Sun, 27 Jul 2008 06:12:49 BST CiteULike: Tag label http://www.citeulike.org/tag/label CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/sarahferriss/article/557530 <i>Conservation Biology, Vol. 20, No. 2. (April 2006), pp. 392-398.</i> The Role of Ecolabeling in Fisheries Management and Conservation Michel Kaiser Gareth Edwards-Jones doi:10.1111/j.1523-1739.2006.00319.x Conservation Biology, Vol. 20, No. 2. (April 2006), pp. 392-398. 2006-03-21T00:01:09-00:00 2006 Conservation Biology 0888-8892 20 2 392 398 Blackwell Publishing certification conservation ecolabeling fish fishery label management http://www.citeulike.org/user/rodney/article/1525956 <i>Advanced Materials, Vol. 16, No. 12. (2004), pp. 961-966.</i><br /><br />No abstract. Intracellular Delivery of Quantum Dots for Live Cell Labeling and Organelle Tracking A M Derfus W C W Chan S N Bhatia doi:10.1002/adma.200306111 Advanced Materials, Vol. 16, No. 12. (2004), pp. 961-966. 2007-08-01T00:04:32-00:00 2004 Advanced Materials 16 12 961 966 cell delivery dots label organelle quantum tracking http://www.citeulike.org/user/Phanix/article/573747 <i>(2001), pp. 41-48.</i><br /><br />Self-Organizing Maps, being used mainly with data that are not pre-labeled, need automatic procedures for extracting keywords as labels for each of the map units. The WEBSOM methodology for building very large text archives has a very slow method for extracting such unit labels. It computes the relative frequencies of all the words of all the documents associated to each unit and then compares these to the relative frequencies of all the words of all the other units of the map. Since maps may... Extracting Meaningful Labels for WEBSOM Text Archives Arnulfo Azcarraga Teddy Yap (2001), pp. 41-48. 2006-04-03T05:48:53-00:00 2001 41 48 extraction label text websom http://www.citeulike.org/user/paulschlesinger/article/2714343 <i>Biophys. J., Vol. 86, No. 1. (1 January 2004), pp. 329-336.</i><br /><br />The interaction of antimicrobial peptides with membranes is a key factor in determining their biological activity. In this study we have synthesized a series of minimized cecropin-mellitin hybrid peptides each containing a single cysteine residue, modified the cysteine with the sulfhydryl-specific methanethiosulfonate spin-label, and used electron paramagnetic resonance spectroscopy to measure membrane-binding affinities and determine the orientation and localization of peptides bound to membranes that mimic the bacterial cytoplasmic membrane. All of the peptides were unstructured in aqueous solution but underwent a significant conformational change upon membrane binding that diminished the rotational mobility of the attached spin-label. Apparent partition coefficients were similar for five of the six constructs examined, indicating that location of the spin-label had little effect on peptide binding as long as the attachment site was in the relatively hydrophobic C-terminal domain. Depth measurements based on accessibility of the spin-labeled sites to oxygen and nickel ethylenediaminediacetate indicated that at high lipid/peptide ratios these peptides form a singlealpha -helix, with the helical axis aligned parallel to the bilayer surface and immersed [~]5 A below the membrane-aqueous interface. Such a localization would provide exposure of charged/polar residues on the hydrophilic face of the amphipathic helix to the aqueous phase, and allow the nonpolar residues along the opposite face of the helix to remain immersed in the hydrophobic phase of the bilayer. These results are discussed with respect to the mechanism of membrane disruption by antimicrobial peptides. Membrane Binding, Structure, and Localization of Cecropin-Mellitin Hybrid Peptides: A Site-Directed Spin-Labeling Study Kalpana Bhargava Jimmy Feix Biophys. J., Vol. 86, No. 1. (1 January 2004), pp. 329-336. 2008-04-24T20:45:58-00:00 2004 Biophys. J. 86 1 329 336 binding cecropin label melittin membrane spin http://www.citeulike.org/user/ngoctt/article/4387 <i>Structural Safety, Vol. 25, No. 4. (October 2003), pp. 317-341.</i><br /><br />In reliability analysis of engineering systems it is conventional to represent the limit state function as a precise surface. Uncertainty in the limit state function may be represented by introducing one or more additional random variables. However, the meaning of the additional random variable(s) is unclear and seldom does justice to the uncertainties in the subtle combination of expert judgement and sometimes scarce data from which the limit state function is constructed. Two new methods based on linguistic covering of the state space with fuzzy labels are introduced and used to generate an imprecise limit state function from very scarce experimental data. An example from flood defence engineering is used to demonstrate how plausible relaxations of the strong assumptions in the conventional probabilistic approach can generate wide bounds on the probability of system failure. Fuzzy label methods for constructing imprecise limit state functions Jim Hall Jonathan Lawry doi:10.1016/S0167-4730(03)00003-1 Structural Safety, Vol. 25, No. 4. (October 2003), pp. 317-341. 2004-12-21T13:36:16-00:00 2003 Structural Safety 25 4 317 341 constructing for functions fuzzy imprecise label limit methods state http://www.citeulike.org/user/myui/article/869943 <i>(2005), pp. 193-204.</i> From region encoding to extended dewey: on efficient processing of XML twig pattern matching Jiaheng Lu Tok Ling Chee-Yong Chan Ting Chen (2005), pp. 193-204. 2006-09-26T09:28:41-00:00 2005 193 204 VLDB Endowment dewey index label twig xml http://www.citeulike.org/user/myui/article/869941 <i>(2004), pp. 903-908.</i> ORDPATHs: insert-friendly XML node labels Patrick O'Neil Elizabeth O'Neil Shankar Pal Istvan Cseri Gideon Schaller Nigel Westbury doi:10.1145/1007568.1007686 (2004), pp. 903-908. 2006-09-26T09:26:44-00:00 2004 903 908 ACM Press 4 dewey index label ordpaths xml http://www.citeulike.org/user/mattcmu/article/942799 <i>Am J Psychol, Vol. 93, No. 3. (September 1980), pp. 505-527.</i><br /><br />Two experiments examined the effects of label retrieval upon subsequent recognition of complex, scenic pictures. Contrary to past research, i.e., Bahrick and Boucher's 1968 study, retrieval of labels which accompanied pictures at input was associated with high recognition of "same-photo" (copy) cues but not false recognition of similar "same-scene" cues on a subsequent "photo" recognition test. The label-retrieval effect can be attributed to actual rehearsal of pictorial information and not to item selection. In addition, the beneficial effects of label retrieval did not vary with the informational content of the label itself, i.e., its power to distinguish between same-photo and same-scene items. However, the effects of label-type as well as label retrieval varied with recognition test instructions. In a "scene" recognition test, requiring recognition of both same-photo and same-scene items, effects of label-type were stronger than in the "photo" test, while effects of label retrieval were not significant. The results highlight the complexity of the relationships between label retrieval and picture recognition and suggest several factors which might determine such relationships. Effects of label distinctiveness and label testing on recognition of complex pictures. JC Bartlett RE Till WC Fields Am J Psychol, Vol. 93, No. 3. (September 1980), pp. 505-527. 2006-11-14T11:28:02-00:00 1980 Am J Psychol 0002-9556 93 3 505 527 distinctiveness imagery label visual http://www.citeulike.org/user/katja/article/2680914 <i>Journal of the American Society for Information Science and Technology, Vol. 9999, No. 9999. (2008), NA.</i><br /><br />Information search and retrieval interactions usually involve information content in the form of document collections, information retrieval systems and interfaces, and the user. To fully understand information search and retrieval interactions between users' cognitive space and the information space, researchers need to turn to cognitive models and theories. In this article, the authors use one of these theories, the basic level theory. Use of the basic level theory to understand human categorization is both appropriate and essential to user-centered design of taxonomies, ontologies, browsing interfaces, and other indexing tools and systems. Analyses of data from two studies involving free sorting by 105 participants of 100 images were conducted. The types of categories formed and category labels were examined. Results of the analyses indicate that image category labels generally belong to superordinate to the basic level, and are generic and interpretive. Implications for research on theories of cognition and categorization, and design of image indexing, retrieval and browsing systems are discussed. Theories of cognition and image categorization: What category labels reveal about basic level theory Abebe Rorissa Hemalata Iyer doi:10.1002/asi.20825 Journal of the American Society for Information Science and Technology, Vol. 9999, No. 9999. (2008), NA. 2008-04-17T07:23:59-00:00 2008 Journal of the American Society for Information Science and Technology 9999 9999 NA category experiment label user http://www.citeulike.org/user/gerry/article/1762097 <i>J. Am. Chem. Soc., Vol. 129, No. 37. (19 September 2007), pp. 11378-11383.</i><br /><br />Abstract: Coordination of metal ions significantly contributes to protein structures and functions. Here we constructed a fusion protein, consisting of a de novo designed, metal-ion-binding, trimeric coiled-coil and a circularly permutated green fluorescent protein (cpGFP), where the fluorescent emission from cpGFP was induced by metal ion coordination to the coiled-coil. A circularly permutated GFP, 191cpGFP190, was constructed by connecting the original N- and C-termini of GFPUV by a GGSGG linker and cleaving it between Asp190 and Gly191. The metal-ion-binding coiled-coil, IZ-HH, was designed to have three -helical structures, with 12 His residues in the hydrophobic core of the coiled-coil structure. IZ-HH exhibited an unfolded structure, whereas it formed the trimeric coiled-coil structure in the presence of divalent metal ions, such as Cu2+, Ni2+, or Zn2+. The fusion protein 191cpGFP190-IZ-HH was constructed, in which 191cpGFP190 was inserted between the second and third -helices of IZ-HH. Escherichia coli cells, expressing 191cpGFP190-IZ-HH, exhibited strong fluorescence when the Cu2+ and Zn2+ ions were present in the medium, indicating that they passed through the cell membrane and induced the proper folding of the 191cpGFP190 domain. This strategy, in which protein function is regulated by a metal-ion-responsive coiled-coil, should be applicable to the design of various metal-ion-responsive, nonnatural proteins that work both in vitro and in vivo. Metal-ion-dependent GFP Emission in Vivo by Combining a Circularly Permutated Green Fluorescent Protein with an Engineered Metal-Ion-Binding Coiled-coil T Mizuno K Murao Y Tanabe M Oda T Tanaka doi:10.1021/ja0685102 J. Am. Chem. Soc., Vol. 129, No. 37. (19 September 2007), pp. 11378-11383. 2007-10-12T22:37:54-00:00 2007 J. Am. Chem. Soc. 129 37 11378 11383 gfp label tag http://www.citeulike.org/user/fryanpan/article/2736580 <i>(1997), pp. 148-157.</i> Map labeling and its generalizations Srinivas Doddi Madhav Marathe Andy Mirzaian Bernard Moret Binhai Zhu (1997), pp. 148-157. 2008-04-30T07:16:47-00:00 1997 148 157 Society for Industrial and Applied Mathematics label map http://www.citeulike.org/user/fryanpan/article/2736579 <i>(2001), pp. 101-110.</i> View management for virtual and augmented reality Blaine Bell Steven Feiner Tobias Höllerer doi:10.1145/502348.502363 (2001), pp. 101-110. 2008-04-30T07:16:42-00:00 2001 101 110 ACM label map placement reality virtual http://www.citeulike.org/user/fryanpan/article/2736611 <i>Visualization and Computer Graphics, IEEE Transactions on, Vol. 12, No. 5. (2006), pp. 773-780.</i><br /><br />We address the problem of filtering, selecting and placing labels on a dynamic map, which is characterized by continuous zooming and panning capabilities. This consists of two interrelated issues. The first is to avoid label popping and other artifacts that cause confusion and interrupt navigation, and the second is to label at interactive speed. In most formulations the static map labeling problem is NP-hard, and a fast approximation might have O(n log n) complexity. Even this is too slow during interaction, when the number of labels shown can be several orders of magnitude less than the number in the map. In this paper we introduce a set of desiderata for "consistent" dynamic map labeling, which has qualities desirable for navigation. We develop a new framework for dynamic labeling that achieves the desiderata and allows for fast interactive display by moving all of the selection and placement decisions into the preprocessing phase. This framework is general enough to accommodate a variety of selection and placement algorithms. It does not appear possible to achieve our desiderata using previous frameworks. Prior to this paper, there were no formal models of dynamic maps or of dynamic labels; our paper introduces both. We formulate a general optimization problem for dynamic map labeling and give a solution to a simple version of the problem. The simple version is based on label priorities and a versatile and intuitive class of dynamic label placements we call "invariant point placements". Despite these restrictions, our approach gives a useful and practical solution. Our implementation is incorporated into the G-Vis system which is a full-detail dynamic map of the continental USA. This demo is available through any browser Dynamic Map Labeling K Been E Daiches Chee Yap doi:10.1109/TVCG.2006.136 Visualization and Computer Graphics, IEEE Transactions on, Vol. 12, No. 5. (2006), pp. 773-780. 2008-04-30T07:34:39-00:00 2006 Visualization and Computer Graphics, IEEE Transactions on 12 5 773 780 infovis interactive label map visualization http://www.citeulike.org/user/fryanpan/article/2739213 <i>(2003)</i> Evaluating Label Placement for Augmented Reality View Management Ronald Azuma Chris Furmanski (2003) 2008-04-30T17:06:53-00:00 2003 IEEE Computer Society label virtual http://www.citeulike.org/user/fryanpan/article/2739211 <i>Computer Aided Design and Computer Graphics, 2005. Ninth International Conference on (2005), 6 pp..</i><br /><br />Most applications in virtual and augmented reality usually need to visualize large amounts of extra text/image/video annotations associated with objects to assist user's navigation. Labeling is one of the most intuitive techniques to achieve this goal, which attaches specific texts to related objects to provide users a clear environmental clue. The basic problem of labeling is the clutters due to unexpected overlapping and occlusion among labels and objects, which makes the environment ambiguous and obscure. In this paper, we present the interactive system of dynamic labeling management to address this problem for virtual environment navigation applications. Our system integrates the techniques of labeling with adaptive placement, view-driven label filtering and structured label searching. These features have been developed in our system with well display of augmented labels in VR applications. Dynamic labeling management in virtual and augmented environments Fan Zhang Hanqiu Sun doi:10.1109/CAD-CG.2005.36 Computer Aided Design and Computer Graphics, 2005. Ninth International Conference on (2005), 6 pp.. 2008-04-30T17:06:30-00:00 2005 Computer Aided Design and Computer Graphics, 2005. Ninth International Conference on 6 pp. label virtual http://www.citeulike.org/user/EvaKaltenborn/article/1585252 <i>Biophys. J., Vol. 77, No. 4. (1 October 1999), pp. 2237-2250.</i><br /><br />Site-directed labeling was used to obtain local information on the binding interface in a receptor-ligand complex. As a model we have chosen the specific association of the extracellular part of tissue factor (sTF) and factor VIIa (FVIIa), the primary initiator of the blood coagulation cascade. Different spectroscopic labels were covalently attached to an engineered cysteine in position 140 in sTF, a position normally occupied by a Phe residue previously characterized as an important contributor to the sTF:FVIIa interaction. Two spin labels, IPSL [N-(1-oxyl-2,2,5,5-tetramethyl-3-pyrrolidinyl)iodoacetamide] and MTSSL [(1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl)methanethiosulfonate], and two fluorescent labels, IAEDANS [5-((((2-iodoacetyl)amino) ethyl)amino)naphthalene-1-sulfonic acid] and BADAN [6-bromoacetyl-2-dimethylaminonaphthalene], were used. Spectral data from electron paramagnetic resonance (EPR) and fluorescence spectroscopy showed a substantial change in the local environment of all labels when the sTF:FVIIa complex was formed. However, the interaction was probed differently by each label and these differences in spectral appearance could be attributed to differences in label properties such as size, polarity, and/or flexibility. Accordingly, molecular modeling data suggest that the most favorable orientations are unique for each label. Furthermore, line-shape simulations of EPR spectra and calculations based on fluorescence depolarization measurements provided additional details of the local environment of the labels, thereby confirming a tight protein-protein interaction between FVIIa and sTF when the complex is formed. The tightness of this local interaction is similar to that seen in the interior of globular proteins. Properties of Spin and Fluorescent Labels at a Receptor-Ligand Interface Rikard Owenius Maria Osterlund Mikael Lindgren Magdalena Svensson Ole Olsen Egon Persson Per-Ola Freskgard Uno Carlsson Biophys. J., Vol. 77, No. 4. (1 October 1999), pp. 2237-2250. 2007-08-23T10:32:07-00:00 1999 Biophys. J. 77 4 2237 2250 epr ipsl label mtsl spin http://www.citeulike.org/user/EvaKaltenborn/article/1617778 <i>Biochemistry, Vol. 44, No. 14. (12 April 2005), pp. 5503-5509.</i><br /><br />Abstract: MsbA is an ABC transporter that transports lipid A across the inner membrane of Gram-negative bacteria such as Escherichia coli. Without functional MsbA present, bacterial cells accumulate a toxic amount of lipid A within their inner membranes. A crystal structure of MsbA was recently obtained that provides an excellent starting point for functional dynamics studies in membranes [Chang and Roth (2001) Science 293, 1793-1800]. Although a structure of MsbA is now available, several functionally important motifs common to ABC transporters are unresolved in the crystal structure. The Walker A domain, one of the ABC transporter consensus motifs that is directly involved in ATP binding, is located within a large unresolved region of the MsbA ATPase domain. Site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy is a powerful technique for characterizing local areas within a large protein structure in addition to detecting and following changes in local structure due to dynamic interactions. MsbA reconstituted into lipid membranes has been evaluated by EPR spectroscopy, and it has been determined that the Walker A domain forms an -helical structure, which is consistent with the structure of this motif observed in other crystallized ABC transporters. In addition, the interaction of the Walker A residues with ATP before, during, and after hydrolysis was followed using SDSL EPR spectroscopy in order to identify the residues directly involved in substrate binding and hydrolysis. Characterization of the Walker A Motif of MsbA Using Site-Directed Spin Labeling Electron Paramagnetic Resonance Spectroscopy AH Buchaklian CS Klug doi:10.1021/bi047568v Biochemistry, Vol. 44, No. 14. (12 April 2005), pp. 5503-5509. 2007-09-04T08:28:57-00:00 2005 Biochemistry 44 14 5503 5509 abc epr label msba spin transporter http://www.citeulike.org/user/EvaKaltenborn/article/2030146 <i>Nucl. Acids Res. (21 May 2007), gkm240.</i><br /><br />In site-directed spin labeling (SDSL), a nitroxide moiety containing a stable, unpaired electron is covalently attached to a specific site within a macromolecule, and structural and dynamic information at the labeling site is obtained via electron paramagnetic resonance (EPR) spectroscopy. Successful SDSL requires efficient site-specific incorporation of nitroxides. Work reported here presents a new method for facile nitroxide labeling at the 5' terminus of nucleic acids of arbitrary sizes. T4-polynucleotide kinase was used to enzymatically substitute a phosphorothioate group at the 5' terminus of a nucleic acid, and the resulting phosphorothioate was then reacted with an iodomethyl derivative of a nitroxide. The method was successfully demonstrated on both chemically synthesized and naturally occurring nucleic acids. The attached nitroxides reported duplex formation as well as tertiary folding of nucleic acids, indicating that they serve as a valid probe in nucleic acid studies. 10.1093/nar/gkm240 A facile method for attaching nitroxide spin labels at the 5' terminus of nucleic acids Gian Grant Peter Qin doi:10.1093/nar/gkm240 Nucl. Acids Res. (21 May 2007), gkm240. 2007-11-30T17:57:54-00:00 2007 Nucl. Acids Res. gkm240 acids label mobility nitroxide nucleic spin http://www.citeulike.org/user/EvaKaltenborn/article/2057635 <i>J. Am. Chem. Soc., Vol. 127, No. 26. (6 July 2005), pp. 9334-9335.</i><br /><br />Abstract: Current SDSL-EPR methods allow measurement of dipolar distances in the 8-70 Å range; however, the use of extrinsic probes complicates the interpretation of these distances in modeling macromolecular structure and conformational changes. The data presented here show that interprobe distances correlate only weakly with C-C distances, especially for distances that are on the order of the spin label tether lengths. Explicitly incorporating the spin label into the modeling process increases the experiment/model correlation 4-fold and reduces the distance error from 6 Å to 3 Å. Explicit Treatment of Spin Labels in Modeling of Distance Constraints from Dipolar EPR and DEER K Sale L Song YS Liu E Perozo P Fajer doi:10.1021/ja051652w J. Am. Chem. Soc., Vol. 127, No. 26. (6 July 2005), pp. 9334-9335. 2007-12-04T17:32:19-00:00 2005 J. Am. Chem. Soc. 127 26 9334 9335 constraints deer distance epr label pulse spin http://www.citeulike.org/user/EvaKaltenborn/article/1617782 <i>Biochemistry, Vol. 43, No. 26. (6 July 2004), pp. 8600-8606.</i><br /><br />Abstract: MsbA is the ABC transporter for lipid A and is found in the inner membranes of Gram-negative bacteria such as Escherichia coli. Without MsbA present, bacterial cells accumulate a toxic amount of lipid A within their inner membranes. A crystal structure of MsbA was recently obtained that provides an excellent starting point for functional dynamics studies in membranes [Chang, and Roth (2001) Science 293, 1793-1800]. Although a structure of MsbA is now available, many questions remain concerning its mechanism of transport. Site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy is a powerful approach for characterizing local areas within a large protein structure in addition to detecting and following changes in local structure due to dynamic interactions within a protein. The quaternary structure of the resting state of the MsbA homodimer reconstituted into lipid membranes has been evaluated by SDSL EPR spectroscopy and chemical cross-linking techniques. SDSL and cross-linking results are consistent with the controversial resting state conformation of the MsbA homodimer found in the crystal structure, with the tips of the transmembrane helices forming a dimer interface. The position of MsbA in the membrane bilayer along with the relative orientation of the transmembrane helical bundles with respect to one another has been determined. Characterization of the resting state of the MsbA homodimer is essential for future studies on the functional dynamics of this membrane transporter. Resting State Conformation of the MsbA Homodimer As Studied by Site-Directed Spin Labeling AH Buchaklian AL Funk CS Klug doi:10.1021/bi0497751 Biochemistry, Vol. 43, No. 26. (6 July 2004), pp. 8600-8606. 2007-09-04T08:30:53-00:00 2004 Biochemistry 43 26 8600 8606 abc epr label msba spin transporter http://www.citeulike.org/user/EvaKaltenborn/article/1741712 <i>Biochemistry, Vol. 36, No. 42. (21 October 1997), pp. 13027-13033.</i><br /><br />Abstract: Electron paramagnetic resonance (EPR) site-directed spin-labeling (SDSL) has been used to characterize a proposed transmembrane -strand of the Escherichia coli ferric enterobactin receptor, FepA. Each of nine consecutive residues was mutated to cysteine and subsequently labeled with the sulfhydryl-specific spin-label methanethiosulfonate (MTSL) and the purified protein reconstituted into liposomes. Continuous wave (CW) power saturation methods were used to determine exposure of the nitroxide side chains to a series of paramagnetic relaxation agents, including nickel acetylacetonate (NiAA), nickel ethylenediaminediacetate (NiEDDA), chromium oxalate (CROX), and molecular oxygen. The spin-label attached to Q245C, L247C, L249C, A251C, and Y253C had higher collision frequencies with molecular oxygen than with polar relaxation agents, indicating that these sites are exposed to the hydrophobic phase of the lipid bilayer. MTSL bound to residues S246C, E248C, E250C, and G252C had higher collision rates with the polar agents than with oxygen, suggesting that these sites are exposed to the aqueous channel. The alternating periodicity observed with the polar relaxation agents, NiAA and NiEDDA, and in opposite phase with oxygen, is consistent with -sheet structure. Depth measurements, based on the reciprocal concentration gradients of NiEDDA and O2 across the bilayer and calibrated for our system with phosphatidylcholine spin-labels, indicated that L249C was nearest the center of the bilayer and that Q245C and Y253C were located just below the bilayer surface in opposite leaflets of the membrane. Thus, we conclude that this approach, through mapping of individual residues, has the capability of defining -sheet secondary structure. Mapping of the Residues Involved in a Proposed &#x03B2;-Strand Located in the Ferric Enterobactin Receptor FepA Using Site-Directed Spin-Labeling CS Klug W Su JB Feix doi:10.1021/bi971232m Biochemistry, Vol. 36, No. 42. (21 October 1997), pp. 13027-13033. 2007-10-08T15:19:36-00:00 1997 Biochemistry 36 42 13027 13033 label mtsl spin http://www.citeulike.org/user/EvaKaltenborn/article/2029816 <i>Journal of Magnetic Resonance, Vol. 185, No. 2. (April 2007), pp. 191-203.</i><br /><br />X- and W-band EPR spectra, at room and low temperatures, are reported for nitroxide spin labels attached to cysteine residues selectively introduced into two proteins, the DNase domain of colicin-E9 and its immunity protein, Im9. The dynamics of each site of attachment on the individual proteins and in the tight DNase-Im9 complex have been analysed by computer simulations of the spectra using a model of Brownian dynamics trajectories for the spin label and protein. Ordering potentials have been introduced to describe mobility of labels restricted by the protein domain. Label mobility varies with position from completely immobilised, to motionally restricted and to freely rotating. Bi-modal dynamics of the spin label have been observed for several sites. We show that W-band spectra are particularly useful for detection of anisotropy of spin label motion. On complex formation significant changes are observed in the dynamics of labels at the binding interface region. This work reveals multi-frequency EPR as a sensitive and valuable tool for detecting conformational changes in protein structure and dynamics especially in protein-protein complexes. Analysis of nitroxide spin label motion in a protein-protein complex using multiple frequency EPR spectroscopy GF White L Ottignon T Georgiou C Kleanthous GR Moore AJ Thomson VS Oganesyan doi:10.1016/j.jmr.2006.12.009 Journal of Magnetic Resonance, Vol. 185, No. 2. (April 2007), pp. 191-203. 2007-11-30T17:29:44-00:00 2007 Journal of Magnetic Resonance 185 2 191 203 epr label nitroxide spin http://www.citeulike.org/user/dlaguardia/article/86799 <i>(2004), pp. 319-326.</i> Labeling images with a computer game Luis von Ahn Laura Dabbish doi:10.1145/985692.985733 (2004), pp. 319-326. 2005-02-01T17:30:04-00:00 2004 319 326 ACM Press esp game label tag http://www.citeulike.org/user/amwands/article/2952322 <i>Protein science : a publication of the Protein Society, Vol. 14, No. 8. (August 2005), pp. 2059-2068.</i><br /><br />Probing structures and dynamics within biomolecules using ensemble and single-molecule fluorescence resonance energy transfer requires the conjugation of fluorophores to proteins in a site-specific and thermodynamically nonperturbative fashion. Using single-molecule fluorescence-aided molecular sorting and the chymotrypsin inhibitor 2-subtilisin BPN' complex as an example, we demonstrate that protein-protein interactions can be exploited to afford site-specific labeling of a recombinant double-cysteine variant of CI2 without the need for extensive and time-consuming chromatography. The use of protein-protein interactions for site-specific labeling of proteins is compatible with and complementary to existing chemistries for selective labeling of N-terminal cysteines, and could be extended to label multiple positions within a given polypeptide chain. Protein-protein interactions as a tool for site-specific labeling of proteins. M Jäger X Michalet S Weiss doi:10.1110/ps.051384705 Protein science : a publication of the Protein Society, Vol. 14, No. 8. (August 2005), pp. 2059-2068. 2008-07-02T14:44:05-00:00 2005 Protein science : a publication of the Protein Society 0961-8368 14 8 2059 2068 label http://www.citeulike.org/user/agallet/article/1093429 <i>Functional Plant Biology, Vol. 26, No. 3. (19 May 1999), pp. 253-264.</i><br /><br />Soluble organic nitrogen, including protein and amino acids, was found to be a ubiquitous form of soil N in diverse Australian environments. Fine roots of species representative of these environments were found to be active in the metabolism of glycine. The ability to incorporate [¹⁵N]glycine was widespread among plant species from subantarctic to tropical communities. In species from subantarctic herbfield, subtropical coral cay, subtropical rainforest and wet heathland, [¹⁵N]glycine incorporation ranged from 26 to 45 % of ¹⁵NH₄⁺ incorporation and was 2- to 3-fold greater than ¹⁵NO₃^- incorporation. Most semiarid mulga and tropical savanna woodland species incorporated [¹⁵N]glycine and ¹⁵NO₃^- in similar amounts, 18–26 % of ¹⁵NH₄⁺ incorporation. We conclude that the potential to utilise amino acids as N sources is of widespread occurrence in plant communities and is not restricted to those from low temperature regimes or where N mineralisation is limited. Seedlings of <i>Hakea</i> (Proteaceae) were shown to metabolise glycine, with a rapid transfer of ¹⁵N from glycine to serine and other amino compounds. The ability to take up and metabolise glycine was unaffected by the presence of equimolar concentrations of NO₃^- and NH₄⁺. Isonicotinic acid hydrazide (INH) did not inhibit the transfer of ¹⁵N- label from glycine to serine indicating that serine hydroxymethyltransferase was not active in glycine catabolism. In contrast aminooxyacetate (AOA) strongly inhibited transfer of ¹⁵N from glycine to serine and labelling of other amino compounds, suggesting that glycine is metabolised in roots and cluster roots of <i>Hakea</i> via an aminotransferase.</p> Glycine metabolism by plant roots and its occurrence in Australian plant communities S Schmidt GR Stewart doi:10.1071/PP98116 Functional Plant Biology, Vol. 26, No. 3. (19 May 1999), pp. 253-264. 2007-02-07T19:46:12-00:00 1999 Functional Plant Biology 26 3 253 264 15n 2007-42 amino-acids aminotransferase glycine label roots http://www.citeulike.org/user/agallet/article/1093624 <i>Functional Ecology, Vol. 14, No. 5. (2000), pp. 645-653.</i><br /><br />Abstract 1. Plant responses after addition of nitrogen-rich complex organic material (Lolium perenne L. shoots), differing in physical (coarsely cut or finely ground) and spatial (uniform dispersion or discrete patches) heterogeneity, were examined. 2. The organic material was added to microcosm units containing L. perenne and Poa pratensis L. as monocultures or mixed swards in order to examine how species composition affected exploitation of the added 15N-labelled N source. 3. Capture of N (as 15N) from the organic material was followed by harvesting individual shoots. Poa pratensis captured more N from the added material when in mixtures with L. perenne than when in monoculture, particularly from the milled material. Capture of N by L. perenne shoots was not affected by either sward composition or method of organic material placement. 4. At final harvest (70 days after addition of the organic material), roots from P. pratensis monocultures had greater dry weights, lengths and N contents than those from L. perenne monocultures; P. pratensis shoot dry weights were also greater. 5. Capture by swards of N from the added organic material was the same (=26% of that originally available) regardless of sward composition or organic material placement. However, within the mixed swards P. pratensis captured more N than L. perenne (=18 and 9%, respectively). Spatial and physical heterogeneity of N supply from soil does not influence N capture by two grass species A Hodge J Stewart D Robinson BS Griffiths AH Fitter doi:10.1046/j.1365-2435.2000.t01-1-00470.x Functional Ecology, Vol. 14, No. 5. (2000), pp. 645-653. 2007-02-07T20:34:15-00:00 2000 Functional Ecology 14 5 645 653 13c15n 2007-44 competition label organic_patches