@article{13431, abstract = {Hydrogel stamps can microstructure solid surfaces, i.e., modify the surface topology of metals, glasses, and crystals. It is demonstrated that stamps soaked in an appropriate etchant can remove material with micrometer-scale precision. The Figure shows an array of concentric circles etched in glass using the immersion wet stamping process described (scale bar: 500 μm).}, author = {Smoukov, S. K. and Bishop, K. J. M. and Klajn, Rafal and Campbell, C. J. and Grzybowski, B. A.}, issn = {1521-4095}, journal = {Advanced Materials}, keywords = {Mechanical Engineering, Mechanics of Materials, General Materials Science}, number = {11}, pages = {1361--1365}, publisher = {Wiley}, title = {{Cutting into solids with micropatterned gels}}, doi = {10.1002/adma.200402086}, volume = {17}, year = {2005}, } @article{13432, abstract = {A new experimental technique is described that uses reaction−diffusion phenomena as a means of one-step microfabrication of complex, multilevel surface reliefs. Thin films of dry gelatin doped with potassium hexacyanoferrate are chemically micropatterned with a solution of silver nitrate delivered from an agarose stamp. Precipitation reaction between the two salts causes the surface to deform. The mechanism of surface deformation is shown to involve a sequence of reactions, diffusion, and gel swelling/contraction. This mechanism is established experimentally and provides a basis of a theoretical lattice-gas model that allows prediction surface topographies emerging from arbitrary geometries of the stamped features. The usefulness of the technique is demonstrated by using it to rapidly prepare two types of mold for passive microfluidic mixers.}, author = {Campbell, Christopher J. and Klajn, Rafal and Fialkowski, Marcin and Grzybowski, Bartosz A.}, issn = {1520-5827}, journal = {Langmuir}, keywords = {Electrochemistry, Spectroscopy, Surfaces and Interfaces, Condensed Matter Physics, General Materials Science}, number = {1}, pages = {418--423}, publisher = {American Chemical Society}, title = {{One-step multilevel microfabrication by reaction−diffusion}}, doi = {10.1021/la0487747}, volume = {21}, year = {2005}, } @article{13433, abstract = {Self-assembled monolayers (SAMs) of alkane thiols on gold and other metals are versatile constructs with which to study interfacial phenomena and reactions at surfaces. Surface properties of SAMs - e.g., wettability, stability in diverse environments, propensity to interact with or to resist adsorption of macromolecules -- depend on and can be controlled flexibly by the properties of the functional (head) groups in the w position of the alkyl chain. SAMs provide a basis for many important scientific and technological applications, ranging from micropatterning methods, through sensing, to biological recognition. Despite their importance, the literature on SAMs and the synthesis of molecules that constitute them remains scattered and often conflicting. The purpose of this Review is (i) to summarize the applications and physical properties of SAMs and (ii) to systematize the strategies of synthesis of ω-functionalized alkane thiols. Generic retrosynthetic scheme is developed that allows efficient synthetic planning. Issues related to the selection of appropriate protecting groups and the ways of introduction of the thiol functionality are discussed in detail, and illustrated with examples of syntheses of several complex alkane thiols.}, author = {Witt, Dariusz and Klajn, Rafal and Barski, Piotr and Grzybowski, Bartosz}, issn = {1875-5348}, journal = {Current Organic Chemistry}, keywords = {Organic Chemistry}, number = {18}, pages = {1763--1797}, publisher = {Bentham Science}, title = {{Applications, properties and synthesis of w-functionalized n-alkanethiols and disulfides - the building blocks of self-assembled monolayers}}, doi = {10.2174/1385272043369421}, volume = {8}, year = {2005}, } @article{9491, abstract = {Cytosine DNA methylation in vertebrates is widespread, but methylation in plants is found almost exclusively at transposable elements and repetitive DNA [1]. Within regions of methylation, methylcytosines are typically found in CG, CNG, and asymmetric contexts. CG sites are maintained by a plant homolog of mammalian Dnmt1 acting on hemi-methylated DNA after replication. Methylation of CNG and asymmetric sites appears to be maintained at each cell cycle by other mechanisms. We report a new type of DNA methylation in Arabidopsis, dense CG methylation clusters found at scattered sites throughout the genome. These clusters lack non-CG methylation and are preferentially found in genes, although they are relatively deficient toward the 5′ end. CG methylation clusters are present in lines derived from different accessions and in mutants that eliminate de novo methylation, indicating that CG methylation clusters are stably maintained at specific sites. Because 5-methylcytosine is mutagenic, the appearance of CG methylation clusters over evolutionary time predicts a genome-wide deficiency of CG dinucleotides and an excess of C(A/T)G trinucleotides within transcribed regions. This is exactly what we find, implying that CG methylation clusters have contributed profoundly to plant gene evolution. We suggest that CG methylation clusters silence cryptic promoters that arise sporadically within transcription units.}, author = {Tran, Robert K. and Henikoff, Jorja G. and Zilberman, Daniel and Ditt, Renata F. and Jacobsen, Steven E. and Henikoff, Steven}, issn = {1879-0445}, journal = {Current Biology}, number = {2}, pages = {154--159}, publisher = {Elsevier}, title = {{DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes}}, doi = {10.1016/j.cub.2005.01.008}, volume = {15}, year = {2005}, } @article{9514, abstract = {Background: DNA methylation occurs at preferred sites in eukaryotes. In Arabidopsis, DNA cytosine methylation is maintained by three subfamilies of methyltransferases with distinct substrate specificities and different modes of action. Targeting of cytosine methylation at selected loci has been found to sometimes involve histone H3 methylation and small interfering (si)RNAs. However, the relationship between different cytosine methylation pathways and their preferred targets is not known. Results: We used a microarray-based profiling method to explore the involvement of Arabidopsis CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related siRNA silencing component (AGO4) in methylating target loci. We found that KYP targets are also CMT3 targets, suggesting that histone methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar proximal distributions that correspond to the overall distribution of transposable elements of all types, whereas DRM targets are distributed more distally along the chromosome. We find an inverse relationship between element size and loss of methylation in ago4 and drm mutants. Conclusion: We conclude that the targets of both DNA methylation and histone H3K9 methylation pathways are transposable elements genome-wide, irrespective of element type and position. Our findings also suggest that RNA-directed DNA methylation is required to silence isolated elements that may be too small to be maintained in a silent state by a chromatin-based mechanism alone. Thus, parallel pathways would be needed to maintain silencing of transposable elements.}, author = {Tran, Robert K. and Zilberman, Daniel and de Bustos, Cecilia and Ditt, Renata F. and Henikoff, Jorja G. and Lindroth, Anders M. and Delrow, Jeffrey and Boyle, Tom and Kwong, Samson and Bryson, Terri D. and Jacobsen, Steven E. and Henikoff, Steven}, issn = {1465-6906}, journal = {Genome Biology}, number = {11}, publisher = {Springer Nature}, title = {{Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis}}, doi = {10.1186/gb-2005-6-11-r90}, volume = {6}, year = {2005}, } @article{9529, abstract = {Eukaryotic organisms have the remarkable ability to inherit states of gene activity without altering the underlying DNA sequence. This epigenetic inheritance can persist over thousands of years, providing an alternative to genetic mutations as a substrate for natural selection. Epigenetic inheritance might be propagated by differences in DNA methylation, post-translational histone modifications, and deposition of histone variants. Mounting evidence also indicates that small interfering RNA (siRNA)-mediated mechanisms play central roles in setting up and maintaining states of gene activity. Much of the epigenetic machinery of many organisms, including Arabidopsis, appears to be directed at silencing viruses and transposable elements, with epigenetic regulation of endogenous genes being mostly derived from such processes.}, author = {Zilberman, Daniel and Henikoff, Steven}, issn = {0959-437X}, journal = {Current Opinion in Genetics and Development}, number = {5}, pages = {557--562}, publisher = {Elsevier}, title = {{Epigenetic inheritance in Arabidopsis: Selective silence}}, doi = {10.1016/j.gde.2005.07.002}, volume = {15}, year = {2005}, } @article{11904, abstract = {Many daily activities present information in the form of a stream of text, and often people can benefit from additional information on the topic discussed. TV broadcast news can be treated as one such stream of text; in this paper we discuss finding news articles on the web that are relevant to news currently being broadcast. We evaluated a variety of algorithms for this problem, looking at the impact of inverse document frequency, stemming, compounds, history, and query length on the relevance and coverage of news articles returned in real time during a broadcast. We also evaluated several postprocessing techniques for improving the precision, including reranking using additional terms, reranking by document similarity, and filtering on document similarity. For the best algorithm, 84–91% of the articles found were relevant, with at least 64% of the articles being on the exact topic of the broadcast. In addition, a relevant article was found for at least 70% of the topics.}, author = {Henzinger, Monika H and Chang, Bay-Wei and Milch, Brian and Brin, Sergey}, issn = {1573-1413}, journal = {World Wide Web}, number = {2}, pages = {101--126}, publisher = {Springer Nature}, title = {{Query-free news search}}, doi = {10.1007/s11280-004-4870-6}, volume = {8}, year = {2005}, } @article{12657, abstract = {An enhanced temperature-index glacier melt model, incorporating incoming shortwave radiation and albedo, is presented. The model is an attempt to combine the high temporal resolution and accuracy of physically based melt models with the lower data requirements and computational simplicity of empirical melt models, represented by the ‘degree-day’ method and its variants. The model is run with both measured and modelled radiation data, to test its applicability to glaciers with differing data availability. Five automatic weather stations were established on Haut Glacier d’Arolla, Switzerland, between May and September 2001. Reference surface melt rates were calculated using a physically based energy-balance melt model. The performance of the enhanced temperature-index model was tested at each of the four validation stations by comparing predicted hourly melt rates with reference melt rates. Predictions made with three other temperature-index models were evaluated in the same way for comparison. The enhanced temperature-index model offers significant improvements over the other temperature-index models, and accounts for 90–95% of the variation in the reference melt rate. The improvement is lower, but still significant, when the model is forced by modelled shortwave radiation data, thus offering a better alternative to existing models that require only temperature data input.}, author = {Pellicciotti, Francesca and Brock, Ben and Strasser, Ulrich and Burlando, Paolo and Funk, Martin and Corripio, Javier}, issn = {1727-5652}, journal = {Journal of Glaciology}, number = {175}, pages = {573--587}, publisher = {Cambridge University Press}, title = {{An enhanced temperature-index glacier melt model including the shortwave radiation balance: Development and testing for Haut Glacier d’Arolla, Switzerland}}, doi = {10.3189/172756505781829124}, volume = {51}, year = {2005}, } @article{1298, abstract = {Genetically encoded fluorescent probes of neural activity represent new promising tools for systems neuroscience. Here, we present a comparative in vivo analysis of 10 different genetically encoded calcium indicators, as well as the pH-sensitive synapto-pHluorin. We analyzed their fluorescence changes in presynaptic boutons of the Drosophila larval neuromuscular junction. Robust neural activity did not result in any or noteworthy fluorescence changes when Flash-Pericam, Camgaroo-1, and Camgaroo-2 were expressed. However, calculated on the raw data, fractional fluorescence changes up to 18% were reported by synapto-pHluorin, Yellow Cameleon 2.0, 2.3, and 3.3, Inverse-Pericam, GCaMP1.3, GCaMP1.6, and the troponin C-based calcium sensor TN-L15. The response characteristics of all of these indicators differed considerably from each other, with GCaMP1.6 reporting high rates of neural activity with the largest and fastest fluorescence changes. However, GCaMP1.6 suffered from photobleaching, whereas the fluorescence signals of the double-chromophore indicators were in general smaller but more photostable and reproducible, with TN-L15 showing the fastest rise of the signals at lower activity rates. We show for GCaMP1.3 and YC3.3 that an expanded range of neural activity evoked fairly linear fluorescence changes and a corresponding linear increase in the signal-to-noise ratio (SNR). The expression level of the indicator biased the signal kinetics and SNR, whereas the signal amplitude was independent. The presented data will be useful for in vivo experiments with respect to the selection of an appropriate indicator, as well as for the correct interpretation of the optical signals.}, author = {Reiff, Dierk F and Ihring, Alexandra and Guerrero, Giovanna and Isacoff, Ehud Y and Maximilian Jösch and Nakai, Junichi and Borst, Alexander}, journal = {Journal of Neuroscience}, number = {19}, pages = {4766 -- 4778}, publisher = {Society for Neuroscience}, title = {{In vivo performance of genetically encoded indicators of neural activity in flies}}, doi = {10.1523/JNEUROSCI.4900-04.2005}, volume = {25}, year = {2005}, } @article{3416, abstract = {In the last decade atomic force microscopy has been used to measure the mechanical stability of single proteins. These force spectroscopy experiments have shown that many water-soluble and membrane proteins unfold via one or more intermediates. Recently, Li and co-workers found a linear correlation between the unfolding force of the native state and the intermediate in fibronectin, which they suggested indicated the presence of a molecular memory or multiple unfolding pathways (1). Here, we apply two independent methods in combination with Monte Carlo simulations to analyze the unfolding of α-helices E and D of bacteriorhodopsin (BR). We show that correlation analysis of unfolding forces is very sensitive to errors in force calibration of the instrument. In contrast, a comparison of relative forces provides a robust measure for the stability of unfolding intermediates. The proposed approach detects three energetically different states of α-helices E and D in trimeric BR. These states are not observed for monomeric BR and indicate that substantial information is hidden in forced unfolding experiments of single proteins.}, author = {Harald Janovjak and Sapra, Tanuj K and Mueller, Daniel J}, journal = {Biophysical Journal}, number = {5}, pages = {37 -- 39}, publisher = {Biophysical Society}, title = {{Complex stability of single proteins explored by forced unfolding experiments}}, doi = {10.1529/biophysj.105.059774}, volume = {88}, year = {2005}, } @article{3417, abstract = {Recently, direct measurements of forces stabilizing single proteins or individual receptor–ligand bonds became possible with ultra-sensitive force probe methods like the atomic force microscope (AFM). In force spectroscopy experiments using AFM, a single molecule or receptor–ligand pair is tethered between the tip of a micromachined cantilever and a supporting surface. While the molecule is stretched, forces are measured by the deflection of the cantilever and plotted against extension, yielding a force spectrum characteristic for each biomolecular system. In order to obtain statistically relevant results, several hundred to thousand single-molecule experiments have to be performed, each resulting in a unique force spectrum. We developed software and algorithms to analyse large numbers of force spectra. Our algorithms include the fitting polymer extension models to force peaks as well as the automatic alignment of spectra. The aligned spectra allowed recognition of patterns of peaks across different spectra. We demonstrate the capabilities of our software by analysing force spectra that were recorded by unfolding single transmembrane proteins such as bacteriorhodopsin and NhaA. Different unfolding pathways were detected by classifying peak patterns. Deviant spectra, e.g. those with no attachment or erratic peaks, can be easily identified. The software is based on the programming language C++, the GNU Scientific Library (GSL), the software WaveMetrics IGOR Pro and available open-source at http://bioinformatics.org/fskit/.}, author = {Kuhn, Michael and Harald Janovjak and Hubain, Maurice and Mueller, Daniel J}, journal = {Journal of Microscopy}, number = {2}, pages = {125 -- 132}, publisher = {Wiley-Blackwell}, title = {{Automated alignment and pattern recognition of single-molecule force spectroscopy data}}, doi = {10.1111/j.1365-2818.2005.01478.x}, volume = {218}, year = {2005}, } @article{3418, abstract = {Atomic force microscopy (AFM) allows the critical forces that unfold single proteins and rupture individual receptor–ligand bonds to be measured. To derive the shape of the energy landscape, the dynamic strength of the system is probed at different force loading rates. This is usually achieved by varying the pulling speed between a few nm/s and a few mgrm/s, although for a more complete investigation of the kinetic properties higher speeds are desirable. Above 10 mgrm/s, the hydrodynamic drag force acting on the AFM cantilever reaches the same order of magnitude as the molecular forces. This has limited the maximum pulling speed in AFM single-molecule force spectroscopy experiments. Here, we present an approach for considering these hydrodynamic effects, thereby allowing a correct evaluation of AFM force measurements recorded over an extended range of pulling speeds (and thus loading rates). To support and illustrate our theoretical considerations, we experimentally evaluated the mechanical unfolding of a multi-domain protein recorded at 30 mgrm/s pulling speed.}, author = {Harald Janovjak and Struckmeier, Jens and Mueller, Daniel J}, journal = {European Biophysics Journal}, number = {1}, pages = {91 -- 96}, publisher = {Springer}, title = {{Hydrodynamic effects in fast AFM single molecule force measurements}}, doi = {10.1007/s00249-004-0430-3}, volume = {34}, year = {2005}, } @article{3426, abstract = {We discuss the formation of graded morphogen profiles in a cell layer by nonlinear transport phenomena, important for patterning developing organisms. We focus on a process termed transcytosis, where morphogen transport results from the binding of ligands to receptors on the cell surface, incorporation into the cell, and subsequent externalization. Starting from a microscopic model, we derive effective transport equations. We show that, in contrast to morphogen transport by extracellular diffusion, transcytosis leads to robust ligand profiles which are insensitive to the rate of ligand production.}, author = {Bollenbach, Mark Tobias and Kruse, Karsten and Pantazis, Periklis and González Gaitán, Marcos and Jülicher, Frank}, journal = {Physical Review Letters}, number = {1}, publisher = {American Physical Society}, title = {{Robust formation of morphogen gradients}}, doi = {10.1103/PhysRevLett.94.018103}, volume = {94}, year = {2005}, } @inbook{3433, author = {Jonathan Bollback}, booktitle = {Statistical methods in Molecular Evolution}, editor = {Nielsen, Rasmus}, pages = {439 -- 462}, publisher = {Springer}, title = {{Posterior mapping and posterior predictive distributions}}, doi = {10.1007/0-387-27733-1}, year = {2005}, } @article{3443, abstract = {In the hippocampal CA1 area, a relatively homogenous population of pyramidal cells is accompanied by a diversity of GABAergic interneurons. Previously, we found that parvalbumin-expressing basket, axo-axonic, bistratified, and oriens-lacunosum moleculare cells, innervating different domains of pyramidal cells, have distinct firing patterns during network oscillations in vivo. A second family of interneurons, expressing cholecystokinin but not parvalbumin, is known to target the same domains of pyramidal cells as do the parvalbumin cells. To test the temporal activity of these independent and parallel GABAergic inputs, we recorded the precise spike timing of identified cholecystokinin interneurons during hippocampal network oscillations in anesthetized rats and determined their molecular expression profiles and synaptic targets. The cells were cannabinoid receptor type 1 immunopositive. Contrary to the stereotyped firing of parvalbumin interneurons, cholecystokinin-expressing basket and dendrite-innervating cells discharge, on average, with 1.7 ± 2.0 Hz during high-frequency ripple oscillations in an episode-dependent manner. During theta oscillations, cholecystokinin- expressing interneurons fire with 8.8 ± 3.3 Hz at a characteristic time on the ascending phase of theta waves (155 ± 81°), when place cells start firing in freely moving animals. The firing patterns of some interneurons recorded in drug-free behaving rats were similar to cholecystokinin cells in anesthetized animals. Our results demonstrate that cholecystokinin- and parvalbumin-expressing interneurons make different contributions to network oscillations and play distinct roles in different brain states. We suggest that the specific spike timing of cholecystokinin interneurons and their sensitivity to endocannabinoids might contribute to differentiate subgroups of pyramidal cells forming neuronal assemblies, whereas parvalbumin interneurons contribute to synchronizing the entire network. Copyright © 2005 Society for Neuroscience.}, author = {Klausberger,Thomas and Marton,Laszlo F and Joseph O'Neill and Huck, Jojanneke H and Dalezios, Yannis and Fuentealba,Pablo and Suen, Wai Yee and Papp, Edit Cs and Kaneko, Takeshi and Watanabe, Masahiko and Jozsef Csicsvari and Somogyi, Péter}, journal = {Journal of Neuroscience}, number = {42}, pages = {9782 -- 9793}, publisher = {Society for Neuroscience}, title = {{Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations}}, doi = {10.1523/JNEUROSCI.3269-05.2005}, volume = {25}, year = {2005}, } @misc{3509, abstract = {Methods, apparatus and computer program products can generate light weight but highly realistic and accurate colored models of three-dimensional colored objects. The colored model may be generated from a second plurality of points that define a coarse digital representation of the surface and at least one texture map containing information derived from a first plurality of colored points that define a fine digital representation of the surface. This derivation is achieved by mapping points within the texture map to the fine digital representation of the three-dimensional surface. Colored scan data may be used to construct the fine digital representation as a triangulated surface (i.e., triangulation) using a wrapping operation.}, author = {Williams, Steven and Edelsbrunner, Herbert and Fu, Ping}, title = {{Methods, apparatus and computer program products for modeling three-dimensional colored objects}}, year = {2005}, } @inproceedings{3557, abstract = {A challenging problem in computer-aided geometric design is the decomposition of a surface into four-sided regions that are then represented by NURBS patches. There are various approaches published in the literature and implemented as commercially available software, but all fall short in either automation or quality of the result. At Raindrop Geomagic, we have recently taken a fresh approach based on concepts from Morse theory. This by itself is not a new idea, but we have some novel ingredients that make this work, one being a rational notion of hierarchy that guides the construction of a simplified decomposition sensitive to only the major critical points.}, author = {Herbert Edelsbrunner}, pages = {9 -- 11}, publisher = {ACM}, title = {{Surface tiling with differential topology}}, doi = {http://dx.doi.org/10.2312/SGP/SGP05/009-011}, year = {2005}, } @inproceedings{3558, abstract = {The tandem algorithm combines the marching cube algorithm for surface extraction and the edge contraction algorithm for surface simplification in lock-step to avoid the costly intermediate step of storing the entire extracted surface triangulation. Beyond this basic strategy, we introduce refinements to prevent artifacts in the resulting triangulation, first, by carefully monitoring the amount of simplification during the process and, second, by driving the simplification toward a compromise between shape approximation and mesh quality. We have implemented the algorithm and used extensive computational experiments to document the effects of various design options and to further fine-tune the algorithm.}, author = {Attali, Dominique and Cohen-Steiner, David and Herbert Edelsbrunner}, pages = {139 -- 148}, publisher = {ACM}, title = {{Extraction and simplification of iso-surfaces in tandem}}, year = {2005}, } @inbook{3576, abstract = {ears of research in biology have established that all cellular functions are deeply connected to the shape and dynamics of their molec- ular actors. As a response, structural molecular biology has emerged as a new line of experimental research focused on revealing the structure of biomolecules. The analysis of these structures has led to the development of computational biology, whose aim is to predict from molecular simulation properties inaccessible to experimental probes. Here we focus on the representation of biomolecules used in these sim- ulations, and in particular on the hard sphere models. We review how the geometry of the union of such spheres is used to model their interactions with their environment, and how it has been included in simulations of molecular dynamics. In parallel, we review our own developments in mathematics and com- puter science on understanding the geometry of unions of balls, and their applications in molecular simulation.}, author = {Herbert Edelsbrunner and Koehl, Patrice}, booktitle = {Combinatorial and Computational Geometry}, pages = {243 -- 275}, publisher = {Cambridge University Press}, title = {{The geometry of biomolecular solvation}}, volume = {52}, year = {2005}, } @inbook{3588, author = {Castanon Ortega, Irinka and Heisenberg, Carl-Philipp J}, booktitle = {Cell Migration in Development and Disease}, editor = {Wedlich, Doris}, pages = {71 -- 105}, publisher = {Wiley-VCH}, title = {{Cell migration during zebrafish gastrulation}}, doi = {10.1002/3527604669}, year = {2005}, }