@article{12203, abstract = {Geranylgeranyl diphosphate synthase (GGPPS, EC: 2.5.1.29) catalyzes the biosynthesis of geranylgeranyl diphosphate (GGPP), which is a key precursor for ginkgolide biosynthesis. Here we reported for the first time the cloning of a new full-length cDNA encoding GGPPS from the living fossil plant Ginkgo biloba. The full-length cDNA encoding G. biloba GGPPS (designated as GbGGPPS) was 1657bp long and contained a 1176bp open reading frame encoding a 391 amino acid protein. Comparative analysis showed that GbGGPPS possessed a 79 amino acid transit peptide at its N-terminal, which directed GbGGPPS to target to the plastids. Bioinformatic analysis revealed that GbGGPPS was a member of polyprenyltransferases with two highly conserved aspartate-rich motifs like other plant GGPPSs. Phylogenetic tree analysis indicated that plant GGPPSs could be classified into two groups, angiosperm and gymnosperm GGPPSs, while GbGGPPS had closer relationship with gymnosperm plant GGPPSs.}, author = {Liao, Zhihua and Chen, Min and Gong, Yifu and Guo, Liang and Tan, Qiumin and Feng, Xiaoqi and Sun, Xiaofen and Tan, Feng and Tang, Kexuan}, issn = {1042-5179}, journal = {DNA Sequence}, keywords = {Endocrinology, Genetics, Molecular Biology, Biochemistry}, number = {2}, pages = {153--158}, publisher = {Informa UK Limited}, title = {{A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides}}, doi = {10.1080/10425170410001667348}, volume = {15}, year = {2004}, } @article{12658, abstract = {[1] During the ablation period 2001 a glaciometeorological experiment was carried out on Haut Glacier d'Arolla, Switzerland. Five meteorological stations were installed on the glacier, and one permanent automatic weather station in the glacier foreland. The altitudes of the stations ranged between 2500 and 3000 m a.s.l., and they were in operation from end of May to beginning of September 2001. The spatial arrangement of the stations and temporal duration of the measurements generated a unique data set enabling the analysis of the spatial and temporal variability of the meteorological variables across an alpine glacier. All measurements were taken at a nominal height of 2 m, and hourly averages were derived for the analysis. The wind regime was dominated by the glacier wind (mean value 2.8 m s−1) but due to erosion by the synoptic gradient wind, occasionally the wind would blow up the valley. A slight decrease in mean 2 m air temperatures with altitude was found, however the 2 m air temperature gradient varied greatly and frequently changed its sign. Mean relative humidity was 71% and exhibited limited spatial variation. Mean incoming shortwave radiation and albedo both generally increased with elevation. The different components of shortwave radiation are quantified with a parameterization scheme. Resulting spatial variations are mainly due to horizon obstruction and reflections from surrounding slopes, i.e., topography. The effect of clouds accounts for a loss of 30% of the extraterrestrial flux. Albedos derived from a Landsat TM image of 30 July show remarkably constant values, in the range 0.49 to 0.50, across snow covered parts of the glacier, while albedo is highly spatially variable below the zone of continuous snow cover. These results are verified with ground measurements and compared with parameterized albedo. Mean longwave radiative fluxes decreased with elevation due to lower air temperatures and the effect of upper hemisphere slopes. It is shown through parameterization that this effect would even be more pronounced without the effect of clouds. Results are discussed with respect to a similar study which has been carried out on Pasterze Glacier (Austria). The presented algorithms for interpolating, parameterizing and simulating variables and parameters in alpine regions are integrated in the software package AMUNDSEN which is freely available to be adapted and further developed by the community.}, author = {Strasser, Ulrich and Corripio, Javier and Pellicciotti, Francesca and Burlando, Paolo and Brock, Ben and Funk, Martin}, issn = {0148-0227}, journal = {Journal of Geophysical Research: Atmospheres}, keywords = {Paleontology, Space and Planetary Science, Earth and Planetary Sciences (miscellaneous), Atmospheric Science, Earth-Surface Processes, Geochemistry and Petrology, Soil Science, Water Science and Technology, Ecology, Aquatic Science, Forestry, Oceanography, Geophysics}, number = {D3}, publisher = {American Geophysical Union}, title = {{Spatial and temporal variability of meteorological variables at Haut Glacier d'Arolla (Switzerland) during the ablation season 2001: Measurements and simulations}}, doi = {10.1029/2003jd003973}, volume = {109}, year = {2004}, } @article{8517, abstract = {We consider the evolution of a connected set on the plane carried by a space periodic incompressible stochastic flow. While for almost every realization of the stochastic flow at time t most of the particles are at a distance of order equation image away from the origin, there is a measure zero set of points that escape to infinity at the linear rate. We study the set of points visited by the original set by time t and show that such a set, when scaled down by the factor of t, has a limiting nonrandom shape.}, author = {Dolgopyat, Dmitry and Kaloshin, Vadim and Koralov, Leonid}, issn = {0010-3640}, journal = {Communications on Pure and Applied Mathematics}, keywords = {Applied Mathematics, General Mathematics}, number = {9}, pages = {1127--1158}, publisher = {Wiley}, title = {{A limit shape theorem for periodic stochastic dispersion}}, doi = {10.1002/cpa.20032}, volume = {57}, year = {2004}, } @article{8518, author = {Koralov, Leonid and Kaloshin, Vadim and Dolgopyat, Dmitry}, issn = {0091-1798}, journal = {The Annals of Probability}, number = {1A}, pages = {1--27}, publisher = {Institute of Mathematical Statistics}, title = {{Sample path properties of the stochastic flows}}, doi = {10.1214/aop/1078415827}, volume = {32}, year = {2004}, } @article{864, abstract = {We present a method for prediction of functional sites in a set of aligned protein sequences. The method selects sites which are both well conserved and clustered together in space, as inferred from the 3D structures of proteins included in the alignment. We tested the method using 86 alignments from the NCBI CDD database, where the sites of experimentally determined ligand and/or macromolecular interactions are annotated. In agreement with earlier investigations, we found that functional site predictions are most successful when overall background sequence conservation is low, such that sites under evolutionary constraint become apparent. In addition, we found that averaging of conservation values across spatially clustered sites improves predictions under certain conditions: that is, when overall conservation is relatively high and when the site in question involves a large macromolecular binding interface. Under these conditions it is better to look for clusters of conserved sites than to look for particular conserved sites.}, author = {Panchenko, Anna R and Fyodor Kondrashov and Bryant, Stephen H}, journal = {Protein Science}, number = {4}, pages = {884 -- 892}, publisher = {Wiley-Blackwell}, title = {{Prediction of functional sites by analysis of sequence and structure conservation}}, doi = {10.1110/ps.03465504}, volume = {13}, year = {2004}, } @article{870, abstract = {Only a fraction of eukaryotic genes affect the phenotype drastically. We compared 18 parameters in 1273 human morbid genes, known to cause diseases, and in the remaining 16 580 unambiguous human genes. Morbid genes evolve more slowly, have wider phylogenetic distributions, are more similar to essential genes of Drosophila melanogaster, code for longer proteins containing more alanine and glycine and less histidine, lysine and methionine, possess larger numbers of longer introns with more accurate splicing signals and have higher and broader expressions. These differences make it possible to classify as non-morbid 34% of human genes with unknown morbidity, when only 5% of known morbid genes are incorrectly classified as non-morbid. This classification can help to identify disease-causing genes among multiple candidates.}, author = {Fyodor Kondrashov and Ogurtsov, Aleksey Yu and Kondrashov, Alexey S}, journal = {Nucleic Acids Research}, number = {5}, pages = {1731 -- 1737}, publisher = {Oxford University Press}, title = {{Bioinformatical assay of human gene morbidity}}, doi = {10.1093/nar/gkh330}, volume = {32}, year = {2004}, } @article{875, abstract = {The dominance of wild-type alleles and the concomitant recessivity of deleterious mutant alleles might have evolved by natural selection or could be a by-product of the molecular and physiological mechanisms of gene action. We compared the properties of human haplosufficient genes, whose wild-type alleles are dominant over loss-of-function alleles, with haploinsufficient (recessive wild-type) genes, which produce an abnormal phenotype when heterozygous for a loss-of-function allele. The fraction of haplosufficient genes is the highest among the genes that encode enzymes, which is best compatible with the physiological theory. Haploinsufficient genes, on average, have more paralogs than haplosufficient genes, supporting the idea that gene dosage could be important for the initial fixation of duplications. Thus, haplo(in)sufficiency of a gene and its propensity for duplication might have a common evolutionary basis.}, author = {Fyodor Kondrashov and Koonin, Eugene V}, journal = {Trends in Genetics}, number = {7}, pages = {287 -- 291}, publisher = {Elsevier}, title = {{A common framework for understanding the origin of genetic dominance and evolutionary fates of gene duplications}}, doi = {10.1016/j.tig.2004.05.001}, volume = {20}, year = {2004}, } @article{889, abstract = {The function of protein and RNA molecules depends on complex epistatic interactions between sites. Therefore, the deleterious effect of a mutation can be suppressed by a compensatory second-site substitution. In relating a list of 86 pathogenic mutations in human IRNAs encoded by mitochondrial genes to the sequences of their mammalian orthologs, we noted that 52 pathogenic mutations were present in normal tRNAs of one or several nonhuman mammals. We found at least five mechanisms of compensation for 32 pathogenic mutations that destroyed a Watson-Crick pair in one of the four tRNA stems: restoration of the affected Watson-Crick interaction (25 cases), strengthening of another pair (4 cases), creation of a new pair (8 cases), changes of multiple interactions in the affected stem (11 cases) and changes involving the interaction between the loop and stem structures (3 cases). A pathogenic mutation and its compensating substitution are fixed in a lineage in rapid succession, and often a compensatory interaction evolves convergently in different clades. At least 10%, and perhaps as many as 50%, of all nucleotide substitutions in evolving mammalian (RNAs participate in such interactions, indicating that the evolution of tRNAs proceeds along highly epistatic fitness ridges.}, author = {Kern, Andrew D and Fyodor Kondrashov}, journal = {Nature Genetics}, number = {11}, pages = {1207 -- 1212}, publisher = {Nature Publishing Group}, title = {{Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs}}, doi = {10.1038/ng1451}, volume = {36}, year = {2004}, } @article{898, abstract = {New alleles become fixed owing to random drift of nearly neutral mutations or to positive selection of substantially advantageous mutations. After decades of debate, the fraction of fixations driven by selection remains uncertain. Within 9,390 genes, we analysed 28,196 codons at which rat and mouse differ from each other at two nucleotide sites and 1,982 codons with three differences. At codons where rat-mouse divergence involved two non-synonymous substitutions, both of them occurred in the same lineage, either rat or mouse, in 64% of cases; however, independent substitutions would occur in the same lineage with a probability of only 50%. All three non-synonymous substitutions occurred in the same lineage for 46% of codons, instead of the 25% expected. Furthermore, comparison of 12 pairs of prokaryotic genomes also shows clumping of multiple non-synonymous substitutions in the same lineage. This pattern cannot be explained by correlated mutation or episodes of relaxed negative selection, but instead indicates that positive selection acts at many sites of rapid, successive amino acid replacement.}, author = {Bazykin, Georgii A and Fyodor Kondrashov and Ogurtsov, Aleksey Yu and Sunyaev, Shamil R and Kondrashov, Alexey S}, journal = {Nature}, number = {6991}, pages = {558 -- 562}, publisher = {Nature Publishing Group}, title = {{Positive selection at sites of multiple amino acid replacements since rat-mouse divergence}}, doi = {10.1038/nature02601}, volume = {429}, year = {2004}, } @article{902, abstract = {We compare the functional spectrum of protein evolution in two separate animal lineages with respect to two hypotheses: (1) rates of divergence are distributed similarly among functional classes within both lineages, indicating that selective pressure on the proteome is largely independent of organismic-level biological requirements; and (2) rates of divergence are distributed differently among functional classes within each lineage, indicating species-specific selective regimes impact genome-wide substitutional patterns. Integrating comparative genome sequence with data from tissue-specific expressed-sequence-tag (EST) libraries and detailed database annotations, we find a functional genomic signature of rapid evolution and selective constraint shared between mammalian and nematode lineages despite their extensive morphological and ecological differences and distant common ancestry. In both phyla, we find evidence of accelerated evolution among components of molecular systems involved in coevolutionary change. In mammals, lineage-specific fast evolving genes include those involved in reproduction, immunity, and possibly, maternal-fetal conflict. Likelihood ratio tests provide evidence for positive selection in these rapidly evolving functional categories in mammals. In contrast, slowly evolving genes, in terms of amino acid or insertion/deletion (indel) change, in both phyla are involved in core molecular processes such as transcription, translation, and protein transport. Thus, strong purifying selection appears to act on the same core cellular processes in both mammalian and nematode lineages, whereas positive and/or relaxed selection acts on different biological processes in each lineage.}, author = {Castillo-Davis, Cristian I and Fyodor Kondrashov and Hartl, Daniel L and Kulathinal, Rob J}, journal = {Genome Research}, number = {5}, pages = {802 -- 811}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint}}, doi = {10.1101/gr.2195604}, volume = {14}, year = {2004}, } @article{7333, abstract = {The analysis of the complete H2/air polymer electrolyte fuel cell system shows that process air humidification is one of the biggest obstacles for a high performance portable system in the kW range. Therefore, a new concept, with passive process air humidification integrated into the stack, has been developed. Humidification in each cell makes the process independent from the number of cells and the operation mode, thus making the concept fully scalable. Without external humidification the system is simpler, smaller, and cheaper. The humidification of the process air is achieved by transfer of product water from the exhaust air, through part of the membrane, to the dry intake air. Tests have shown that cells using the concept of internal humidification and operated with dry air at 70 ° have almost the same performance as when operated with external humidification. A 42‐cell stack with this internal humidification concept was built and integrated into a portable 1 kW power generator system.}, author = {Santis, M. and Schmid, D. and Ruge, M. and Freunberger, Stefan Alexander and Büchi, F.N.}, issn = {1615-6846}, journal = {Fuel Cells}, number = {3}, pages = {214--218}, publisher = {Wiley}, title = {{Modular stack-internal air humidification concept-verification in a 1 kW stack}}, doi = {10.1002/fuce.200400028}, volume = {4}, year = {2004}, } @article{7334, abstract = {Fundamental and phenomenological models for cells, stacks, and complete systems of PEFC and SOFC are reviewed and their predictive power is assessed by comparing model simulations against experiments. Computationally efficient models suited for engineering design include the (1+1) dimensionality approach, which decouples the membrane in-plane and through-plane processes, and the volume-averaged-method (VAM) that considers only the lumped effect of pre-selected system components. The former model was shown to capture the measured lateral current density inhomogeneities in a PEFC and the latter was used for the optimization of commercial SOFC systems. State Space Modeling (SSM) was used to identify the main reaction pathways in SOFC and, in conjunction with the implementation of geometrically well-defined electrodes, has opened a new direction for the understanding of electrochemical reactions. Furthermore, SSM has advanced the understanding of the COpoisoning-induced anode impedance in PEFC. Detailed numerical models such as the Lattice Boltzmann (LB) method for transport in porous media and the full 3-D Computational Fluid Dynamics (CFD) Navier-Stokes simulations are addressed. These models contain all components of the relevant physics and they can improve the understanding of the related phenomena, a necessary condition for the development of both appropriate simplified models as well as reliable technologies. Within the LB framework, a technique for the characterization and computer-reconstruction of the porous electrode structure was developed using advanced pattern recognition algorithms. In CFD modeling, 3-D simulations were used to investigate SOFC with internal methane steam reforming and have exemplified the significance of porous and novel fractal channel distributors for the fuel and oxidant delivery, as well as for the cooling of PEFC. As importantly, the novel concept has been put forth of functionally designed, fractal-shaped fuel cells, showing promise of significant performance improvements over the conventional rectangular shaped units. Thermo-economic modeling for the optimization of PEFC is finally addressed. }, author = {Mantzaras, John and Freunberger, Stefan Alexander and Büchi, Felix N. and Roos, Markus and Brandstätter, Wilhelm and Prestat, Michel and Gauckler, Ludwig J. and Andreaus, Bernhard and Hajbolouri, Faegheh and Senn, Stephan M. and Poulikakos, Dimos and Chaniotis, Andreas K. and Larrain, Diego and Autissier, Nordahl and Maréchal, François}, issn = {0009-4293}, journal = {CHIMIA International Journal for Chemistry}, number = {12}, pages = {857--868}, publisher = {Swiss Chemical Society}, title = {{Fuel cell modeling and simulations}}, doi = {10.2533/000942904777677029}, volume = {58}, year = {2004}, } @article{7706, abstract = {The Sir2 deacetylase modulates organismal life-span in various species. However, the molecular mechanisms by which Sir2 increases longevity are largely unknown. We show that in mammalian cells, the Sir2 homolog SIRT1 appears to control the cellular response to stress by regulating the FOXO family of Forkhead transcription factors, a family of proteins that function as sensors of the insulin signaling pathway and as regulators of organismal longevity. SIRT1 and the FOXO transcription factor FOXO3 formed a complex in cells in response to oxidative stress, and SIRT1 deacetylated FOXO3 in vitro and within cells. SIRT1 had a dual effect on FOXO3 function: SIRT1 increased FOXO3's ability to induce cell cycle arrest and resistance to oxidative stress but inhibited FOXO3's ability to induce cell death. Thus, one way in which members of the Sir2 family of proteins may increase organismal longevity is by tipping FOXO-dependent responses away from apoptosis and toward stress resistance.}, author = {Brunet, Anne and Sweeney, Lora Beatrice Jaeger and Sturgill, J Fitzhugh and Chua, Katrin and Greer, Paul and Lin, Yingxi and Tran, Hien and Ross, Sarah and Mostoslavsky, Raul and Cohen, Haim and Hu, Linda and Chen, Hwei-Ling and Jedrychowski, Mark and Gygi, Steven and Sinclair, David and Alt, Frederick and Greenberg, Michael}, issn = {0036-8075}, journal = {Science}, number = {5666}, pages = {2011--2015}, publisher = {American Association for the Advancement of Science}, title = {{Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase}}, doi = {10.1126/science.1094637}, volume = {303}, year = {2004}, } @article{1963, abstract = {The mechanism coupling electron transfer and proton pumping in respiratory complex I (NADH-ubiquinone oxidoreductase) has not been established, but it has been suggested that it involves conformational changes. Here, the influence of substrates on the conformation of purified complex I from Escherichia coli was studied by cross-linking and electron microscopy. When a zero-length cross-linking reagent was used, the presence of NAD(P)H, in contrast to that of NAD+, prevented the formation of cross-links between the hydrophilic subunits of the complex, including NuoB, NuoI, and NuoCD. Comparisons using different cross-linkers suggested that NuoB, which is likely to coordinate the key iron-sulfur cluster N2, is the most mobile subunit. The presence of NAD(P)H led also to enhanced proteolysis of subunit NuoG. These data indicate that upon NAD(P)H binding, the peripheral arm of the complex adopts a more open conformation, with increased distances between subunits. Single particle analysis showed the nature of this conformational change. The enzyme retains its L-shape in the presence of NADH, but exhibits a significantly more open or expanded structure both in the peripheral arm and, unexpectedly, in the membrane domain also.}, author = {Mamedova, Aygun A and Holt, Peter J and Carroll, Joe D and Leonid Sazanov}, journal = {Journal of Biological Chemistry}, number = {22}, pages = {23830 -- 23836}, publisher = {American Society for Biochemistry and Molecular Biology}, title = {{Substrate-induced conformational change in bacterial complex I}}, doi = {10.1074/jbc.M401539200}, volume = {279}, year = {2004}, } @article{13434, abstract = {Thin films of ionically doped gelatin have been color-patterned with submicrometer precision using the wet-stamping technique. Inorganic salts are delivered onto the gelatin surface from an agarose stamp, and diffuse into the gelatine layer, producting deeply colored precipitates. Reaction fronts originating from different features of the stamp cease within < 1 μm of each other, leaving sharp, transparent regions in between.}, author = {Campbell, C. J. and Fialkowski, M. and Klajn, Rafal and Bensemann, I. T. and Grzybowski, B. A.}, issn = {1521-4095}, journal = {Advanced Materials}, keywords = {Mechanical Engineering, Mechanics of Materials, General Materials Science}, number = {21}, pages = {1912--1917}, publisher = {Wiley}, title = {{Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts}}, doi = {10.1002/adma.200400383}, volume = {16}, year = {2004}, } @article{13435, abstract = {Micropatterning of surfaces with several chemicals at different spatial locations usually requires multiple stamping and registration steps. Here, we describe an experimental method based on reaction–diffusion phenomena that allows for simultaneous micropatterning of a substrate with several coloured chemicals. In this method, called wet stamping (WETS), aqueous solutions of two or more inorganic salts are delivered onto a film of dry, ionically doped gelatin from an agarose stamp patterned in bas relief. Once in conformal contact, these salts diffuse into the gelatin, where they react to give deeply coloured precipitates. Separation of colours in the plane of the surface is the consequence of the differences in the diffusion coefficients, the solubility products, and the amounts of different salts delivered from the stamp, and is faithfully reproduced by a theoretical model based on a system of reaction–diffusion partial differential equations. The multicolour micropatterns are useful as non-binary optical elements, and could potentially form the basis of new applications in microseparations and in controlled delivery.}, author = {Klajn, Rafal and Fialkowski, Marcin and Bensemann, Igor T. and Bitner, Agnieszka and Campbell, C. J. and Bishop, Kyle and Smoukov, Stoyan and Grzybowski, Bartosz A.}, issn = {1476-4660}, journal = {Nature Materials}, keywords = {Mechanical Engineering, Mechanics of Materials, Condensed Matter Physics, General Materials Science, General Chemistry}, pages = {729--735}, publisher = {Springer Nature}, title = {{Multicolour micropatterning of thin films of dry gels}}, doi = {10.1038/nmat1231}, volume = {3}, year = {2004}, } @article{1456, abstract = {We study the space of L2 harmonic forms on complete manifolds with metrics of fibred boundary or fibred cusp type. These metrics generalize the geometric structures at infinity of several different well-known classes of metrics, including asymptotically locally Euclidean manifolds, the (known types of) gravitational instantons, and also Poincaré metrics on ℚ-rank 1 ends of locally symmetric spaces and on the complements of smooth divisors in Kähler manifolds. The answer in all cases is given in terms of intersection cohomology of a stratified compactification of the manifold. The L2 signature formula implied by our result is closely related to the one proved by Dai and more generally by Vaillant and identifies Dai's τ-invariant directly in terms of intersection cohomology of differing perversities. This work is also closely related to a recent paper of Carron and the forthcoming paper of Cheeger and Dai. We apply our results to a number of examples, gravitational instantons among them, arising in predictions about L2 harmonic forms in duality theories in string theory.}, author = {Tamas Hausel and Hunsicker, Eugénie and Mazzeo, Rafe R}, journal = {Duke Mathematical Journal}, number = {3}, pages = {485 -- 548}, publisher = {Duke University Press}, title = {{Hodge cohomology of gravitational instantons}}, doi = {10.1215/S0012-7094-04-12233-X}, volume = {122}, year = {2004}, } @article{1464, abstract = {The moduli space of stable vector bundles on a Riemann surface is smooth when the rank and degree are coprime, and is diffeomorphic to the space of unitary connections of central constant curvature. A classic result of Newstead and Atiyah and Bott asserts that its rational cohomology ring is generated by the universal classes, that is, by the Kunneth components of the Chern classes of the universal bundle. This paper studies the larger, non-compact moduli space of Higgs bundles, as introduced by Hitchin and Simpson, with values in the canonical bundle K. This is diffeomorphic to the space of all connections of central constant curvature, whether unitary or not. The main result of the paper is that, in the rank 2 case, the rational cohomology ring of this space is again generated by universal classes. The spaces of Higgs bundles with values in K(n) for n > 0 turn out to be essential to the story. Indeed, we show that their direct limit has the homotopy type of the classifying space of the gauge group, and hence has cohomology generated by universal classes. 2000 Mathematics Subject Classification 14H60 (primary), 14D20, 14H81, 32Q55, 58D27 (secondary). }, author = {Tamas Hausel and Thaddeus, Michael}, journal = {Proceedings of the London Mathematical Society}, number = {3}, pages = {632 -- 658}, publisher = {Oxford University Press}, title = {{Generators for the cohomology ring of the moduli space of rank 2 higgs bundles}}, doi = {10.1112/S0024611503014618}, volume = {88}, year = {2004}, } @article{6155, abstract = {The genome of the nematode Caenorhabditis elegans encodes seven soluble guanylate cyclases (sGCs) [1]. In mammals, sGCs function as α/β heterodimers activated by gaseous ligands binding to a haem prosthetic group 2, 3. The principal activator is nitric oxide, which acts through sGCs to regulate diverse cellular events. In C. elegans the function of sGCs is mysterious: the worm genome does not appear to encode nitric oxide synthase, and all C. elegans sGC subunits are more closely related to mammalian β than α subunits [1]. Here, we show that two of the seven C. elegans sGCs, GCY-35 and GCY-36, promote aggregation behavior. gcy-35 and gcy-36 are expressed in a small number of neurons. These include the body cavity neurons AQR, PQR, and URX, which are directly exposed to the blood equivalent of C. elegans and regulate aggregation behavior [4]. We show that GCY-35 and GCY-36 act as α-like and β-like sGC subunits and that their function in the URX sensory neurons is sufficient for strong nematode aggregation. Neither GCY-35 nor GCY-36 is absolutely required for C. elegans to aggregate. Instead, these molecules may transduce one of several pathways that induce C. elegans to aggregate or may modulate aggregation by responding to cues in C. elegans body fluid.}, author = {Cheung, Benny H.H and Arellano-Carbajal, Fausto and Rybicki, Irene and de Bono, Mario}, issn = {0960-9822}, journal = {Current Biology}, number = {12}, pages = {1105--1111}, publisher = {Elsevier}, title = {{Soluble guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation behavior}}, doi = {10.1016/j.cub.2004.06.027}, volume = {14}, year = {2004}, } @article{9454, author = {Chan, Simon W.-L. and Zilberman, Daniel and Xie, Zhixin and Johansen, Lisa K. and Carrington, James C. and Jacobsen, Steven E.}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {5662}, pages = {1336}, publisher = {American Association for the Advancement of Science}, title = {{RNA silencing genes control de novo DNA methylation}}, doi = {10.1126/science.1095989}, volume = {303}, year = {2004}, }