@inbook{6323, abstract = {This paper surveys recent progress towards the Manin conjecture for (singular and non-singular) del Pezzo surfaces. To illustrate some of the techniques available, an upper bound of the expected order of magnitude is established for a singular del Pezzo surface of degree four.}, author = {Browning, Timothy D}, booktitle = {A Tribute to Gauss and Dirichlet}, pages = {39--56}, publisher = {American Mathematical Society}, title = {{An overview of Manin's conjecture for del Pezzo surfaces}}, volume = {7}, year = {2007}, } @article{13424, abstract = {Changing shapes: Metastable spherical aggregates of gold nanoparticles undergo a one-to-one, thermally induced transformation into heterodimers comprising connected plate and spherical domains. By controlling the reaction time, it is possible to isolate a variety of structures differing in the relative sizes of the domains and in the overall optical properties (see picture).}, author = {Klajn, Rafal and Pinchuk, Anatoliy O. and Schatz, George C. and Grzybowski, Bartosz A.}, issn = {1521-3773}, journal = {Angewandte Chemie International Edition}, keywords = {General Chemistry, Catalysis}, number = {44}, pages = {8363--8367}, publisher = {Wiley}, title = {{Synthesis of heterodimeric sphere–prism nanostructures via metastable gold supraspheres}}, doi = {10.1002/anie.200702570}, volume = {46}, year = {2007}, } @article{13425, abstract = {Nanoparticles (NPs) decorated with ligands combining photoswitchable dipoles and covalent cross-linkers can be assembled by light into organized, three-dimensional suprastructures of various types and sizes. NPs covered with only few photoactive ligands form metastable crystals that can be assembled and disassembled “on demand” by using light of different wavelengths. For higher surface concentrations, self-assembly is irreversible, and the NPs organize into permanently cross-linked structures including robust supracrystals and plastic spherical aggregates.}, author = {Klajn, Rafal and Bishop, Kyle J. M. and Grzybowski, Bartosz A.}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, keywords = {Multidisciplinary}, number = {25}, pages = {10305--10309}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Light-controlled self-assembly of reversible and irreversible nanoparticle suprastructures}}, doi = {10.1073/pnas.0611371104}, volume = {104}, year = {2007}, } @article{13426, abstract = {Photoswelling of thin films of dichromated gelatin provides a basis for fabrication of multilevel surface reliefs via sequential UV illumination through different photomasks. The remarkable feature of this simple, benchtop technique is that by adjusting irradiation times, film thickness, or its hydration state the heights of the developed features can be varied from few nanometers to tens of microns. After UV exposure, the surface structures can be replicated faithfully into either soft or hard PDMS stamps.}, author = {Paszewski, Maciej and Smoukov, Stoyan K. and Klajn, Rafal and Grzybowski, Bartosz A.}, issn = {1520-5827}, journal = {Langmuir}, keywords = {Electrochemistry, Spectroscopy, Surfaces and Interfaces, Condensed Matter Physics, General Materials Science}, number = {10}, pages = {5419--5422}, publisher = {American Chemical Society}, title = {{Multilevel surface nano- and microstructuring via sequential photoswelling of dichromated gelatin}}, doi = {10.1021/la062982c}, volume = {23}, year = {2007}, } @article{13427, abstract = {Deformable, spherical aggregates of metal nanoparticles connected by long-chain dithiol ligands self-assemble into nanostructured materials of macroscopic dimensions. These materials are plastic and moldable against arbitrarily shaped masters and can be thermally hardened into polycrystalline metal structures of controllable porosity. In addition, in both plastic and hardened states, the assemblies are electrically conductive and exhibit Ohmic characteristics down to ∼20 volts per meter. The self-assembly method leading to such materials is applicable both to pure metals and to bimetallic structures of various elemental compositions.}, author = {Klajn, Rafal and Bishop, Kyle J. M. and Fialkowski, Marcin and Paszewski, Maciej and Campbell, Christopher J. and Gray, Timothy P. and Grzybowski, Bartosz A.}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {5822}, pages = {261--264}, publisher = {American Association for the Advancement of Science}, title = {{Plastic and moldable metals by self-assembly of sticky nanoparticle aggregates}}, doi = {10.1126/science.1139131}, volume = {316}, year = {2007}, } @article{904, abstract = {Background: Independently evolving lineages mostly accumulate different changes, which leads to their gradual divergence. However, parallel accumulation of identical changes is also common, especially in traits with only a small number of possible states. Results: We characterize parallelism in evolution of coding sequences in three four-species sets of genomes of mammals, Drosophila, and yeasts. Each such set contains two independent evolutionary paths, which we call paths I and II. An amino acid replacement which occurred along path I also occurs along path II with the probability 50-8211;80% of that expected under selective neutrality. Thus, the per site rate of parallel evolution of proteins is several times higher than their average rate of evolution, but still lower than the rate of evolution of neutral sequences. This deficit may be caused by changes in the fitness landscape, leading to a replacement being possible along path I but not along path II. However, constant, weak selection assumed by the nearly neutral model of evolution appears to be a more likely explanation. Then, the average coefficient of selection associated with an amino acid replacement, in the units of the effective population size, must exceed ∼0.4, and the fraction of effectively neutral replacements must be below ∼30%. At a majority of evolvable amino acid sites, only a relatively small number of different amino acids is permitted. Conclusion: High, but below-neutral, rates of parallel amino acid replacements suggest that a majority of amino acid replacements that occur in evolution are subject to weak, but non-trivial, selection, as predicted by Ohta's nearly-neutral theory.}, author = {Bazykin, Georgii A and Fyodor Kondrashov and Brudno, Michael and Poliakov, Alexander V and Dubchak, Inna L and Kondrashov, Alexey S}, journal = {Biology Direct}, publisher = {BioMed Central}, title = {{Extensive parallelism in protein evolution}}, doi = {10.1186/1745-6150-2-20}, volume = {2}, year = {2007}, } @article{9149, abstract = {The interaction of tidal currents with sea-floor topography results in the radiation of internal gravity waves into the ocean interior. These waves are called internal tides and their dissipation due to nonlinear wave breaking and concomitant three-dimensional turbulence could play an important role in the mixing of the abyssal ocean, and hence in controlling the large-scale ocean circulation. As part of on-going work aimed at providing a theory for the vertical distribution of wave breaking over sea-floor topography, in this paper we investigate the instability of internal tides in a very simple linear model that helps us to relate the formation of unstable regions to simple features in the sea-floor topography. For two-dimensional tides over one-dimensional topography we find that the formation of overturning instabilities is closely linked to the singularities in the topography shape and that it is possible to have stable waves at the sea floor and unstable waves in the ocean interior above. For three-dimensional tides over two-dimensional topography there is in addition an effect of geometric focusing of wave energy into localized regions of high wave amplitude, and we investigate this focusing effect in simple examples. Overall, we find that the distribution of unstable wave breaking regions can be highly non-uniform even for very simple idealized topography shapes.}, author = {Bühler, Oliver and Muller, Caroline J}, issn = {0022-1120}, journal = {Journal of Fluid Mechanics}, keywords = {mechanical engineering, mechanics of materials, condensed matter physics}, pages = {1--28}, publisher = {Cambridge University Press}, title = {{Instability and focusing of internal tides in the deep ocean}}, doi = {10.1017/s0022112007007410}, volume = {588}, year = {2007}, } @article{9487, abstract = {Cytosine DNA methylation is considered to be a stable epigenetic mark, but active demethylation has been observed in both plants and animals. In Arabidopsis thaliana, DNA glycosylases of the DEMETER (DME) family remove methylcytosines from DNA. Demethylation by DME is necessary for genomic imprinting, and demethylation by a related protein, REPRESSOR OF SILENCING1, prevents gene silencing in a transgenic background. However, the extent and function of demethylation by DEMETER-LIKE (DML) proteins in WT plants is not known. Using genome-tiling microarrays, we mapped DNA methylation in mutant and WT plants and identified 179 loci actively demethylated by DML enzymes. Mutations in DML genes lead to locus-specific DNA hypermethylation. Reintroducing WT DML genes restores most loci to the normal pattern of methylation, although at some loci, hypermethylated epialleles persist. Of loci demethylated by DML enzymes, >80% are near or overlap genes. Genic demethylation by DML enzymes primarily occurs at the 5′ and 3′ ends, a pattern opposite to the overall distribution of WT DNA methylation. Our results show that demethylation by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis genome to protect genes from potentially deleterious methylation.}, author = {Penterman, Jon and Zilberman, Daniel and Huh, Jin Hoe and Ballinger, Tracy and Henikoff, Steven and Fischer, Robert L.}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {16}, pages = {6752--6757}, publisher = {National Academy of Sciences}, title = {{DNA demethylation in the Arabidopsis genome}}, doi = {10.1073/pnas.0701861104}, volume = {104}, year = {2007}, } @misc{9504, author = {Zilberman, Daniel}, booktitle = {Nature Genetics}, issn = {1546-1718}, number = {4}, pages = {442--443}, publisher = {Nature Publishing Group}, title = {{The human promoter methylome}}, doi = {10.1038/ng0407-442}, volume = {39}, year = {2007}, } @article{9524, abstract = {Cytosine methylation is the most common covalent modification of DNA in eukaryotes. DNA methylation has an important role in many aspects of biology, including development and disease. Methylation can be detected using bisulfite conversion, methylation-sensitive restriction enzymes, methyl-binding proteins and anti-methylcytosine antibodies. Combining these techniques with DNA microarrays and high-throughput sequencing has made the mapping of DNA methylation feasible on a genome-wide scale. Here we discuss recent developments and future directions for identifying and mapping methylation, in an effort to help colleagues to identify the approaches that best serve their research interests.}, author = {Zilberman, Daniel and Henikoff, Steven}, issn = {1477-9129}, journal = {Development}, number = {22}, pages = {3959--3965}, publisher = {The Company of Biologists}, title = {{Genome-wide analysis of DNA methylation patterns}}, doi = {10.1242/dev.001131}, volume = {134}, year = {2007}, } @article{1035, abstract = {We explore the rich internal structure of Cs2 Feshbach molecules. Pure ultracold molecular samples are prepared in a CO2 -laser trap, and a multitude of weakly bound states is populated by elaborate magnetic-field ramping techniques. Our methods use different Feshbach resonances as input ports and various internal level crossings for controlled state transfer. We populate higher partial-wave states of up to eight units of rotational angular momentum (l -wave states). We investigate the molecular structure by measurements of the magnetic moments for various states. Avoided level crossings between different molecular states are characterized through the changes in magnetic moment and by a Landau-Zener tunneling method. Based on microwave spectroscopy, we present a precise measurement of the magnetic-field-dependent binding energy of the weakly bound s -wave state that is responsible for the large background scattering length of Cs. This state is of particular interest because of its quantum-halo character.}, author = {Mark, Michael and Ferlaino, Francesca and Knoop, Steven and Danzl, Johann G and Kraemer, Tobias and Chin, Cheng and Nägerl, Hanns and Grimm, Rudolf}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {4}, publisher = {American Physical Society}, title = {{Spectroscopy of ultracold trapped cesium Feshbach molecules}}, doi = {10.1103/PhysRevA.76.042514}, volume = {76}, year = {2007}, } @article{11884, abstract = {About 20% of the world's population uses the Web, and a large majority thereof uses Web search engines to find information. As a result, many Web researchers are devoting much effort to improving the speed and capability of search technology.}, author = {Henzinger, Monika H}, issn = {1095-9203}, journal = {Science}, number = {5837}, pages = {468--471}, publisher = {American Association for the Advancement of Science}, title = {{Search technologies for the internet}}, doi = {10.1126/science.1126557}, volume = {317}, year = {2007}, } @inproceedings{11924, abstract = {How much can smart combinatorial algorithms improve web search engines? To address this question we will describe three algorithms that have had a positive impact on web search engines: The PageRank algorithm, algorithms for finding near-duplicate web pages, and algorithms for index server loadbalancing.}, author = {Henzinger, Monika H}, booktitle = {18th Annual ACM-SIAM Symposium on Discrete Algorithms}, isbn = {9780898716245}, location = {New Orleans, LA, United States}, pages = {1022--1026}, publisher = {Society for Industrial & Applied Mathematics}, title = {{Combinatorial algorithms for web search engines: three success stories}}, year = {2007}, } @article{12201, abstract = {The development of plant lateral organs is interesting because, although many of the same genes seem to be involved in the early growth of primordia, completely different gene combinations are required for the complete development of organs such as leaves and stamens. Thus, the genes common to the development of most organs, which generally form and polarize the primordial ‘envelope’, must at some stage interact with those that ‘install’ the functional content of the organ – in the case of the stamen, the four microsporangia. Although distinct genetic pathways of organ initiation, polarity establishment and setting up the reproductive cell line can readily be recognized, they do not occur sequentially. Rather, they are activated early and run in parallel. There is evidence for continuing crosstalk between these pathways.}, author = {Feng, Xiaoqi and Dickinson, Hugh G.}, issn = {0168-9525}, journal = {Trends in Genetics}, keywords = {Genetics}, number = {10}, pages = {503--510}, publisher = {Elsevier BV}, title = {{Packaging the male germline in plants}}, doi = {10.1016/j.tig.2007.08.005}, volume = {23}, year = {2007}, } @article{128, abstract = {A 671 nm diode laser with a mode-hop-free tuning range of 40 GHz is described. This long tuning range is achieved by simultaneously ramping the external cavity length with the laser injection current. The laser output pointing remains fixed, independent of its frequency because of the cover slip cavity design. This system is simple, economical, robust, and easy to use for spectroscopy, as we demonstrate with lithium vapor and lithium atom beam experiments. }, author = {Carr, Adra and Serchest, Yancey and Waitukaitis, Scott R and Perreault, John and Lonij, Vincent and Cronin, Alexander}, journal = {Review of Scientific Instruments}, number = {10}, publisher = {American Institute of Physics}, title = {{Cover slip external cavity diode laser}}, doi = {10.1063/1.2801006}, volume = {78}, year = {2007}, } @article{1297, abstract = {In flies, the large tangential cells of the lobula plate represent an important processing center for visual navigation based on optic flow. Although the visual response properties of these cells have been well studied in blowflies, information on their synaptic organization is mostly lacking. Here we study the distribution of presynaptic release and postsynaptic inhibitory sites in the same set of cells in Drosophila melanogaster. By making use of transgenic tools and immunohistochemistry, our results suggest that HS and VS cells of Drosophila express γ-aminobutyric acid (GABA) receptors in their dendritic region within the lobula plate, thus being postsynaptic to inhibitory input there. At their axon terminals in the protocerebrum, both cell types express synaptobrevin, suggesting the presence of presynaptic specializations there. HS- and VS-cell terminals additionally show evidence for postsynaptic GABAergic input, superimposed on this synaptic polarity. Our findings are in line with the general circuit for visual motion detection and receptive field properties as postulated from electrophysiological and optical recordings in blowflies, suggesting a similar functional organization of lobula plate tangential cells in the two species.}, author = {Raghu, Shamprasad V and Maximilian Jösch and Borst, Alexander and Reiff, Dierk F}, journal = {Journal of Comparative Neurology}, number = {4}, pages = {598 -- 610}, publisher = {Wiley-Blackwell}, title = {{Synaptic organization of lobula plate tangential cells in Drosophila: γ-aminobutyric acid receptors and chemical release sites}}, doi = {10.1002/cne.21319}, volume = {502}, year = {2007}, } @article{3411, abstract = {Mechanical single-molecule techniques offer exciting possibilities to investigate protein folding and stability in native environments at submolecular resolution. By applying a free-energy reconstruction procedure developed by Hummer and Szabo, which is based on a statistical theorem introduced by Jarzynski, we determined the unfolding free energy of the membrane proteins bacteriorhodopsin (BR), halorhodopsin, and the sodium-proton antiporter NhaA. The calculated energies ranged from 290.5kcal/mol for BR to 485.5kcal/mol for NhaA. For the remarkably stable BR, the equilibrium unfolding free energy was independent of pulling rate and temperature ranging between 18 and 42°C. Our experiments also revealed heterogeneous energetic properties in individual transmembrane helices. In halorhodopsin, the stabilization of a short helical segment yielded a characteristic signature in the energy profile. In NhaA, a pronounced peak was observed at a functionally important site in the protein. Since a large variety of single- and multispan membrane proteins can be tackled in mechanical unfolding experiments, our approach provides a basis for systematically elucidating energetic properties of membrane proteins with the resolution of individual secondary-structure elements.}, author = {Preiner, Johannes and Harald Janovjak and Rankl, Christian and Knaus, Helene and Cisneros, David A and Kedrov, Alexej and Kienberger, Ferry and Mueller, Daniel J and Hinterdorfer, Peter}, journal = {Biophysical Journal}, number = {3}, pages = {930 -- 937}, publisher = {Biophysical Society}, title = {{Free energy of membrane protein unfolding derived from single-molecule force measurements}}, doi = {10.1529/biophysj.106.096982}, volume = {93}, year = {2007}, } @misc{3412, abstract = {Molecular interactions are the basic language of biological processes. They establish the forces interacting between the building blocks of proteins and other macromolecules, thus determining their functional roles. Because molecular interactions trigger virtually every biological process, approaches to decipher their language are needed. Single-molecule force spectroscopy (SMFS) has been used to detect and characterize different types of molecular interactions that occur between and within native membrane proteins. The first experiments detected and localized molecular interactions that stabilized membrane proteins, including how these interactions were established during folding of α-helical secondary structure elements into the native protein and how they changed with oligomerization, temperature, and mutations. SMFS also enables investigators to detect and locate molecular interactions established during ligand and inhibitor binding. These exciting applications provide opportunities for studying the molecular forces of life. Further developments will elucidate the origins of molecular interactions encoded in their lifetimes, interaction ranges, interplay, and dynamics characteristic of biological systems.}, author = {Kedrov, Alexej and Harald Janovjak and Sapra, Tanuj K and Mueller, Daniel J}, booktitle = {Annual Review of Biophysics}, pages = {233 -- 260}, publisher = {Annual Reviews}, title = {{Deciphering molecular interactions of native membrane proteins by single-molecule force spectroscopy}}, doi = {10.1146/annurev.biophys.36.040306.132640}, volume = {36}, year = {2007}, } @article{3427, abstract = {We present a general theoretical framework to discuss mechanisms of morphogen transport and gradient formation in a cell layer. Trafficking events on the cellular scale lead to transport on larger scales. We discuss in particular the case of transcytosis where morphogens undergo repeated rounds of internalization into cells and recycling. Based on a description on the cellular scale, we derive effective nonlinear transport equations in one and two dimensions which are valid on larger scales. We derive analytic expressions for the concentration dependence of the effective diffusion coefficient and the effective degradation rate. We discuss the effects of a directional bias on morphogen transport and those of the coupling of the morphogen and receptor kinetics. Furthermore, we discuss general properties of cellular transport processes such as the robustness of gradients and relate our results to recent experiments on the morphogen Decapentaplegic (Dpp) that acts in the wing disk of the fruit fly Drosophila. © 2007 The American Physical Society}, author = {Bollenbach, Mark Tobias and Kruse, Karsten and Pantazis, Periklis and Gonzalez Gaitan, Marcos and Julicher, Frank}, journal = {Physical Review E Statistical Nonlinear and Soft Matter Physics}, number = {1}, publisher = {American Institute of Physics}, title = {{Morphogen transport in epithelia}}, doi = {10.1103/PhysRevE.75.011901}, volume = {75}, year = {2007}, } @inbook{3432, abstract = {Evolution has left its signature on the molecules and morphology of living organisms. Ancestral reconstruction offers an excellent tool for understanding the process of evolution using comparative information. Methods for ancestral reconstruction have generally focused on reconstructing the ancestral states at the internal nodes of a phylogeny. Often, we are not interested in particular nodes of the phylogeny but the whole history of a character. This chapter focuses on a Bayesian method for estimating these histories, or mutational paths, on phylogenies. Mutational path methods differ most notably from other approaches in their ability to estimate not only the ancestral states at the internal nodes of a phylogeny, but also the order and timing of mutational changes across the phylogeny. The chapter provides a concise introduction to the statistical tools needed for sampling mutational paths on a phylogeny.}, author = {Jonathan Bollback and Gardner, Paul P and Nielsen, Rasmus}, booktitle = {Ancestral Sequence Reconstruction}, editor = {Liberles, David A}, pages = {69 -- 79}, publisher = {Oxford University Press}, title = {{Estimating the history of mutations on a phylogeny}}, doi = {10.1093/acprof:oso/9780199299188.003.0006}, year = {2007}, }