynthesis

    SciTech Connect

    Li, Zhi; Rupasinghe, Sanjeewa G.; Schuler, Mary A.; Nair, Satish K.

    2012-02-08

    The lipoglycopeptide antibiotic teicoplanin has proven efficacy against gram-positive pathogens. Teicoplanin is distinguished from the vancomycin-type glycopeptide antibiotics, by the presence of an additional cross-link between the aromatic amino acids 1 and 3 that is catalyzed by the cytochrome P450 monooxygenase Orf6* (CYP165D3). As a goal towards understanding the mechanism of this phenol-coupling reaction, we have characterized recombinant Orf6* and determined its crystal structure to 2.2-{angstrom} resolution. Although the structure of Orf6* reveals the core fold common to other P450 monooxygenases, there are subtle differences in the disposition of secondary structure elements near the active site cavity necessary to accommodate its complex heptapeptide substrate. Specifically, the orientation of the F and G helices in Orf6* results in a more closed active site than found in the vancomycin oxidative enzymes OxyB and OxyC. In addition, Met226 in the I helix replaces the more typical Gly/Ala residue that is positioned above the heme porphyrin ring, where it forms a hydrogen bond with a heme iron-bound water molecule. Sequence comparisons with other phenol-coupling P450 monooxygenases suggest that Met226 plays a role in determining the substrate regiospecificity of Orf6*. These features provide further insights into the mechanism of the cross-linking mechanisms that occur during glycopeptide antibiotics biosynthesis.

  10. Water-membrane partition thermodynamics of an amphiphilic lipopeptide: an enthalpy-driven hydrophobic effect.

    PubMed

    Gorfe, Alemayehu A; Baron, Riccardo; McCammon, J Andrew

    2008-10-01

    To shed light on the driving force for the hydrophobic effect that partitions amphiphilic lipoproteins between water and membrane, we carried out an atomically detailed thermodynamic analysis of a triply lipid modified H-ras heptapeptide anchor (ANCH) in water and in a DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) bilayer. Combining molecular mechanical and continuum solvent approaches with an improved technique for solute entropy calculation, we obtained an overall transfer free energy of approximately -13 kcal mol(-1). This value is in qualitative agreement with free energy changes derived from a potential of mean force calculation and indirect experimental observations. Changes in free energies of solvation and ANCH conformational reorganization are unfavorable, whereas ANCH-DMPC interactions-especially van der Waals-favor insertion. These results are consistent with an enthalpy-driven hydrophobic effect, in accord with earlier calorimetric data on the membrane partition of other amphiphiles. Furthermore, structural and entropic analysis of molecular dynamics-generated ensembles suggests that conformational selection may play a hitherto unappreciated role in membrane insertion of lipid-modified peptides and proteins.

  11. Potentiometric and spectroscopic studies on the copper(II) complexes of rat amylin fragments. The anchoring ability of specific non-coordinating side chains.

    PubMed

    Dávid, Ágnes; Kállay, Csilla; Sanna, Daniele; Lihi, Norbert; Sóvágó, Imre; Várnagy, Katalin

    2015-10-21

    Copper(ii) complexes of peptides modelling the sequence of the 17-22 residues of rat amylin have been studied by potentiometric, UV-Vis, CD and ESR spectroscopic methods. The peptides were synthesized in N-terminally free forms, NH2-VRSSNN-NH2, NH2-VRSSAA-NH2, NH2-VRAANN-NH2, NH2-VRSS-NH2, NH2-SSNN-NH2, NH2-SSNA-NH2 and NH2-AANN-NH2, providing a possibility for the comparison of the metal binding abilities of the amino terminus and the -SSNN- domain. The amino terminus was the primary ligating site in all cases and the formation of only mononuclear complexes was obtained for the tetrapeptides. The thermodynamic stability of the (NH2, N(-), N(-)) coordinated complexes was, however, enhanced by the asparaginyl moiety in the case of NH2-SSNN-NH2, NH2-SSNA-NH2 and NH2-AANN-NH2. Among the hexapeptides the formation of dinuclear complexes was characteristic for NH2-VRSSNN-NH2 demonstrating the anchoring ability of the -SSNN- (SerSerAsnAsn) domain. The complexes of the heptapeptide NH2-GGHSSNN-NH2 were also studied and the data supported the above mentioned anchoring ability of the -SSNN- site.

  12. Alteration in the Expression of Cytochrome P450s (CYP1A1, CYP2E1, and CYP3A11) in the Liver of Mouse Induced by Microcystin-LR

    PubMed Central

    Zhang, Bangjun; Liu, Yang; Li, Xiaoyu

    2015-01-01

    Microcystins (MCs) are cyclic heptapeptide toxins and can accumulate in the liver. Cytochrome P450s (CYPs) play an important role in the biotransformation of endogenous substances and xenobiotics in animals. It is unclear if the CYPs are affected by MCs exposure. The objective of this study was to evaluate the effects of microcystin-LR (MCLR) on cytochrome P450 isozymes (CYP1A1, CYP2E1, and CYP3A11) at mRNA level, protein content, and enzyme activity in the liver of mice the received daily, intraperitoneally, 2, 4, and 8 µg/kg body weight of MCLR for seven days. The result showed that MCLR significantly decreased ethoxyresorufin-O-deethylase (EROD) (CYP1A1) and erythromycin N-demthylase (ERND) (CYP3A11) activities and increased aniline hydroxylase (ANH) activity (CYP2E1) in the liver of mice during the period of exposure. Our findings suggest that MCLR exposure may disrupt the function of CYPs in liver, which may be partly attributed to the toxicity of MCLR in mice. PMID:25831226

  13. Colocalization of Amanitin and a Candidate Toxin-Processing Prolyl Oligopeptidase in Amanita Basidiocarps ▿

    PubMed Central

    Luo, Hong; Hallen-Adams, Heather E.; Scott-Craig, John S.; Walton, Jonathan D.

    2010-01-01

    Fungi in the basidiomycetous genus Amanita owe their high mammalian toxicity to the bicyclic octapeptide amatoxins such as α-amanitin. Amatoxins and the related phallotoxins (such as the heptapeptide phalloidin) are encoded by members of the “MSDIN” gene family and are synthesized on ribosomes as short (34- to 35-amino-acid) proproteins. Antiamanitin antibodies and confocal microscopy were used to determine the cellular and subcellular localizations of amanitin accumulation in basidiocarps (mushrooms) of the Eastern North American destroying angel (Amanita bisporigera). Consistent with previous studies, amanitin is present throughout the basidiocarp (stipe, pileus, lamellae, trama, and universal veil), but it is present in only a subset of cells within these tissues. Restriction of amanitin to certain cells is especially marked in the hymenium. Several lines of evidence implicate a specific prolyl oligopeptidase, A. bisporigera POPB (AbPOPB), in the initial processing of the amanitin and phallotoxin proproteins. The gene for AbPOPB is restricted taxonomically to the amatoxin-producing species of Amanita and is clustered in the genome with at least one expressed member of the MSDIN gene family. Immunologically, amanitin and AbPOPB show a high degree of colocalization, indicating that toxin biosynthesis and accumulation occur in the same cells and possibly in the same subcellular compartments. PMID:20889720

  14. Primary structures of skin antimicrobial peptides indicate a close, but not conspecific, phylogenetic relationship between the leopard frogs Lithobates onca and Lithobates yavapaiensis (Ranidae).

    PubMed

    Conlon, J Michael; Coquet, Laurent; Leprince, Jérôme; Jouenne, Thierry; Vaudry, Hubert; King, Jay D

    2010-04-01

    The phylogenetic relationship between the relict leopard frog Lithobates (Rana) onca (Cope, 1875) and the lowland leopard frog Lithobates (Rana) yavapaiensis (Platz and Frost, 1984) is unclear. Chromatographic analysis of norepinephrine-stimulated skin secretions from L. onca led to the identification of six peptides with antimicrobial activity. Determination of their primary structures indicated that four of the peptides were identical to brevinin-1Ya, brevinin-1Yb, brevinin-1Yc and ranatuerin-2Ya previously isolated from skin secretions of L. yavapaiensis. However, a peptide belonging to the temporin family (temporin-ONa: FLPTFGKILSGLF.NH(2)) and an atypical member of the ranatuerin-2 family containing a C-terminal cyclic heptapeptide domain (ranatuerin-2ONa: GLMDTVKNAAKNLAGQMLDKLKCKITGSC) were isolated from the L. onca secretions but were not present in the L. yavapaiensis secretions. Ranatuerin-2ONa inhibited the growth of Escherichia coli (MIC=50muM) and Candida albicans (MIC=100muM ) and showed hemolytic activity (LC(50)=90muM) but was inactive against Staphylococcus aureus. The data indicate a close phylogenetic relationship between L. onca and L. yavapaiensis but suggest that they are not conspecific species.

  15. Conserved hydrogen bonds and water molecules in MDR HIV-1 protease substrate complexes

    SciTech Connect

    Liu, Zhigang; Wang, Yong; Yedidi, Ravikiran S.; Dewdney, Tamaria G.; Reiter, Samuel J.; Brunzelle, Joseph S.; Kovari, Iulia A.; Kovari, Ladislau C.

    2012-12-19

    Success of highly active antiretroviral therapy (HAART) in anti-HIV therapy is severely compromised by the rapidly developing drug resistance. HIV-1 protease inhibitors, part of HAART, are losing their potency and efficacy in inhibiting the target. Multi-drug resistant (MDR) 769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, 90) was selected for the present study to understand the binding to its natural substrates. The nine crystal structures of MDR769 HIV-1 protease substrate hepta-peptide complexes were analyzed in order to reveal the conserved structural elements for the purpose of drug design against MDR HIV-1 protease. Our structural studies demonstrated that highly conserved hydrogen bonds between the protease and substrate peptides, together with the conserved crystallographic water molecules, played a crucial role in the substrate recognition, substrate stabilization and protease stabilization. Additionally, the absence of the key flap-ligand bridging water molecule might imply a different catalytic mechanism of MDR769 HIV-1 protease compared to that of wild type (WT) HIV-1 protease.

  16. Nine Crystal Structures Determine the Substrate Envelope of the MDR HIV-1 Protease

    SciTech Connect

    Liu, Zhigang; Wang, Yong; Brunzelle, Joseph; Kovari, Iulia A.; Kovari, Ladislau C.

    2012-03-27

    Under drug selection pressure, emerging mutations render HIV-1 protease drug resistant, leading to the therapy failure in anti-HIV treatment. It is known that nine substrate cleavage site peptides bind to wild type (WT) HIV-1 protease in a conserved pattern. However, how the multidrug-resistant (MDR) HIV-1 protease binds to the substrate cleavage site peptides is yet to be determined. MDR769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, and 90) was selected for present study to understand the binding to its natural substrates. MDR769 HIV-1 protease was co-crystallized with nine substrate cleavage site hepta-peptides. Crystallographic studies show that MDR769 HIV-1 protease has an expanded substrate envelope with wide open flaps. Furthermore, ligand binding energy calculations indicate weaker binding in MDR769 HIV-1 protease-substrate complexes. These results help in designing the next generation of HIV-1 protease inhibitors by targeting the MDR HIV-1 protease.

  17. A comprehensive immunoassay for the detection of microcystins in waters based on polyclonal antibodies.

    PubMed

    Sheng, Jian-Wu; He, Miao; Shi, Han-Chang; Qian, Yi

    2006-07-21

    Microcystins (MCs) are a group of closely related toxic cyclic heptapeptides produced by common cyanobacteria (blue-green algae), and microcystin-leucine-arginine (MC-LR) is among the most frequent and most toxic microcystin congeners. In this study, a free amino group was introduced to MC-LR at its seventh amino acid residue with 2-mercaptoethylamine, and the product aminoethyl-MC-LR was coupled to bovine serum albumin (BSA) and horseradish peroxidise (HRP) by glutaraldehyde to be complete antigen (MC-LR-BSA) and labelled hapten (MC-LR-HRP), respectively. Polyclonal antibodies against MC-LR were generated by immunization with MC-LR-BSA. A direct competitive enzyme-linked immunosorbent assay (dc-ELISA) was established to detect the MCs in waters, which showed a good cross-reactivity with MC-LR, MC-RR, MC-YR, MC-LF, MC-LW and nodularin, and have a detection limit for MC-LR 0.12 microg L(-1), the 50% inhibition concentration (IC50) for MC-LR was 0.63+/-0.06 microg L(-1) and the quantitative detection range was from 0.17 to 2.32 microg L(-1), the analysis result of water samples showed good recovery and reliability. So the comprehensive and reliable dc-ELISA will well potentially suit for sensitive analysis for total MCs in drinking as well as resource water samples.

  18. Structural studies of α-melanocyte-stimulating hormone and a novel β-melanocyte-stimulating hormone from the neurointermediate lobe of the pituitary of the dogfish Squalus acanthias

    PubMed Central

    Bennett, Hugh P. J.; Lowry, Philip J.; McMartin, Colin; Scott, Alexander P.

    1974-01-01

    A melanocyte-stimulating hormone (MSH) has been isolated from extracts of the neurointermediate lobe of the pituitary of the dogfish Squalus acanthias by gel-filtration and ion-exchange chromatography. It had approximately 1% of the potency of mammalian α-MSH on bioassays in vitro on frog skin and dogfish skin. Sequence analysis revealed it to be a hexadecapeptide with the following primary structure: Asp-Gly-Asp-Asp-Tyr-Lys-Phe-Gly-His-Phe-Arg-Trp-Ser-Val-Pro-Leu. It appears to be related to the β-MSH species of mammalian species but has only the sequence -His-Phe-Arg-Trp- in common with the heptapeptide core -Met-Glu-His-Phe-Arg-Trp-Gly- which is characteristic not only of the MSH peptides but also of the adrenocorticotrophins and lipotrophins studied so far. An α-MSH was also isolated, 50% of which was amidated at the C-terminus group. Sequence data from this study taken in conjunction with those from a previous study (Lowry & Chadwick, 1970b) revealed it to be a tridecapeptide which is identical with the N-terminal sequence of dogfish adrenocorticotrophin. PMID:4375978

  19. Amelioratory effect of coenzyme Q10 on potential human carcinogen Microcystin-LR induced toxicity in mice.

    PubMed

    Lone, Yaqoob; Bhide, Mangla; Koiri, Raj Kumar

    2017-04-01

    Microcystins are a group of cyclic heptapeptide toxins produced by cyanobacteria. More than 100 microcystin analogues have been detected, among which microcystin-LR is the most abundant and toxic variant. Present study was designed to reveal whether potential human carcinogen microcystin-LR could imbalance the glycolytic-oxidative-nitrosative status of heart, kidney and spleen of mice and also to explore the amelioratory effect of coenzyme Q10 on microcystin-LR induced toxicity. Microcystin-LR was administered at a dose of 10 μg/kg bw/day, ip for 14 days in male mice. In microcystin-LR treated mice as compared to control, significant increase in the level of lipid peroxidation, hydrogen peroxide, lactate dehydrogenase, nitric oxide with a concomitant decrease in the level of glutathione was observed, suggesting microcystin-LR induced toxicity via induction of oxidative-nitrosative-glycolytic pathway. Although several studies have evaluated numerous antioxidants but still there is no effective chemoprotectant against microcystin-LR induced toxicity. When microcystin-LR treated mice were co-administered coenzyme Q10 (10 mg/kg bw/day, im) for 14 days, it was observed that coenzyme Q10 ameliorates microcystin-LR induced toxicity via modulation of glycolytic-oxidative-nitrosative stress pathway. Thus, the results suggest that coenzyme Q10 has a potential to be developed as preventive agent against microcystin-LR induced toxicity. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Enhanced legumain-recognition and NIR controlled released of cisplatin-indocyanine nanosphere against gastric carcinoma.

    PubMed

    Shi, Tianyi; Gu, Lianshuai; Sun, Yu; Wang, Senlin; You, Chaoqun; Zhang, Xiangyang; Zhu, Jin; Sun, Baiwang

    2017-01-05

    Cisplatin-therapy has faced limitations in the gastric cancer therapy. To settle the bottleneck, enhanced specificity and controlled-release property are choosen. We synthesize cisplatin and indocyanine green (ICG) loaded PLGA-(DSPE-PEG2000) nanoparticles, which is abbreviated as CINPs. And we conjugate the Gly-Cys-Gly-Ala-Ala-Asn-Leu (GCGAANL) heptapeptide upon the surface of CINPs, the product is abbreviated as ACINPs. ACINPs with nearly 110nm exhibit good monodispersity and size stability. The EE (efficiency of encapsulation) and LE (loading of encapsulation) of cisplatin loaded into ACINPs are optimized as 29.81% and 3.88%. MGC803 cells overexpressing the legumain and MKN28 cells, which negatively express the legumain as well as the normal stomach cells, are selected. In vitro studies have suggested ACINPs, compared with CINPs, could be recognized by MGC803 cells and efficiently killed the cancer cells, while be harmless to MKN28 cells, which indicates the specificity and safety of ACINPs. Under irradiation of 808nm NIR irradiation, ICG loaded in ACINPs could rapidly transform the light to heat up to 60℃. Nanoparticles compared with non-irraditaion group could be quickly disrupted and release the cisplatin which could enhance the controlled-release ability. Hence, the ACINPs exhibit great potential in avoiding the side effects and enhancing the therapy ability of cisplatin.

  1. Sulfide oxidations for LC-MS analysis of methionine-containing microcystins in Dolichospermum flos-aquae NIVA-CYA 656.

    PubMed

    Miles, Christopher O; Melanson, Jeremy E; Ballot, Andreas

    2014-11-18

    Microcystins are cyclic heptapeptides produced by a range of cyanobacteria. More than 150 microcystin analogues have been reported from cultures, algal blooms, or other contaminated samples. Relatively few analytical standards are available, making identification and quantitation of these toxins a challenge, even with LC-MS technology. We developed a two-step oxidative procedure that allows LC-MS identification of microcystins containing methionine and methionine sulfoxide, and reveals the oxidation state of the methionyl sulfur atom. The procedure was used in parallel with mercaptoethanol derivatization and LC-MS(2) analysis to demonstrate the presence of [Asp(3)]MC-MR (12) and MC-MR (17) in a culture of Dolichospermum flos-aquae, together with low levels of [Asp(3)]MC-M(O)R (5) and MC-M(O)R (7), as well as 20 other microcystins. Fresh culture contained only traces of sulfoxides 5 and 7, but these increased during storage or sample extraction and preparation. This suggests that microcystins containing methionine sulfoxide are primarily postextraction oxidation artifacts, rather than being produced by biosynthesis in cyanobacteria. A simple, rapid extraction under inert gas followed promptly by LC-MS analysis minimized oxidation artifacts for D. flos-aquae.

  2. Are fish fed with cyanobacteria safe, nutritious and delicious? A laboratory study.

    PubMed

    Liang, Hualei; Zhou, Wenshan; Zhang, Yulei; Qiao, Qin; Zhang, Xuezhen

    2015-10-16

    Toxic cyanobacterial blooms, which produce cyclic heptapeptide toxins known as microcystins, are worldwide environmental problems. On the other hand, the cyanobacteria protein (30-50%) has been recommended as substitute protein for aquaculture. The present laboratory study verified the feasibility of cyanobacteria protein substitution and risk assessment. Goldfish were fed diets supplemented lyophilised cyanobacteria powder for 16 weeks with the various doses: 0% (control), 10%, 20%, 30% and 40%. Low doses (10% and 20%) promoted growth whereas high doses (30% and 40%) inhibited growth. In cyanobacteria treated fish, the proximate composition of ash, crude fat content and crude protein content decreased in 16 weeks; the saturated fatty acid (SFA) content significantly increased; the n-3 polyunsaturated fatty acid content, collagen content and muscle pH significantly decreased; cooking loss percents increased significantly. Muscle fiber diameter and myofibril length were negatively correlation. Additionally, flavour compounds (e.g., amino acids, nucleotides, organic acids and carnosine) changed significantly in the treated fish, and odour compounds geosmin and 2-methylisoborneol increased significantly. The estimated daily intake (EDI) of microcystins in muscle was close to or exceeded the World Health Organization (WHO) tolerable daily intake (TDI), representing a great health risk. Cyanobacterie is not feasible for protein sources use in aquaculture.

  3. Label-Free Electrical Immunosensor for Highly Sensitive and Specific Detection of Microcystin-LR in Water Samples.

    PubMed

    Tan, Feng; Saucedo, Nuvia Maria; Ramnani, Pankaj; Mulchandani, Ashok

    2015-08-04

    Microcystin-LR (MCLR) is one of the most commonly detected and toxic cyclic heptapeptide cyanotoxins released by cyanobacterial blooms in surface waters, for which sensitive and specific detection methods are necessary to carry out its recognition and quantification. Here, we present a single-walled carbon nanotube (SWCNTs)-based label-free chemiresistive immunosensor for highly sensitive and specific detection of MCLR in different source waters. MCLR was initially immobilized on SWCNTs modified interdigitated electrode, followed by incubation with monoclonal anti-MCLR antibody. The competitive binding of MCLR in sample solutions induced departure of the antibody from the antibody-antigen complexes formed on SWCNTs, resulting in change in the conductivity between source and drain of the sensor. The displacement assay greatly improved the sensitivity of the sensor compared with direct immunoassay on the same device. The immunosensor exhibited a wide linear response to log value of MCLR concentration ranging from 1 to 1000 ng/L, with a detection limit of 0.6 ng/L. This method showed good reproducibility, stability and recovery. The proposed method provides a powerful tool for rapid and sensitive monitoring of MCLR in environmental samples.

  4. Conserved hydrogen bonds and water molecules in MDR HIV-1 protease substrate complexes.

    PubMed

    Liu, Zhigang; Wang, Yong; Yedidi, Ravikiran S; Dewdney, Tamaria G; Reiter, Samuel J; Brunzelle, Joseph S; Kovari, Iulia A; Kovari, Ladislau C

    2013-01-18

    The success of highly active antiretroviral therapy (HAART) in anti-HIV therapy is severely compromised by the rapidly developing drug resistance. HIV-1 protease inhibitors, part of HAART, are losing their potency and efficacy in inhibiting the target. Multi-drug resistant (MDR) 769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, 90) was selected for the present study to understand the binding to its natural substrates. The nine crystal structures of MDR769 HIV-1 protease substrate hepta-peptide complexes were analyzed in order to reveal the conserved structural elements for the purpose of drug design against MDR HIV-1 protease. Our structural studies demonstrated that highly conserved hydrogen bonds between the protease and substrate peptides, together with the conserved crystallographic water molecules, played a crucial role in the substrate recognition, substrate stabilization and protease stabilization. In addition, the absence of the key flap-ligand bridging water molecule might imply a different catalytic mechanism of MDR769 HIV-1 protease compared to that of wild type (WT) HIV-1 protease.

  5. Gene family encoding the major toxins of lethal Amanita mushrooms.

    PubMed

    Hallen, Heather E; Luo, Hong; Scott-Craig, John S; Walton, Jonathan D

    2007-11-27

    Amatoxins, the lethal constituents of poisonous mushrooms in the genus Amanita, are bicyclic octapeptides. Two genes in A. bisporigera, AMA1 and PHA1, directly encode alpha-amanitin, an amatoxin, and the related bicyclic heptapeptide phallacidin, a phallotoxin, indicating that these compounds are synthesized on ribosomes and not by nonribosomal peptide synthetases. alpha-Amanitin and phallacidin are synthesized as proproteins of 35 and 34 amino acids, respectively, from which they are predicted to be cleaved by a prolyl oligopeptidase. AMA1 and PHA1 are present in other toxic species of Amanita section Phalloidae but are absent from nontoxic species in other sections. The genomes of A. bisporigera and A. phalloides contain multiple sequences related to AMA1 and PHA1. The predicted protein products of this family of genes are characterized by a hypervariable "toxin" region capable of encoding a wide variety of peptides of 7-10 amino acids flanked by conserved sequences. Our results suggest that these fungi have a broad capacity to synthesize cyclic peptides on ribosomes.

  6. Ribosomal biosynthesis of the cyclic peptide toxins of Amanita mushrooms.

    PubMed

    Walton, Jonathan D; Hallen-Adams, Heather E; Luo, Hong

    2010-01-01

    Some species of mushrooms in the genus Amanita are extremely poisonous and frequently fatal to mammals including humans and dogs. Their extreme toxicity is due to amatoxins such as alpha- and beta-amanitin. Amanita mushrooms also biosynthesize a chemically related group of toxins, the phallotoxins, such as phalloidin. The amatoxins and phallotoxins (collectively known as the Amanita toxins) are bicyclic octa- and heptapeptides, respectively. Both contain an unusual Trp-Cys crossbridge known as tryptathionine. We have shown that, in Amanita bisporigera, the amatoxins and phallotoxins are synthesized as proproteins on ribosomes and not by nonribosomal peptide synthetases. The proproteins are 34-35 amino acids in length and have no predicted signal peptides. The genes for alpha-amanitin (AMA1) and phallacidin (PHA1) are members of a large family of related genes, characterized by highly conserved amino acid sequences flanking a hypervariable "toxin" region. The toxin regions are flanked by invariant proline (Pro) residues. An enzyme that could cleave the proprotein of phalloidin was purified from the phalloidin-producing lawn mushroom Conocybe apala. The enzyme is a serine protease in the prolyl oligopeptidase (POP) subfamily. The same enzyme cuts at both Pro residues to release the linear hepta- or octapeptide.

  7. Decreasing oxidative stress and neuroinflammation with a multifunctional peptide rescues memory deficits in mice with Alzheimer disease.

    PubMed

    Zhou, Wei-wei; Lu, Shuai; Su, Ya-jing; Xue, Di; Yu, Xiao-lin; Wang, Shao-wei; Zhang, He; Xu, Peng-xin; Xie, Xi-xiu; Liu, Rui-tian

    2014-09-01

    Alzheimer disease (AD) is characterized by extracellular senile plaques, intracellular neurofibrillary tangles, and memory loss. Aggregated amyloid-β (Aβ), oxidative stress, and inflammation have pivotal roles in the pathogenesis of AD. Therefore, the inhibition of Aβ-induced neurotoxicity, oxidative stress, and inflammation is a potential therapeutic strategy for the treatment of AD. In this study, a heptapeptide, isolated from a Ph.D.-C7C library by phage display, attenuated Aβ42-induced cytotoxicity in SH-SY5Y neuroblastoma cells and reduced Aβ42-induced oxidative stress by decreasing the production of reactive oxygen species and glutathione disulfide. As a result, glutathione level increased and superoxide dismutase and glutathione peroxidase activities were enhanced in vitro and in vivo. This peptide also suppressed the inflammatory response by decreasing the release of proinflammatory cytokines, such as tumor necrosis factor α and interleukin 1β, in microglia and by reducing microgliosis and astrogliosis in AD transgenic mice. This peptide was intracerebroventricularly administered to APPswe/PS1dE9 transgenic mice. We found that this peptide significantly improved spatial memory and reduced the amyloid plaque burden and soluble and insoluble Aβ levels. Our findings suggest that this multifunctional peptide has therapeutic potential for an Aβ-targeted treatment of AD. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. The Periplasmic Bacterial Molecular Chaperone SurA Adapts Its Structure to Bind Peptides in Different Conformations to Assert a Sequence Preference for Aromatic Residues

    SciTech Connect

    Xu, X.; Wang, S.; Hu, Y.-X.; McKay, D.B.

    2009-06-04

    The periplasmic molecular chaperone protein SurA facilitates correct folding and maturation of outer membrane proteins in Gram-negative bacteria. It preferentially binds peptides that have a high fraction of aromatic amino acids. Phage display selections, isothermal titration calorimetry and crystallographic structure determination have been used to elucidate the basis of the binding specificity. The peptide recognition is imparted by the first peptidyl-prolyl isomerase (PPIase) domain of SurA. Crystal structures of complexes between peptides of sequence WEYIPNV and NFTLKFWDIFRK with the first PPIase domain of the Escherichia coli SurA protein at 1.3 A resolution, and of a complex between the dodecapeptide and a SurA fragment lacking the second PPIase domain at 3.4 A resolution, have been solved. SurA binds as a monomer to the heptapeptide in an extended conformation. It binds as a dimer to the dodecapeptide in an alpha-helical conformation, predicated on a substantial structural rearrangement of the SurA protein. In both cases, side-chains of aromatic residues of the peptides contribute a large fraction of the binding interactions. SurA therefore asserts a recognition preference for aromatic amino acids in a variety of sequence configurations by adopting alternative tertiary and quaternary structures to bind peptides in different conformations.

  9. Structure and function of the proline-rich region of myelin basic protein.

    PubMed

    Fraser, P E; Deber, C M

    1985-08-13

    Myelin basic protein (MBP)--the major extrinsic membrane protein of central nervous system myelin--from several species contains a rarely encountered highly conserved triproline segment as residues 99-101 of its 170-residue sequence. Cis peptide bonds are known to arise at X-Pro junctions in proteins and may be of functional significance in protein folding, chain reversal, and/or maintenance of tertiary structure. We have examined the conformation of this proline-rich region using principally 13C nuclear magnetic resonance spectroscopy (125 MHz) both in intact bovine MBP and in several MBP fragment peptides which we synthesized, including octapeptide 97-104 (Arg-Thr-Pro-Pro-Pro-Ser-Gln-Gly). Results suggested an all-trans conformation in aqueous solution for the triproline segment in MBP hexapeptide (99-104), heptapeptide (98-104), and octapeptide. Comparison with the 13C spectrum of intact MBP (125 MHz) suggested that the proline-rich region, as well as all other X-Pro MBP peptide junctures, was also essentially all trans in aqueous solution. Although experiments in which octapeptide 97-104 was bound to a lipid preparation (4:1 dipalmitoylphosphatidylcholine/dimyristoylphosphatidic acid) demonstrated that cis-proline bonds do arise (to the extent of ca. 5%) in the membrane environment, a role of linear chain propagation is suggested for the triproline segment of myelin basic protein.

  10. Tachykinins activate guinea-pig alveolar macrophages: involvement of NK2 and NK1 receptors.

    PubMed Central

    Brunelleschi, S.; Vanni, L.; Ledda, F.; Giotti, A.; Maggi, C. A.; Fantozzi, R.

    1990-01-01

    1. The effects of substance P (SP), neurokinin A (NKA) and neurokinin B (NKB) were evaluated on superoxide anion (O2-.) production by guinea-pig alveolar macrophages (AM). 2. SP dose-dependently (ED50 = 0.7 nM) evoked O2-. production from guinea-pig AM; the N-terminal heptapeptide, SP(1-7), was ineffective. In the presence of thiorphan (10(-5) M), an enkephalinase inhibitor, the stimulating effects of SP were not significantly modified. NKA and NKB were both able to induce O2-. production from guinea-pig AM, ED50 values being 0.1 and 1.3 nM, respectively. Therefore, the rank order of activity of natural tachykinins was NKA greater than SP greater than NKB. Tachykinin-evoked effects were quantitatively similar to those elicited by the autacoid mediator PAF-acether and less than those induced by the synthetic peptide N-formylmethionyl-leucyl-phenylalanine (FMLP). 3. The NK2 receptor agonist [beta-Ala8]-NKA (4-10) dose-dependently evoked O2-. production from guinea-pig AM; the NK1 receptor agonist [Pro9]-SP sulphone acted only at high concentrations, while the NK3 receptor agonist [Me,Phe7]-NKB was ineffective. 4. These findings indicate that guinea-pig AM possess NK2 and possibly some NK1 tachykinin receptors and further suggest tachykinin involvement in lung pathophysiology. PMID:1697194

  11. A universal RNA polymerase II CTD cycle is orchestrated by complex interplays between kinase, phosphatase, and isomerase enzymes along genes.

    PubMed

    Bataille, Alain R; Jeronimo, Célia; Jacques, Pierre-Étienne; Laramée, Louise; Fortin, Marie-Ève; Forest, Audrey; Bergeron, Maxime; Hanes, Steven D; Robert, François

    2012-01-27

    Transcription by RNA polymerase II (RNAPII) is coupled to mRNA processing and chromatin modifications via the C-terminal domain (CTD) of its largest subunit, consisting of multiple repeats of the heptapeptide YSPTSPS. Pioneering studies showed that CTD serines are differentially phosphorylated along genes in a prescribed pattern during the transcription cycle. Genome-wide analyses challenged this idea, suggesting that this cycle is not uniform among different genes. Moreover, the respective role of enzymes responsible for CTD modifications remains controversial. Here, we systematically profiled the location of the RNAPII phosphoisoforms in wild-type cells and mutants for most CTD modifying enzymes. Together with results of in vitro assays, these data reveal a complex interplay between the modifying enzymes, and provide evidence that the CTD cycle is uniform across genes. We also identify Ssu72 as the Ser7 phosphatase and show that proline isomerization is a key regulator of CTD dephosphorylation at the end of genes. Copyright © 2012 Elsevier Inc. All rights reserved.

  12. Evidence for a "wattle and daub" model of the cyst wall of entamoeba.

    PubMed

    Chatterjee, Anirban; Ghosh, Sudip K; Jang, Ken; Bullitt, Esther; Moore, Landon; Robbins, Phillips W; Samuelson, John

    2009-07-01

    The cyst wall of Entamoeba invadens (Ei), a model for the human pathogen Entamoeba histolytica, is composed of fibrils of chitin and three chitin-binding lectins called Jacob, Jessie3, and chitinase. Here we show chitin, which was detected with wheat germ agglutinin, is made in secretory vesicles prior to its deposition on the surface of encysting Ei. Jacob lectins, which have tandemly arrayed chitin-binding domains (CBDs), and chitinase, which has an N-terminal CBD, were each made early during encystation. These results are consistent with their hypothesized roles in cross-linking chitin fibrils (Jacob lectins) and remodeling the cyst wall (chitinase). Jessie3 lectins likely form the mortar or daub of the cyst wall, because 1) Jessie lectins were made late during encystation; 2) the addition to Jessie lectins to the cyst wall correlated with a marked decrease in the permeability of cysts to nucleic acid stains (DAPI) and actin-binding heptapeptide (phalloidin); and 3) recombinant Jessie lectins, expressed as a maltose-binding proteins in the periplasm of Escherichia coli, caused transformed bacteria to agglutinate in suspension and form a hard pellet that did not dissociate after centrifugation. Jessie3 appeared as linear forms and rosettes by negative staining of secreted recombinant proteins. These findings provide evidence for a "wattle and daub" model of the Entamoeba cyst wall, where the wattle or sticks (chitin fibrils likely cross-linked by Jacob lectins) is constructed prior to the addition of the mortar or daub (Jessie3 lectins).

  13. UV-B Exposure Affects the Biosynthesis of Microcystin in Toxic Microcystis aeruginosa Cells and Its Degradation in the Extracellular Space.

    PubMed

    Yang, Zhen; Kong, Fanxiang

    2015-10-20

    Microcystins (MCs) are cyclic hepatotoxic heptapeptides produced by cyanobacteria that can be toxic to aquatic and terrestrial organisms. MC synthesis and degradation are thought to be influenced by several different physical and environmental parameters. In this study, the effects of different intensities of UV-B radiation on MC biosynthesis in Microcystis cells and on its extracellular degradation were investigated by mRNA analysis and degradation experiments. Exposure to UV-B at intensities of 1.02 and 1.45 W/m² not only remarkably inhibited the growth of Microcystis, but also led to a decrease in the MC concentration. In addition, mcyD transcription was decreased under the same UV-B intensities. These results demonstrated that the effects of UV-B exposure on the biosynthesis of MCs in Microcystis cells could be attributed to the regulation of mcy gene transcription. Moreover, the MC concentration was decreased significantly after exposure to different intensities of UV-B radiation. Of the three MC variants (MC-LR, -RR and -YR, L, R and Y are abbreviations of leucine, arginine and tyrosine), MC-LR and MC-YR were sensitive to UV-B radiation, whereas MC-RR was not. In summary, our results showed that UV-B radiation had a negative effect on MC production in Microcystis cells and MC persistence in the extracellular space.

  14. Pheromone killing of multidrug-resistant Enterococcus faecalis V583 by native commensal strains.

    PubMed

    Gilmore, Michael S; Rauch, Marcus; Ramsey, Matthew M; Himes, Paul R; Varahan, Sriram; Manson, Janet M; Lebreton, Francois; Hancock, Lynn Ernest

    2015-06-09

    Multidrug-resistant Enterococcus faecalis possess numerous mobile elements that encode virulence and antibiotic resistance traits as well as new metabolic pathways, often constituting over one-quarter of the genome. It was of interest to determine how this large accretion of mobile elements affects competitive growth in the gastrointestinal (GI) tract consortium. We unexpectedly observed that the prototype clinical isolate strain V583 was actively killed by GI tract flora, whereas commensal enterococci flourished. It was found that killing of V583 resulted from lethal cross-talk between accumulated mobile elements and that this cross-talk was induced by a heptapeptide pheromone produced by native E. faecalis present in the fecal consortium. These results highlight two important aspects of the evolution of multidrug-resistant enterococci: (i) the accretion of mobile elements in E. faecalis V583 renders it incompatible with commensal strains, and (ii) because of this incompatibility, multidrug-resistant strains sharing features found in V583 cannot coexist with commensal strains. The accumulation of mobile elements in hospital isolates of enterococci can include those that are inherently incompatible with native flora, highlighting the importance of maintaining commensal populations as means of preventing colonization and subsequent infection by multidrug-resistant strains.

  15. The toxicology of microcystin-LR: occurrence, toxicokinetics, toxicodynamics, diagnosis and treatment.

    PubMed

    Bischoff, K

    2001-10-01

    Cyanobacterial blooms occur worldwide and present an increasing problem due to eutrophication of lakes. Microcystins, especially microcystin-LR, are microcyclic heptapeptide hepatotoxins and are the most common and potent toxins associated with cyanobacteria. Microcystin is rapidly taken up by hepatocytes through carrier-mediated transport. Once in the hepatocyte, microcystin causes structural damage to the cell indirectly by inhibiting protein phosphorylases 1 and 2A, which are needed for regulation of structural proteins of the cell. Acute liver hemorrhage and death occur with high doses of microcystin-LR, which is also a potent tumor promoter in laboratory rats. The significance of microcystin to human health has been debated; however, poisoning in humans has occurred due to contaminated dialysis water. Microcystin in contaminated drinking water may be the cause of elevated rates of primary liver cancer in some areas of China. Problems with hepatotoxic cyanobacteria have been most seen in livestock. Treatment of confirmed microcystin toxicosis in livestock is likely to be unrewarding, so prevention is important. Wild mammals, birds, fish, insects, and microinvertebrates may also be affected by microcystin.

  16. Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells.

    PubMed

    Dias, João D; Rito, Tiago; Torlai Triglia, Elena; Kukalev, Alexander; Ferrai, Carmelo; Chotalia, Mita; Brookes, Emily; Kimura, Hiroshi; Pombo, Ana

    2015-12-19

    Dynamic post-translational modification of RNA polymerase II (RNAPII) coordinates the co-transcriptional recruitment of enzymatic complexes that regulate chromatin states and processing of nascent RNA. Extensive phosphorylation of serine residues at the largest RNAPII subunit occurs at its structurally-disordered C-terminal domain (CTD), which is composed of multiple heptapeptide repeats with consensus sequence Y1-S2-P3-T4-S5-P6-S7. Serine-5 and Serine-7 phosphorylation mark transcription initiation, whereas Serine-2 phosphorylation coincides with productive elongation. In vertebrates, the CTD has eight non-canonical substitutions of Serine-7 into Lysine-7, which can be acetylated (K7ac). Here, we describe mono- and di-methylation of CTD Lysine-7 residues (K7me1 and K7me2). K7me1 and K7me2 are observed during the earliest transcription stages and precede or accompany Serine-5 and Serine-7 phosphorylation. In contrast, K7ac is associated with RNAPII elongation, Serine-2 phosphorylation and mRNA expression. We identify an unexpected balance between RNAPII K7 methylation and acetylation at gene promoters, which fine-tunes gene expression levels.

  17. Comparison of the temporary dynamics of NGF and BDNF gene expression in rat hippocampus, frontal cortex, and retina under Semax action.

    PubMed

    Shadrina, Maria; Kolomin, Timur; Agapova, Tamara; Agniullin, Yan; Shram, Stanislav; Slominsky, Petr; Lymborska, Svetlana; Myasoedov, Nikolay

    2010-05-01

    Neurotrophins are a family of structurally related proteins that regulate the survival, differentiation, and maintenance of function of different neuron populations. Some peptides are able to affect the production and activity of neurotrophins. One of these synthetic peptides is heptapeptide Semax, an analog of the N-terminal adrenocorticotropic hormone fragment 4-10. It is known that Semax has effects on learning and memory formation and exerts some neuroprotective effects in rodents and humans. Male Wistar rats were treated for 20 min, 40 min, 90 min, 3 h, 8 h, and 24 h with Semax. Nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF) gene expression in rat brain and retina was analyzed by real-time polymerase chain reaction. It was revealed that after Semax administration the multidirectional activation of the expression of the genes under investigation in the hippocampus, frontal cortex, and retina was observed. The expression of both neurotrophin genes was decreased in rat hippocampus and retina 20 min after Semax administration and was increased in the frontal cortex. The expression levels of NGF remained practically constant in the retina at the initial stage, whereas the expression levels of BDNF were significantly increased 90 min after Semax administration.

  18. Neurotrophin gene expression in rat brain under the action of Semax, an analogue of ACTH 4-10.

    PubMed

    Agapova, T Y; Agniullin, Y V; Shadrina, M I; Shram, S I; Slominsky, P A; Lymborska, S A; Myasoedov, N F

    2007-05-01

    The heptapeptide Semax, an analogue of the N-terminal adrenocorticotropic hormone fragment (4-10) (ACTH(4-10)), has been shown to exert a number of neuroprotective effects. There are some investigations that connected these effects with the increase of neurotrophin gene expression under the peptide drug application in neuron cell cultures [M.I. Shadrina, O.V. Dolotov, I.A. Grivennikov, P.A. Slominsky, L.A. Andreeva, L.S. Inozemtseva, S.A. Limborska, N.F. Myasoedov, Rapid induction of neurotrophin mRNAs in rat glial cell cultures by Semax, an adrenocorticotropic hormone analogue, Neurosci. Lett. 308 (2001) (2) 115-118]. In this work, we examined the action of Semax on rapid changes of nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF) gene expression in vivo. Male Wistar rats were treated for 1h with Semax (50 microg/kg, single intranasal application) and neurotrophin gene expression in rat brain was analyzed by real-time polymerase chain reaction (PCR). It was revealed that an intranasal application of Semax increased the expression of both neurotrophin genes in rat hippocampus. Bdnf gene expression also increased in the brainstem and cerebellum. Ngf gene expression decreased in rat frontal cortex. Thus, Semax induces rapid, gene- and region-specific changes in neurotrophin gene expression in normal rat brain.

  19. Semax, an analogue of adrenocorticotropin (4-10), is a potential agent for the treatment of attention-deficit hyperactivity disorder and Rett syndrome.

    PubMed

    Tsai, Shih-Jen

    2007-01-01

    Psychostimulants, such as methylphenidate, are currently the most common used drug therapy for children with attention-deficit hyperactivity disorder (ADHD). However, a number of patients with ADHD either fail to respond to these drugs or experience side effects that preclude their use. The heptapeptide Semax is an analogue of the N-terminal fragment (4-10) of adrenocorticotropic hormone, but is completely devoid of any hormonal activity. It has been found to stimulate memory and attention in rodents and humans after intranasal application. Evidence from animal studies revealed that Semax can augment the effects of psychostimulants on central dopamine release and also stimulates central brain-derived neurotrophic factor (BDNF) synthesis. In addition, Semax could improve selective attention and modulate brain development. Since ADHD is likely to be a neurodevelopmental disorder with disturbance in dopamine and BDNF function, it is proposed in this paper that Semax may have good therapeutic potential in ADHD. Furthermore, increased BDNF activity is found to improve Rett syndrome, a severe neurodevelopmental disorder which is, in the majority of cases, caused by mutations in the gene encoding methyl-CpG-binding protein 2 (MECP2). The potential therapeutic effect of Semax in Rett syndrome by increasing central BDNF activity may be of interest for further exploration in animal models of Rett syndrome.

  20. Human intoxication by microcystins during renal dialysis treatment in Caruaru-Brazil.

    PubMed

    Azevedo, Sandra M F O; Carmichael, Wayne W; Jochimsen, Elise M; Rinehart, Kenneth L; Lau, Sharon; Shaw, Glen R; Eaglesham, Geoff K

    2002-12-27

    In February 1996, an outbreak of illness occurred at a hemodialysis clinic in Caruaru, Pernambuco State-Brazil. At this clinic 116 (89%) of 131 patients experienced visual disturbances, nausea, vomiting, and muscle weakness, following routine haemodialysis treatment. Subsequently, 100 patients developed acute liver failure. As of December 1996, 52 of the deaths could be attributed to a common syndrome now called 'Caruaru Syndrome'. Examination of previous years' phytoplankton counts showed that cyanobacteria were dominant in the water supply reservoir since 1990. Analyses of carbon and other resins from the clinic's water treatment system plus serum and liver tissue of patients led to the identification of two groups of hepatotoxic cyanotoxins: microcystins (cyclic heptapeptides) in all of these samples and cylindrospermopsin (alkaloid hepatotoxic) in the carbon and resins. Comparison of victims symptoms and pathology with animal studies on these two cyanotoxins, leads us to conclude that the major contributing factor to death of the dialysis patients was intravenous exposure to microcystins, specifically microcystin-YR, -LR and -AR. In 2000, a review of the Brazilian regulation for drinking water quality, promoted by Brazilian Health Ministry with collaboration of PAHO, incorporated cyanobacteria and cyanotoxins into this new regulation as parameters that must to be monitored for water quality control.

  1. Amyloid β-sheet mimics that antagonize protein aggregation and reduce amyloid toxicity

    NASA Astrophysics Data System (ADS)

    Cheng, Pin-Nan; Liu, Cong; Zhao, Minglei; Eisenberg, David; Nowick, James S.

    2012-11-01

    The amyloid protein aggregation associated with diseases such as Alzheimer's, Parkinson's and type II diabetes (among many others) features a bewildering variety of β-sheet-rich structures in transition from native proteins to ordered oligomers and fibres. The variation in the amino-acid sequences of the β-structures presents a challenge to developing a model system of β-sheets for the study of various amyloid aggregates. Here, we introduce a family of robust β-sheet macrocycles that can serve as a platform to display a variety of heptapeptide sequences from different amyloid proteins. We have tailored these amyloid β-sheet mimics (ABSMs) to antagonize the aggregation of various amyloid proteins, thereby reducing the toxicity of amyloid aggregates. We describe the structures and inhibitory properties of ABSMs containing amyloidogenic peptides from the amyloid-β peptide associated with Alzheimer's disease, β2-microglobulin associated with dialysis-related amyloidosis, α-synuclein associated with Parkinson's disease, islet amyloid polypeptide associated with type II diabetes, human and yeast prion proteins, and Tau, which forms neurofibrillary tangles.

  2. High-Throughput Genetic and Gene Expression Analysis of the RNAPII-CTD Reveals Unexpected Connections to SRB10/CDK8

    PubMed Central

    Aristizabal, Maria J.; Negri, Gian Luca; Benschop, Joris J.; Holstege, Frank C. P.; Krogan, Nevan J.; Kobor, Michael S.

    2013-01-01

    The C-terminal domain (CTD) of RNA polymerase II (RNAPII) is composed of heptapeptide repeats, which play a key regulatory role in gene expression. Using genetic interaction, chromatin immunoprecipitation followed by microarrays (ChIP-on-chip) and mRNA expression analysis, we found that truncating the CTD resulted in distinct changes to cellular function. Truncating the CTD altered RNAPII occupancy, leading to not only decreases, but also increases in mRNA levels. The latter were largely mediated by promoter elements and in part were linked to the transcription factor Rpn4. The mediator subunit Cdk8 was enriched at promoters of these genes, and its removal not only restored normal mRNA and RNAPII occupancy levels, but also reduced the abnormally high cellular amounts of Rpn4. This suggested a positive role of Cdk8 in relationship to RNAPII, which contrasted with the observed negative role at the activated INO1 gene. Here, loss of CDK8 suppressed the reduced mRNA expression and RNAPII occupancy levels of CTD truncation mutants. PMID:24009531

  3. Tyrosine phosphorylation of RNA polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells

    PubMed Central

    Descostes, Nicolas; Heidemann, Martin; Spinelli, Lionel; Schüller, Roland; Maqbool, Muhammad Ahmad; Fenouil, Romain; Koch, Frederic; Innocenti, Charlène; Gut, Marta; Gut, Ivo; Eick, Dirk; Andrau, Jean-Christophe

    2014-01-01

    In mammals, the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II consists of 52 conserved heptapeptide repeats containing the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Post-translational modifications of the CTD coordinate the transcription cycle and various steps of mRNA maturation. Here we describe Tyr1 phosphorylation (Tyr1P) as a hallmark of promoter (5′ associated) Pol II in mammalian cells, in contrast to what was described in yeast. Tyr1P is predominantly found in antisense orientation at promoters but is also specifically enriched at active enhancers. Mutation of Tyr1 to phenylalanine (Y1F) prevents the formation of the hyper-phosphorylated Pol IIO form, induces degradation of Pol II to the truncated Pol IIB form, and results in a lethal phenotype. Our results suggest that Tyr1P has evolved specialized and essential functions in higher eukaryotes associated with antisense promoter and enhancer transcription, and Pol II stability. DOI: http://dx.doi.org/10.7554/eLife.02105.001 PMID:24842994

  4. The Ssu72 Phosphatase Mediates the RNA Polymerase II Initiation-Elongation Transition*

    PubMed Central

    Rosado-Lugo, Jesús D.; Hampsey, Michael

    2014-01-01

    Transitions between the different stages of the RNAPII transcription cycle involve the recruitment and exchange of factors, including mRNA capping enzymes, elongation factors, splicing factors, 3′-end-processing complexes, and termination factors. These transitions are coordinated by the dynamic phosphorylation of the C-terminal domain (CTD) of the largest subunit of RNAPII (Rpb1). The CTD is composed of reiterated heptapeptide repeats (Y1S2P3T4S5P6S7) that undergo phosphorylation and dephosphorylation as RNAPII transitions through the transcription cycle. An essential phosphatase in this process is Ssu72, which exhibits catalytic specificity for Ser(P)5 and Ser(P)7. Ssu72 is unique in that it is specific for Ser(P)5 in one orientation of the CTD and for Ser(P)7 when bound in the opposite orientation. Moreover, Ssu72 interacts with components of the initiation machinery and affects start site selection yet is an integral component of the CPF 3′-end-processing complex. Here we provide a comprehensive view of the effects of Ssu72 with respect to its Ser(P)5 phosphatase activity. We demonstrate that Ssu72 dephosphorylates Ser(P)5 at the initiation-elongation transition. Furthermore, Ssu72 indirectly affects the levels of Ser(P)2 during the elongation stage of transcription but does so independent of its catalytic activity. PMID:25339178

  5. A rule-based kinetic model of RNA polymerase II C-terminal domain phosphorylation

    PubMed Central

    Aitken, Stuart; Alexander, Ross D.; Beggs, Jean D.

    2013-01-01

    The complexity of many RNA processing pathways is such that a conventional systems modelling approach is inadequate to represent all the molecular species involved. We demonstrate that rule-based modelling permits a detailed model of a complex RNA signalling pathway to be defined. Phosphorylation of the RNA polymerase II (RNAPII) C-terminal domain (CTD; a flexible tail-like extension of the largest subunit) couples pre-messenger RNA capping, splicing and 3′ end maturation to transcriptional elongation and termination, and plays a central role in integrating these processes. The phosphorylation states of the serine residues of many heptapeptide repeats of the CTD alter along the coding region of genes as a function of distance from the promoter. From a mechanistic perspective, both the changes in phosphorylation and the location at which they take place on the genes are a function of the time spent by RNAPII in elongation as this interval provides the opportunity for the kinases and phosphatases to interact with the CTD. On this basis, we synthesize the available data to create a kinetic model of the action of the known kinases and phosphatases to resolve the phosphorylation pathways and their kinetics. PMID:23804443

  6. Functional characterization of βC1 gene of Cotton leaf curl Multan betasatellite.

    PubMed

    Tiwari, Neha; Sharma, P K; Malathi, V G

    2013-02-01

    Whitefly-transmitted Begomoviruses having circular single stranded DNA genome cause severe leaf curl diseases in the tropical and subtropical region. The majority of Old World monopartite begomoviruses with DNA A component is associated with a satellite DNA of 1.3 kb length referred to as betasatellites. The presence of betasatellite is required to express typical symptoms in the primary hosts. Increased symptom expression in betasatellite's presence is attributed to a 13-15 kDa βC1 protein encoded by the βC1 gene on complementary sense strand. The exact mechanism by which the βC1 protein contributes to the symptoms' severity and helper viral DNA's accumulation is not yet understood. Here, we studied the βC1 protein of Cotton leaf curl Multan betasatellite, associated with mono and bipartite begomoviruses. The βC1 protein was expressed in prokaryotic system as 6XHis-βC1 fusion protein and recombinant protein showed size- and sequence-specific DNA binding activity. The host proteins which may interact with βC1 were identified by binding βC1 recombinant protein with heptapeptide in phage display library. The βC1-interacting host proteins predicted belong to metabolic and defense pathways, indicating that βC1 protein has a pivotal role in viral pathogenicity.

  7. Interactions between lipid-free apolipoprotein-AI and a lipopeptide incorporating the RGDS cell adhesion motif

    NASA Astrophysics Data System (ADS)

    Castelletto, V.; Hamley, I. W.; Reza, M.; Ruokolainen, J.

    2014-11-01

    The interaction of a designed bioactive lipopeptide C16-GGGRGDS, comprising a hexadecyl lipid chain attached to a functional heptapeptide, with the lipid-free apoliprotein, Apo-AI, is examined. This apolipoprotein is a major component of high density lipoprotein and it is involved in lipid metabolism and may serve as a biomarker for cardiovascular disease and Alzheimers' disease. We find via isothermal titration calorimetry that binding between the lipopeptide and Apo-AI occurs up to a saturation condition, just above equimolar for a 10.7 μM concentration of Apo-AI. A similar value is obtained from circular dichroism spectroscopy, which probes the reduction in α-helical secondary structure of Apo-AI upon addition of C16-GGGRGDS. Electron microscopy images show a persistence of fibrillar structures due to self-assembly of C16-GGGRGDS in mixtures with Apo-AI above the saturation binding condition. A small fraction of spheroidal or possibly ``nanodisc'' structures was observed. Small-angle X-ray scattering (SAXS) data for Apo-AI can be fitted using a published crystal structure of the Apo-AI dimer. The SAXS data for the lipopeptide/Apo-AI mixtures above the saturation binding conditions can be fitted to the contribution from fibrillar structures coexisting with flat discs corresponding to Apo-AI/lipopeptide aggregates.

  8. Structure and expression of the gene coding for the alpha-subunit of DNA-dependent RNA polymerase from the chloroplast genome of Zea mays.

    PubMed Central

    Ruf, M; Kössel, H

    1988-01-01

    The rpoA gene coding for the alpha-subunit of DNA-dependent RNA polymerase located on the DNA of Zea mays chloroplasts has been characterized with respect to its position on the chloroplast genome and its nucleotide sequence. The amino acid sequence derived for a 39 Kd polypeptide shows strong homology with sequences derived from the rpoA genes of other chloroplast species and with the amino acid sequence of the alpha-subunit from E. coli RNA polymerase. Transcripts of the rpoA gene were identified by Northern hybridization and characterized by S1 mapping using total RNA isolated from maize chloroplasts. Antibodies raised against a synthetic C-terminal heptapeptide show cross reactivity with a 39 Kd polypeptide contained in the stroma fraction of maize chloroplasts. It is concluded that the rpoA gene is a functional gene and that therefore, at least the alpha-subunit of plastidic RNA polymerase, is expressed in chloroplasts. Images PMID:3399379

  9. Structural diversity of the microbial surfactin derivatives from selective esterification approach.

    PubMed

    Shao, Chuanshi; Liu, Lin; Gang, Hongze; Yang, Shizhong; Mu, Bozhong

    2015-01-15

    Surfactin originated from genus Bacillus is composed of a heptapeptide moiety bonded to the carboxyl and hydroxyl groups of a β-hydroxy fatty acid and it can be chemically modified to prepare the derivatives with different structures, owing to the existence of two free carboxyl groups in its peptide loop. This article presents the chemical modification of surfactin esterified with three different alcohols, and nine novel surfactin derivatives have been separated from products by the high performance liquid chromatography (HPLC). The novel derivatives, identified with Fourier transform infrared spectroscopy (FT-IR) and electrospray ionization mass spectrometry (ESI-MS), are the mono-hexyl-surfactin C14 ester, mono-hexyl-surfactin C15 ester, mono-2-methoxy-ethyl-surfactin C14 ester, di-hexyl-surfactin C14 ester, di-hexyl-surfactin ester C15, di-2-methoxy-ethyl-surfactin ester C14, di-2-methoxy-ethyl-surfactin ester C15, di-6-hydoxyl-hexyl-surfactin C14 ester and, di-6-hydoxyl-hexyl-surfactin C15 ester. The reaction conditions for esterification were optimized and the dependence of yields on different alcohols and catalysts were discussed. This study shows that esterification is one of the most efficient ways of chemical modification for surfactin and it can be used to prepare more derivatives to meet the needs of study in biological and interfacial activities.

  10. RPRD1A and RPRD1B Are Human RNA Polymerase II C-Terminal Domain Scaffolds for Ser5 Dephosphorylation

    PubMed Central

    Guo, Xinghua; Hunter, Gerald O.; Kuznetsova, Olga V.; Tempel, Wolfram; Marcon, Edyta; Zhong, Guoqing; Guo, Hongbo; Kuo, Wei-Hung William; Li, Joyce; Young, Peter; Olsen, Jonathan B.; Wan, Cuihong; Loppnau, Peter; El Bakkouri, Majida; Senisterra, Guillermo A.; He, Hao; Huang, Haiming; Sidhu, Sachdev S.; Emili, Andrew; Murphy, Shona; Mosley, Amber L.; Arrowsmith, Cheryl H.; Min, Jinrong; Greenblatt, Jack F.

    2014-01-01

    SUMMARY The RNA polymerase II (RNAPII) carboxyl-terminal domain (CTD) heptapeptide repeats (Y1-S2-P3-T4-S5-P6-S7) undergo dynamic phosphorylation and dephosphorylation during the transcription cycle to recruit factors that regulate transcription, RNA processing and chromatin modification. We show here that RPRD1A and RPRD1B form homodimers and heterodimers through their coiled-coil domains and interact preferentially via CTD interaction domains (CIDs) with CTD repeats phosphorylated at S2 and S7. Our high resolution crystal structures of the RPRD1A, RPRD1B and RPRD2 CIDs, alone and in complex with CTD phosphoisoforms, elucidate the molecular basis of CTD recognition. In an interesting example of cross-talk between different CTD modifications, our data also indicate that RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and, by interacting with CTD repeats where phospho-S2 and/or phospho-S7 bracket a phospho-S5 residue, serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. PMID:24997600

  11. UV-B Exposure Affects the Biosynthesis of Microcystin in Toxic Microcystis aeruginosa Cells and Its Degradation in the Extracellular Space

    PubMed Central

    Yang, Zhen; Kong, Fanxiang

    2015-01-01

    Microcystins (MCs) are cyclic hepatotoxic heptapeptides produced by cyanobacteria that can be toxic to aquatic and terrestrial organisms. MC synthesis and degradation are thought to be influenced by several different physical and environmental parameters. In this study, the effects of different intensities of UV-B radiation on MC biosynthesis in Microcystis cells and on its extracellular degradation were investigated by mRNA analysis and degradation experiments. Exposure to UV-B at intensities of 1.02 and 1.45 W/m2 not only remarkably inhibited the growth of Microcystis, but also led to a decrease in the MC concentration. In addition, mcyD transcription was decreased under the same UV-B intensities. These results demonstrated that the effects of UV-B exposure on the biosynthesis of MCs in Microcystis cells could be attributed to the regulation of mcy gene transcription. Moreover, the MC concentration was decreased significantly after exposure to different intensities of UV-B radiation. Of the three MC variants (MC-LR, -RR and -YR, L, R and Y are abbreviations of leucine, arginine and tyrosine), MC-LR and MC-YR were sensitive to UV-B radiation, whereas MC-RR was not. In summary, our results showed that UV-B radiation had a negative effect on MC production in Microcystis cells and MC persistence in the extracellular space. PMID:26492272

  12. Pheromone killing of multidrug-resistant Enterococcus faecalis V583 by native commensal strains

    PubMed Central

    Gilmore, Michael S.; Rauch, Marcus; Ramsey, Matthew M.; Himes, Paul R.; Varahan, Sriram; Manson, Janet M.; Lebreton, Francois; Hancock, Lynn Ernest

    2015-01-01

    Multidrug-resistant Enterococcus faecalis possess numerous mobile elements that encode virulence and antibiotic resistance traits as well as new metabolic pathways, often constituting over one-quarter of the genome. It was of interest to determine how this large accretion of mobile elements affects competitive growth in the gastrointestinal (GI) tract consortium. We unexpectedly observed that the prototype clinical isolate strain V583 was actively killed by GI tract flora, whereas commensal enterococci flourished. It was found that killing of V583 resulted from lethal cross-talk between accumulated mobile elements and that this cross-talk was induced by a heptapeptide pheromone produced by native E. faecalis present in the fecal consortium. These results highlight two important aspects of the evolution of multidrug-resistant enterococci: (i) the accretion of mobile elements in E. faecalis V583 renders it incompatible with commensal strains, and (ii) because of this incompatibility, multidrug-resistant strains sharing features found in V583 cannot coexist with commensal strains. The accumulation of mobile elements in hospital isolates of enterococci can include those that are inherently incompatible with native flora, highlighting the importance of maintaining commensal populations as means of preventing colonization and subsequent infection by multidrug-resistant strains. PMID:26039987

  13. A Fhit-mimetic peptide suppresses annexin A4-mediated chemoresistance to paclitaxel in lung cancer cells.

    PubMed

    Gaudio, Eugenio; Paduano, Francesco; Ngankeu, Apollinaire; Ortuso, Francesco; Lovat, Francesca; Pinton, Sandra; D'Agostino, Sabrina; Zanesi, Nicola; Aqeilan, Rami I; Campiglia, Pietro; Novellino, Ettore; Alcaro, Stefano; Croce, Carlo M; Trapasso, Francesco

    2016-05-24

    We recently reported that Fhit is in a molecular complex with annexin A4 (ANXA4); following to their binding, Fhit delocalizes ANXA4 from plasma membrane to cytosol in paclitaxel-resistant lung cancer cells, thus restoring their chemosensitivity to the drug. Here, we demonstrate that Fhit physically interacts with A4 through its N-terminus; molecular dynamics simulations were performed on a 3D Fhit model to rationalize its mechanism of action. This approach allowed for the identification of the QHLIKPS heptapeptide (position 7 to 13 of the wild-type Fhit protein) as the smallest Fhit sequence still able to preserve its ability to bind ANXA4. Interestingly, Fhit peptide also recapitulates the property of the native protein in inhibiting Annexin A4 translocation from cytosol to plasma membrane in A549 and Calu-2 lung cancer cells treated with paclitaxel. Finally, the combination of Tat-Fhit peptide and paclitaxel synergistically increases the apoptotic rate of cultured lung cancer cells and blocks in vivo tumor formation.Our findings address to the identification of chemically simplified Fhit derivatives that mimic Fhit tumor suppressor functions; intriguingly, this approach might lead to the generation of novel anticancer drugs to be used in combination with conventional therapies in Fhit-negative tumors to prevent or delay chemoresistance.

  14. A Fhit-mimetic peptide suppresses annexin A4-mediated chemoresistance to paclitaxel in lung cancer cells

    PubMed Central

    Ngankeu, Apollinaire; Ortuso, Francesco; Lovat, Francesca; Pinton, Sandra; D'Agostino, Sabrina; Zanesi, Nicola; Aqeilan, Rami I.; Campiglia, Pietro; Novellino, Ettore; Alcaro, Stefano; Croce, Carlo M.; Trapasso, Francesco

    2016-01-01

    We recently reported that Fhit is in a molecular complex with annexin A4 (ANXA4); following to their binding, Fhit delocalizes ANXA4 from plasma membrane to cytosol in paclitaxel-resistant lung cancer cells, thus restoring their chemosensitivity to the drug. Here, we demonstrate that Fhit physically interacts with A4 through its N-terminus; molecular dynamics simulations were performed on a 3D Fhit model to rationalize its mechanism of action. This approach allowed for the identification of the QHLIKPS heptapeptide (position 7 to 13 of the wild-type Fhit protein) as the smallest Fhit sequence still able to preserve its ability to bind ANXA4. Interestingly, Fhit peptide also recapitulates the property of the native protein in inhibiting Annexin A4 translocation from cytosol to plasma membrane in A549 and Calu-2 lung cancer cells treated with paclitaxel. Finally, the combination of Tat-Fhit peptide and paclitaxel synergistically increases the apoptotic rate of cultured lung cancer cells and blocks in vivo tumor formation. Our findings address to the identification of chemically simplified Fhit derivatives that mimic Fhit tumor suppressor functions; intriguingly, this approach might lead to the generation of novel anticancer drugs to be used in combination with conventional therapies in Fhit-negative tumors to prevent or delay chemoresistance. PMID:27166255

  15. Factors affecting the retention of rennet in cheese curd.

    PubMed

    Bansal, Nidhi; Fox, Patrick F; McSweeney, Paul L H

    2007-10-31

    The coagulant retained in cheese curd is a major contributor to proteolysis during ripening. The objective of this study was to quantify the effects of several milk-related factors and parameters during cheese manufacture on the retention of coagulant in cheese curd. The amount of coagulant retained in curd was determined by its activity on a synthetic heptapeptide (Pro-Thr-Glu-Phe-[NO2-Phe]-Arg-Leu) using reversed-phase HPLC. The retention of chymosin in cheese curd increased significantly when the pH of milk was reduced at rennet addition below pH 6.1, the pH at whey drainage below pH 5.7, or the average casein micelle size in milk and when the ionic strength of milk was increased. The casein content of milk and the quantity of chymosin added to milk had no significant effect on the retention of chymosin in curd; the quantity of coagulant bound per gram of casein remained unchanged.

  16. Semax, an ACTH4-10 peptide analog with high affinity for copper(II) ion and protective ability against metal induced cell toxicity.

    PubMed

    Tabbì, Giovanni; Magrì, Antonio; Giuffrida, Alessandro; Lanza, Valeria; Pappalardo, Giuseppe; Naletova, Irina; Nicoletti, Vincenzo Giuseppe; Attanasio, Francesco; Rizzarelli, Enrico

    2015-01-01

    Heptapeptide Semax, encompassing the sequence 4-7 of N-terminal domain of the adrenocorticotropic hormone (ACTH) and a C-terminal Pro-Gly-Pro tripeptide, belongs to a short regulatory peptides family. This compound has been found to affect learning processes and to exert marked neuroprotective activities on cognitive brain functions. Dys-homeostasis of metal ions is involved in several neurodegenerative disorders and growing evidences have showed that brain is a specialized organ able to concentrate metal ions. In this work, the metal binding ability and protective activity of Semax and its metal complexes were studied. The equilibrium study clearly demonstrated the presence of three complex species. Two minor species [CuL] and [CuLH-1]- co-exist together with the [CuLH-2]2- in the pH range from 3.6 to 5. From pH5 the [CuLH-2]2- species becomes predominant with the donor atoms around copper arranged in a 4N planar coordination mode. Noteworthy, a reduced copper induced cytotoxicity was observed in the presence of Semax by MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] assay on a SHSY5Y neuroblastoma and RBE4 endothelial cell lines.

  17. [The role of opioid system in peculiarities of anti-anxiety effect of peptide anxiolytic selank].

    PubMed

    Kozlovskiĭ, I I; Andreeva, L A; Kozlovskaia, M M; Nadorova, A V; Kolik, L G

    2012-01-01

    Peculiarities of the anxiolytic effects of selank (heptapeptide analog of taftsin) under reduced activity of opioid system upon acute administration of naloxone have been studied in BALB/C and C57BL/6 inbred mice with high and low levels of anxiety, with passive and active emotional stress reaction phenotypes in the open field (OF) test. Selank (0.25 mg/kg, i.p.) per se exhibited anxiolytic effect in BALB/C mice by increasing the general locomotor activity, with no effects on the behavior of C57BL/6 mice in the OF test. Naloxone (1.0 mg/kg, i.p.) per se evoked swift runaway in OF peripheral areas in BALB/C mice while "freezing" the reaction in C57BL/6 mice with active response to stress under the same conditions. Pretreatment with naloxone attenuated the sensitivity to selank in BALB/C mice whereas the response to anxiolytic effects of peptide was increased in C57BL/6 mice. The data obtained reveal a new target for selank in CNS and indicate significance of the activity of enkephalin-opioid system in individual sensitivity to selank.

  18. Construction and analysis of liver suppression subtractive hybridization library of silver carp (Hypophthalmichthys molitrix) intraperitoneally injected with microcystin-LR.

    PubMed

    Qu, Xiancheng; Zhang, Kaiyue; Cui, Zhihui; Zhang, Yong; Jiang, Jiaoyun; Feng, Long; Liu, Qigen

    2011-09-01

    Microcystin-LR (MC-LR) is the most frequently studied cyclic heptapeptide hepatotoxin produced by cyanobacteria. The toxin accumulates rapidly in the liver where it exerts most of its damage, but the molecular mechanisms behind its toxicity remain unclear. Here, suppression subtractive hybridization (SSH) was used to identify alterations in gene transcription of the silver carp (Hypophthalmichthys molitrix) after exposure to MC-LR. After hybridization and cloning, the forward and reverse subtractive cDNA libraries were obtained. At random, 150 positive clones (70 forward and 80 reverse) were selected and sequenced from the subtractive libraries, which gave a total of 88 gene fragment sequences (48 forward and 40 reverse). Sequencing analysis and homology searches showed that these ESTs represented 75 unique genes and 13 duplicates. Of the 75 unique genes, 38 shared high homology with fish genes of known functions, including immune-related genes, transporters and some involved in cell metabolism. Four sequenced genes (Fs59, Fs70, Rs2 and Rs15) were analyzed further using semi-quantitative RT-PCR. The genes from the forward library (Fs59 and Fs70) were found to be transcriptionally upregulated, while the genes from the reverse library (Rs2 and Rs15) were found to be transcriptionally downregulated. These results confirmed the successful construction of the subtractive cDNA library that was enriched for genes that were differentially transcribed in the silver carp liver challenged with MC-LR.

  19. Identification of microcystins in a Lake Victoria cyanobacterial bloom using LC-MS with thiol derivatization.

    PubMed

    Miles, Christopher O; Sandvik, Morten; Nonga, Hezron E; Rundberget, Thomas; Wilkins, Alistair L; Rise, Frode; Ballot, Andreas

    2013-08-01

    Microcystins are cyclic heptapeptides from cyanobacteria which are responsible for poisonings of livestock and humans. Cyanobacteria also produce a range of peptides and other compounds that can result in complex chromatograms when samples are analysed by LC-MS. Thiol derivatization of the α,β-unsaturated amide present in most microcystins was recently shown to simplify analysis of LC-MS chromatograms of a Microcystis culture, making it easier to identify peaks corresponding to microcystins in complex mixtures. This method was applied to analysis of extracts taken from a natural cyanobacteria bloom in Mwanza Gulf, Lake Victoria, Tanzania, in 2010, revealing the presence of numerous putative microcystin analogues in the sample. Results were verified using LC-MS², LC-MS/MS with precursor-ion scanning, and LC-HRMS, leading to identification of 8 major and 17 minor microcystins in the sample, including analogues of microcystin-RY, -RL and -RA. Microcystin-YR (2), -RR (3), and -RY (9) were isolated from bloom material from Lake Victoria, and the structure of 9 was confirmed by NMR spectroscopic analysis and NMR spectral comparison with 2 and 3. Confirmation of the structure of MC-RY (9) facilitated detailed analysis of its MS² spectrum, thereby supporting the structures of related analogues tentatively established on the basis of MS analyses. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Molecular cloning, expression analysis and cellular localization of an LFRFamide gene in the cuttlefish Sepiella japonica.

    PubMed

    Cao, Zi-Hao; Sun, Lian-Lian; Chi, Chang-Feng; Liu, Hui-Hui; Zhou, Li-Qing; Lv, Zhen-Ming; Wu, Chang-Wen

    2016-06-01

    Neuropeptides are important regulators of physiological processes in metazoans, such as feeding, reproduction, and heart activities. In this study, an LFRFamide gene was identified from the cuttlefish Sepiella japonica (designated as SjLFRFamide). The full-length sequence of SjLFRFamide cDNA has 841bp, and the open reading frame contains 567bp encoding 188 amino acids, which shared high similarity with precursor SOFaRP2 from Sepia officinalis. The deduced SjLFRFamdie precursor protein contains a signal peptide and four different FLPs (FMRFamide-like peptides): one pentapeptide (TIFRFamide), two hexapeptides (NSLFRFamide and GNLFRFamide) and one heptapeptide (PHTPFRFamide). Multiple sequence alignment showed that SjLFRFamide contains rather conserved mature peptides, which all ended in FRF. The phylogenetic analysis suggests that SjLFRFamide belongs to the LFRFamide subfamily. The tissue distribution analysis through quantitative real-time PCR method showed that SjLFRFamide mRNA is significantly expressed in the brain, and slight trace are detected in female nidamental gland and accessory nidamental gland. In situ hybridization assay of the brain indicated that SjLFRFamide is transcribed in several different functional lobes, suggesting SjLFRFamide might associate with multiple physiological regulations, such as feeding, chromatophore regulation and reproduction. This is the first study describing LFRFamide in S. japonica, which might have great importance for cuttlefish artificial breeding. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. AVE 0991, a non-peptide Mas-receptor agonist, facilitates penile erection.

    PubMed

    da Costa Gonçalves, Andrey C; Fraga-Silva, Rodrigo A; Leite, Romulo; Santos, Robson A S

    2013-03-01

    The renin-angiotensin system plays a crucial role in erectile function. It has been shown that elevated levels of angiotensin II contribute to the development of erectile dysfunction both in humans and in aminals. On the contrary, the heptapeptide angiotensin-(1-7) appears to mediate penile erection by activation of the Mas receptor. Recently, we have shown that the erectile function of Mas gene-deleted mice was substantially reduced, which was associated with a marked increase in fibrous tissue in the corpus cavernosum. We have hypothesized that the synthetic non-peptide Mas agonist, AVE 0991, would potentiate penile erectile function. We showed that intracavernosal injection of AVE 0991 potentiated the erectile response of anaesthetized Wistar rats, measured as the ratio between corpus cavernosum pressure and mean arterial pressure, upon electrical stimulation of the major pelvic ganglion. The facilitatory effect of AVE 0991 on erectile function was dose dependent and completely blunted by the nitric oxide synthesis inhibitor, l-NAME. Importantly, concomitant intracavernosal infusion of the specific Mas receptor blocker, A-779, abolished the effect of AVE 0991. We demonstrated that AVE 0991 potentiates the penile erectile response through Mas in an NO-dependent manner. Importantly, these results suggest that Mas agonists, such as AVE 0991, might have significant therapeutic benefits for the treatment of erectile dysfunction.

  2. Engineering a bioluminescent indicator for cyclic AMP-dependent protein kinase.

    PubMed Central

    Sala-Newby, G B; Campbell, A K

    1991-01-01

    cDNA coding for the luciferase in the firefly Photinus pyralis was amplified in vitro to generate cyclic AMP-dependent protein kinase phosphorylation sites. The DNA was transcribed and translated to generate light-emitting protein. A valine at position 217 was mutated to arginine to generate a site RRFS and the heptapeptide kemptide, the phosphorylation site of the porcine pyruvate kinase, was added at the N- or C-terminus of the luciferase. The proteins carrying phosphorylation sites were characterized for their specific activity, pI, effect of pH on the colour of the light emitted and effect of the catalytic subunit of protein kinase A in the presence of ATP. Only one of the recombinant proteins (RRFS) was significantly different from wild-type luciferase. The RRFS mutant had a lower specific activity, lower pH optimum, emitted greener light at low pH and when phosphorylated it decreased its activity by up to 80%. This latter effect was reversed by phosphatase. This recombinant protein is a good candidate to measure for the first time cyclic AMP-dependent phosphorylation in live cells. Images Fig. 1. Fig. 2. Fig. 3. PMID:1953665

  3. Discovery of rare and highly toxic microcystins from lichen-associated cyanobacterium Nostoc sp. strain IO-102-I.

    PubMed

    Oksanen, Ilona; Jokela, Jouni; Fewer, David P; Wahlsten, Matti; Rikkinen, Jouko; Sivonen, Kaarina

    2004-10-01

    The production of hepatotoxic cyclic heptapeptides, microcystins, is almost exclusively reported from planktonic cyanobacteria. Here we show that a terrestrial cyanobacterium Nostoc sp. strain IO-102-I isolated from a lichen association produces six different microcystins. Microcystins were identified with liquid chromatography-UV mass spectrometry by their retention times, UV spectra, mass fragmentation, and comparison to microcystins from the aquatic Nostoc sp. strain 152. The dominant microcystin produced by Nostoc sp. strain IO-102-I was the highly toxic [ADMAdda(5)]microcystin-LR, which accounted for ca. 80% of the total microcystins. We assigned a structure of [DMAdda(5)]microcystin-LR and [d-Asp(3),ADMAdda(5)]microcystin-LR and a partial structure of three new [ADMAdda(5)]-XR type of microcystin variants. Interestingly, Nostoc spp. strains IO-102-I and 152 synthesized only the rare ADMAdda and DMAdda subfamilies of microcystin variants. Phylogenetic analyses demonstrated congruence between genes involved directly in microcystin biosynthesis and the 16S rRNA and rpoC1 genes of Nostoc sp. strain IO-102-I. Nostoc sp. strain 152 and the Nostoc sp. strain IO-102-I are distantly related, revealing a sporadic distribution of toxin production in the genus Nostoc. Nostoc sp. strain IO-102-I is closely related to Nostoc punctiforme PCC 73102 and other symbiotic Nostoc strains and most likely belongs to this species. Together, this suggests that other terrestrial and aquatic strains of the genus Nostoc may have retained the genes necessary for microcystin biosynthesis.

  4. Biocombinatorial Synthesis of Novel Lipopeptides by COM Domain-Mediated Reprogramming of the Plipastatin NRPS Complex

    PubMed Central

    Liu, Hongxia; Gao, Ling; Han, Jinzhi; Ma, Zhi; Lu, Zhaoxin; Dai, Chen; Zhang, Chong; Bie, Xiaomei

    2016-01-01

    Both donors and acceptors of communication-mediating (COM) domains are essential for coordinating intermolecular communication within nonribosomal peptides synthetases (NRPSs) complexes. Different sets of COM domains provide selectivity, allowing NRPSs to utilize different natural biosynthetic templates. In this study, novel lipopeptides were synthesized by reprogramming the plipastatin biosynthetic machinery. A Thr-to-Asp point mutation was sufficient to shift the selectivity of the donor COM domain of ppsB toward that of ppsD. Deletion and/or interchangeability established donor and acceptor function. Variations in acceptor COM domain did not result in novel product formation in the presence of its partner donor, whereas plipastatin formation was completely abrogated by altering donor modules. Five novel lipopeptides (cyclic pentapeptide, linear hexapeptide, nonapeptide, heptapeptide, and cyclic octapeptide) were identified and verified by high-resolution LC-ESI-MS/MS. In addition, we demonstrated the potential to generate novel strains with the antimicrobial activity by selecting compatible COM domains, and the novel lipopeptides exhibited antimicrobial activity against five of the fungal species at a contention of 31.25–125 μg/ml. PMID:27909427

  5. Transcriptional and Behavioral Responses of Zebrafish Larvae to Microcystin-LR Exposure

    PubMed Central

    Tzima, Eleni; Serifi, Iliana; Tsikari, Ioanna; Alzualde, Ainhoa; Leonardos, Ioannis; Papamarcaki, Thomais

    2017-01-01

    Microcystins are cyclic heptapeptides that constitute a diverse group of toxins produced by cyanobacteria. One of the most toxic variants of this family is microcystin-LR (MCLR) which is a potent inhibitor of protein phosphatase 2A (PP2A) and induces cytoskeleton alterations. In this study, zebrafish larvae exposed to 500 μg/L of MCLR for four days exhibited a 40% reduction of PP2A activity compared to the controls, indicating early effects of the toxin. Gene expression profiling of the MCLR-exposed larvae using microarray analysis revealed that keratin 96 (krt96) was the most downregulated gene, consistent with the well-documented effects of MCLR on cytoskeleton structure. In addition, our analysis revealed upregulation in all genes encoding for the enzymes of the retinal visual cycle, including rpe65a (retinal pigment epithelium-specific protein 65a), which is critical for the larval vision. Quantitative real-time PCR (qPCR) analysis confirmed the microarray data, showing that rpe65a was significantly upregulated at 50 μg/L and 500 μg/L MCLR in a dose-dependent manner. Consistent with the microarray data, MCLR-treated larvae displayed behavioral alterations such as weakening response to the sudden darkness and hypoactivity in the dark. Our work reveals new molecular targets for MCLR and provides further insights into the molecular mechanisms of MCLR toxicity during early development. PMID:28208772

  6. Can we effectively degrade microcystins?--Implications on human health.

    PubMed

    de la Cruz, Armah A; Antoniou, Maria G; Hiskia, Anastasia; Pelaez, Miguel; Song, Weihua; O'Shea, Kevin E; He, Xuexiang; Dionysiou, Dionysios D

    2011-01-01

    Microcystins are cyclic heptapeptide toxins produced by a number of genera of cyanobacteria. They are ubiquitous in bodies of water worldwide and pose significant hazard to human, plant, and animal health. Microcystins are primarily hepatotoxins known to inhibit serine-threonine phosphatases leading to the disruption of cascade of events important in the regulation and control of cellular processes. Covalent binding of microcystins with phosphatases is thought to be responsible for the cytotoxic and genotoxic effects of microcystins. In addition, microcystins can trigger oxidative stress in cells resulting in necrosis or apoptosis. Their cyclic structure and novel amino acids enhance their stability and persistence in the environment. Humans are primarily exposed to microcystins via drinking water consumption and accidental ingestion of recreational water. Recreational exposure by skin contact or inhalation to microcystins is now recognized to cause a wide range of acute illnesses which can be life-threatening. Microcystins are primarily degraded by microorganisms in the environment, while sunlight can cause the isomerization of the double bonds and hydroxylation in the presence of pigments. Attempts to utilize these organisms in sand and membrane filters to treat water contaminated with microcystins showed complete removal and detoxification. Conventional water treatment processes may not fully eliminate microcystins when there are high levels of organic compounds especially during harmful bloom events. Combination of conventional and advanced oxidation technologies can potentially remove 100% of microcystins in water even in turbid conditions. This review covers selected treatment technologies to degrade microcystins in water.

  7. Are fish fed with cyanobacteria safe, nutritious and delicious? A laboratory study

    PubMed Central

    Liang, Hualei; Zhou, Wenshan; Zhang, Yulei; Qiao, Qin; Zhang, Xuezhen

    2015-01-01

    Toxic cyanobacterial blooms, which produce cyclic heptapeptide toxins known as microcystins, are worldwide environmental problems. On the other hand, the cyanobacteria protein (30–50%) has been recommended as substitute protein for aquaculture. The present laboratory study verified the feasibility of cyanobacteria protein substitution and risk assessment. Goldfish were fed diets supplemented lyophilised cyanobacteria powder for 16 weeks with the various doses: 0% (control), 10%, 20%, 30% and 40%. Low doses (10% and 20%) promoted growth whereas high doses (30% and 40%) inhibited growth. In cyanobacteria treated fish, the proximate composition of ash, crude fat content and crude protein content decreased in 16 weeks; the saturated fatty acid (SFA) content significantly increased; the n-3 polyunsaturated fatty acid content, collagen content and muscle pH significantly decreased; cooking loss percents increased significantly. Muscle fiber diameter and myofibril length were negatively correlation. Additionally, flavour compounds (e.g., amino acids, nucleotides, organic acids and carnosine) changed significantly in the treated fish, and odour compounds geosmin and 2-methylisoborneol increased significantly. The estimated daily intake (EDI) of microcystins in muscle was close to or exceeded the World Health Organization (WHO) tolerable daily intake (TDI), representing a great health risk. Cyanobacterie is not feasible for protein sources use in aquaculture. PMID:26470644

  8. The structural basis for peptidomimetic inhibition of eukaryotic ribonucleotide reductase: a conformationally flexible pharmacophore.

    PubMed

    Xu, Hai; Fairman, James W; Wijerathna, Sanath R; Kreischer, Nathan R; LaMacchia, John; Helmbrecht, Elizabeth; Cooperman, Barry S; Dealwis, Chris

    2008-08-14

    Eukaryotic ribonucleotide reductase (RR) catalyzes nucleoside diphosphate conversion to deoxynucleoside diphosphate. Crucial for rapidly dividing cells, RR is a target for cancer therapy. RR activity requires formation of a complex between subunits R1 and R2 in which the R2 C-terminal peptide binds to R1. Here we report crystal structures of heterocomplexes containing mammalian R2 C-terminal heptapeptide, P7 (Ac-1FTLDADF7) and its peptidomimetic P6 (1Fmoc(Me)PhgLDChaDF7) bound to Saccharomyces cerevisiae R1 (ScR1). P7 and P6, both of which inhibit ScRR, each bind at two contiguous sites containing residues that are highly conserved among eukaryotes. Such binding is quite distinct from that reported for prokaryotes. The Fmoc group in P6 peptide makes several hydrophobic interactions that contribute to its enhanced potency in binding to ScR1. Combining all of our results, we observe three distinct conformations for peptide binding to ScR1. These structures provide pharmacophores for designing highly potent nonpeptide class I RR inhibitors.

  9. Biochemical and structural characterisation of the second oxidative crosslinking step during the biosynthesis of the glycopeptide antibiotic A47934

    PubMed Central

    Ulrich, Veronika; Brieke, Clara

    2016-01-01

    The chemical complexity and biological activity of the glycopeptide antibiotics (GPAs) stems from their unique crosslinked structure, which is generated by the actions of cytochrome P450 (Oxy) enzymes that affect the crosslinking of aromatic side chains of amino acid residues contained within the GPA heptapeptide precursor. Given the crucial role peptide cyclisation plays in GPA activity, the characterisation of this process is of great importance in understanding the biosynthesis of these important antibiotics. Here, we report the cyclisation activity and crystal structure of StaF, the D-O-E ring forming Oxy enzyme from A47934 biosynthesis. Our results show that the specificity of StaF is reduced when compared to Oxy enzymes catalysing C-O-D ring formation and that this activity relies on interactions with the non-ribosomal peptide synthetase via the X-domain. Despite the interaction of StaF with the A47934 X-domain being weaker than for the preceding Oxy enzyme StaH, StaF retains higher levels of in vitro activity: we postulate that this is due to the ability of the StaF/X-domain complex to allow substrate reorganisation after initial complex formation has occurred. These results highlight the importance of testing different peptide/protein carrier constructs for in vitro GPA cyclisation assays and show that different Oxy homologues can display significantly different catalytic propensities despite their overall similarities. PMID:28144358

  10. Suppression Analysis Reveals a Functional Difference between the Serines in Positions Two and Five in the Consensus Sequence of the C-Terminal Domain of Yeast RNA Polymerase II

    PubMed Central

    Yuryev, A.; Corden, J. L.

    1996-01-01

    The largest subunit of RNA polymerase II contains a repetitive C-terminal domain (CTD) consisting of tandem repeats of the consensus sequence Tyr(1)Ser(2)Pro(3)Thr(4) Ser(5)Pro(6) Ser(7). Substitution of nonphosphorylatable amino acids at positions two or five of the Saccharomyces cerevisiae CTD is lethal. We developed a selection ssytem for isolating suppressors of this lethal phenotype and cloned a gene, SCA1 (suppressor of CTD alanine), which complements recessive suppressors of lethal multiple-substitution mutations. A partial deletion of SCA1 (sca1Δ::hisG) suppresses alanine or glutamate substitutions at position two of the consensus CTD sequence, and a lethal CTD truncation mutation, but SCA1 deletion does not suppress alanine or glutamate substitutions at position five. SCA1 is identical to SRB9, a suppressor of a cold-sensitive CTD truncation mutation. Strains carrying dominant SRB mutations have the same suppression properties as a sca1Δ::hisG strain. These results reveal a functional difference between positions two and five of the consensus CTD heptapeptide repeat. The ability of SCA1 and SRB mutant alleles to suppress CTD truncation mutations suggest that substitutions at position two, but not at position five, cause a defect in RNA polymerase II function similar to that introduced by CTD truncation. PMID:8725217

  11. RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation.

    PubMed

    Ni, Zuyao; Xu, Chao; Guo, Xinghua; Hunter, Gerald O; Kuznetsova, Olga V; Tempel, Wolfram; Marcon, Edyta; Zhong, Guoqing; Guo, Hongbo; Kuo, Wei-Hung William; Li, Joyce; Young, Peter; Olsen, Jonathan B; Wan, Cuihong; Loppnau, Peter; El Bakkouri, Majida; Senisterra, Guillermo A; He, Hao; Huang, Haiming; Sidhu, Sachdev S; Emili, Andrew; Murphy, Shona; Mosley, Amber L; Arrowsmith, Cheryl H; Min, Jinrong; Greenblatt, Jack F

    2014-08-01

    The RNA polymerase II (RNAPII) C-terminal domain (CTD) heptapeptide repeats (1-YSPTSPS-7) undergo dynamic phosphorylation and dephosphorylation during the transcription cycle to recruit factors that regulate transcription, RNA processing and chromatin modification. We show here that RPRD1A and RPRD1B form homodimers and heterodimers through their coiled-coil domains and interact preferentially via CTD-interaction domains (CIDs) with RNAPII CTD repeats phosphorylated at S2 and S7. Crystal structures of the RPRD1A, RPRD1B and RPRD2 CIDs, alone and in complex with RNAPII CTD phosphoisoforms, elucidate the molecular basis of CTD recognition. In an example of cross-talk between different CTD modifications, our data also indicate that RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and, by interacting with CTD repeats where phospho-S2 and/or phospho-S7 bracket a phospho-S5 residue, serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2.

  12. Properties of a homogeneous C-lobe prepared by introduction of a TEV cleavage site between the lobes of human transferrin1

    PubMed Central

    Steere, Ashley N.; Roberts, Samantha E.; Byrne, Shaina L.; Chasteen, N. Dennis; Bobst, Cedric E.; Kaltashov, Igor A; Smith, Valerie C.; MacGillivray, Ross T. A.; Mason, Anne B.

    2010-01-01

    Essential to iron transport and delivery, human serum transferrin (hTF) is a bilobal glycoprotein capable of reversibly binding one ferric ion in each lobe (the N- and C-lobes). A complete description of iron release from hTF, as well as insight into the physiological significance of the bilobal structure, demands characterization of the isolated lobes. Although production of large amounts of isolated N-lobe and full-length hTF has been well documented, attempts to produce the C-lobe (by recombinant and/or proteolytic approaches) have met with more limited success. Our new strategy involves replacing the hepta-peptide, PEAPTDE (comprising the bridge between the lobes) with the sequence ENLYFQ/G in a His-tagged non-glycosylated monoferric hTF construct, designated FeChTF. The new bridge sequence of this construct, designated FeCTEV hTF, is readily cleaved by the tobacco etch virus (TEV) protease yielding non-glycosylated C-lobe. Following nickel column chromatography (to remove the N-lobe and the TEV protease which are both His tagged), the homogeneity of the C-lobe has been confirmed by mass spectroscopy. Differing reactivity with a monoclonal antibody specific to the C-lobe indicates that introduction of the TEV cleavage site into the bridge alters its conformation. The spectral and kinetic properties of the isolated C-lobe differ significantly from those of the isolated N-lobe. PMID:20064616

  13. Development of an analytical method for the unambiguous structure elucidation of cyclic peptides with special appliance for hepatotoxic desmethylated microcystins.

    PubMed

    Krüger, Thomas; Christian, Bernd; Luckas, Bernd

    2009-09-01

    The periodical occurrence of harmful algal blooms (HABs) in freshwater lakes requires the determination of potential cyanobacterial toxins, especially microcystins (MCs). On demand of an adequate risk assessment, the high diversity of these hepatotoxic cyclic heptapeptides implicates the need of an unambiguous detection of their specific structural variants. Therefore, LC-MS and LC-MS/MS methods are the approaches of choice for determination of MCs. In contrast, even tandem mass spectromic fragmentation patterns are not even sufficient in any kind of structural determination requirements, whereas NMR methods require very high amounts of MCs. In this study, we present a novel method for chromatographic separation of desmethylated microcystins (dm-MCs). Based on the isolation of the specific structural variants using semi-preparative HPLC, a method was developed for the structure elucidation of cyclic peptides with special appliance for the determination of dm-MCs via analysis of the specific amino acid composition after peptide hydrolysis followed by stereospecific detection of the amino acids and resulting keto acids. On the basis of this method it is demonstrated that dm-MC-RR with the structure [Dha(7)]MC-RR represented the major compound in the microcystin pattern of Microcystis aeruginosa bloom events in 2005 and 2006 in Lake Senftenberg, Germany.

  14. Mass spectrometry and biochemical analysis of RNA polymerase II: targeting by protein phosphatase-1

    PubMed Central

    Jerebtsova, Marina; Klotchenko, Sergei A.; Artamonova, Tatiana O.; Ammosova, Tatiana; Washington, Kareem; Egorov, Vladimir V.; Shaldzhyan, Aram A.; Sergeeva, Maria V.; Zatulovskiy, Evgeny A.; Temkina, Olga A.; Petukhov, Mikhail G.; Vasin, Andrei V.; Khodorkovskii, Mikhail A.; Orlov, Yuri N.

    2011-01-01

    Transcription of eukaryotic genes is regulated by phosphorylation of serine residues of heptapeptide repeats of the carboxyterminal domain (CTD) of RNA polymerase II (RNAPII). We previously reported that protein phosphatase-1 (PP1) dephosphorylates RNAPII CTD in vitro and inhibition of nuclear PP1-blocked viral transcription. In this article, we analyzed the targeting of RNAPII by PP1 using biochemical and mass spectrometry analysis of RNAPII-associated regulatory subunits of PP1. Immunoblotting showed that PP1 co-elutes with RNAPII. Mass spectrometry approach showed the presence of U2 snRNP. Co-immunoprecipitation analysis points to NIPP1 and PNUTS as candidate regulatory subunits. Because NIPP1 was previously shown to target PP1 to U2 snRNP, we analyzed the effect of NIPP1 on RNAPII phosphorylation in cultured cells. Expression of mutant NIPP1 promoted RNAPII phosphorylation suggesting that the deregulation of cellular NIPP1/PP1 holoenzyme affects RNAPII phosphorylation and pointing to NIPP1 as a potential regulatory factor in RNAPII-mediated transcription. PMID:20941529

  15. A fluorescent peptide substrate for the surface metalloprotease of Leishmania.

    PubMed

    Bouvier, J; Schneider, P; Malcolm, B

    1993-03-01

    A fluorescent oligopeptide substrate for the promastigote surface protease (PSP) of Leishmania was designed using the data reported for the substrate specificity of the enzyme (Bouvier, J., Schneider, P., Etges, R. J., and Bordier, C. 1990. Biochemistry 29, 10113-10119). The indole fluorescence of the tryptophan residue was efficiently quenched through resonance energy transfer by an N-terminal dansyl group located five amino acid residues away. The heptapeptide, dansyl-A-Y-L-K-K-W-V-NH2, was cleaved by PSP between the tyrosine and leucine residues with a kcat/Km ratio of 8.8 x 10(6) M-1sec-1. Hydrolysis by the enzyme results in a time-dependent increase of fluorescence intensity of 3.7-fold. Assays can be designed based on the tryptophan fluorescence at 360 nm or by individual product analyses using thin-layer chromatography. The synthetic substrate is readily cleaved by the metalloprotease at the surface of fixed promastigotes. The specificity and sensitivity of such internally quenched fluorescent peptide substrate will facilitate the identification of novel inhibitors for the enzyme and aid in detailed studies on its enzymology.

  16. Biologically functionalized nanochannels on ferroelectric lead zirconium titanate surfaces.

    SciTech Connect

    Ocola, L. E.; Pan, W. C.; Kuo, M.; Tirumala, V. R.; Reiss, B. D.; Firestone, M. A.; Illinois Mathematics and Science Academy

    2005-01-01

    We recently started a program at Argonne to exploit patterned, polarizable ferroelectric surfaces, such as lead zirconium titanate (PZT), as a means to create field-responsive inorganic-biomolecule interfaces to study and manipulate biomatter on surfaces. In this paper we will discuss the integration of nanochannels on the surface of PZT films and their selective functionalization to create nanovalves to control nanofluidic flow. Microfluidic devices have been fabricated using a variety of methods, ranging from thermal decomposition of buried patterned channels, to fabricating trenches via plasma etch or hot embossing followed by trench capping. Our work focuses on an alternative method by using a bilayer resist in an inverted configuration normally used for T- and Gamma- gate fabrication. This method is capable of yielding sub-100 nm nanochannels with high aspect ratios and sub-500nm alignment. We have recently demonstrated that the polarization hysteresis loop of PZT is the same before and after exposure to an aqueous environment. This opens the possibility of selective surface modification of PZT via coupling of a wide range of biomolecules (e.g., peptides, proteins) and the use of the electric-field-responsive properties of PZT to manipulate the function (e.g., orientation) of the tethered biomolecules. We have used phage display techniques to evolve specific peptide motifs that selectively bind to PZT. The optimum heptapeptide that facilitates both the attachment of functional biological molecules to the surface of PZT has been identified.

  17. Structural Basis for Microcin C7 Inactivation by the MccE Acetyltransferase

    SciTech Connect

    Agarwal, Vinayak; Metlitskaya, Anastasiya; Severinov, Konstantin; Nair, Satish K.

    2015-10-15

    The antibiotic microcin C7 (McC) acts as a bacteriocide by inhibiting aspartyl-tRNA synthetase and stalling the protein translation machinery. McC is synthesized as a heptapeptide-nucleotide conjugate, which is processed by cellular peptidases within target strains to yield the biologically active compound. As unwanted processing of intact McC can result in self-toxicity, producing strains utilize multiple mechanisms for autoimmunity against processed McC. We have shown previously that the mccE gene within the biosynthetic cluster can inactivate processed McC by acetylating the antibiotic. Here, we present the characterization of this acetylation mechanism through biochemical and structural biological studies of the MccE acetyltransferase domain (MccE{sup AcTase}). We have also determined five crystal structures of the MccE-acetyl-CoA complex with bound substrates, inhibitor, and reaction product. The structural data reveal an unexpected mode of substrate recognition through p-stacking interactions similar to those found in cap-binding proteins and nucleotidyltransferases. These studies provide a rationale for the observation that MccE{sup AcTase} can detoxify a range of aminoacylnucleotides, including those that are structurally distinct from microcin C7.

  18. Roles of miRNAs in microcystin-LR-induced Sertoli cell toxicity

    SciTech Connect

    Zhou, Yuan; Wang, Hui; Wang, Cong; Qiu, Xuefeng; Benson, Mikael; Yin, Xiaoqin; Xiang, Zou; Li, Dongmei; and others

    2015-08-15

    Microcystin (MC)-LR, a cyclic heptapeptide, is a potent reproductive system toxin. To understand the molecular mechanisms of MC-induced reproductive system cytotoxicity, we evaluated global changes of miRNA and mRNA expression in mouse Sertoli cells following MC-LR treatment. Our results revealed that the exposure to MC-LR resulted in an altered miRNA expression profile that might be responsible for the modulation of mRNA expression. Bio-functional analysis indicated that the altered genes were involved in specific cellular processes, including cell death and proliferation. Target gene analysis suggested that junction injury in Sertoli cells exposed to MC-LR might be mediated by miRNAs through the regulation of the Sertoli cell-Sertoli cell pathway. Collectively, these findings may enhance our understanding on the modes of action of MC-LR on mouse Sertoli cells as well as the molecular mechanisms underlying the toxicity of MC-LR on the male reproductive system. - Highlights: • miRNAs were altered in Sertoli cells exposed to MC-LR. • Alerted genes were involved in different cell functions including the cell morphology. • MC-LR adversely affected Sertoli cell junction formation through the regulating miRNAs.

  19. Fast and sensitive analysis of dermorphin and HYP6-dermorphin in equine plasma using liquid chromatography tandem mass spectrometry.

    PubMed

    Wang, Caroline C; Hartmann-Fischbach, Petra; Krueger, Tim R; Wells, Terry L; Feineman, Amy R; Compton, Joanne C

    2014-04-01

    Dermorphin and HYP(6) -dermorphin are hepta-peptides and natural opioids originally isolated from the skin of South American frogs. They are more potent than morphine but less likely to produce drug tolerance and addiction. These properties make them ideal candidates for the doping of racehorses to enhance performance during competition. Dermorphin was recently classified as a Class I drug by Racing Commissioners International (RCI), indicating that it is a banned substance in equine athletes. To enforce this ban, a fast and sensitive method was developed for dermorphin and HYP(6)-dermorphin analysis in equine plasma. Equine plasma (2 ml) was extracted on a mixed mode cation exchange solid-phase column. After extraction, dermorphin and HYP(6)-dermorphin were separated and detected using a liquid chromatography (LC) triple quadrupole linear ion trap mass spectrometry in positive multiple-reaction-monitoring (MRM) mode. Each analysis was 3.5 min. Four MRM transitions were used for identification of each compound. The extraction procedure was efficient and the limits of detection (LOD) were 2 pg/ml and 10 pg/ml for dermorphin and HYP(6)-dermorphin, respectively. The method has good selectivity and precision. Results of stability studies showed that both analytes were stable at low temperature. This is the first report of dermorphin and HYP(6)-dermorphin analysis in equine plasma, which could be adopted as a regular screening or confirmation method for controlling the abuse of these compounds in equine sports. Copyright © 2013 John Wiley & Sons, Ltd.

  20. Identification and characterization of antimicrobial peptides from the skin of the endangered frog Odorrana ishikawae.

    PubMed

    Iwakoshi-Ukena, Eiko; Ukena, Kazuyoshi; Okimoto, Aiko; Soga, Miyuki; Okada, Genya; Sano, Naomi; Fujii, Tamotsu; Sugawara, Yoshiaki; Sumida, Masayuki

    2011-04-01

    The endangered anuran species, Odorrana ishikawae, is endemic to only two small Japanese Islands, Amami and Okinawa. To assess the innate immune system in this frog, we investigated antimicrobial peptides in the skin using artificially bred animals. Nine novel antimicrobial peptides containing the C-terminal cyclic heptapeptide domain were isolated on the basis of antimicrobial activity against Escherichia coli. The peptides were members of the esculentin-1 (two peptides), esculentin-2 (one peptide), palustrin-2 (one peptide), brevinin-2 (three peptides) and nigrocin-2 (two peptides) antimicrobial peptide families. They were named esculentin-1ISa, esculentin-1ISb, esculentin-2ISa, palustrin-2ISa, brevinin-2ISa, brevinin-2ISb, brevinin-2ISc, nigrocin-2ISa and nigrocin-2ISb. Peptide primary structures suggest a close relationship with the Asian odorous frogs, Odorrana grahami and Odorrana hosii. These antimicrobial peptides possessed a broad-spectrum of growth inhibition against five microorganisms (E. coli, Staphylococcus aureus, methicillin-resistant S. aureus, Bacillus subtilis and Candida albicans). Nine different cDNAs encoding the precursor proteins were also cloned and showed that the precursor proteins exhibited a signal peptide, an N-terminal acidic spacer domain, a Lys-Arg processing site and an antimicrobial peptide at the C-terminus. Copyright © 2010 Elsevier Inc. All rights reserved.

  1. Identification and structure-activity relationship of an antimicrobial peptide of the palustrin-2 family isolated from the skin of the endangered frog Odorrana ishikawae.

    PubMed

    Iwakoshi-Ukena, Eiko; Okada, Genya; Okimoto, Aiko; Fujii, Tamotsu; Sumida, Masayuki; Ukena, Kazuyoshi

    2011-10-01

    Recently, we identified nine novel antimicrobial peptides from the skin of the endangered anuran species, Odorrana ishikawae, to assess its innate immune system. In this study an additional antimicrobial peptide was initially isolated based on antimicrobial activity against Escherichia coli. The new antimicrobial peptide belonging to the palustrin-2 family was named palustrin-2ISb. It consists of 36 amino acid residues including 7 amino acids C-terminal to the cyclic heptapeptide Rana box domain. The peptide's primary structure suggests a close relationship with the Chinese odorous frog, Odorrana grahami. The cloned cDNA encoding the precursor protein contained a signal peptide, an N-terminal acidic spacer domain, a Lys-Arg processing site and the C-terminal precursor antimicrobial peptide. It also contained 3 amino acid residues at the C-terminus not found in the mature peptide. Finally, the antimicrobial activities against four microorganisms (E. coli, Staphylococcus aureus, methicillin-resistant S. aureus and Candida albicans) were investigated using several synthetic peptides. A 29 amino acid truncated form of the peptide, lacking the 7 amino acids C-terminal to the Rana box, possessed greater antimicrobial activities than the native structure. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. Molecular and cellular mechanisms of the inhibitory effects of ACE-2/ANG1-7/Mas axis on lung injury.

    PubMed

    Gopallawa, Indiwari; Uhal, Bruce D

    2014-01-01

    An established body of recent literature has demonstrated potent inhibitory effects of the angiotensin converting enzyme-2 (ACE-2)/ANG1-7/ Mas axis on acute lung injury and lung fibrogenesis. One of the mechanisms of this inhibition is the enzymatic action of ACE-2 to degrade its main substrate angiotensin (ANG) II, thereby reducing the injurious and profibrotic activities of this octapeptide. Another, potentially more important mechanism is the production by ACE-2 of the heptapeptide ANG1-7, which inhibits the actions of ANGII through its own receptor Mas, the product of the oncogene of the same name. Very recent efforts to define the molecular and cellular mechanisms of ANG1-7/Mas action have revealed a number of similar, but mechanistically distinct, pathways by which ANG1-7 and Mas act on various lung cell types to inhibit lung injury and fibrosis. In this review we summarize the beneficial actions of the ANG1-7/Mas pathway, specifically on lung cells in non-neoplastic lung injury. We also review the currently known downstream signaling mechanisms of the ANG1-7/Mas pathway in various lung cell types known to be key in acute injury and fibrogenesis.

  3. Characterization and significance of ACE2 and Mas receptor in human colon adenocarcinoma.

    PubMed

    Bernardi, Stella; Zennaro, Cristina; Palmisano, Silvia; Velkoska, Elena; Sabato, Nicoletta; Toffoli, Barbara; Giacomel, Greta; Buri, Luigi; Zanconati, Fabrizio; Bellini, Giuseppe; Burrell, Louise M; De Manzini, Nicolò; Fabris, Bruno

    2012-03-01

    A new arm of the renin-angiotensin system (RAS) has been recently characterized; this includes angiotensin converting enzyme (ACE)2 and angiotensin (Ang)1-7, a heptapeptide acting through the Mas receptor (MasR). Recent studies show that Ang1-7 has an antiproliferative action on lung adenocarcinoma cells. The aim of this study was to characterize RAS expression in human colon adenocarcinoma and to investigate whether Ang1-7 exerts an antiproliferative effect on human colon adenocarcinoma cells. Gene, protein expression and enzymatic activity of the main components of the RAS were determined on non-neoplastic colon mucosa as well as on the tumor mass and the mucosa taken 5 cm distant from it, both collected from patients with colon adenocarcinoma. Two different human colon cancer cell lines were treated with AngII and Ang1-7. The novel finding of this study was that MasR was significantly upregulated in colon adenocarcinoma compared with non-neoplastic colon mucosa, which showed little or no expression of it. ACE gene expression and enzymatic activity were also increased in the tumors. However, AngII and Ang1-7 did not have any pro-/antiproliferative effects in the cell lines studied. The data suggest that upregulation of the MasR could be used as a diagnostic marker of colon adenocarcinoma.

  4. Stress Induces Changes in the Phosphorylation of Trypanosoma cruzi RNA Polymerase II, Affecting Its Association with Chromatin and RNA Processing

    PubMed Central

    Rocha, Antônio Augusto; Moretti, Nilmar Silvio

    2014-01-01

    The phosphorylation of the carboxy-terminal heptapeptide repeats of the largest subunit of RNA polymerase II (Pol II) controls several transcription-related events in eukaryotes. Trypanosomatids lack these typical repeats and display an unusual transcription control. RNA Pol II associates with the transcription site of the spliced leader (SL) RNA, which is used in the trans-splicing of all mRNAs transcribed on long polycistronic units. We found that Trypanosoma cruzi RNA Pol II associated with chromatin is highly phosphorylated. When transcription is inhibited by actinomycin D, the enzyme runs off from SL genes, remaining hyperphosphorylated and associated with polycistronic transcription units. Upon heat shock, the enzyme is dephosphorylated and remains associated with the chromatin. Transcription is partially inhibited with the accumulation of housekeeping precursor mRNAs, except for heat shock genes. DNA damage caused dephosphorylation and transcription arrest, with RNA Pol II dissociating from chromatin although staying at the SL. In the presence of calyculin A, the hyperphosphorylated form detached from chromatin, including the SL loci. These results indicate that in trypanosomes, the unusual RNA Pol II is phosphorylated during the transcription of SL and polycistronic operons. Different types of stresses modify its phosphorylation state, affecting pre-RNA processing. PMID:24813189

  5. Novel fluorescently labeled peptide compounds for detection of oxidized low-density lipoprotein at high specificity.

    PubMed

    Sato, Akira; Yamanaka, Hikaru; Oe, Keitaro; Yamazaki, Yoji; Ebina, Keiichi

    2014-10-01

    The probes for specific detection of oxidized low-density lipoprotein (ox-LDL) in plasma and in atherosclerotic plaques are expected to be useful for the identification, diagnosis, prevention, and treatment for atherosclerosis. In this study, to develop a fluorescent peptide probe for specific detection of ox-LDL, we investigated the interaction of fluorescein isothiocyanate (FITC)-labeled peptides with ox-LDL using polyacrylamide gel electrophoresis. Two heptapeptides (KWYKDGD and KP6) coupled through the ε-amino group of K at the N-terminus to FITC in the presence/absence of 6-amino-n-caproic acid (AC) linker to FITC--(FITC-AC)KP6 and (FITC)KP6--both bound with high specificity to ox-LDL in a dose-dependent manner. In contrast, a tetrapeptide (YKDG) labeled with FITC at the N-terminus and a pentapeptide (YKDGK) coupled through the ε-amino group of K at the C-terminus to FITC did not bind selectively to ox-LDL. Furthermore, (FITC)KP6 and (FITC-AC)KP6 bound with high specificity to the protein in mouse plasma (probably ox-LDL fraction). These findings strongly suggest that (FITC)KP6 and (FITC-AC)KP6 may be effective novel fluorescent probes for specific detection of ox-LDL.

  6. Collision induced dissociation-based characterization of nucleotide peptides: fragmentation patterns of microcin C7-C51, an antimicrobial peptide produced by Escherichia coli.

    PubMed

    Petit, Vanessa W; Zirah, Séverine; Rebuffat, Sylvie; Tabet, Jean-Claude

    2008-08-01

    Covalent protein-nucleic acid conjugates form an original class of compounds that occur in nature or can be generated in vitro through cross-linking to investigate domains involved in protein/nucleic acid interactions. Their mass spectrometry fragmentation patterns are poorly characterized. We have used electrospray-ionization mass spectrometry (ESI-MS) combined with collision-induced dissociation (CID) to characterize microcin C7-C51, an antimicrobial nucleotide peptide that targets aspartyl-tRNA synthetase and inhibits translation. The fragments of microcin C7-C51 were analyzed in positive- and negative-ion modes and compared with those of the corresponding unmodified heptapeptide and to the derived aspartyl-adenylate. The positive- and negative-ion mode fragments of microcin C7-C51 provided information on both the nucleotide and peptide moieties. Accurate mass measurement obtained using an LTQ Orbitrap instrument was a key factor for a comprehensive interpretation of the fragments. The experimental results obtained permitted the proposal of stepwise fragmentation pathways involving ion-dipole complexes. The data provide a better understanding of nucleotide peptide fragmentation in the gas phase.

  7. Characterization of the surfactin synthetase C-terminal thioesterase domain as a cyclic depsipeptide synthase.

    PubMed

    Tseng, Claire C; Bruner, Steven D; Kohli, Rahul M; Marahiel, Mohamed A; Walsh, Christopher T; Sieber, Stephan A

    2002-11-12

    The C-terminal thioesterase domain of the nonribosomal peptide synthetase producing the lipopetide surfactin (Srf TE) retains autonomous ability to generate the cyclic peptidolactone skeleton of surfactin when provided with a soluble beta-hydroxy-butyryl-heptapeptidyl thioester substrate. Utilizing the recently solved crystal structure [Bruner, S. D., et al. (2002) Structure 10, 301-310], the active-site nucleophile, Ser80, was changed to Cys, and the other members of the catalytic triad, Asp107 and His207, were changed to Ala, with the resulting mutants lacking detectable activity. Two cationic side chains in the active site, Lys111 and Arg120, were changed to Ala, causing an increased partitioning of the product to hydrolysis, as did a P26G mutant, mimicking the behavior of lipases. To evaluate recognition elements in substrates used by Srf TE, alterations to the fatty acyl group, the heptapeptide, and the thioester leaving group were made, and the resulting substrates were characterized for kinetic competency and flux of product to cyclization or hydrolysis. Alterations that could be accepted for cyclization were identified in all three parts of the substrate, although tolerance limits for changes varied. In addition, cocrystal structures of Srf TE with dipeptidyl boronate inhibitors were solved, illustrating the critical binding determinants of the substrate. On the basis of the structures and biochemical data, the cyclizing conformation of the surfactin peptide was modeled into the enzyme active site.

  8. Rtr1 is a dual specificity phosphatase that dephosphorylates Tyr1 and Ser5 on the RNA Polymerase II CTD

    PubMed Central

    Hsu, Peter L.; Yang, Fan; Smith-Kinnaman, Whitney; Yang, Wen; Song, Jae-Eun; Mosley, Amber L.; Varani, Gabriele

    2014-01-01

    The phosphorylation state of heptapeptide repeats within the C-terminal domain (CTD) of the largest subunit of RNA Polymerase II (PolII) controls the transcription cycle and is maintained by the competing action of kinases and phosphatases. Rtr1 was recently proposed to be the enzyme responsible for the transition of PolII into the elongation and termination phases of transcription by removing the phosphate marker on Serine 5, but this attribution was questioned by the apparent lack of enzymatic activity. Here we demonstrate that Rtr1 is a phosphatase of new structure that is auto-inhibited by its own C-terminus. The enzymatic activity of the protein in vitro is functionally important in vivo as well: a single amino acid mutation that reduces activity leads to the same phenotype in vivo as deletion of the protein-coding gene from yeast. Surprisingly, Rtr1 dephosphorylates not only Serine 5 on the CTD, but also the newly described anti-termination Tyrosine 1 marker, supporting the hypothesis that Rtr1 and its homologs promote the transition from transcription to termination. PMID:24951832

  9. Sulforaphane protects Microcystin-LR-induced toxicity through activation of the Nrf2-mediated defensive response

    SciTech Connect

    Gan Nanqin; Mi Lixin; Sun Xiaoyun; Dai Guofei; Chung Funglung; Song Lirong

    2010-09-01

    Microcystins (MCs), a cyclic heptapeptide hepatotoxins, are mainly produced by the bloom-forming cyanobacerium Microcystis, which has become an environmental hazard worldwide. Long term consumption of MC-contaminated water may induce liver damage, liver cancer, and even human death. Therefore, in addition to removal of MCs in drinking water, novel strategies that prevent health damages are urgently needed. Sulforaphane (SFN), a natural-occurring isothiocyanate from cruciferous vegetables, has been reported to reduce and eliminate toxicities from xenobiotics and carcinogens. The purpose of the present study was to provide mechanistic insights into the SFN-induced antioxidative defense system against MC-LR-induced cytotoxicity. We performed cell viability assays, including MTS assay, colony formation assay and apoptotic cell sorting, to study MC-LR-induced cellular damage and the protective effects by SFN. The results showed that SFN protected MC-LR-induced damages at a nontoxic and physiological relevant dose in HepG2, BRL-3A and NIH 3 T3 cells. The protection was Nrf2-mediated as evident by transactivation of Nrf2 and activation of its downstream genes, including NQO1 and HO-1, and elevated intracellular GSH level. Results of our studies indicate that pretreatment of cells with 10 {mu}M SFN for 12 h significantly protected cells from MC-LR-induced damage. SFN-induced protective response was mediated through Nrf2 pathway.

  10. Targeting the ACE2-Ang-(1–7) Pathway in Cardiac Fibroblasts to Treat Cardiac Remodeling and Heart Failure

    PubMed Central

    Iwata, Michikado; Cowling, Randy T.; Yeo, Seon Ju; Greenberg, Barry

    2011-01-01

    Fibroblasts play a pivotal role in cardiac remodeling and the development of heart failure through the deposition of extra-cellular matrix (ECM) proteins and also by affecting cardiomyocyte growth and function. The renin-angiotensin system (RAS) is a key regulator of the cardiovascular system in health and disease and many of its effects involve cardiac fibroblasts. Levels of angiotensin II (Ang II), the main effector molecule of the RAS, are elevated in the failing heart and there is a substantial body of evidence indicating that this peptide contributes to changes in cardiac structure and function which ultimately lead to progressive worsening in heart failure. A pathway involving angiotensin converting enzyme 2 (ACE2) has the capacity to break down Ang II while generating angiotensin-(1–7) (Ang-(1–7), a heptapeptide, which in contrast to Ang II, has cardioprotective and anti-remodeling effects. Many Ang-(1–7) actions involve cardiac fibroblasts and there is information indicating that it reduces collagen production and also may protect against cardiac hypertrophy. This report describes the effects of ACE2 and Ang-(1–7) that appear to be relevant in cardiac remodeling and heart failure and explores potential therapeutic strategies designed to increase ACE2 activity and Ang-(1–7) levels to treat these conditions. PMID:21147120

  11. A novel submandibular gland peptide protects against endotoxic and anaphylactic shock.

    PubMed

    Mathison, R D; Befus, A D; Davison, J S

    1997-09-01

    Submandibular glands release peptides and proteins that, through exocrine and endocrine actions, facilitate tissue repair in the oral cavity, gastrointestinal tract, and more distal sites such as liver. It has been shown that salivary gland factors also modulate inflammatory responses, because we found that removal of the submandibular glands increases the hypotensive responses to endotoxin. From this observation we proposed that these glands contain a factor that regulates cardiovascular response to shock. With the use of classical peptide isolation procedures, a heptapeptide (TDIFEGG) called submandibular gland peptide T was identified in rat submandibular glands. A synthetic form of this peptide reduced endotoxic shock in sialadenectomized rats by 50% at doses as low as 1 microgram/kg and prevented allergen-induced hypotension by 90% in rats with intact salivary glands at a dose of 100 micrograms/kg. This novel peptide is probably generated from a prohormone, submandibular gland rat 1 protein, a product of the VCSA1 gene. These data indicate that submandibular glands participate in the regulation of systemic homeostasis.

  12. Versatility of prolyl oligopeptidase B in peptide macrocyclization.

    PubMed

    Sgambelluri, Robert Michael; Smith, Miranda O; Walton, Jonathan D

    2017-09-02

    Cyclic peptides are promising compounds for new chemical biological tools and therapeutics due to their structural diversity, resistance to proteases, and membrane permeability. Amatoxins, the toxic principles of poisonous mushrooms, are biosynthesized on ribosomes as 35-mer precursor peptides which are ultimately converted to hydroxylated bicyclic octapeptides. The initial cyclization steps, catalyzed by a dedicated prolyl oligopeptidase (POPB), involves removal of the 10-amino acid leader sequence from the precursor peptide and transpeptidation to produce a monocyclic octapeptide intermediate. The utility of POPB as a general catalyst for peptide cyclization was systematically characterized using a range of precursor peptide substrates produced either in E. coli or chemically. Substrates produced in E. coli were expressed either individually or in mixtures produced by codon mutagenesis. A total of 127 novel peptide substrates were tested, of which POPB could cyclize 100. Peptides of 7 to 16 residues were cyclized at least partially. Synthetic 25mer precursor peptide substrates containing modified amino acids including D-Ala, β-Ala, N-methyl-Ala, and 4-hydroxy-Pro were also successfully cyclized. Although a phalloidin heptapeptide with all L amino acids was not cyclized, partial cyclization was seen when L-Thr at position #5 was replaced with the naturally occurring D amino acid. POPB should have broad applicability as a general catalyst for macrocyclization of peptides containing 7 to at least 16 amino acids, with an optimum of 8-9 residues.

  13. Loss of Internal Backbone Carbonyls: Additional Evidence for Sequence-Scrambling in Collision-Induced Dissociation of y-Type Ions

    NASA Astrophysics Data System (ADS)

    Harper, Brett; Miladi, Mahsan; Solouki, Touradj

    2014-10-01

    It is shown that y-type ions, after losing C-terminal H2O or NH3, can lose an internal backbone carbonyl (CO) from different peptide positions and yield structurally different product fragment ions upon collision-induced dissociation (CID). Such CO losses from internal peptide backbones of y-fragment ions are not unique to a single peptide and were observed in four of five model peptides studied herein. Experimental details on examples of CO losses from y-type fragment ions for an isotopically labeled AAAAH AA-NH2 heptapeptide and des-acetylated-α-melanocyte-stimulating hormone (dα-MSH) (SYSMEHFRWGKPV-NH2) are reported. Results from isotope labeling, tandem mass spectrometry (MSn), and ion mobility-mass spectrometry (IM-MS) confirm that CO losses from different amino acids of m/ z-isolated y-type ions yield structurally different ions. It is shown that losses of internal backbone carbonyls (as CID products of m/ z-isolated y-type ions) are among intermediate steps towards formation of rearranged or permutated product fragment ions. Possible mechanisms for generation of the observed sequence-scrambled a-"like" ions, as intermediates in sequence-scrambling pathways of y-type ions, are proposed and discussed.

  14. Localization of the genes encoding the melanocortin-2 (Adrenocorticotropic hormone) and melanocortin-3 receptors to chromosomes 18p11. 2 and 20q13. 2-q13. 3 by fluorescence in situ hybridization

    SciTech Connect

    Gantz, I.; Tashiro, Takao; Konda, Yoshitaka; Shimoto, Yoshimasa; Miwa, Hiroto; Munzert, G.; Barcroft, C.; Glover, T.; Yamada, Tadataka )

    1993-10-01

    Adrenocorticotropic hormone (ACTH) and [alpha]-, [beta]-, and [gamma]-melanocyte-stimulating hormone (MSH) are products of propiomelanocortin post-translational processing. These compounds are collectively labeled as melanocortins (MC). Aside from their established effects on the regulation of the adrenal cortex (ACTH) and melanocytes ([alpha]-MSH), the melanocortins have been implicated in a broad array of physiological events. Melanocortins mediate their effects through cell membrane receptors belonging to the superfamily of seven transmembrane G-protein-linked receptors. Using the technique of polymerase chain reaction with primers based on conserved areas of the seven transmembrane G-protein-linked receptor family, the authors recently isolated an [open quotes]orphan[close quotes] subfamily of this receptor group. Within the past year, two of these receptors were identified as specific for [alpha]-MSH (MC1) and ACTH (MC2). They have recently described a third melanocortin receptor (MC3) that appears to recognize the core heptapeptide sequence of melanocortins with equal potency and efficacy and identified its presence in the brain, placenta, and gut. Using the FISH technique, they localized the ACTH and the melanocortin-3 receptors to chromosome loci 18p11.2 and 20q12.3-q13.2, respectively. 19 refs., 1 fig.

  15. Mapping of the gene encoding the melanocortin-1 ([alpha]-melanocyte stimulating hormone) receptor (MC1R) to human chromosome 16q24. 3 by fluorescence in situ hybridization

    SciTech Connect

    Gantz, I.; Yamada, Tadataka; Tashiro, Takao; Konda, Yoshitaka; Shimoto, Yoshimasa; Miwa, Hiroto; Trent, J.M. )

    1994-01-15

    [alpha]-Melanocyte stimulating hormone ([alpha]-MSH), a hormone originally named for its ability to regulate pigmentation of melanocytes, is a 13-amino-acid post-translational product of the pro-opiomelanocortin (POMC) gene. [alpha]-MSH and the other products of POMC processing, which share the core heptapeptide amino acid sequence Met-Glu (Gly)-His-Phe-Arg-Trp-Gly (Asp), the adrenocorticotropic hormone (ACTH), [beta]-MSH, and [gamma]-MSH, are collectively referred to as melanocortins. While best known for their effects on the melanocyte (pigmentation) and adrenal cortical cells (steroidogenesis), melanocortins have been postulated to function in diverse activities, including enhancement of learning and memory, control of the cardiovascular system, analgesia, thermoregulation, immunomodulation, parturition, and neurotrophism. To identify the chromosomal band encoding the human melanocortin-1 receptor gene, 1 [mu]g of an EMBL clone coding region of the human MC1R and approximately 15 kb of surrounding DNA was labeled with biotin and hybridized to human metaphase chromosomes as previously described. The results indicate that the human MC1R gene is localized to 16q24.3. 15 refs., 1 fig.

  16. Renin Angiotensin System and cytokines in chronic kidney disease: Clinical and experimental evidence.

    PubMed

    Silva, Ariadna Andrade Saldanha; Finotti, Beranardo Bahia; Lauar, Amanda Oliveira; Prestes, Thiago Ruiz Rodrigues; Silva, Ana Cristina Simões E

    2017-08-18

    Chronic kidney disease (CKD) has become a major public health problem in Brazil and worldwide. There are many causes of CKD, being the congenital anomalies of the kidney and urinary tract and the glomerular diseases very common in pediatric patients, while diabetic nephropathy, CKD due to chronic arterial hypertension and glomerular diseases are predominant in adult patients. Many endogenous mediators have been related to the pathophysiology of CKD, being relevant the effects of the renin-angiotensin system (RAS) and the immune-inflammatory mediators including cytokines. Several experimental and clinical studies have shown the role of the cytokines and RAS peptides in the pathophysiology of CKD. The blockade of the classical RAS axis, comprising angiotensin converting enzyme (ACE), the octapeptide Angiotensin II and the angiotensin type 1 (AT1) receptor, delays the development of CKD through multiple mechanisms, including the control of inflammatory response mediated by cytokines. On the other hand, the counterregulatory RAS axis, formed by the enzyme homologue to ACE named ACE2, the heptapeptide Angiotensin-(1-7) and its G-protein coupled receptor, the receptor Mas, exerts several renoprotective actions, mostly related to the inhibition of renal tissue inflammation and fibrosis. This review aims to report clinical and experimental evidence of the interaction between both RAS axes and cytokines in the pathophysiology of CKD. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  17. Genetic Polymorphism of Plasmodium vivax msp1p, a Paralog of Merozoite Surface Protein 1, from Worldwide Isolates

    PubMed Central

    Wang, Yue; Kaneko, Osamu; Sattabongkot, Jetsumon; Chen, Jun-Hu; Lu, Feng; Chai, Jong-Yil; Takeo, Satoru; Tsuboi, Takafumi; Ayala, Francisco J.; Chen, Yong; Lim, Chae Seung; Han, Eun-Taek

    2011-01-01

    Plasmodium vivax msp1p, a paralog of the candidate vaccine antigen P. vivax merozoite surface protein 1, possesses a signal peptide at its N-terminus and two epidermal growth factor–like domains at its C-terminus with a glycosylphosphatidylinositol attachment site. The msp1p gene locus may have originated by a duplication of the msp1 gene locus in a common ancestor of the analyzed Plasmodium species and lost from P. yoelii, P. berghei, and P. falciparum during their evolutionary history. Full-length sequences of the msp1p gene were generally highly conserved; they had a few amino acid substitutions, one highly polymorphic E/Q-rich region, and a single-to-triple hepta-peptide repeat motif. Twenty-one distinguishable allelic types (A1–A21) of the E/Q-rich region were identified from worldwide isolates. Among them, four types were detected in isolates from South Korea. The length polymorphism of the E/Q-rich region might be useful as a genetic marker for population structure studies in malaria-endemic areas. PMID:21292901

  18. Tracking the interplay between bound peptide and the lid domain of DnaK, using molecular dynamics.

    PubMed

    Azoulay, Itzhaq; Kucherenko, Nataly; Nachliel, Esther; Gutman, Menachem; Azem, Abdussalam; Tsfadia, Yossi

    2013-06-17

    Hsp70 chaperones consist of two functional domains: the 44 kDa Nucleotide Binding Domain (NBD), that binds and hydrolyses ATP, and the 26 kDa Substrate Binding Domain (SBD), which binds unfolded proteins and reactivates them, utilizing energy obtained from nucleotide hydrolysis. The structure of the SBD of the bacterial Hsp70, DnaK, consists of two sub-domains: A β-sandwich part containing the hydrophobic cavity to which the hepta-peptide NRLLLTG (NR) is bound, and a segment made of 5 α-helices, called the "lid" that caps the top of the β-sandwich domain. In the present study we used the Escherichia coli Hsp70, DnaK, as a model for Hsp70 proteins, focusing on its SBD domain, examining the changes in the lid conformation. We deliberately decoupled the NBD from the SBD, limiting the study to the structure of the SBD section, with an emphasis on the interaction between the charges of the peptide with the residues located in the lid. Molecular dynamics simulations of the complex revealed significant mobility within the lid structure; as the structure was released from the forces operating during the crystallization process, the two terminal helices established a contact with the positive charge at the tip of the peptide. This contact is manifested only in the presence of electrostatic attraction. The observed internal motions within the lid provide a molecular role for the function of this sub-domain during the reaction cycle of Hsp 70 chaperones.

  19. Epitope mapping of B-cell determinants on the 15-kilodalton lipoprotein of Treponema pallidum (Tpp15) with synthetic peptides.

    PubMed Central

    Baughn, R E; Demecs, M; Taber, L H; Musher, D M

    1996-01-01

    The antigenicity of the 15-kDa lipoprotein of Treponema pallidum (Tpp15 or TpN15) was comprehensively evaluated in epitope-scanning studies with overlapping deca- and octapeptides and polygonal rabbit and human infant immunoglobulins (Igs) and antisera. This approach enabled us to identify potentially important regions and to determine the optimal dilutions of Igs or antisera for use in further studies. IgM and IgG from both species were capable of recognizing multiple, continuous epitopes. A total of 13 peptides, principally clustered in the central regions of the protein, were recognized by all syphilitic sera and Ig fractions. On the basis of window analyses, frequency profiles, and alanine substitution studies, five heptapeptides were selected for mimetic studies. Two of these five immunodominant, continuous epitopes initially appeared to be species specific; however, antisera elicited against mimetics of all five epitopes were polyspecific, recognizing similar motifs on several other treponemal proteins, including those of avirulent organisms. The only mimetic which yielded positive reactions with infant IgM and syphilitic sera in the absence of cross-reactions with rabbit antisera to avirulent treponemes was the variant of the VMYASSG motif. These findings are relevant to the development of simple, inexpensive assays for the serodiagnosis of active syphilis. PMID:8698467

  20. Evolution of the RNA polymerase II C-terminal domain

    PubMed Central

    Stiller, John W.; Hall, Benjamin D.

    2002-01-01

    In recent years a great deal of biochemical and genetic research has focused on the C-terminal domain (CTD) of the largest subunit (RPB1) of DNA-dependent RNA polymerase II. This strongly conserved domain of tandemly repeated heptapeptides has been linked functionally to important steps in the initiation and processing of mRNA transcripts in both animals and fungi. Although they are absolutely required for viability in these organisms, C-terminal tandem repeats do not occur in RPB1 sequences from diverse eukaryotic taxa. Here we present phylogenetic analyses of RPB1 sequences showing that canonical CTD heptads are strongly conserved in only a subset of eukaryotic groups, all apparently descended from a single common ancestor. Moreover, eukaryotic groups in which the most complex patterns of ontogenetic development occur are descended from this CTD-containing ancestor. Consistent with the results of genetic and biochemical investigations of CTD function, these analyses suggest that the enhanced control over RNA polymerase II transcription conveyed by acquired CTD/protein interactions was an important step in the evolution of intricate patterns of gene expression that are a hallmark of large, developmentally complex eukaryotic organisms. PMID:11972039

  1. Exploration and Pharmacokinetic Profiling of Phenylalanine Based Carbamates as Novel Substance P 1–7 Analogues

    PubMed Central

    2014-01-01

    The bioactive metabolite of Substance P, the heptapeptide SP1–7 (H-Arg-Pro-Lys-Pro-Gln-Gln-Phe-OH), has been shown to attenuate signs of hyperalgesia in diabetic mice, which indicate a possible use of compounds targeting the SP1–7 binding site as analgesics for neuropathic pain. Aiming at the development of drug-like SP1–7 peptidomimetics we have previously reported on the discovery of H-Phe-Phe-NH2 as a high affinity lead compound. Unfortunately, the pharmacophore of this compound was accompanied by a poor pharmacokinetic (PK) profile. Herein, further lead optimization of H-Phe-Phe-NH2 by substituting the N-terminal phenylalanine for a benzylcarbamate group giving a new type of SP1–7 analogues with good binding affinities is reported. Extensive in vitro as well as in vivo PK characterization is presented for this compound. Evaluation of different C-terminal functional groups, i.e., hydroxamic acid, acyl sulfonamide, acyl cyanamide, acyl hydrazine, and oxadiazole, suggested hydroxamic acid as a bioisosteric replacement for the original primary amide. PMID:25516784

  2. Discovery of Rare and Highly Toxic Microcystins from Lichen-Associated Cyanobacterium Nostoc sp. Strain IO-102-I

    PubMed Central

    Oksanen, Ilona; Jokela, Jouni; Fewer, David P.; Wahlsten, Matti; Rikkinen, Jouko; Sivonen, Kaarina

    2004-01-01

    The production of hepatotoxic cyclic heptapeptides, microcystins, is almost exclusively reported from planktonic cyanobacteria. Here we show that a terrestrial cyanobacterium Nostoc sp. strain IO-102-I isolated from a lichen association produces six different microcystins. Microcystins were identified with liquid chromatography-UV mass spectrometry by their retention times, UV spectra, mass fragmentation, and comparison to microcystins from the aquatic Nostoc sp. strain 152. The dominant microcystin produced by Nostoc sp. strain IO-102-I was the highly toxic [ADMAdda5]microcystin-LR, which accounted for ca. 80% of the total microcystins. We assigned a structure of [DMAdda5]microcystin-LR and [d-Asp3,ADMAdda5]microcystin-LR and a partial structure of three new [ADMAdda5]-XR type of microcystin variants. Interestingly, Nostoc spp. strains IO-102-I and 152 synthesized only the rare ADMAdda and DMAdda subfamilies of microcystin variants. Phylogenetic analyses demonstrated congruence between genes involved directly in microcystin biosynthesis and the 16S rRNA and rpoC1 genes of Nostoc sp. strain IO-102-I. Nostoc sp. strain 152 and the Nostoc sp. strain IO-102-I are distantly related, revealing a sporadic distribution of toxin production in the genus Nostoc. Nostoc sp. strain IO-102-I is closely related to Nostoc punctiforme PCC 73102 and other symbiotic Nostoc strains and most likely belongs to this species. Together, this suggests that other terrestrial and aquatic strains of the genus Nostoc may have retained the genes necessary for microcystin biosynthesis. PMID:15466511

  3. Identification, functional gastrointestinal stability and molecular docking studies of lentil peptides with dual antioxidant and angiotensin I converting enzyme inhibitory activities.

    PubMed

    García-Mora, Patricia; Martín-Martínez, Mercedes; Angeles Bonache, María; González-Múniz, Rosario; Peñas, Elena; Frias, Juana; Martinez-Villaluenga, Cristina

    2017-04-15

    The objective was to identify peptides with dual antioxidant and angiotensin I converting enzyme (ACE) inhibitory activities released from lentil proteins by Savinase®. The influence of gastrointestinal digestion on peptide bioactivity was also assayed. Fragments from vicilin, convicilin and legumin were the most abundant peptides identified. Peptides LLSGTQNQPSFLSGF, NSLTLPILRYL, TLEPNSVFLPVLLH showed the highest antioxidant (0.013-1.432μmol Trolox eq./μmol peptide) and ACE inhibitory activities (IC50=44-120μM). Gastrointestinal digestion of peptides improved their dual activity (10-14μmol Trolox eq./μmol peptide; IC50=11-21μM). In general, C-terminal heptapeptide was crucial for their dual activity. ACE inhibition relies on the formation of hydrogen bonds between C-terminal residues of lentil peptides and residues of the ACE catalytic site. The present study helps clarifying the relationship between structure and dual antioxidant/antihypertensive activity of lentil peptides opening new opportunities to food industry such as the application of lentil protein hydrolysates as ingredients for development of functional foods. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Kinetics of the phosphotransferase reaction of the catalytic subunit of the tick salivary gland cAMP-dependent protein kinase

    SciTech Connect

    Mane, S.D.; Essenberg, R.C.; Sauer, J.R.

    1986-05-01

    The catalytic subunit of the cAMP dependent protein kinase was purified 100-fold from tick salivary glands. The enzyme mechanism of the phosphotransferase reaction catalyzed by this subunit was investigated. Highly purified enzyme did not show ATP-ase activity in the absence of protein substrates. Initial velocities were measured using histone H-1 or a synthetic heptapeptide, Kemptide, as P/sub i/ acceptors and (..gamma..-/sup 32/P) ATP as a phosphodonor. Patterns were consistent with a sequential, but not a ping pong mechanism. At high concentration (>2Km), histone showed substrate inhibition which was noncompetitive versus ATP. Product inhibition by Mg.ADP was competitive versus ATP and noncompetitive with respect to H-1. Phosphohistone on the other hand was noncompetitive with respect to H-1, but gave parabolic competitive inhibition against ATP. Dead-end inhibition by AMP-PNP, an analogue of ATP, was competitive and noncompetitive against ATP and H-1, respectively. The inhibitory of cAMP dependent protein kinase was noncompetitive with ATP and competitive with histone. These studies strongly suggest that the tick salivary gland protein kinase has a sequential mechanism with primarily ordered addition of ATP followed by protein substrate and ordered release of phosphoprotein and ADP, but some random character.

  5. Crystal Structure of Vancosaminyltransferase GtfD from the Vancomycin Biosynthetic Pathway: Interactions with Acceptor and Nucleotide Ligands

    SciTech Connect

    Mulichak, A.M.; Lu, W.; Losey, H.C.; Walsh, C.T.; Garavito, R.M.

    2010-03-08

    The TDP-vancosaminyltransferase GtfD catalyzes the attachment of L-vancosamine to a monoglucosylated heptapeptide intermediate during the final stage of vancomycin biosynthesis. Glycosyltransferases from this and similar antibiotic pathways are potential tools for the design of new compounds that are effective against vancomycin resistant bacterial strains. We have determined the X-ray crystal structure of GtfD as a complex with TDP and the natural glycopeptide substrate at 2.0 {angstrom} resolution. GtfD, a member of the bidomain GT-B glycosyltransferase superfamily, binds TDP in the interdomain cleft, while the aglycone acceptor binds in a deep crevice in the N-terminal domain. However, the two domains are more interdependent in terms of substrate binding and overall structure than was evident in the structures of closely related glycosyltransferases GtfA and GtfB. Structural and kinetic analyses support the identification of Asp13 as a catalytic general base, with a possible secondary role for Thr10. Several residues have also been identified as being involved in donor sugar binding and recognition.

  6. High affinity recognition of a Phytophthora protein by Arabidopsis via an RGD motif.

    PubMed

    Senchou, V; Weide, R; Carrasco, A; Bouyssou, H; Pont-Lezica, R; Govers, F; Canut, H

    2004-02-01

    The RGD tripeptide sequence, a cell adhesion motif present in several extracellular matrix proteins of mammalians, is involved in numerous plant processes. In plant-pathogen interactions, the RGD motif is believed to reduce plant defence responses by disrupting adhesions between the cell wall and plasma membrane. Photoaffinity cross-linking of [125I]-azido-RGD heptapeptide in the presence of purified plasma membrane vesicles of Arabidopsis thaliana led to label incorporation into a single protein with an apparent molecular mass of 80 kDa. Incorporation could be prevented by excess RGD peptides, but also by the IPI-O protein, an RGD-containing protein secreted by the oomycete plant pathogen Phytophthora infestans. Hydrophobic cluster analysis revealed that the RGD motif of IPI-O (positions 53-56) is readily accessible for interactions. Single amino acid mutations in the RGD motif in IPI-O (of Asp56 into Glu or Ala) resulted in the loss of protection of the 80-kDa protein from labelling. Thus, the interaction between the two proteins is mediated through RGD recognition and the 80-kDa RGD-binding protein has the characteristics of a receptor for IPI-O. The IPI-O protein also disrupted cell wall-plasma membrane adhesions in plasmolysed A. thaliana cells, whereas IPI-O proteins mutated in the RGD motif (D56A and D56E) did not.

  7. Are fish fed with cyanobacteria safe, nutritious and delicious? A laboratory study

    NASA Astrophysics Data System (ADS)

    Liang, Hualei; Zhou, Wenshan; Zhang, Yulei; Qiao, Qin; Zhang, Xuezhen

    2015-10-01

    Toxic cyanobacterial blooms, which produce cyclic heptapeptide toxins known as microcystins, are worldwide environmental problems. On the other hand, the cyanobacteria protein (30-50%) has been recommended as substitute protein for aquaculture. The present laboratory study verified the feasibility of cyanobacteria protein substitution and risk assessment. Goldfish were fed diets supplemented lyophilised cyanobacteria powder for 16 weeks with the various doses: 0% (control), 10%, 20%, 30% and 40%. Low doses (10% and 20%) promoted growth whereas high doses (30% and 40%) inhibited growth. In cyanobacteria treated fish, the proximate composition of ash, crude fat content and crude protein content decreased in 16 weeks; the saturated fatty acid (SFA) content significantly increased; the n-3 polyunsaturated fatty acid content, collagen content and muscle pH significantly decreased; cooking loss percents increased significantly. Muscle fiber diameter and myofibril length were negatively correlation. Additionally, flavour compounds (e.g., amino acids, nucleotides, organic acids and carnosine) changed significantly in the treated fish, and odour compounds geosmin and 2-methylisoborneol increased significantly. The estimated daily intake (EDI) of microcystins in muscle was close to or exceeded the World Health Organization (WHO) tolerable daily intake (TDI), representing a great health risk. Cyanobacterie is not feasible for protein sources use in aquaculture.

  8. Immunochemical detection of 4-hydroxynonenal protein adducts in oxidized hepatocytes.

    PubMed

    Uchida, K; Szweda, L I; Chae, H Z; Stadtman, E R

    1993-09-15

    We report here the development of an immunochemical procedure that uses an antibody specific to the 4-hydroxynonenal (HNE) moiety for the detection of HNE-protein adducts. The HNE-specific antibody was prepared by immunizing rabbits with a HNE-keyhole limpet hemocyanin conjugate and purifying the rabbit serum on an affinity gel prepared by covalent attachment of a HNE-conjugated heptapeptide. When various preparations of glyceraldehyde-3-phosphate dehydrogenase containing 0-7.0 equivalent of HNE-histidine residues per subunit were obtained by incubating samples of glyceraldehyde-3-phosphate dehydrogenase with increased amounts of HNE and subjected to immunoblotting with the HNE-specific antibody, the intensities of the blots were directly proportional to the number of HNE-histidine adducts as measured directly by amino acid analysis. Binding of the HNE-conjugated glyceraldehyde-3-phosphate dehydrogenase to the HNE-specific antibody could be completely inhibited by HNE-N-acetylhistidine, HNE-N-acetyllysine, or HNE-glutathione, suggesting that the antigenic determinant recognized by the antibody is the HNE moiety, not the HNE-amino acid conjugates, such as HNE-histidine, HNE-lysine, and HNE-cysteine. The utility of the HNE-specific antibody was demonstrated by its ability to react selectively with a number of HNE-protein adducts in immunoblot analyses of crude homogenates of rat liver hepatocytes that had been exposed to HNE or oxidative stresses with tert-butylhydroperoxide or metal-ion-catalyzed oxidation systems.

  9. Class I release factors in ciliates with variant genetic codes

    PubMed Central

    Inagaki, Yuji; Doolittle, W. Ford

    2001-01-01

    In eukaryotes with the universal genetic code a single class I release factor (eRF1) most probably recognizes all stop codons (UAA, UAG and UGA) and is essential for termination of nascent peptide synthesis. It is well established that stop codons have been reassigned to amino acid codons at least three times among ciliates. The codon specificities of ciliate eRF1s must have been modified to accommodate the variant codes. In this study we have amplified, cloned and sequenced eRF1 genes of two hypotrichous ciliates, Oxytricha trifallax (UAA and UAG for Gln) and Euplotes aediculatus (UGA for Cys). We also sequenced/identified three protist and two archaeal class I RF genes to enlarge the database of eRF1/aRF1s with the universal code. Extensive comparisons between universal code eRF1s and those of Oxytricha, Euplotes and Tetrahymena, which represent three lineages that acquired variant codes independently, provide important clues to identify stop codon-binding regions in eRF1. Domain 1 in the five ciliate eRF1s, particulary the TASNIKS heptapeptide and its adjacent region, differs significantly from domain 1 in universal code eRF1s. This observation suggests that domain 1 contains the codon recognition site, but that the mechanism of eRF1 codon recognition may be more complex than proposed by Nakamura et al. or Knight and Landweber. PMID:11160924

  10. The Structural Basis for Peptidomimetic Inhibition of Eukaryotic Ribonucleotide Reductase: A Conformationally Flexible Pharmacophore

    SciTech Connect

    Xu, Hai; Fairman, James W.; Wijerathna, Sanath R.; Kreischer, Nathan R.; LaMacchia, John; Helmbrecht, Elizabeth; Cooperman, Barry S.; Dealwis, Chris

    2008-08-19

    Eukaryotic ribonucleotide reductase (RR) catalyzes nucleoside diphosphate conversion to deoxynucleoside diphosphate. Crucial for rapidly dividing cells, RR is a target for cancer therapy. RR activity requires formation of a complex between subunits R1 and R2 in which the R2 C-terminal peptide binds to R1. Here we report crystal structures of heterocomplexes containing mammalian R2 C-terminal heptapeptide, P7 (Ac-{sup 1}FTLDADF{sup 7}) and its peptidomimetic P6 ({sup 1}Fmoc(Me)PhgLDChaDF{sup 7}) bound to Saccharomyces cerevisiae R1 (ScR1). P7 and P6, both of which inhibit ScRR, each bind at two contiguous sites containing residues that are highly conserved among eukaryotes. Such binding is quite distinct from that reported for prokaryotes. The Fmoc group in P6 peptide makes several hydrophobic interactions that contribute to its enhanced potency in binding to ScR1. Combining all of our results, we observe three distinct conformations for peptide binding to ScR1. These structures provide pharmacophores for designing highly potent nonpeptide class I RR inhibitors.

  11. Structural Dimorphism of Achiral α,γ-Hybrid Peptide Foldamers: Coexistence of 12- and 15/17-Helices.

    PubMed

    Misra, Rajkumar; Saseendran, Abhijith; George, Gijo; Veeresh, Kuruva; Raja, K Muruga Poopathi; Raghothama, Srinivasarao; Hofmann, Hans-Jörg; Gopi, Hosahudya N

    2017-03-13

    Here, novel 12-helices in α,γ-hybrid peptides composed of achiral α-aminoisobutyric acid (Aib) and 4-aminoisocaproic acid (Aic, doubly homologated Aib) monomers in 1:1 alternation are reported. The 12-helices were indicated by solution and crystal structural analyses of tetra- and heptapeptides. Surprisingly, single crystals of the longer nonapeptide displayed two different helix types: the novel 12-helix and an unprecedented 15/17-helix. Quantum chemical calculations on both helix types in a series of continuously lengthened Aib/Aic-hybrid peptides confirm that the 12-helix is more stable than the 15/17-helix in shorter peptides, whereas the 15/17-helix is more stable in longer sequences. Thus, the coexistence of both helix types can be expected within a definite range of sequence lengths. The novel 15/17- and 12-helices in α,γ-hybrid peptides with 5→1 and 4→1 hydrogen-bonding patterns, respectively, can be viewed as backbone-expanded analogues of native α- and 310 -helices. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Angioedema induced by a peptide derived from complement component C2

    PubMed Central

    1988-01-01

    Synthetic peptides that correspond to the COOH-terminal portion of C2b enhance vascular permeability in human and guinea pig skin. In human studies, 1 nmol of the most active peptide of 25-amino acid residues produced substantial local edema. A pentapeptide and a heptapeptide corresponding to the COOH-terminal sequence of C2b each induced contraction of estrous rat uterus in the micromole range; a peptide of 25 amino acids from this region induced a like contraction of rat uterus at a concentration 20-fold lower than the smaller peptides. The vascular permeability of guinea pig skin was enhanced by doses of these synthetic peptides in a similar fashion as that observed for the concentration of rat uterus. The induction of localized edema by intradermal injection in both the guinea pig and the human proceeds in the presence of antihistaminic drugs, suggesting that there is a histamine-independent component to the observed increase in vascular permeability. Cleavage of C2 with the enzymic subcomponent of C1, C1s, yields only C2a and C2b, and no small peptides, whereas cleavage of C2 with C1s and plasmin yields a set of small peptides. These plasmin- cleaved peptides are derived from the COOH terminus of C2b, and they induce the contraction of estrous rat uterus. PMID:2972793

  13. Structural and functional analysis of Aplysia attractins, a family of water-borne protein pheromones with interspecific attractiveness

    PubMed Central

    Painter, Sherry D.; Cummins, Scott F.; Nichols, Amy E.; Akalal, David-B. G.; Schein, Catherine H.; Braun, Werner; Smith, John S.; Susswein, Abraham J.; Levy, Miriam; de Boer, Pamela A. C. M.; ter Maat, Andries; Miller, Mark W.; Scanlan, Cory; Milberg, Richard M.; Sweedler, Jonathan V.; Nagle, Gregg T.

    2004-01-01

    Mate attraction in Aplysia involves a long-distance water-borne signal (the protein pheromone attractin), which is released during egg laying. Aplysia californica attractin attracts species that produce closely related attractins, such as Aplysia brasiliana, whose geographic distribution does not overlap that of A. californica. This finding suggests that other mollusks release attractin-related pheromones to form and maintain breeding aggregations. We describe four additional members of the attractin family: A. brasiliana, Aplysia fasciata, Aplysia depilans (which aggregates with A. fasciata aggregations), and Aplysia vaccaria (which aggregates with A. californica aggregations). On the basis of their sequence similarity with A. californica attractin, the attractin proteins fall into two groups: A. californica, A. brasiliana, and A. fasciata (91–95% identity), and A. depilans and A. vaccaria (41–43% identity). The sequence similarity within the attractin family, the conserved six cysteines, and the compact fold of the NMR solution structure of A. californica attractin suggest a common fold for this pheromone family containing two antiparallel helices. The second helix contains the IEECKTS sequence conserved in Aplysia attractins. Mutating surface-exposed charged residues within this heptapeptide sequence abolishes attractin activity, suggesting that the second helix is an essential part of the receptor-binding interface. PMID:15118100

  14. Design of a hydroxyapatite-binding antimicrobial peptide with improved retention and antibacterial efficacy for oral pathogen control

    PubMed Central

    Huang, Zhi-bin; Shi, Xin; Mao, Jing; Gong, Shi-qiang

    2016-01-01

    Controlling and reducing the formation of pathogenic biofilm on tooth surface is the key to the prevention and treatment of the biofilm-associated oral diseases. Antimicrobial peptides (AMPs), considered as possible future alternatives for conventional antibiotics, have been extensively studied for the control of bacterial infection. Due to the rapid dilution and degradation by human saliva, AMP preparations designed for oral use with longer retention and higher efficacy are in urgent need. To this end, a hydroxyapatite (HAp)-binding antimicrobial peptide (HBAMP), which is based on the fusion of a specific HAp-binding heptapeptide (HBP7) domain and a broad-spectrum antimicrobial peptide (KSLW) domain, has been developed in our laboratory. HBAMP was supposed to form a contact-active antibacterial interface on tooth surface to inhibit the formation of biofilms. In this study, we investigated its binding behaviour, antibacterial activity against bacteria in both planktonic and sessile states, enzymatic stability in human saliva, and cytocompatibility to human gingival fibroblasts (HGFs). Our findings suggest that HBAMP could adsorb on tooth surface to provide effective antibacterial activity with improved retention. This study provides a proof-of-concept on using conjugated molecules to promote antibacterial efficacy by synergistically actions of HBAMP free in solution and bound on tooth surface. PMID:27910930

  15. Detection of colonic dysplasia in patients with ulcerative colitis using a targeted fluorescent peptide and confocal laser endomicroscopy: A pilot study.

    PubMed

    De Palma, Giovanni Domenico; Colavita, Irene; Zambrano, Gerardo; Giglio, Mariano Cesare; Maione, Francesco; Luglio, Gaetano; Sarnelli, Giovanni; Rispo, Antonio; Schettino, Pietro; D'Armiento, Francesco Paolo; De Palma, Fatima Domenica Elisa; D'Argenio, Valeria; Salvatore, Francesco

    2017-01-01

    Targeted molecular probes have been used to detect sporadic colonic dysplasia during confocal laser endomicroscopy (CLE) with promising results. This is a feasibility pilot study aiming to assess the potential role of CLE combined with a fluorescent-labeled peptide to stain and detect dysplasia associated with Ulcerative Colitis. A phage-derived heptapeptide with predicted high binding affinity for dysplastic tissue, was synthesized and labeled with fluorescein. Eleven lesions with suspected dysplasia at endoscopy were excised from nine patients with long-standing ulcerative colitis. Specimens were sprayed with the peptide and examined by CLE. The CLE images were then compared to the corresponding histological sections. At definitive histology, 4 lesions were diagnosed as inflammatory polyps, 6 as dysplastic lesions and one as invasive cancer. In inflammatory polyps, the fluorescence signal came from peri-cryptal spaces and crypt lumen due to passive accumulation of the peptide in these areas. Dysplasia was associated with active binding of the peptide to dysplastic colonocytes. Ex vivo staining of ulcerative colitis-associated dysplasia using a fluorescent labeled molecular probe and CLE is feasible. In vivo studies on larger populations are required to evaluate the safety and the effective contribution of molecular probes in cancer surveillance of ulcerative colitis.

  16. Genetic relationship between cultured populations of Pacific oyster revealed by RAPD analysis.

    PubMed

    Aranishi, Futoshi; Okimoto, Takane

    2004-01-01

    We developed random amplified polymorphic DNA (RAPD) analysis for the assessment of the genetic relationship between cultured populations of the Pacific oyster Crassostrea gigas Thunberg in Hiroshima and Goseong, the largest oyster farming areas in Japan and Korea, respectively. Of 25 arbitrary primers comprising decamer nucleotides of random sequences, polymerase chain reaction amplifications with 5 different primers gave reproducible electrophoretic patterns. A total of 49 RAPD markers were clearly identified for the Hiroshima and Goseong populations, and 46 markers were polymorphic presenting mean polymorphism rates of the respective populations at 92.29% and 93.32%. Pairwise genetic distances of each 20 individuals from these populations served to produce a UPGMA dendrogram. The dendrogram comprised two main clusters, one of which was a nested cluster including all individuals of the Hiroshima population along with 12 individuals of the Goseong population, and the other cluster included the remaining individuals of the Goseong population. Results indicate that RAPD markers are useful for the assessment of the genetic relationships between populations of the Pacific oyster and further that a significant portion of oysters imported from Korea could be genetically related to the Hiroshima population.

  17. Conformational studies of d-(AAAAATTTTT) sub 2 using constraints from nuclear Overhauser effects and from quantitative analysis of the cross-peak fine structures in two-dimensional H nuclear magnetic resonance spectra

    SciTech Connect

    Celda, B.; Widmer, H.; Leupin, W.; Chazin, W.J.; Denny, W.A.; Wuethrich, K. )

    1989-02-21

    The conformation at the dA-dT junction in k-(AAAAATTTTT){sub 2} was investigated by using a variety of phase-sensitive two-dimensional nuclear magnetic resonance experiments at 500 MHz for detailed studies of the deoxyribose ring puckers. Conformational constraints were collected from two-dimensional nuclear Overhauser enhancement spectra recorded with short mixing times and from quantitative simulations of the cross-peaks in two-dimensional correlated spectra. Overall, the decamer duplex adopts a conformation of the B-DNA type, and for dA{sub 4} and dA{sub 5} the pseudorotation phase angle P is in the standard range 150-180{degree}. The deoxyribose puckers for the other nucleotides deviate significantly from the standard B-DNA structure. Spectrum simulations assuming either static deviations from standard B-DNA or a simple two-state dynamic equilibrium between the C2'-endo and C3'-endo forms of the deoxyribose were used to analyze the experimental data. In agreement with recent papers on related duplexes containing (dA){sub n} tracts, the authors observed prominent nuclear Overhauser effects between adenine-2H and deoxyribose-1'H, which could be largely due to pronounced propeller twisting as observed in the crystal structures of (dA){sub n}-containing compounds.

  18. 2-Aminopurine optical spectra: Solvent, pentose ring, and DNA helix melting dependence.

    PubMed

    Evans, K; Xu, D; Kim, Y; Nordlund, T M

    1992-12-01

    2-Aminopurine (2AP) absorption and fluorescence excitation and emission spectra in a series of solvents have been measured to assess effects of solvent polarity. Emission spectra of the free base shift to the red in solvents of a higher dielectric constant, including water but excepting dioxane. Excitation spectra also red-shift, except in water. A change in dipole moment of 2.8 D upon excitation is obtained from a Bilot-Kawski plot which includes data from potentially anomolous solvents such as alcohols but which excludes dioxane and aqueous solvents. Attachment of ribose or 2'-deoxyribose causes 1 to 2-nm shifts in the position of fluorescence excitation and emission spectra of 2AP in water and little change in fluorescence yield. Melting of the DNA duplex d[CTGA(2AP)TTCAG]2 yields a blue shift of the excitation and no shift of the emission spectrum-results consistent with increased exposure to water and formation of 2AP-water H bonds in the ground state. The spectral shift occurs 5°C or more below the helix melting temperature, implying a premelting structural change in the decamer.

  19. Different water clusters dependent on long-chain dicarboxylates in two Ag(I) coordination polymers: Synthesis, structure and thermal stability

    NASA Astrophysics Data System (ADS)

    Sun, Di; Liu, Fu-Jing; Hao, Hong-Jun; Huang, Rong-Bin; Zheng, Lan-Sun

    2011-10-01

    Two mixed-ligand Ag(I) coordination polymers (CPs), [Ag 2(bipy) 2(sub)·5H 2O] n ( 1), [Ag 2(bipy) 2(aze)·3H 2O] n ( 2), (bipy = 4,4'-bipyridine, H 2sub = suberic acid, H 2aze = azelaic acid) have been synthesized and structurally characterized by elemental analysis, infrared (IR) spectroscopy, powder X-ray diffraction (PXRD), thermogravimetric (TG) analysis, and single crystal X-ray diffraction. Both 1 and 2 are two-dimensional (2D) sheets based on infinite [Ag(bipy)] n double chain incorporating Ag⋯Ag interactions. Interestingly, two different water clusters are encapsulated in the voids between the sheets of 1 and 2. For 1, one water decamer (H 2O) 10 based on a cyclic water tetramer was hydrogen-bonded with the host 2D sheet. While, one water hexamer (H 2O) 6 also based on a cyclic water tetramer was observed in 2. Comparing the experimental results, it is comprehensible that the dicarboxylates play a crucial role in the formation of the different water clusters. Moreover, the thermal stabilities of them were also discussed.

  20. Phenotypic differences of human neutrophils of carriers of the PSGL-1 A and B-allele in binding to immobilised P-selectin under flow conditions.

    PubMed

    Meyer dos Santos, Sascha; Klinkhardt, Ute; Lang, Katharina; Parisius, Jeannine; Kuczka, Karina; Harder, Sebastian

    2011-02-01

    P-selectin glycoprotein ligand-1 (PSGL-1) interacts with P-selectin expressed on endothelial cells and platelets. PSGL-1 extracellular mucin-like domain displays a variable number of tandem repeats (VNTRs) polymorphism. The wildtype consists of 16 decameric repeats (designated A isoforms) and variants with 15 (B allele) and 14 (C allele) repeats that are assumed to be associated with reduced risk of vascular disease. We investigated the adhesion of these natural variants to P-selectin in native human neutrophils. Healthy volunteers were genotyped and the adhesion of neutrophils expressing the PSGL-1 isoforms A/A, A/B and B/B were studied under static and physiologic flow conditions. Homozygous B/B neutrophils attached significantly weaker to P-selectin at elevated shear rates from 24 up to 64 dyn/cm(2) than A/A and A/B neutrophils. No difference in adhesion rate was found under static conditions and shear stress below 24 dyn/cm(2), but B/B neutrophils rolled significantly faster than A/A neutrophils at shear stress ≥ 12 dyn/cm(2). There was no difference in the adhesive capacity between A/A an A/B neutrophils. These data support the view that the role of the decamers is to extend the ligand binding domain far above the cell surface to support stable leukocyte adhesion and rolling.

  1. The HPr(Ser) Kinase of Streptococcus salivarius: Purification, Properties, and Cloning of the hprK Gene

    PubMed Central

    Brochu, Denis; Vadeboncoeur, Christian

    1999-01-01

    In gram-positive bacteria, HPr, a protein of the phosphoenolpyruvate:sugar phosphotransferase system, is phosphorylated on a serine residue at position 46 by an ATP-dependent protein kinase. The HPr(Ser) kinase of Streptococcus salivarius ATCC 25975 was purified, and the encoding gene (hprK) was cloned by using a nucleotide probe designed from the N-terminal amino acid sequence. The predicted amino acid sequence of the S. salivarius enzyme showed 45% identity with the Bacillus subtilis enzyme, the conserved residues being located mainly in the C-terminal half of the protein. The predicted hprK gene product has a molecular mass of 34,440 Da and a pI of 5.6. These values agree well with those found experimentally by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate, molecular sieve chromatography in the presence of guanidine hydrochloride, and chromatofocusing using the purified protein. The native protein migrates on a Superdex 200 HR column as a 330,000-Da protein, suggesting that the HPr(Ser) kinase is a decamer. The enzyme requires Mg2+ for activity and functions optimally at pH 7.5. Unlike the enzyme from other gram-positive bacteria, the HPr(Ser) kinase from S. salivarius is not stimulated by FDP or other glycolytic intermediates. The enzyme is inhibited by inorganic phosphate, and its Kms for HPr and ATP are 31 μM and 1 mM, respectively. PMID:9922231

  2. Filament formation by metabolic enzymes is a specific adaptation to an advanced state of cellular starvation

    PubMed Central

    Petrovska, Ivana; Nüske, Elisabeth; Munder, Matthias C; Kulasegaran, Gayathrie; Malinovska, Liliana; Kroschwald, Sonja; Richter, Doris; Fahmy, Karim; Gibson, Kimberley; Verbavatz, Jean-Marc; Alberti, Simon

    2014-01-01

    One of the key questions in biology is how the metabolism of a cell responds to changes in the environment. In budding yeast, starvation causes a drop in intracellular pH, but the functional role of this pH change is not well understood. Here, we show that the enzyme glutamine synthetase (Gln1) forms filaments at low pH and that filament formation leads to enzymatic inactivation. Filament formation by Gln1 is a highly cooperative process, strongly dependent on macromolecular crowding, and involves back-to-back stacking of cylindrical homo-decamers into filaments that associate laterally to form higher order fibrils. Other metabolic enzymes also assemble into filaments at low pH. Hence, we propose that filament formation is a general mechanism to inactivate and store key metabolic enzymes during a state of advanced cellular starvation. These findings have broad implications for understanding the interplay between nutritional stress, the metabolism and the physical organization of a cell. DOI: http://dx.doi.org/10.7554/eLife.02409.001 PMID:24771766

  3. Characterization of Aspartate Kinase from Corynebacterium pekinense and the Critical Site of Arg169

    PubMed Central

    Min, Weihong; Li, Huiying; Li, Hongmei; Liu, Chunlei; Liu, Jingsheng

    2015-01-01

    Aspartate kinase (AK) is the key enzyme in the biosynthesis of aspartate-derived amino acids. Recombinant AK was efficiently purified and systematically characterized through analysis under optimal conditions combined with steady-state kinetics study. Homogeneous AK was predicted as a decamer with a molecular weight of ~48 kDa and a half-life of 4.5 h. The enzymatic activity was enhanced by ethanol and Ni2+. Moreover, steady-state kinetic study confirmed that AK is an allosteric enzyme, and its activity was inhibited by allosteric inhibitors, such as Lys, Met, and Thr. Theoretical results indicated the binding mode of AK and showed that Arg169 is an important residue in substrate binding, catalytic domain, and inhibitor binding. The values of the kinetic parameter Vmax of R169 mutants, namely, R169Y, R169P, R169D, and R169H AK, with l-aspartate as the substrate, were 4.71-, 2.25-, 2.57-, and 2.13-fold higher, respectively, than that of the wild-type AK. Furthermore, experimental and theoretical data showed that Arg169 formed a hydrogen bond with Glu92, which functions as the entrance gate. This study provides a basis to develop new enzymes and elucidate the corresponding amino acid production. PMID:26633359

  4. Characterization of Aspartate Kinase from Corynebacterium pekinense and the Critical Site of Arg169.

    PubMed

    Min, Weihong; Li, Huiying; Li, Hongmei; Liu, Chunlei; Liu, Jingsheng

    2015-11-27

    Aspartate kinase (AK) is the key enzyme in the biosynthesis of aspartate-derived amino acids. Recombinant AK was efficiently purified and systematically characterized through analysis under optimal conditions combined with steady-state kinetics study. Homogeneous AK was predicted as a decamer with a molecular weight of ~48 kDa and a half-life of 4.5 h. The enzymatic activity was enhanced by ethanol and Ni(2+). Moreover, steady-state kinetic study confirmed that AK is an allosteric enzyme, and its activity was inhibited by allosteric inhibitors, such as Lys, Met, and Thr. Theoretical results indicated the binding mode of AK and showed that Arg169 is an important residue in substrate binding, catalytic domain, and inhibitor binding. The values of the kinetic parameter Vmax of R169 mutants, namely, R169Y, R169P, R169D, and R169H AK, with l-aspartate as the substrate, were 4.71-, 2.25-, 2.57-, and 2.13-fold higher, respectively, than that of the wild-type AK. Furthermore, experimental and theoretical data showed that Arg169 formed a hydrogen bond with Glu92, which functions as the entrance gate. This study provides a basis to develop new enzymes and elucidate the corresponding amino acid production.

  5. The First Data Release of the Survey of the MAgellanic Stellar History (SMASH)

    NASA Astrophysics Data System (ADS)

    Nidever, David L.; SMASH

    2017-01-01

    Our knowledge of the formation and evolution of dwarf galaxies is limited. To gain a better understanding of the formation history of the nearby Small and Large Magellanic Clouds, SMASH (Survey of the MAgellanic Stellar History) has imaged ~2400 square degrees (at 20% filling factor) to 24th mag in gri (uz~23). These observations are alllowing us to map the expected stellar debris, extended stellar populations, and star formation histories of the Clouds with unprecedented fidelity. We are announcing the first SMASH data release, which features catalogs from ~70 DECam fields. This release highlights the new data publication functionality of the NOAO Data Lab. The SMASH catalogs of forced-PSF photometry have high photometric precision (~0.2%) and accuracy (~1-2%) with exceptional astrometry (~20 mas) using Gaia reference stars. Our initial results include the discovery of (1) an extended stellar population around the Large Magellanic Cloud to ~19 kpc in many directions, (2) the Milky Way dwarf spheroidal galaxy Hydra II, and (3) a tidally disrupting globular cluster of the Large Magellanic Cloud (SMASH 1).

  6. SMASH: The Survey of the MAgellanic Stellar History

    NASA Astrophysics Data System (ADS)

    Olsen, Knut A.; Nidever, D. L.; Gruendl, R. A.; Blum, R. D.; Walker, A. R.; Saha, A.; Olszewski, E. W.; Munoz, R.; Kunder, A. M.; Kaleida, C. C.; Conn, B.; Besla, G.; Majewski, S. R.; Gallart, C.; Monelli, M.; Stringfellow, G. S.; Zaritsky, D. F.; Chu, Y.; Van Der Marel, R. P.; Martin, N.; Noel, N.; Jin, S.; Kim, H.; Cioni, M.; Bell, E. F.; Monachesi, A.; Vivas, K.; de Boer, T.

    2014-01-01

    We report on early pilot program results and progress made in the Survey of the Magellanic Stellar History (SMASH). SMASH is an NOAO community survey that is using the Dark Energy Camera (DECam) to map a 2400 deg^2 area (at 20% filling factor, or 480 deg^2 total) of the Magellanic Clouds and their periphery in ugriz. With depths of gri 24 and 23, SMASH will: (1) map the stellar periphery of the Clouds with old main sequence turnoff stars to a surface brightness limit of 35mag/arcsec^2,(2) identify the stellar component of the Magellanic Stream and Leading Arm for the first time, if they exist, and (3) derive spatially-resolved star formation histories covering all ages out to large radius from the Cloud centers. Combined with the Dark Energy Survey, SMASH will explore a vast area for hidden Magellanic Cloud populations, providing new insight into the complex and dramatic history of these two iconic dwarf galaxies.

  7. First Results from the Survey of the MAgellanic Stellar History (SMASH)

    NASA Astrophysics Data System (ADS)

    Nidever, David L.; Olsen, Knut A.; Gruendl, Robert A.; Besla, Gurtina; Saha, Abi; Olszewski, Edward; Munoz, Ricardo; Gallart, Carme; Monelli, Matteo; Walker, Alistair R.; Blum, Robert D.; Kaleida, Catherine C.; Vivas, Kathy; Majewski, Steven R.; Zaritsky, Dennis F.; van der Marel, Roeland P.; Bell, Eric F.; Conn, Blair; Stringfellow, Guy S.; Jin, Shoko; Monteagudo Nervion, Lara; Cioni, Maria-Rosa; Noel, Noelia; Martin, Nicolas; Monachesi, Antonela; de Boer, Thomas; Chu, You-Hua; Kim, Hwihyun; Martinez-Delgado, David; Johnson, Lent C.; Kunder, Andrea; Smash

    2015-01-01

    Clear observational signatures of hierarchical galaxy formation have been found around the Milky Way and other nearby massive galaxies. However, the build-up of smaller dwarf galaxies and the extent to which they harbor relics of past interactions such as stellar halos and substructure is not well-known. In an effort to observationally constrain structure formation on small scales, SMASH (Survey of the MAgellanic Stellar History), an approved NOAO community DECam survey, is imaging ~2400 square degrees (at 20% filling factor) to 24th mag in gri (uz~23) allowing us to map the expected stellar debris and extended stellar populations of the Clouds with unprecedented fidelity. SMASH will (a) search for the stellar components of the Magellanic Stream and Leading Arm, (b) detect and map the extended smooth components and substructure of the Magellanic Clouds, and (c) derive spatially resolved, precise star formation histories out to large radii. Our first year of data reveal (1) Large Magellanic Cloud (LMC) stellar populations extending out to a radius of at least 19 deg (~17 kpc) in several directions, (2) clear signatures of two dominant LMC star formation episodes at intermediate radii as revealed by multiple subgiant branches, and (3) evidence for an expansive stellar substructure in the Milky Way halo at a distance of ~30 kpc.

  8. The Magellanic Satellites Survey: Searching for Hierarchical Structure Formation within the Local Group

    NASA Astrophysics Data System (ADS)

    Bechtol, Keith; Magellanic Satellites Survey (MagLiteS)

    2017-01-01

    A generic prediction of galaxy formation in the standard cosmological model with cold dark matter is the hierarchical assembly of structure on mass scales ranging from ultra-faint galaxies to galaxy clusters. In the Local Group, dozens of galaxies have been found orbiting the Milky Way and Andromeda. The question of whether the largest Milky Way satellites, the Large and Small Magellanic Clouds, brought in their own entourage of satellites has been a long standing puzzle, and has garnered renewed interest following the recent discovery of more than a dozen ultra-faint galaxy candidates in the southern hemisphere. The on-going Magellanic Satellites Survey (MagLiteS) aims to complete an annulus of contiguous deep optical imaging with Blanco/DECam around the periphery of the Magellanic Clouds, enabling a systematic search for ultra-faint galaxies and other low-surface-brightness stellar substructures associated with the Magellanic system. I will report on the progress of MagLiteS and discuss science highlights from the first observing season, including a new ultra-faint galaxy candidate located ~11 kpc from the Large Magellanic Cloud.

  9. Identification and detection of genetic relatedness among important varieties of pea (Pisum sativum L.) grown in India.

    PubMed

    Choudhury, P Ray; Tanveer, Hasan; Dixit, G P

    2007-06-01

    Among the cool season legume crops grown in India and the Indian sub-continent, peas are very popular and preferred by the growers as well as consumers for various uses. The third largest area in pea cultivation is occupied by India after Canada and Russia. Among the important and popular varieties of peas that are grown in India, several are from exotic background. But very little work has been done to carry out the genetic diversity present in the widely adapted Indian pea varieties using DNA markers. Twenty-four most popular and widely adapted varieties were subjected to RAPD analysis to find out the genetic relatedness among them using 60 decamer primers. All the primers used in our study were found to be polymorphic and seven of them showed 100% polymorphism. Out of 579 amplified products, 433 showed polymorphism (74.8%). On an average, 9.65 bands were amplified per primer. Cluster analysis based on Jaccard's similarity coefficient using UPGMA grouped all the tall type varieties together, whereas, dwarf types formed two different clusters based upon their pedigree. The arithmetic mean heterozygosity (Hav) value and marker index (MI) was found to be 0.496 and 4.787, respectively, thus this indicated the efficiency of RAPD as a marker system. Moreover, the calculated value of probability of identical match by chance suggested that about 10(53) genotypes can be unambiguously distinguish by employing 60 RAPD primers.

  10. Human melanoma patients recognize an HLA-A1-restricted CTL epitope from tyrosinase containing two cysteine residues: implications for tumor vaccine development.

    PubMed

    Kittlesen, D J; Thompson, L W; Gulden, P H; Skipper, J C; Colella, T A; Shabanowitz, J; Hunt, D F; Engelhard, V H; Slingluff, C L; Shabanowitz, J A

    1998-03-01

    To identify shared epitopes for melanoma-reactive CTL restricted by MHC molecules other than HLA-A*0201, six human melanoma patient CTL lines expressing HLA-A1 were screened for reactivity against the melanocyte differentiation proteins Pmel-17/gp100, MART-1/Melan-A, and tyrosinase, expressed via recombinant vaccinia virus vectors. CTL from five of the six patients recognized epitopes from tyrosinase, and recognition of HLA-A1+ target cells was strongly correlated with tyrosinase expression. Restriction by HLA-A1 was further demonstrated for two of those tyrosinase-reactive CTL lines. Screening of 119 synthetic tyrosinase peptides with the HLA-A1 binding motif demonstrated that nonamer, decamer, and dodecamer peptides containing the sequence KCDICTDEY (residues 243-251) all reconstituted the CTL epitope in vitro. Epitope reconstitution in vitro required high concentrations of these peptides, which was hypothesized to be a result of spontaneous modification of cysteine residues, interfering with MHC binding. Substitution of serine or alanine for the more N-terminal cysteine prevented modification at that residue and permitted target cell sensitization at peptide concentrations 2 to 3 orders of magnitude lower than that required for the wild-type peptide. Because spontaneous modification of sulfhydryl groups may also occur in vivo, tumor vaccines using this or other cysteine-containing peptides may be improved by amino acid substitutions at cysteine residues.

  11. Impact of processing on the bioavailability and vascular effects of blueberry (poly)phenols.

    PubMed

    Rodriguez-Mateos, Ana; Del Pino-García, Raquel; George, Trevor W; Vidal-Diez, Alberto; Heiss, Christian; Spencer, Jeremy P E

    2014-10-01

    Blueberries are a rich source of flavonoids and phenolic acids. Currently, little information is available regarding the impact of processing on the bioavailability and the bioactivity of blueberry (poly)phenols. In a randomized, controlled crossover trial, ten healthy volunteers consumed (a) blueberry-containing baked products, (b) an unprocessed blueberry drink containing the same amount of freeze-dried blueberry powder as used in the baked products, and (c) matched control baked products. Endothelial function was measured as flow-mediated dilation (FMD) and plasma samples taken at baseline and at 1, 2, 4, and 6 h postconsumption. Although processing did not significantly change the total (poly)phenolic amount, the processed products contained significantly less anthocyanins (-42%), more chlorogenic acid (23%), no flavanol nonamers or decamers, and significantly more flavanol dimers and trimers (36% and 28%, respectively). FMD increased after 1, 2, and 6 h consumption of the baked products to a similar degree as the unprocessed blueberries, despite significant differences in the levels of individual plasma metabolites. No changes were observed after the consumption of the control product. Careful processing can preserve important biological activities of blueberries despite changing the blueberry (poly)phenol composition and plasma metabolite profile. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes.

    SciTech Connect

    Robinson, H.; Gao, Y.-G.; Sanishvili, R.; Joachimiak, A.; Wang, A. H.-J.; Univ. of Illinois; Northwestern Univ.

    2000-01-01

    Magnesium ions play important roles in the structure and function of nucleic acids. Whereas the tertiary folding of RNA often requires magnesium ions binding to tight places where phosphates are clustered, the molecular basis of the interactions of magnesium ions with RNA helical regions is less well understood. We have refined the crystal structures of four decamer oligonucleotides, d(ACCGGCCGGT), r(GCG)d(TATACGC), r(GC)d(GTATACGC) and r(G)d(GCGTATACGC) with bound hexahydrated magnesium ions at high resolution. The structures reveal that A-form nucleic acid has characteristic [Mg(H2O)6]2+ binding modes. One mode has the ion binding in the deep major groove of a GpN step at the O6/N7 sites of guanine bases via hydrogen bonds. Our crystallographic observations are consistent with the recent NMR observations that in solution [Co(NH3)6]3+, a model ion of [Mg(H2O)6]2+, binds in an identical manner. The other mode involves the binding of the ion to phosphates, bridging across the outer mouth of the narrow major groove. These [Mg(H2O)6]2+ ions are found at the most negative electrostatic potential regions of A-form duplexes. We propose that these two binding modes are important in the global charge neutralization, and therefore stability, of A-form duplexes.

  13. Light Echoes of Galactic Explosions and Eruptions

    NASA Astrophysics Data System (ADS)

    Rest, Armin; Bianco, Federica; Chornock, Ryan; Foley, Ryan; Matheson, Thomas; Olsen, Knut; Prieto, Jose Luis; Sinnott, Brendan; Smith, Chris; Smith, Nathan; Welch, Doug

    2013-02-01

    We propose to continue our search for the first light echoes (LEs) associated with historical Galactic supernovae and LBV outbursts: SN 1006, Kepler's SN, RCW 86, Crab Nebula, and P Cygni. In previously granted NOAO time, we have discovered light echoes of three ancient SNe in the LMC as well as from the historic SN events of Cas A and Tycho [2, 3], which allowed their spectroscopic classification [6, 7, 10] and 3D spectroscopy [8, 9]. Most recently, we discovered light echoes of the mid-19th-century Great Eruption of eta Carinae using CTIO 4m Mosaic images [11]. Subsequent spectroscopic follow-up of Eta Carinae revealed that its outburst spectral type was most similar to those of G-type supergiants, rather than reported LBV outburst spectral types of F-type (or earlier) [11]. We propose to continue our search for light echoes of the remaining historical events. With DECam, we have a 10-15 fold improvement in efficiency over the retired Mosaic camera, which allows us to cover the bigger search areas of most of the remaining targets. The study of scattered-light echoes from these Galactic supernovae and eruptions will give us the opportunity to directly compare the original outburst and its current remnant, and in favorable cases (like Eta Carinae), it provides a three-dimensional view of the event and/or a spectral time series.

  14. Crystallization and X-ray diffraction analysis of the Trp/amber editing site of hepatitis delta virus (+)RNA: a case of rational design

    SciTech Connect

    MacElrevey, Celeste; Wedekind, Joseph E.

    2005-12-01

    Well diffracting decamer crystals of the hepatitis delta virus RNA-editing site were prepared, but exhibited merohedral twinning and base averaging owing to duplex symmetry. A longer asymmetric construct that includes additional flanking RNA sequences has been crystallized that does not appear to exhibit these defects. RNA editing by mammalian ADAR1 (Adenosine Deaminase Acting on RNA) is required for the life cycle of the hepatitis delta virus (HDV). Editing extends the single viral open reading frame to yield two protein products of alternate length. ADARs are believed to recognize double-stranded RNA substrates via a ‘structure-based’ readout mechanism. Crystals of 10-mer duplexes representing the HDV RNA-editing site diffracted to 1.35 Å resolution, but suffered from merohedral twinning and averaging of the base registry. Expansion of the construct to include two flanking 3 × 1 internal loops yielded crystals in the primitive tetragonal space group P4{sub 1}2{sub 1}2 or P4{sub 3}2{sub 1}2. X-ray diffraction data were collected to 2.8 Å resolution, revealing a unit cell with parameters a = 62.5, c = 63.5 Å. The crystallization and X-ray analysis of multiple forms of the HDV RNA-editing substrate, encounters with common RNA crystal-growth defects and a strategy to overcome these problems are reported.

  15. Peptide Array on Cellulose Support—A Screening Tool to Identify Peptides with Dipeptidyl-Peptidase IV Inhibitory Activity within the Sequence of α-Lactalbumin

    PubMed Central

    Lacroix, Isabelle M. E.; Li-Chan, Eunice C. Y.

    2014-01-01

    The inhibition of the enzyme dipeptidyl-peptidase IV (DPP-IV) is an effective pharmacotherapeutic approach for the management of type 2 diabetes. Recent findings have suggested that dietary proteins, including bovine α-lactalbumin, could be precursors of peptides able to inhibit DPP-IV. However, information on the location of active peptide sequences within the proteins is far from being comprehensive. Moreover, the traditional approach to identify bioactive peptides from foods can be tedious and long. Therefore, the objective of this study was to use peptide arrays to screen α-lactalbumin-derived peptides for their interaction with DPP-IV. Deca-peptides spanning the entire α-lactalbumin sequence, with a frame shift of 1 amino acid between successive sequences, were synthesized on cellulose membranes using “SPOT” technology, and their binding to and inhibition of DPP-IV was studied. Among the 114 α-lactalbumin-derived decamers investigated, the peptides 60WCKDDQNPHS69 (αKi = 76 µM), 105LAHKALCSEK114 (Ki = 217 µM) and 110LCSEKLDQWL119 (Ki = 217 µM) were among the strongest DPP-IV inhibitors. While the SPOT- and traditionally-synthesized peptides showed consistent trends in DPP-IV inhibitory activity, the cellulose-bound peptides’ binding behavior was not correlated to their ability to inhibit the enzyme. This research showed, for the first time, that peptide arrays are useful screening tools to identify DPP-IV inhibitory peptides from dietary proteins. PMID:25402645

  16. The Extended Globular Cluster System of NGC3923

    NASA Astrophysics Data System (ADS)

    Ahumada, Tomás; Miller, Bryan; Candlish, Graeme; McGaugh, Stacy S.; Mihos, Chris; Smith, Rory; Puzia, Thomas H.; Taylor, Matthew

    2017-01-01

    In the LambdaCMD paradigm of galaxy formation galaxy halos and their globular clusters systems build up over time by the accretion of small satellites. We can learn about this process in detail by observing systems with ongoing accretion events and comparing the data with simulations. Elliptical shell galaxies are systems that are thought to be due to ongoing or recent minor mergers. We present preliminary results of an investigation of the entire globular cluster system of the shell galaxy NGC3923 from deep DECam g and i-band imaging. Cluster candidates are selected using Principal Component Analysis of Sextractor/PSFEx parameters. We will present the 2D and radial distributions of the globular cluster candidates out to a projected radius of about 130kpc, or 26Re, making this one of the most extended cluster systems studied. We find that the bluer globular cluster candidates have a shallower radial distribution than the red cluster candidates, in agreement with many previous studies.

  17. Detecting Mass Loss in Main Belt Asteroids

    NASA Astrophysics Data System (ADS)

    Sandberg, Erik; Rajagopal, Jayadev; Ridgway, Susan E.; Kotulla, Ralf C.; Valdes, Francisco; Allen, Lori

    2016-01-01

    Sandberg, E., Rajagopal, J., Ridgway, S.E, Kotulla, R., Valdes, F., Allen, L.The Dark Energy Camera (DECam) on the 4m Blanco telescope at the Cerro Tololo Inter-American Observatory (CTIO) is being used for a survey of Near Earth Objects (NEOs). Here we attempt to identify mass loss in main belt asteroids (MBAs) from these data. A primary motivation is to understand the role that asteroids may play in supplying dust and gas for debris disks. This work focuses on finding methods to automatically pick out asteroids that have qualities indicating possible mass loss. Two methods were chosen: looking for flux above a certain threshold in the asteroid's radial profile, and comparing its PSF to that of a point source. After sifting through 490 asteroids, several have passed these tests and should be followed up with a more rigorous analysis.Sandberg was supported by the NOAO/KPNO Research Experience for Undergraduates (REU) Program which is funded by the National Science Foundation Research Experiences for Undergraduates Program (AST-1262829)

  18. Stabilization, Characterization, and Selective Removal of Cystatin C Amyloid Oligomers*

    PubMed Central

    Östner, Gustav; Lindström, Veronica; Hjort Christensen, Per; Kozak, Maciej; Abrahamson, Magnus; Grubb, Anders

    2013-01-01

    The pathophysiological process in amyloid disorders usually involves the transformation of a functional monomeric protein via potentially toxic oligomers into amyloid fibrils. The structure and properties of the intermediary oligomers have been difficult to study due to their instability and dynamic equilibrium with smaller and larger species. In hereditary cystatin C amyloid angiopathy, a cystatin C variant is deposited in arterial walls and cause brain hemorrhage in young adults. In the present investigation, we use redox experiments of monomeric cystatin C, stabilized against domain swapping by an intramolecular disulfide bond, to generate stable oligomers (dimers, trimers, tetramers, decamers, and high molecular weight oligomers). These oligomers were characterized concerning size by gel filtration, polyacrylamide gel electrophoresis, and mass spectrometry, shape by electron and atomic force microscopy, and, function by assays of their capacity to inhibit proteases. The results showed the oligomers to be highly ordered, domain-swapped assemblies of cystatin C and that the oligomers could not build larger oligomers, or fibrils, without domain swapping. The stabilized oligomers were used to induce antibody formation in rabbits. After immunosorption, using immobilized monomeric cystatin C, and elution from columns with immobilized cystatin C oligomers, oligomer-specific antibodies were obtained. These could be used to selectively remove cystatin C dimers from biological fluids containing both dimers and monomers. PMID:23629649

  19. Analysis of genetic diversity among selected grasspea (Lathyrus sativus L.) genotypes using RAPD markers.

    PubMed

    Barik, Durga P; Acharya, Laxmikanta; Mukherjee, Arup K; Chand, Pradeep K

    2007-01-01

    Randomly amplified polymorphic DNA (RAPD) technique was applied to assess the genetic variability among five selected genotypes of grasspea. Out of 30 random decamer primers tested for the present investigation 20 showed reproducible DNA amplification. A total of 257 loci were amplified of which 159 were polymorphic including 57 genotype-specific unique bands. Amplicons had molecular weights ranging from 3.0 kb to 0.1 kb. Majority amplicons were shared by most of the genotypes which indicated a very narrow genetic gap between them. The dendrogram constructed on the basis of RAPD data showed two clusters. The local genotype collected from Nayagarh was grouped along with IC-120451 and IC-120453, sharing a common node at an 82% similarity level. The other genotypes, IC-120478 and IC-120487, were located in the second clade having a common node at 84% similarity level. The investigation showed that though all the genotypes of grasspea were of apparently similar morphology there exists polymorphism at the molecular level, which can be exploited in breeding programmes aimed at crop improvement.

  20. Conservation of structure and mechanism within the transaldolase enzyme family.

    PubMed

    Samland, Anne K; Baier, Shiromi; Schürmann, Melanie; Inoue, Tomoyuki; Huf, Sabine; Schneider, Gunter; Sprenger, Georg A; Sandalova, Tatyana

    2012-03-01

    Transaldolase (Tal) is involved in the central carbon metabolism, i.e. the non-oxidative pentose phosphate pathway, and is therefore a ubiquitous enzyme. However, Tals show a low degree in sequence identity and vary in length within the enzyme family which previously led to the definition of five subfamilies. We wondered how this variation is conserved in structure and function. To answer this question we characterised and compared the Tals from Bacillus subtilis, Corynebacterium glutamicum and Escherichia coli, each belonging to a different subfamily, with respect to their biochemical properties and structures. The overall structure of the Tal domain, a (β/α)(8) -barrel fold, is well conserved between the different subfamilies but the enzymes show different degrees of oligomerisation (monomer, dimer and decamer). The substrate specificity of the three enzymes investigated is quite similar which is reflected in the conservation of the active site, the phosphate binding site as well as the position of a catalytically important water molecule. All decameric enzymes characterised so far appear to be heat stable no matter whether they originate from a mesophilic or thermophilic organism. Hence, the thermostability might be due to the structural properties, i.e. tight packing, of these enzymes. Database The crystal structures have been deposited in the Protein Data Bank with accession code 3R8R for BsTal and 3R5E for CgTal. © 2011 The Authors Journal compilation © 2011 FEBS.

  1. Supramolecular assembled of hexameric water clusters into a 1D chain containing (H2O)6 and [(H2O)4O2] stabilized by hydrogen bonding in a copper complex

    PubMed Central

    2012-01-01

    Background Various water clusters including hexamers, heptamers, octamers, decamers and 1D or 2D infinite water chains in a number of organic and inorganic-organic hybrid hosts, have been reported. Results {[Cu(pydc)(amp)].3H2O}n has been hydrothermally synthesized and characterized by elemental analysis and by IR spectroscopy. A wide range of hydrogen bonds (of the O-H...O, N-H...O and N-H...N type) are present in the crystal structure. Hydrogen bond interactions between the co-crystallized water molecules led to formation of six-membered rings with chair conformation. Conclusion In {[Cu(pydc)(amp)].3H2O}n, there are three uncoordinated water molecules. Thermal methods confirm number of co-crystallized water molecules in polymer. Hydrogen bond interactions between the co-crystallized water molecules led to the formation of a six-membered ring with the chair conformation. These rings are part of a 1D chain containing six-membered O6 rings, which are alternately made from (H2O)6 and [(H2O)4O2] rings. [(H2O)4O2] rings are also in chair conformation. PMID:22264401

  2. Impact of gamma rays on the Phaffia rhodozyma genome revealed by RAPD-PCR

    PubMed Central

    Najafi, N; Hosseini, Ramin; Ahmadi, AR

    2011-01-01

    Background and Objectives Phaffia rhodozyma is a red yeast which produces astaxanthin as the major carotenoid pigment. Astaxanthin is thought to reduce the incidence of cancer and degenerative diseases in man. It also enhances the immune response and acts as a free-radical quencher, a precursor of vitamin A, or a pigment involved in the visual attraction of animals as mating partners. The impact of gamma irradiation was studied on the Phaffia rhodozyma genome. Materials and Methods Ten mutant strains, designated Gam1-Gam10, were obtained using gamma irradiation. Ten decamer random amplified polymorphic DNA (RAPD) primers were employed to assess genetic changes. Results Nine primers revealed scorable polymorphisms and a total of 95 band positions were scored; amongst which 38 bands (37.5%) were polymorphic. Primer F with 3 bands and primer J20 with 13 bands produced the lowest and the highest number of bands, respectively. Primer A16 produced the highest number of polymorphic bands (70% polymorphism) and primer F showed the lowest number of polymorphic bands (0% polymorphism). Genetic distances were calculated using Jaccard's coefficient and the UPGMA method. A dendrogram was created using SPSS (version 11.5) and the strains were clustered into four groups. Conclusion RAPD markers could distinguish between the parental and the mutant strains of P. rhodozyma. RAPD technique showed that some changes had occurred in the genome of the mutated strains. This technique demonstrated the capability to differentiate between the parental and the mutant strains. PMID:22530091

  3. Electrostatic Forces as Dominant Interactions Between Proteins and Polyanions: an ESI MS Study of Fibroblast Growth Factor Binding to Heparin Oligomers

    NASA Astrophysics Data System (ADS)

    Minsky, Burcu Baykal; Dubin, Paul L.; Kaltashov, Igor A.

    2017-04-01

    The interactions between fibroblast growth factors (FGFs) and their receptors (FGFRs) are facilitated by heparan sulfate (HS) and heparin (Hp), highly sulfated biological polyelectrolytes. The molecular basis of FGF interactions with these polyelectrolytes is highly complex due to the structural heterogeneity of HS/Hp, and many details still remain elusive, especially the significance of charge density and minimal chain length of HS/Hp in growth factor recognition and multimerization. In this work, we use electrospray ionization mass spectrometry (ESI MS) to investigate the association of relatively homogeneous oligoheparins (octamer, dp8, and decamer, dp10) with acidic fibroblast growth factor (FGF-1). This growth factor forms 1:1, 2:1, and 3:1 protein/heparinoid complexes with both dp8 and dp10, and the fraction of bound protein is highly dependent on protein/heparinoid molar ratio. Multimeric complexes are preferentially formed on the highly sulfated Hp oligomers. Although a variety of oligomers appear to be binding-competent, there is a strong correlation between the affinity and the overall level of sulfation (the highest charge density polyanions binding FGF most strongly via multivalent interactions). These results show that the interactions between FGF-1 and Hp oligomers are primarily directed by electrostatics, and also demonstrate the power of ESI MS as a tool to study multiple binding equilibria between proteins and structurally heterogeneous polyanions.

  4. Genetic diversity of eggplant (Solanum melongena) germplasm from Turkey assessed by SSR and RAPD markers.

    PubMed

    Demir, K; Bakir, M; Sarikamiş, G; Acunalp, S

    2010-08-10

    Eggplant is a major crop in Turkey, which produces more of this crop than all of Europe; consequently, germplasm resources are of concern for the country. Molecular characterization of eggplant genotypes collected from different geographical regions of Turkey was carried out using SSR and RAPD markers. With amplification of five SSR loci, the number of alleles per microsatellite locus ranged from 2 to 10, with a total of 24 alleles. The greatest number of alleles was found at the emf21H22 locus (10 alleles); followed by emh11O01 and emf21C11 as five and four alleles, respectively. The average number of alleles per locus was 4.8. Using 11 decamer RAPD primers, 100 bands were amplified, among which 29 were polymorphic. The number of bands per primer ranged from seven (OPH10, OPH19, OPH20, OPH03) to 14 (OPB07). Primer OPB07 was the most polymorphic, generating 64% polymorphic bands; the rest of the primers gave less than 50% polymorphism. UPGMA dendrograms were used to examine the genetic relatedness of the genotypes.

  5. Profiles and α-amylase inhibition activity of proanthocyanidins in unripe Manilkara zapota (chiku).

    PubMed

    Wang, Hongyu; Liu, Tingting; Song, Lixia; Huang, Dejian

    2012-03-28

    Proanthocyanidins in unripe Manilkara zapota (chiku) were isolated using solvent extraction followed by Sephadex LH-20 fractionation with a yield of 0.9%. HPLC analysis using a diol column revealed well-resolved oligomers ranging from dimer to hexamer. The majority of the proanthocyanidins are composed of higher-degree oligomers appearing as one large peak in the chromatogram. Analysis of the proanthocyanidins using LC/MS showed that (epi)gallocatechins were the dominant extension unit in the proanthocyanidins. In agreement with this result, thiolysis treatment of the proanthocyanidins using mercaptoacetic acid produced thioether derivatives of (epi)gallocatechins as the major product and (epi)gallocatechin gallate derivatives as the minor product. The mean of the degree of polymerization was estimated to be 9.0. From MALDI-TOF MS, B-type gallocatechin oligomers up to decamer could be detected. The unripe chiku proanthocyanidins are thus good starting material for preparation of (epi)gallocatechin derivatives. The proanthocyanidins was shown to inhibit α-amylase with an IC(50) value of 4.2 ± 0.2 μg/mL and inhibit α-glucosidase with an IC(50) of 16.6 ± 0.3 μg/mL.

  6. Structural investigation into physiological DNA phosphorothioate modification

    PubMed Central

    Lan, Wenxian; Hu, Zhongpei; Shen, Jie; Wang, Chunxi; Jiang, Feng; Liu, Huili; Long, Dewu; Liu, Maili; Cao, Chunyang

    2016-01-01

    DNA phosphorothioate (PT) modification, with sulfur replacing a nonbridging phosphate oxygen in a sequence and stereo specific manner, is a novel physiological variation in bacteria. But what effects on DNA properties PT modification has is still unclear. To address this, we prepared three double-stranded (ds) DNA decamers, d(CGPXGCCGCCGA) with its complementary strand d(TCGGCGPXGCCG) (where X = O or S, i.e., PT-free dsDNA, [Sp, Sp]-PT dsDNA or [Rp, Rp]-PT dsDNA) located in gene of Streptomyces lividans. Their melting temperature (Tm) measurement indicates that [Rp, Rp]-PT dsDNA is most unstable. Their electron transfer potential detection presents an order of anti-oxidation properties: Sp-PT DNA > Rp-PT DNA > PT-free DNA. Their NMR structures demonstrate that PT modification doesn’t change their B-form conformation. The sulfur in [Rp, Rp]-PT dsDNA locates in the major groove, with steric effects on protons in the sugar close to modification sites, resulting in its unstability, and facilitating its selectively interactions with ScoMcrA. We thought that PT modification was dialectical to the bacteria. It protects the hosting bacteria by working as antioxidant against H2O2, and acts as a marker, directing restriction enzyme observed in other hosts, like ScoMcrA, to correctly cleave the PT modified DNA, so that bacteria cannot spread and survive. PMID:27169778

  7. Peptide array on cellulose support--a screening tool to identify peptides with dipeptidyl-peptidase IV inhibitory activity within the sequence of α-lactalbumin.

    PubMed

    Lacroix, Isabelle M E; Li-Chan, Eunice C Y

    2014-11-13

    The inhibition of the enzyme dipeptidyl-peptidase IV (DPP-IV) is an effective pharmacotherapeutic approach for the management of type 2 diabetes. Recent findings have suggested that dietary proteins, including bovine α-lactalbumin, could be precursors of peptides able to inhibit DPP-IV. However, information on the location of active peptide sequences within the proteins is far from being comprehensive. Moreover, the traditional approach to identify bioactive peptides from foods can be tedious and long. Therefore, the objective of this study was to use peptide arrays to screen α-lactalbumin-derived peptides for their interaction with DPP-IV. Deca-peptides spanning the entire α-lactalbumin sequence, with a frame shift of 1 amino acid between successive sequences, were synthesized on cellulose membranes using "SPOT" technology, and their binding to and inhibition of DPP-IV was studied. Among the 114 α-lactalbumin-derived decamers investigated, the peptides 60WCKDDQNPHS69 (αK(i) = 76 µM), 105LAHKALCSEK114 (K(i) = 217 µM) and 110LCSEKLDQWL119 (K(i) = 217 µM) were among the strongest DPP-IV inhibitors. While the SPOT- and traditionally-synthesized peptides showed consistent trends in DPP-IV inhibitory activity, the cellulose-bound peptides' binding behavior was not correlated to their ability to inhibit the enzyme. This research showed, for the first time, that peptide arrays are useful screening tools to identify DPP-IV inhibitory peptides from dietary proteins.

  8. The Dark Energy Survey and Operations: Years 1 to 3

    SciTech Connect

    Diehl, H. T.

    2016-01-01

    The Dark Energy Survey (DES) is an operating optical survey aimed at understanding the accelerating expansion of the universe using four complementary methods: weak gravitational lensing, galaxy cluster counts, baryon acoustic oscillations, and Type Ia supernovae. To perform the 5000 sq-degree wide field and 30 sq-degree supernova surveys, the DES Collaboration built the Dark Energy Camera (DECam), a 3 square-degree, 570-Megapixel CCD camera that was installed at the prime focus of the Blanco 4-meter telescope at the Cerro Tololo Inter-American Observatory (CTIO). DES has completed its third observing season out of a nominal five. This paper describes DES “Year 1” (Y1) to “Year 3” (Y3), the strategy, an outline of the survey operations procedures, the efficiency of operations and the causes of lost observing time. It provides details about the quality of the first three season's data, and describes how we are adjusting the survey strategy in the face of the El Niño Southern Oscillation

  9. Surface adhesion of fusion proteins containing the hydrophobins HFBI and HFBII from Trichoderma reesei

    PubMed Central

    Linder, Markus; Szilvay, Geza R.; Nakari-Setälä, Tiina; Söderlund, Hans; Penttilä, Merja

    2002-01-01

    Hydrophobins are surface-active proteins produced by filamentous fungi, where they seem to be ubiquitous. They have a variety of roles in fungal physiology related to surface phenomena, such as adhesion, formation of surface layers, and lowering of surface tension. Hydrophobins can be divided into two classes based on the hydropathy profile of their primary sequence. We have studied the adhesion behavior of two Trichoderma reesei class II hydrophobins, HFBI and HFBII, as isolated proteins and as fusion proteins. Both hydrophobins were produced as C-terminal fusions to the core of the hydrolytic enzyme endoglucanase I from the same organism. It was shown that as a fusion partner, HFBI causes the fusion protein to efficiently immobilize to hydrophobic surfaces, such as silanized glass and Teflon. The properties of the surface-bound protein were analyzed by the enzymatic activity of the endoglucanase domain, by surface plasmon resonance (Biacore), and by a quartz crystal microbalance. We found that the HFBI fusion forms a tightly bound, rigid surface layer on a hydrophobic support. The HFBI domain also causes the fusion protein to polymerize in solution, possibly to a decamer. Although isolated HFBII binds efficiently to surfaces, it does not cause immobilization as a fusion partner, nor does it cause polymerization of the fusion protein in solution. The findings give new information on how hydrophobins function and how they can be used to immobilize fusion proteins. PMID:12192081

  10. SOURCE EXPLORER: Towards Web Browser Based Tools for Astronomical Source Visualization and Analysis

    NASA Astrophysics Data System (ADS)

    Young, M. D.; Hayashi, S.; Gopu, A.

    2014-05-01

    As a new generation of large format, high-resolution imagers come online (ODI, DECAM, LSST, etc.) we are faced with the daunting prospect of astronomical images containing upwards of hundreds of thousands of identifiable sources. Visualizing and interacting with such large datasets using traditional astronomical tools appears to be unfeasible, and a new approach is required. We present here a method for the display and analysis of arbitrarily large source datasets using dynamically scaling levels of detail, enabling scientists to rapidly move from large-scale spatial overviews down to the level of individual sources and everything in-between. Based on the recognized standards of HTML5+JavaScript, we enable observers and archival users to interact with their images and sources from any modern computer without having to install specialized software. We demonstrate the ability to produce large-scale source lists from the images themselves, as well as overlaying data from publicly available source ( 2MASS, GALEX, SDSS, etc.) or user provided source lists. A high-availability cluster of computational nodes allows us to produce these source maps on demand and customized based on user input. User-generated source lists and maps are persistent across sessions and are available for further plotting, analysis, refinement, and culling.

  11. Calcium and Magnesium Ions Modulate the Oligomeric State and Function of Mitochondrial 2-Cys Peroxiredoxins in Leishmania Parasites.

    PubMed

    Morais, Mariana A B; Giuseppe, Priscila O; Souza, Tatiana A C B; Castro, Helena; Honorato, Rodrigo V; Oliveira, Paulo S L; Netto, Luis E S; Tomas, Ana M; Murakami, Mario T

    2017-03-14

    Leishmania parasites have evolved a number of strategies to cope with the harsh environmental changes during mammalian infection. One of these mechanisms involves the functional gain that allowed mitochondrial 2-Cys peroxiredoxins to act as molecular chaperones when forming decamers. This function was demonstrated to be critical for the parasite infectivity in mammals and its activation was considered to be controlled exclusively by the enzyme redox state under physiological conditions. Herein, we revealed that magnesium and calcium ions play a major role in modulating the ability of these enzymes to act as molecular chaperones, surpassing the redox effect. These ions are directly involved in the mitochondrial metabolism and now also integrate a novel mechanism to stabilize the decameric form of 2-Cys peroxiredoxins in Leishmania mitochondrion. Moreover, we demonstrated that a constitutively dimeric Prx1m mutant impairs Leishmania's survival under heat stress, supporting the central role of chaperone function of Prx1m for Leishmania parasites during the transition from insect to mammalian hosts.

  12. SDSS-IV eBOSS emission-line galaxy pilot survey

    NASA Astrophysics Data System (ADS)

    Comparat, J.; Delubac, T.; Jouvel, S.; Raichoor, A.; Kneib, J.-P.; Yèche, C.; Abdalla, F. B.; Le Cras, C.; Maraston, C.; Wilkinson, D. M.; Zhu, G.; Jullo, E.; Prada, F.; Schlegel, D.; Xu, Z.; Zou, H.; Bautista, J.; Bizyaev, D.; Bolton, A.; Brownstein, J. R.; Dawson, K. S.; Escoffier, S.; Gaulme, P.; Kinemuchi, K.; Malanushenko, E.; Malanushenko, V.; Mariappan, V.; Newman, J. A.; Oravetz, D.; Pan, K.; Percival, W. J.; Prakash, A.; Schneider, D. P.; Simmons, A.; Abbott, T. M. C.; Allam, S.; Banerji, M.; Benoit-Lévy, A.; Bertin, E.; Brooks, D.; Capozzi, D.; Carnero Rosell, A.; Carrasco Kind, M.; Carretero, J.; Castander, F. J.; Cunha, C. E.; da Costa, L. N.; Desai, S.; Doel, P.; Eifler, T. F.; Estrada, J.; Flaugher, B.; Fosalba, P.; Frieman, J.; Gaztanaga, E.; Gerdes, D. W.; Gruen, D.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; James, D. J.; Kuehn, K.; Kuropatkin, N.; Lahav, O.; Lima, M.; Maia, M. A. G.; March, M.; Marshall, J. L.; Miquel, R.; Plazas, A. A.; Reil, K.; Roe, N.; Romer, A. K.; Roodman, A.; Rykoff, E. S.; Sako, M.; Sanchez, E.; Scarpine, V.; Sevilla-Noarbe, I.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thaler, J.; Thomas, D.; Walker, A. R.; Zhang, Y.

    2016-08-01

    The Sloan Digital Sky Survey IV extended Baryonic Oscillation Spectroscopic Survey (SDSS-IV/eBOSS) will observe 195 000 emission-line galaxies (ELGs) to measure the baryonic acoustic oscillation (BAO) standard ruler at redshift 0.9. To test different ELG selection algorithms, 9000 spectra were observed with the SDSS spectrograph as a pilot survey based on data from several imaging surveys. First, using visual inspection and redshift quality flags, we show that the automated spectroscopic redshifts assigned by the pipeline meet the quality requirements for a reliable BAO measurement. We also show the correlations between sky emission, signal-to-noise ratio in the emission lines, and redshift error. Then we provide a detailed description of each target selection algorithm we tested and compare them with the requirements of the eBOSS experiment. As a result, we provide reliable redshift distributions for the different target selection schemes we tested. Finally, we determine an target selection algorithms that is best suited to be applied on DECam photometry because they fulfill the eBOSS survey efficiency requirements. The catalog is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/592/A121

  13. The alignment and assembly of the DESI prime focus corrector

    NASA Astrophysics Data System (ADS)

    Brooks, David; Doel, Peter; Besuner, Robert; Flaugher, Brenna; Gallo, Giuseppe; Gutierrez, Gaston; Kent, Stephen; Lampton, Michael; Levi, Michael; Liang, Ming; Miller, Timothy N.; Sprayberry, David; Stefanik, Andrew

    2016-08-01

    The Dark Energy Spectroscopic Instrument (DESI), which is currently under construction, is designed to measure the expansion history of the Universe using the Baryon Acoustic Oscillation technique. The spectra of 40 million galaxies over 14000 sq deg will be measured during the life of the experiment. A new prime focus corrector for the KPNO Mayall telescope will deliver light to 5000 fibre optic positioners. The fibres in turn feed ten broad-band spectrographs. The prime focus corrector for DESI consists of six lenses that range in diameter from 0.80 - 1.14 meters and from 83 - 237 kg in weight. The alignment of the large lenses of the optical corrector poses a significant challenge as in order to meet the fibre throughput requirements they have to be aligned to within a tolerance of 50 micrometres. This paper details the design for the cells that will hold the lenses and the alignment and assembly procedure for the mounting of the lenses into the cells and into the complete barrel assembly. This is based on the experience obtained from the alignment of the Dark Energy Camera (DECam) instrument which was successfully assembled and aligned by the same team and we include in the paper the lessons learnt and design modifications that will be implemented on the DESI system.

  14. The structure of Medicago truncatula δ1-pyrroline-5-carboxylate reductase provides new insights into regulation of proline biosynthesis in plants

    DOE PAGES

    Ruszkowski, Milosz; Nocek, Boguslaw; Forlani, Giuseppe; ...

    2015-10-30

    The two pathways for proline biosynthesis in higher plants share the last step, the conversion of δ1-pyrroline-5-carboxylate (P5C) to L-proline, which is catalyzed by P5C reductase (P5CR, EC 1.5.1.2) with the use of NAD(P)H as a coenzyme. There is increasing amount of evidence to suggest a complex regulation of P5CR activity at the post-translational level, yet the molecular basis of these mechanisms is unknown. Here we report the three-dimensional structure of the P5CR enzyme from the model legume Medicago truncatula (Mt). The crystal structures of unliganded MtP5CR decamer, and its complexes with the products NAD+, NADP+, and L-proline were refinedmore » using x-ray diffraction data (at 1.7, 1.85, 1.95, and 2.1 Å resolution, respectively). Based on the presented structural data, the coenzyme preference for NADPH over NADH was explained, and NADPH is suggested to be the only coenzyme used by MtP5CR in vivo. Moreover, the insensitivity of MtP5CR to feed-back inhibition by proline, revealed by enzymatic analysis, was correlated with structural features. Additionally, a mechanism for the modulation of enzyme activity by chloride anions is discussed, as well as the rationale for the possible development of effective enzyme inhibitors.« less

  15. Ring-expanding olefin metathesis: a route to highly active unsymmetrical macrocyclic oligomeric co-salen catalysts for the hydrolytic kinetic resolution of epoxides.

    PubMed

    Zheng, Xiaolai; Jones, Christopher W; Weck, Marcus

    2007-02-07

    In the presence of the third generation Grubbs catalyst, the ring-expanding olefin metathesis of a monocyclooct-4-en-1-yl functionalized salen ligand and the corresponding Co(II)(salen) complex at low monomer concentrations results in the exclusive formation of macrocyclic oligomeric structures with the salen moieties being attached in an unsymmetrical, flexible, pendent manner. The TOF-MALDI mass spectrometry reveals that the resulting macrocyclic oligomers consist predominantly of dimeric to tetrameric species, with detectable traces of higher homologues up to a decamer. Upon activation under aerobic and acidic conditions, these Co(salen) macrocycles exhibit extremely high reactivities and selectivities in the hydrolytic kinetic resolution (HKR) of a variety of racemic terminal epoxides under neat conditions with very low catalyst loadings. The excellent catalytic properties can be explained in terms of the new catalyst's appealing structural features, namely, the flexible oligomer backbone, the unsymmetrical pendent immobilization motif of the catalytic sites, and the high local concentration of Co(salen) species resulting from the macrocyclic framework. This ring-expanding olefin metathesis is suggested to be a simple way to prepare tethered metal complexes that are endowed with key features--(i) a high local concentration of metal complexes and (ii) a flexible, single point of attachment to the support--that facilitate rapid and efficient catalysis when a bimetallic transition state is required.

  16. The Dark Energy Survey and operations: Year 1

    NASA Astrophysics Data System (ADS)

    Diehl, H. T.; Abbott, T. M. C.; Annis, J.; Armstrong, R.; Baruah, L.; Bermeo, A.; Bernstein, G.; Beynon, E.; Bruderer, C.; Buckley-Geer, E. J.; Campbell, H.; Capozzi, D.; Carter, M.; Casas, R.; Clerkin, L.; Covarrubias, R.; Cuhna, C.; D'Andrea, C.; da Costa, L.; Das, R.; DePoy, D. L.; Dietrich, J.; Drlica-Wagner, A.; Elliott, A.; Eifler, T.; Estrada, J.; Etherington, J.; Flaugher, B. L.; Frieman, J.; Fausti Neto, A.; Gelman, M.; Gerdes, D.; Gruen, D.; Gruendl, R.; Hao, J.; Head, H.; Helsby, J.; Hoffman, K.; Honscheid, K.; James, D.; Johnson, M.; Kacprzac, T.; Katsaros, J.; Kennedy, R.; Kent, S.; Kessler, R.; Kim, A.; Krause, E.; Kron, R.; Kuhlmann, S.; Kunder, A.; Li, T.; Lin, H.; Maccrann, N.; March, M.; Marshall, J.; Neilsen, E.; Nugent, P.; Martini, P.; Melchior, P.; Menanteau, F.; Nichol, R. C.; Nord, B.; Ogando, R.; Old, L.; Papadopoulos, A.; Patton, K.; Petravick, D.; Plazas, A. A.; Poulton, R.; Pujol, A.; Reil, K.; Rigby, T.; Romer, A.; Roodman, A.; Rooney, P.; Sanchez Alvaro, E.; Serrano, S.; Sheldon, E.; Smith, A.; Smith, R. C.; Soares-Santos, M.; Soumagnac, M.; Spinka, H.; Suchyta, E.; Tucker, D.; Walker, A. R.; Wester, W.; Wiesner, M.; Wilcox, H.; Williams, R.; Yanny, B.; Zhang, Y.-.

    2014-08-01

    The Dark Energy Survey (DES) is a next generation optical survey aimed at understanding the accelerating expansion of the universe using four complementary methods: weak gravitational lensing, galaxy cluster counts, baryon acoustic oscillations, and Type Ia supernovae. To perform the 5000 sq-degree wide field and 30 sq-degree supernova surveys, the DES Collaboration built the Dark Energy Camera (DECam), a 3 square-degree, 570-Megapixel CCD camera that was installed at the prime focus of the Blanco 4-meter telescope at the Cerro Tololo Inter-American Observatory (CTIO). DES started its first observing season on August 31, 2013 and observed for 105 nights through mid-February 2014. This paper describes DES "Year 1" (Y1), the strategy and goals for the first year's data, provides an outline of the operations procedures, lists the efficiency of survey operations and the causes of lost observing time, provides details about the quality of the first year's data, and hints at the "Year 2" plan and outlook.

  17. Fischer carbene mediated covalent grafting of a peptide nucleic acid on gold surfaces and IR optical detection of DNA hybridization with a transition metalcarbonyl label

    NASA Astrophysics Data System (ADS)

    Srivastava, Pratima; Ghasemi, Mahsa; Ray, Namrata; Sarkar, Amitabha; Kocabova, Jana; Lachmanova, Stepanka; Hromadova, Magdalena; Boujday, Souhir; Cauteruccio, Silvia; Thakare, Pramod; Licandro, Emanuela; Fosse, Céline; Salmain, Michèle

    2016-11-01

    Amine-reactive surfaces comprising N-hydroxysuccinimide ester groups as well as much more unusual Fischer alkoxymetallocarbene groups were generated on gold-coated surfaces via self-assembled monolayers of carboxy- and azido-terminated thiolates, respectively. These functions were further used to immobilize homothymine peptide nucleic acid (PNA) decamer in a covalent fashion involving the primary amine located at its N-terminus. These stepwise processes were monitored by polarization modulation reflection - absorption infrared spectroscopy (PM-RAIRS) that gave useful information on the molecular composition of the organic layers. PNA grafting and hybridization with complementary DNA strand were successfully transduced by quartz crystal microbalance (QCM) measurements. Unfortunately, attempts to transduce the hybridization optically by IR in a label-free fashion were inconclusive. Therefore we undertook to introduce an IR reporter group, namely a transition metalcarbonyl (TMC) entity at the 5‧ terminus of complementary DNA. Evidence for the formation of PNA-DNA heteroduplex was brought by the presence of ν(Ctbnd O) bands in the 2000 cm-1 region of the IR spectrum of the gold surface owing to the metalcarbonyl label.

  18. Genetic diversity in mesoamerican populations of mahogany (Swietenia macrophylla), assessed using RAPDs.

    PubMed

    Gillies, A C; Navarro, C; Lowe, A J; Newton, A C; Hernández, M; Wilson, J; Cornelius, J P

    1999-12-01

    Swietenia macrophylla King, a timber species native to tropical America, is threatened by selective logging and deforestation. To quantify genetic diversity within the species and monitor the impact of selective logging, populations were sampled across Mesoamerica, from Mexico to Panama, and analysed for RAPD DNA variation. Ten decamer primers generated 102 polymorphic RAPD bands and pairwise distances were calculated between populations according to Nei, then used to construct a radial neighbour-joining dendrogram and examine intra- and interpopulation variance coefficients, by analysis of molecular variation (AMOVA). Populations from Mexico clustered closely together in the dendrogram and were distinct from the rest of the populations. Those from Belize also clustered closely together. Populations from Panama, Guatemala, Costa Rica, Nicaragua and Honduras, however, did not cluster closely by country but were more widely scattered throughout the dendrogram. This result was also reflected by an autocorrelation analysis of genetic and geographical distance. Genetic diversity estimates indicated that 80% of detected variation was maintained within populations and regression analysis demonstrated that logging significantly decreased population diversity (P = 0.034). This study represents one of the most wide-ranging surveys of molecular variation within a tropical tree species to date. It offers practical information for the future conservation of mahogany and highlights some factors that may have influenced the partitioning of genetic diversity in this species across Mesoamerica.

  19. Large Scale Structure in the Epoch of Reionization

    NASA Astrophysics Data System (ADS)

    Koekemoer, Anton; Mould, Jeremy; Cooke, Jeffrey; Wyithe, Stuart; Lidman, Christopher; Trenti, Michele; Abbott, Tim; Kunder, Andrea; Barone-Nugent, Robert; Tescari, Edoardo; Katsianis, Antonios

    2014-02-01

    We propose to capitalize on the high red sensitivity and large field of view of DECam to detect the brightest and rarest galaxies at z=6-7. Our 2012 results show the signature of large scale structure with wavenumber of order 0.1 inverse Mpc in line with expectations of primordial non-gaussianity. But the signal to noise in one deep field from two nights' data is insufficient for a robust conclusion. Ten nights' data will do the job. These data will also constrain the galaxy contribution to reionization by enabling a tighter constraint on the full galaxy luminosity function, including the faint end. The observations will be executed with a cadence and depth that will enable the detection of super-luminous supernovae at z=6-7. Super-luminous supernovae are a recently observed class of supernovae that are 10-100x more luminous than typical supernovae. This class includes pair- instability supernovae that are a rare, third type of supernova explosion in which only 3 events are known. The proposed observations will greatly extend the current reach of supernovae research, examining their occurrence rate and properties near the epoch of reionization.

  20. Mitochondrial peroxiredoxin functions as crucial chaperone reservoir in Leishmania infantum

    PubMed Central

    Teixeira, Filipa; Castro, Helena; Cruz, Tânia; Tse, Eric; Koldewey, Philipp; Southworth, Daniel R.; Tomás, Ana M.; Jakob, Ursula

    2015-01-01

    Cytosolic eukaryotic 2-Cys-peroxiredoxins have been widely reported to act as dual-function proteins, either detoxifying reactive oxygen species or acting as chaperones to prevent protein aggregation. Several stimuli, including peroxide-mediated sulfinic acid formation at the active site cysteine, have been proposed to trigger the chaperone activity. However, the mechanism underlying this activation and the extent to which the chaperone function is crucial under physiological conditions in vivo remained unknown. Here we demonstrate that in the vector-borne protozoan parasite Leishmania infantum, mitochondrial peroxiredoxin (Prx) exerts intrinsic ATP-independent chaperone activity, protecting a wide variety of different proteins against heat stress-mediated unfolding in vitro and in vivo. Activation of the chaperone function appears to be induced by temperature-mediated restructuring of the reduced decamers, promoting binding of unfolding client proteins in the center of Prx’s ringlike structure. Client proteins are maintained in a folding-competent conformation until restoration of nonstress conditions, upon which they are released and transferred to ATP-dependent chaperones for refolding. Interference with client binding impairs parasite infectivity, providing compelling evidence for the in vivo importance of Prx’s chaperone function. Our results suggest that reduced Prx provides a mitochondrial chaperone reservoir, which allows L. infantum to deal successfully with protein unfolding conditions during the transition from insect to the mammalian hosts and to generate viable parasites capable of perpetuating infection. PMID:25646478