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  • 1
    Publication Date: 1999-05-29
    Description: Plants constantly monitor their light environment in order to grow and develop optimally, in part through use of the phytochromes, which sense red/far-red light. A phytochrome binding protein, PKS1 (phytochrome kinase substrate 1), was identified that is a substrate for light-regulated phytochrome kinase activity in vitro. In vivo experiments suggest that PKS1 is phosphorylated in a phytochrome-dependent manner and negatively regulates phytochrome signaling. The data suggest that phytochromes signal by serine-threonine phosphorylation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fankhauser, C -- Yeh, K C -- Lagarias, J C -- Zhang, H -- Elich, T D -- Chory, J -- R01GM52413/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 May 28;284(5419):1539-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Biology Laboratory, Howard Hughes Medical Institute, Salk Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10348744" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; *Arabidopsis Proteins ; Carrier Proteins/chemistry/genetics/*metabolism ; Genes, Plant ; *Intracellular Signaling Peptides and Proteins ; *Light ; Molecular Sequence Data ; Mutation ; Phosphoproteins/chemistry/genetics/*metabolism ; Phosphorylation ; *Photoreceptor Cells ; Phytochrome/*metabolism ; Phytochrome A ; Phytochrome B ; *Plant Proteins ; Protein Kinases/metabolism ; Protein-Serine-Threonine Kinases/metabolism ; Recombinant Fusion Proteins/metabolism ; *Signal Transduction ; *Transcription Factors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1997-09-05
    Description: The biliprotein phytochrome regulates plant growth and developmental responses to the ambient light environment through an unknown mechanism. Biochemical analyses demonstrate that phytochrome is an ancient molecule that evolved from a more compact light sensor in cyanobacteria. The cyanobacterial phytochrome Cph1 is a light-regulated histidine kinase that mediates red, far-red reversible phosphorylation of a small response regulator, Rcp1 (response regulator for cyanobacterial phytochrome), encoded by the adjacent gene, thus implicating protein phosphorylation-dephosphorylation in the initial step of light signal transduction by phytochrome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yeh, K C -- Wu, S H -- Murphy, J T -- Lagarias, J C -- 1 P41 RR06009/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1997 Sep 5;277(5331):1505-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9278513" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Bacterial Proteins ; Cloning, Molecular ; Cyanobacteria/chemistry/genetics/*metabolism ; Genes, Bacterial ; *Light ; Molecular Sequence Data ; Operon ; Phosphorylation ; Protein Kinases/chemistry/genetics/*metabolism ; Proteins ; Recombinant Fusion Proteins/chemistry/metabolism ; Sequence Deletion ; Signal Transduction
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2010-05-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gleick, P H -- Adams, R M -- Amasino, R M -- Anders, E -- Anderson, D J -- Anderson, W W -- Anselin, L E -- Arroyo, M K -- Asfaw, B -- Ayala, F J -- Bax, A -- Bebbington, A J -- Bell, G -- Bennett, M V L -- Bennetzen, J L -- Berenbaum, M R -- Berlin, O B -- Bjorkman, P J -- Blackburn, E -- Blamont, J E -- Botchan, M R -- Boyer, J S -- Boyle, E A -- Branton, D -- Briggs, S P -- Briggs, W R -- Brill, W J -- Britten, R J -- Broecker, W S -- Brown, J H -- Brown, P O -- Brunger, A T -- Cairns, J Jr -- Canfield, D E -- Carpenter, S R -- Carrington, J C -- Cashmore, A R -- Castilla, J C -- Cazenave, A -- Chapin, F S 3rd -- Ciechanover, A J -- Clapham, D E -- Clark, W C -- Clayton, R N -- Coe, M D -- Conwell, E M -- Cowling, E B -- Cowling, R M -- Cox, C S -- Croteau, R B -- Crothers, D M -- Crutzen, P J -- Daily, G C -- Dalrymple, G B -- Dangl, J L -- Darst, S A -- Davies, D R -- Davis, M B -- De Camilli, P V -- Dean, C -- DeFries, R S -- Deisenhofer, J -- Delmer, D P -- DeLong, E F -- DeRosier, D J -- Diener, T O -- Dirzo, R -- Dixon, J E -- Donoghue, M J -- Doolittle, R F -- Dunne, T -- Ehrlich, P R -- Eisenstadt, S N -- Eisner, T -- Emanuel, K A -- Englander, S W -- Ernst, W G -- Falkowski, P G -- Feher, G -- Ferejohn, J A -- Fersht, A -- Fischer, E H -- Fischer, R -- Flannery, K V -- Frank, J -- Frey, P A -- Fridovich, I -- Frieden, C -- Futuyma, D J -- Gardner, W R -- Garrett, C J R -- Gilbert, W -- Goldberg, R B -- Goodenough, W H -- Goodman, C S -- Goodman, M -- Greengard, P -- Hake, S -- Hammel, G -- Hanson, S -- Harrison, S C -- Hart, S R -- Hartl, D L -- Haselkorn, R -- Hawkes, K -- Hayes, J M -- Hille, B -- Hokfelt, T -- House, J S -- Hout, M -- Hunten, D M -- Izquierdo, I A -- Jagendorf, A T -- Janzen, D H -- Jeanloz, R -- Jencks, C S -- Jury, W A -- Kaback, H R -- Kailath, T -- Kay, P -- Kay, S A -- Kennedy, D -- Kerr, A -- Kessler, R C -- Khush, G S -- Kieffer, S W -- Kirch, P V -- Kirk, K -- Kivelson, M G -- Klinman, J P -- Klug, A -- Knopoff, L -- Kornberg, H -- Kutzbach, J E -- Lagarias, J C -- Lambeck, K -- Landy, A -- Langmuir, C H -- Larkins, B A -- Le Pichon, X T -- Lenski, R E -- Leopold, E B -- Levin, S A -- Levitt, M -- Likens, G E -- Lippincott-Schwartz, J -- Lorand, L -- Lovejoy, C O -- Lynch, M -- Mabogunje, A L -- Malone, T F -- Manabe, S -- Marcus, J -- Massey, D S -- McWilliams, J C -- Medina, E -- Melosh, H J -- Meltzer, D J -- Michener, C D -- Miles, E L -- Mooney, H A -- Moore, P B -- Morel, F M M -- Mosley-Thompson, E S -- Moss, B -- Munk, W H -- Myers, N -- Nair, G B -- Nathans, J -- Nester, E W -- Nicoll, R A -- Novick, R P -- O'Connell, J F -- Olsen, P E -- Opdyke, N D -- Oster, G F -- Ostrom, E -- Pace, N R -- Paine, R T -- Palmiter, R D -- Pedlosky, J -- Petsko, G A -- Pettengill, G H -- Philander, S G -- Piperno, D R -- Pollard, T D -- Price, P B Jr -- Reichard, P A -- Reskin, B F -- Ricklefs, R E -- Rivest, R L -- Roberts, J D -- Romney, A K -- Rossmann, M G -- Russell, D W -- Rutter, W J -- Sabloff, J A -- Sagdeev, R Z -- Sahlins, M D -- Salmond, A -- Sanes, J R -- Schekman, R -- Schellnhuber, J -- Schindler, D W -- Schmitt, J -- Schneider, S H -- Schramm, V L -- Sederoff, R R -- Shatz, C J -- Sherman, F -- Sidman, R L -- Sieh, K -- Simons, E L -- Singer, B H -- Singer, M F -- Skyrms, B -- Sleep, N H -- Smith, B D -- Snyder, S H -- Sokal, R R -- Spencer, C S -- Steitz, T A -- Strier, K B -- Sudhof, T C -- Taylor, S S -- Terborgh, J -- Thomas, D H -- Thompson, L G -- Tjian, R T -- Turner, M G -- Uyeda, S -- Valentine, J W -- Valentine, J S -- Van Etten, J L -- van Holde, K E -- Vaughan, M -- Verba, S -- von Hippel, P H -- Wake, D B -- Walker, A -- Walker, J E -- Watson, E B -- Watson, P J -- Weigel, D -- Wessler, S R -- West-Eberhard, M J -- White, T D -- Wilson, W J -- Wolfenden, R V -- Wood, J A -- Woodwell, G M -- Wright, H E Jr -- Wu, C -- Wunsch, C -- Zoback, M L -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 May 7;328(5979):689-90. doi: 10.1126/science.328.5979.689.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20448167" target="_blank"〉PubMed〈/a〉
    Keywords: *Climate Change ; Politics ; Public Policy ; Research/standards ; Research Personnel
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2014-09-13
    Description: Cyanobacteria are unique among bacteria in performing oxygenic photosynthesis, often together with nitrogen fixation and, thus, are major primary producers in many ecosystems. The cyanobacterium, Leptolyngbya sp. strain JSC-1, exhibits an extensive photoacclimative response to growth in far-red light that includes the synthesis of chlorophylls d and f. During far-red acclimation, transcript levels increase more than twofold for ~900 genes and decrease by more than half for ~2000 genes. Core subunits of photosystem I, photosystem II, and phycobilisomes are replaced by proteins encoded in a 21-gene cluster that includes a knotless red/far-red phytochrome and two response regulators. This acclimative response enhances light harvesting for wavelengths complementary to the growth light (lambda = 700 to 750 nanometers) and enhances oxygen evolution in far-red light.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gan, Fei -- Zhang, Shuyi -- Rockwell, Nathan C -- Martin, Shelley S -- Lagarias, J Clark -- Bryant, Donald A -- New York, N.Y. -- Science. 2014 Sep 12;345(6202):1312-7. doi: 10.1126/science.1256963. Epub 2014 Aug 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. ; Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA. ; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA. dab14@psu.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25214622" target="_blank"〉PubMed〈/a〉
    Keywords: *Acclimatization ; Chlorophyll/biosynthesis ; Cyanobacteria/enzymology/*physiology/radiation effects ; Light ; Molecular Sequence Data ; Multigene Family/physiology ; Oxygen/*physiology ; Photosynthesis/genetics/*physiology/radiation effects ; Photosystem I Protein Complex/genetics/*physiology ; Photosystem II Protein Complex/genetics/*physiology ; Phycobilisomes/metabolism/*physiology ; Phylogeny ; *Phytochrome/chemistry/classification/genetics ; Protein Structure, Tertiary
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Discrete & computational geometry 8 (1992), S. 171-189 
    ISSN: 1432-0444
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science , Mathematics
    Notes: Abstract LetB be a compact convex body symmetric around0 in ℝ2 which has nonempty interior, i.e., the unit ball of a two-dimensional Minkowski space. The self-packing radiusρ(m,B) is the smallestt such thatt B can be packed withm translates of the interior ofB. Form≤6 we show that the self-packing radiusρ(m,B)=1+2/α(m,B) whereα(m,B) is the Minkowski length of the side of the largest equilateralm-gon inscribed inB (measured in the Minkowski metric determined byB). We showρ(6,B)=ρ(7,B)=3 for allB, and determine most of the largest and smallest values ofρ(m,B) form≤7. For allm we have $$\left( {\frac{m}{{\delta (B)}}} \right)^{{1 \mathord{\left/ {\vphantom {1 2}} \right. \kern-\nulldelimiterspace} 2}} - \frac{3}{2} \leqslant \rho (m,B) \leqslant \left( {\frac{m}{{\delta (B)}}} \right)^{{1 \mathord{\left/ {\vphantom {1 2}} \right. \kern-\nulldelimiterspace} 2}} + 1,$$ whereδ(B) is the packing density ofB in ℝ2.
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Discrete & computational geometry 21 (1999), S. 161-191 
    ISSN: 1432-0444
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science , Mathematics
    Notes: Abstract. This paper studies three classes of discrete sets X in $\Bbb R$ n which have a weak translational order imposed by increasingly strong restrictions on their sets of interpoint vectors X-X . A finitely generated Delone set is one such that the abelian group [X-X] generated by X-X is finitely generated, so that [X-X] is a lattice or a quasilattice. For such sets the abelian group [X] is finitely generated, and by choosing a basis of [X] one obtains a homomorphism $\varphi : [X] \rightarrow {\Bbb Z}^s$ . A Delone set of finite type is a Delone set X such that X-X is a discrete closed set. A Meyer set is a Delone set X such that X-X is a Delone set. Delone sets of finite type form a natural class for modeling quasicrystalline structures, because the property of being a Delone set of finite type is determined by ``local rules.'' That is, a Delone set X is of finite type if and only if it has a finite number of neighborhoods of radius 2R , up to translation, where R is the relative denseness constant of X . Delone sets of finite type are also characterized as those finitely generated Delone sets such that the map ϕ satisfies the Lipschitz-type condition ||ϕ (x) - ϕ (x')|| 〈 C ||x - x'|| for x, x' ∈X , where the norms || . . . || are Euclidean norms on $\Bbb R$ s and $\Bbb R$ n , respectively. Meyer sets are characterized as the subclass of Delone sets of finite type for which there is a linear map $\tilde{L} : {\Bbb R}^n \rightarrow {\Bbb R}^s$ and a constant C such that ||ϕ (x) - $\tilde{L}$ (x)|| $\leq C$ for all x∈X . Suppose that X is a Delone set with an inflation symmetry, which is a real number η 〉 1 such that $\eta X \subseteq X$ . If X is a finitely generated Delone set, then η must be an algebraic integer; if X is a Delone set of finite type, then in addition all algebraic conjugates | η ' | $\leq$ η; and if X is a Meyer set, then all algebraic conjugates | η ' | $\leq$ 1.
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Discrete & computational geometry 18 (1997), S. 53-82 
    ISSN: 1432-0444
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science , Mathematics
    Notes: Abstract. The d-step conjecture is one of the fundamental open problems concerning the structure of convex polytopes. Let Δ (d,n) denote the maximum diameter of a graph of a d-polytope that has n facets. The d-step conjecture Δ (d,2d) = d is proved equivalent to the following statement: For each ``general position'' $(d-1)\times (d-1)$ real matrix M there are two matrices $Q_{\tau}, Q_{\sigma}$ drawn from a finite group $\hat{S}_d$ of $(d-1)\times (d-1)$ matrices isomorphic to the symmetric group $\mathop{\rm Sym}\nolimits (d)$ on d letters, such that $Q_{\tau} MQ_{\sigma}$ has the Gaussian elimination factorization L -1 U in which L and U are lower triangular and upper triangular matrices, respectively, that have positive nontriangular elements. If #(M) is the number of pairs $(\sigma,\tau) \in \mathop{\rm Sym}\nolimits(d) \times \mathop{\rm Sym}\nolimits (d)$ giving a positive L -1 U factorization, then #(M) equals the number of d-step paths between two vertices of an associated Dantzig figure. One consequence is that #(M)≤ d!. Numerical experiments all satisfied #(M) ≥ 2 d-1 , including examples attaining equality for 3 ≤ d ≤ 15. The inequality #(M) ≥ 2 d-1 is proved for d=3. For d≥ 4, examples with #(M) =2 d-1 exhibit a large variety of combinatorial types of associated Dantzig figures. These experiments and other evidence suggest that the d-step conjecture may be true in all dimensions, in the strong form #(M) ≥ 2 d-1 .
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Discrete & computational geometry 19 (1998), S. 19-31 
    ISSN: 1432-0444
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science , Mathematics
    Notes: Abstract. The d -step conjecture asserts that every d -polytope P with 2d facets has an edge-path of at most d steps between any two of its vertices. Klee and Walkup showed that to prove the d -step conjecture, it suffices to verify it for all Dantzig figures (P, w 1 , w 2 ) , which are simple d -polytopes with 2d facets together with distinguished vertices w 1 and w 2 which have no common facet, and to consider only paths between w 1 and w 2 . This paper counts the number of d -step paths between w 1 and w 2 for certain Dantzig figures (P, w 1 , w 2 ) which are extremal in the sense that P has the minimal and maximal vertices possible among such d -polytopes with 2d facets, which are d 2 - d + 2 vertices (lower bound theorem) and $2 { \lfloor \frac{3}{2} d - \frac{1}{2} \rfloor \choose \lfloor \frac{d}{2} \rfloor}$ vertices (upper bound theorem), respectively. These Dantzig figures have exactly 2 d-1 d -step paths.
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Discrete & computational geometry 21 (1999), S. 345-372 
    ISSN: 1432-0444
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science , Mathematics
    Notes: Abstract. The atomic structures of quasicrystalline materials exhibit long range order under translations. It is believed that such materials have atomic structures which approximately obey local rules restricting the location of nearby atoms. These local constraints are typically invariant under rotations, and it is of interest to establish conditions under which such local rules can nevertheless enforce order under translations in any structure that satisfies them. A set of local rules $ \cal L $ in $ {\frak R}^n $ is a finite collection of discrete sets {Y i } containing 0, each of which is contained in the ball of radius ρ around 0 in $ {\frak R}^n $ . A set X satisfies the local rules $ \cal L $ under isometries if the ρ -neighborhood of each $ {\bf x} \in X $ is isometric to an element of $ \cal L $ . This paper gives sufficient conditions on a set of local rules $ \cal L $ such that if X satisfies $ \cal L $ under isometries, then X has a weak long-range order under translations, in the sense that X is a Delone set of finite type. A set X is a Delone set of finite type if it is a Delone set whose interpoint distance set X-X is a discrete closed set. We show for each minimal Delone set of finite type X that there exists a set of local rules $ \cal L $ such that X satisfies $ \cal L $ under isometries and all other Y that satisfy $ \cal L $ under isometries are Delone sets of finite type. A set of perfect local rules (under isometries or under translations, respectively) is a set of local rules $ \cal L $ such that all structures X that satisfy $ \cal L $ are in the same local isomorphism class (under isometries or under translations, respectively). If a Delone set of finite type has a set of perfect local rules under translations, then it has a set of perfect local rules under isometries, and conversely.
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Discrete & computational geometry 20 (1998), S. 477-498 
    ISSN: 1432-0444
    Source: Springer Online Journal Archives 1860-2000
    Topics: Computer Science , Mathematics
    Notes: Abstract. This paper gives several conditions in geometric crystallography which force a structure X in R n to be an ideal crystal. An ideal crystal in R n is a finite union of translates of a full-dimensional lattice. An (r,R) -set is a discrete set X in R n such that each open ball of radius r contains at most one point of X and each closed ball of radius R contains at least one point of X . A multiregular point system X is an (r,R) -set whose points are partitioned into finitely many orbits under the symmetry group Sym(X) of isometries of R n that leave X invariant. Every multiregular point system is an ideal crystal and vice versa. We present two different types of geometric conditions on a set X that imply that it is a multiregular point system. The first is that if X ``looks the same'' when viewed from n+2 points { y i : 1 \leq i \leq n + 2 } , such that one of these points is in the interior of the convex hull of all the others, then X is a multiregular point system. The second is a ``local rules'' condition, which asserts that if X is an (r,R) -set and all neighborhoods of X within distance ρ of each x∈X are isometric to one of k given point configurations, and ρ exceeds CRk for C = 2(n 2 +1) log 2 (2R/r+2) , then X is a multiregular point system that has at most k orbits under the action of Sym(X) on R n . In particular, ideal crystals have perfect local rules under isometries.
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