@article{1842, abstract = {We prove polynomial upper bounds of geometric Ramsey numbers of pathwidth-2 outerplanar triangulations in both convex and general cases. We also prove that the geometric Ramsey numbers of the ladder graph on 2n vertices are bounded by O(n3) and O(n10), in the convex and general case, respectively. We then apply similar methods to prove an (Formula presented.) upper bound on the Ramsey number of a path with n ordered vertices.}, author = {Cibulka, Josef and Gao, Pu and Krcál, Marek and Valla, Tomáš and Valtr, Pavel}, journal = {Discrete & Computational Geometry}, number = {1}, pages = {64 -- 79}, publisher = {Springer}, title = {{On the geometric ramsey number of outerplanar graphs}}, doi = {10.1007/s00454-014-9646-x}, volume = {53}, year = {2014}, } @article{18423, abstract = {We present a method for supervised learning of shape descriptors for shape retrieval applications. Many content-based shape retrieval approaches follow the bag-of-features (BoF) paradigm commonly used in text and image retrieval by first computing local shape descriptors, and then representing them in a ‘geometric dictionary’ using vector quantization. A major drawback of such approaches is that the dictionary is constructed in an unsupervised manner using clustering, unaware of the last stage of the process (pooling of the local descriptors into a BoF, and comparison of the latter using some metric). In this paper, we replace the clustering with dictionary learning, where every atom acts as a feature, followed by sparse coding and pooling to get the final BoF descriptor. Both the dictionary and the sparse codes can be learned in the supervised regime via bi-level optimization using a task-specific objective that promotes invariance desired in the specific application. We show significant performance improvement on several standard shape retrieval benchmarks.}, author = {Litman, Roee and Bronstein, Alexander and Bronstein, Michael and Castellani, Umberto}, issn = {1467-8659}, journal = {Computer Graphics Forum}, number = {5}, pages = {127--136}, publisher = {Wiley}, title = {{Supervised learning of bag‐of‐features shape descriptors using sparse coding}}, doi = {10.1111/cgf.12438}, volume = {33}, year = {2014}, } @article{1844, abstract = {Local protein interactions ("molecular context" effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations.}, author = {Risso, Valeria and Manssour Triedo, Fadia and Delgado Delgado, Asuncion and Arco, Rocio and Barroso Deljesús, Alicia and Inglés Prieto, Álvaro and Godoy Ruiz, Raquel and Gavira, Josè and Gaucher, Eric and Ibarra Molero, Beatriz and Sánchez Ruiz, Jose}, journal = {Molecular Biology and Evolution}, number = {2}, pages = {440 -- 455}, publisher = {Oxford University Press}, title = {{Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history}}, doi = {10.1093/molbev/msu312}, volume = {32}, year = {2014}, } @article{1852, abstract = {To control morphogenesis, molecular regulatory networks have to interfere with the mechanical properties of the individual cells of developing organs and tissues, but how this is achieved is not well known. We study this issue here in the shoot meristem of higher plants, a group of undifferentiated cells where complex changes in growth rates and directions lead to the continuous formation of new organs [1, 2]. Here, we show that the plant hormone auxin plays an important role in this process via a dual, local effect on the extracellular matrix, the cell wall, which determines cell shape. Our study reveals that auxin not only causes a limited reduction in wall stiffness but also directly interferes with wall anisotropy via the regulation of cortical microtubule dynamics. We further show that to induce growth isotropy and organ outgrowth, auxin somehow interferes with the cortical microtubule-ordering activity of a network of proteins, including AUXIN BINDING PROTEIN 1 and KATANIN 1. Numerical simulations further indicate that the induced isotropy is sufficient to amplify the effects of the relatively minor changes in wall stiffness to promote organogenesis and the establishment of new growth axes in a robust manner.}, author = {Sassi, Massimiliano and Ali, Olivier and Boudon, Frédéric and Cloarec, Gladys and Abad, Ursula and Cellier, Coralie and Chen, Xu and Gilles, Benjamin and Milani, Pascale and Friml, Jirí and Vernoux, Teva and Godin, Christophe and Hamant, Olivier and Traas, Jan}, journal = {Current Biology}, number = {19}, pages = {2335 -- 2342}, publisher = {Cell Press}, title = {{An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis}}, doi = {10.1016/j.cub.2014.08.036}, volume = {24}, year = {2014}, } @inproceedings{1853, abstract = {Wireless sensor networks (WSNs) composed of low-power, low-cost sensor nodes are expected to form the backbone of future intelligent networks for a broad range of civil, industrial and military applications. These sensor nodes are often deployed through random spreading, and function in dynamic environments. Many applications of WSNs such as pollution tracking, forest fire detection, and military surveillance require knowledge of the location of constituent nodes. But the use of technologies such as GPS on all nodes is prohibitive due to power and cost constraints. So, the sensor nodes need to autonomously determine their locations. Most localization techniques use anchor nodes with known locations to determine the position of remaining nodes. Localization techniques have two conflicting requirements. On one hand, an ideal localization technique should be computationally simple and on the other hand, it must be resistant to attacks that compromise anchor nodes. In this paper, we propose a computationally light-weight game theoretic secure localization technique and demonstrate its effectiveness in comparison to existing techniques.}, author = {Jha, Susmit and Tripakis, Stavros and Seshia, Sanjit and Chatterjee, Krishnendu}, location = {Cambridge, USA}, pages = {85 -- 90}, publisher = {IEEE}, title = {{Game theoretic secure localization in wireless sensor networks}}, doi = {10.1109/IOT.2014.7030120}, year = {2014}, } @article{1854, abstract = {In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching. In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching.}, author = {Guerrero, Paul and Auzinger, Thomas and Wimmer, Michael and Jeschke, Stefan}, journal = {Computer Graphics Forum}, number = {1}, pages = {239 -- 252}, publisher = {Wiley}, title = {{Partial shape matching using transformation parameter similarity}}, doi = {10.1111/cgf.12509}, volume = {34}, year = {2014}, } @article{1862, abstract = {The prominent and evolutionarily ancient role of the plant hormone auxin is the regulation of cell expansion. Cell expansion requires ordered arrangement of the cytoskeleton but molecular mechanisms underlying its regulation by signalling molecules including auxin are unknown. Here we show in the model plant Arabidopsis thaliana that in elongating cells exogenous application of auxin or redistribution of endogenous auxin induces very rapid microtubule re-orientation from transverse to longitudinal, coherent with the inhibition of cell expansion. This fast auxin effect requires auxin binding protein 1 (ABP1) and involves a contribution of downstream signalling components such as ROP6 GTPase, ROP-interactive protein RIC1 and the microtubule-severing protein katanin. These components are required for rapid auxin-and ABP1-mediated re-orientation of microtubules to regulate cell elongation in roots and dark-grown hypocotyls as well as asymmetric growth during gravitropic responses.}, author = {Chen, Xu and Grandont, Laurie and Li, Hongjiang and Hauschild, Robert and Paque, Sébastien and Abuzeineh, Anas and Rakusova, Hana and Benková, Eva and Perrot Rechenmann, Catherine and Friml, Jirí}, issn = {1476-4687}, journal = {Nature}, number = {729}, pages = {90 -- 93}, publisher = {Nature Publishing Group}, title = {{Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules}}, doi = {10.1038/nature13889}, volume = {516}, year = {2014}, } @inproceedings{1869, abstract = {Boolean controllers for systems with complex datapaths are often very difficult to implement correctly, in particular when concurrency is involved. Yet, in many instances it is easy to formally specify correctness. For example, the specification for the controller of a pipelined processor only has to state that the pipelined processor gives the same results as a non-pipelined reference design. This makes such controllers a good target for automated synthesis. However, an efficient abstraction for the complex datapath elements is needed, as a bit-precise description is often infeasible. We present Suraq, the first controller synthesis tool which uses uninterpreted functions for the abstraction. Quantified firstorder formulas (with specific quantifier structure) serve as the specification language from which Suraq synthesizes Boolean controllers. Suraq transforms the specification into an unsatisfiable SMT formula, and uses Craig interpolation to compute its results. Using Suraq, we were able to synthesize a controller (consisting of two Boolean signals) for a five-stage pipelined DLX processor in roughly one hour and 15 minutes.}, author = {Hofferek, Georg and Gupta, Ashutosh}, booktitle = {HVC 2014}, editor = {Yahav, Eran}, location = {Haifa, Israel}, pages = {68 -- 74}, publisher = {Springer}, title = {{Suraq - a controller synthesis tool using uninterpreted functions}}, doi = {10.1007/978-3-319-13338-6_6}, volume = {8855}, year = {2014}, } @inproceedings{1870, abstract = {We investigate the problem of checking if a finite-state transducer is robust to uncertainty in its input. Our notion of robustness is based on the analytic notion of Lipschitz continuity - a transducer is K-(Lipschitz) robust if the perturbation in its output is at most K times the perturbation in its input. We quantify input and output perturbation using similarity functions. We show that K-robustness is undecidable even for deterministic transducers. We identify a class of functional transducers, which admits a polynomial time automata-theoretic decision procedure for K-robustness. This class includes Mealy machines and functional letter-to-letter transducers. We also study K-robustness of nondeterministic transducers. Since a nondeterministic transducer generates a set of output words for each input word, we quantify output perturbation using setsimilarity functions. We show that K-robustness of nondeterministic transducers is undecidable, even for letter-to-letter transducers. We identify a class of set-similarity functions which admit decidable K-robustness of letter-to-letter transducers.}, author = {Henzinger, Thomas A and Otop, Jan and Samanta, Roopsha}, booktitle = {Leibniz International Proceedings in Informatics, LIPIcs}, location = {Delhi, India}, pages = {431 -- 443}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Lipschitz robustness of finite-state transducers}}, doi = {10.4230/LIPIcs.FSTTCS.2014.431}, volume = {29}, year = {2014}, } @inproceedings{1872, abstract = {Extensionality axioms are common when reasoning about data collections, such as arrays and functions in program analysis, or sets in mathematics. An extensionality axiom asserts that two collections are equal if they consist of the same elements at the same indices. Using extensionality is often required to show that two collections are equal. A typical example is the set theory theorem (∀x)(∀y)x∪y = y ∪x. Interestingly, while humans have no problem with proving such set identities using extensionality, they are very hard for superposition theorem provers because of the calculi they use. In this paper we show how addition of a new inference rule, called extensionality resolution, allows first-order theorem provers to easily solve problems no modern first-order theorem prover can solve. We illustrate this by running the VAMPIRE theorem prover with extensionality resolution on a number of set theory and array problems. Extensionality resolution helps VAMPIRE to solve problems from the TPTP library of first-order problems that were never solved before by any prover.}, author = {Gupta, Ashutosh and Kovács, Laura and Kragl, Bernhard and Voronkov, Andrei}, booktitle = {ATVA 2014}, editor = {Cassez, Franck and Raskin, Jean-François}, location = {Sydney, Australia}, pages = {185 -- 200}, publisher = {Springer}, title = {{Extensional crisis and proving identity}}, doi = {10.1007/978-3-319-11936-6_14}, volume = {8837}, year = {2014}, } @article{12632, abstract = {We investigate the performance of five glacier melt models over a multi-decadal period in order to assess their ability to model future glacier response. The models range from a simple degree-day model, based solely on air temperature, to more-sophisticated models, including the full shortwave radiation balance. In addition to the empirical models, the performance of a physically based energy-balance (EB) model is examined. The melt models are coupled to an accumulation and a surface evolution model and applied in a distributed manner to Rhonegletscher, Switzerland, over the period 1929–2012 at hourly resolution. For calibration, seasonal mass-balance measurements (2006–12) are used. Decadal ice volume changes for six periods in the years 1929–2012 serve for model validation. Over the period 2006–12, there are almost no differences in performance between the models, except for EB, which is less consistent with observations, likely due to lack of meteorological in situ data. However, simulations over the long term (1929–2012) reveal that models which include a separate term for shortwave radiation agree best with the observed ice volume changes, indicating that their melt relationships are robust in time and thus suitable for long-term modelling, in contrast to more empirical approaches that are oversensitive to temperature fluctuations.}, author = {Gabbi, Jeannette and Carenzo, Marco and Pellicciotti, Francesca and Bauder, Andreas and Funk, Martin}, issn = {1727-5652}, journal = {Journal of Glaciology}, keywords = {Earth-Surface Processes}, number = {224}, pages = {1140--1154}, publisher = {International Glaciological Society}, title = {{A comparison of empirical and physically based glacier surface melt models for long-term simulations of glacier response}}, doi = {10.3189/2014jog14j011}, volume = {60}, year = {2014}, } @article{12634, abstract = {Glaciers in the Andes of Chile seem to be shrinking and possibly loosing mass, but the number and types of studies conducted, constrained mainly by data availability, are not sufficient to provide a synopsis of glacier changes for the past or future or explain in an explicit way causes of the observed changes. In this paper, we provide a systematic review of changes in glaciers for the entire country, followed by a discussion of the studies that have provided evidence of such changes. We identify a missing type of work in distributed, physically-oriented modelling studies that are needed to bridge the gap between the numerous remote sensing studies and the specific, point scale works focused on process understanding. We use an advanced mass balance model applied to one of the best monitored glaciers in the region to investigate four main research issues that should be addressed in modelling studies for a sound assessment of glacier changes: 1) the use of physically-based models of glacier ablation (energy balance models) versus more empirical models (enhanced temperature index approaches); 2) the importance of the correct extrapolation of air temperature forcing on glaciers and in high elevation areas and the large uncertainty in model outputs associated with it; 3) the role played by snow gravitational redistribution; and 4) the uncertainty associated with future climate scenarios. We quantify differences in model outputs associated with each of these choices, and conclude with suggestions for future work directions.}, author = {Pellicciotti, Francesca and Ragettli, S. and Carenzo, M. and McPhee, J.}, issn = {0048-9697}, journal = {Science of The Total Environment}, keywords = {Pollution, Waste Management and Disposal, Environmental Chemistry, Environmental Engineering}, pages = {1197--1210}, publisher = {Elsevier}, title = {{Changes of glaciers in the Andes of Chile and priorities for future work}}, doi = {10.1016/j.scitotenv.2013.10.055}, volume = {493}, year = {2014}, } @article{12635, abstract = {Switzerland is one of the countries with some of the longest and best glaciological data sets. Its glaciers and their changes in response to climate have been extensively investigated, and the number and quality of related studies are notable. However, a comprehensive review of glacier changes and their impact on the hydrology of glacierised catchments for Switzerland is missing and we use the opportunity provided by the EU-FP7 ACQWA project to review the current state of knowledge about past changes and future projections. We examine the type of models that have been applied to infer glacier evolution and identify knowledge gaps that should be addressed in future research in addition to those indicated in previous publications. Common characteristics in long-term series of projected future glacier runoff are an initial peak followed by a decline, associated with shifts in seasonality, earlier melt onset and reduced summer runoff. However, the quantitative predictions are difficult to compare, as studies differ in terms of model structure, calibration strategies, input data, temporal and spatial resolution as well as future scenarios used for impact studies. We identify two sources of uncertainties among those emerging from recent research, and use simulations over four glaciers to: i) quantify the importance of the correct extrapolation of air temperature, and ii) point at the key role played by debris cover in modulating glacier response.}, author = {Pellicciotti, Francesca and Carenzo, M. and Bordoy, R. and Stoffel, M.}, issn = {0048-9697}, journal = {Science of The Total Environment}, keywords = {Pollution, Waste Management and Disposal, Environmental Chemistry, Environmental Engineering}, pages = {1152--1170}, publisher = {Elsevier}, title = {{Changes in glaciers in the Swiss Alps and impact on basin hydrology: Current state of the art and future research}}, doi = {10.1016/j.scitotenv.2014.04.022}, volume = {493}, year = {2014}, } @article{12636, abstract = {Himalayan glacier tongues are commonly debris covered and they are an important source of melt water. However, they remain relatively unstudied because of the inaccessibility of the terrain and the difficulties in field work caused by the thick debris mantles. Observations of debris-covered glaciers are therefore scarce and airborne remote sensing may bridge the gap between scarce field observations and coarse resolution space-borne remote sensing. In this study we deploy an Unmanned Aerial Vehicle (UAV) before and after the melt and monsoon season (May and October 2013) over the debris-covered tongue of the Lirung Glacier in Nepal. Based on stereo-imaging and the structure for motion algorithm we derive highly detailed ortho-mosaics and digital elevation models (DEMs), which we geometrically correct using differential GPS observations collected in the field. Based on DEM differencing and manual feature tracking we derive the mass loss and the surface velocity of the glacier at a high spatial accuracy. On average, mass loss is limited and the surface velocity is very small. However, the spatial variability of melt rates is very high, and ice cliffs and supra-glacial ponds show mass losses that can be an order of magnitude higher than the average. We suggest that future research should focus on the interaction between supra-glacial ponds, ice cliffs and englacial hydrology to further understand the dynamics of debris-covered glaciers. Finally, we conclude that UAV deployment has large potential in glaciology and it may revolutionize methods currently applied in studying glacier surface features.}, author = {Immerzeel, W.W. and Kraaijenbrink, P.D.A. and Shea, J.M. and Shrestha, A.B. and Pellicciotti, Francesca and Bierkens, M.F.P. and de Jong, S.M.}, issn = {0034-4257}, journal = {Remote Sensing of Environment}, keywords = {Computers in Earth Sciences, Geology, Soil Science}, number = {7}, pages = {93--103}, publisher = {Elsevier}, title = {{High-resolution monitoring of Himalayan glacier dynamics using unmanned aerial vehicles}}, doi = {10.1016/j.rse.2014.04.025}, volume = {150}, year = {2014}, } @article{12637, abstract = {The performance of glaciohydrological models which simulate catchment response to climate variability depends to a large degree on the data used to force the models. The forcing data become increasingly important in high-elevation, glacierized catchments where the interplay between extreme topography, climate, and the cryosphere is complex. It is challenging to generate a reliable forcing data set that captures this spatial heterogeneity. In this paper, we analyze the results of a 1 year field campaign focusing on air temperature and precipitation observations in the Langtang valley in the Nepalese Himalayas. We use the observed time series to characterize both temperature lapse rates (LRs) and precipitation gradients (PGs). We study their spatial and temporal variability, and we attempt to identify possible controlling factors. We show that very clear LRs exist in the valley and that there are strong seasonal differences related to the water vapor content in the atmosphere. Results also show that the LRs are generally shallower than the commonly used environmental lapse rates. The analysis of the precipitation observations reveals that there is great variability in precipitation over short horizontal distances. A uniform valley wide PG cannot be established, and several scale-dependent mechanisms may explain our observations. We complete our analysis by showing the impact of the observed LRs and PGs on the outputs of the TOPKAPI-ETH glaciohydrological model. We conclude that LRs and PGs have a very large impact on the water balance composition and that short-term monitoring campaigns have the potential to improve model quality considerably.}, author = {Immerzeel, W. W. and Petersen, L. and Ragettli, S. and Pellicciotti, Francesca}, issn = {1944-7973}, journal = {Water Resources Research}, keywords = {Water Science and Technology}, number = {3}, pages = {2212--2226}, publisher = {American Geophysical Union}, title = {{The importance of observed gradients of air temperature and precipitation for modeling runoff from a glacierized watershed in the Nepalese Himalayas}}, doi = {10.1002/2013wr014506}, volume = {50}, year = {2014}, } @article{1309, abstract = {We show that weak solutions of the Derrida-Lebowitz-Speer-Spohn (DLSS) equation display infinite speed of support propagation. We apply our method to the case of the quantum drift-diffusion equation which augments the DLSS equation with a drift term and possibly a second-order diffusion term. The proof is accomplished using weighted entropy estimates, Hardy's inequality and a family of singular weight functions to derive a differential inequality; the differential inequality shows exponential growth of the weighted entropy, with the growth constant blowing up very fast as the singularity of the weight becomes sharper. To the best of our knowledge, this is the first example of a nonnegativity-preserving higher-order parabolic equation displaying infinite speed of support propagation.}, author = {Julian Fischer}, journal = {Nonlinear Differential Equations and Applications}, number = {1}, pages = {27 -- 50}, publisher = {Birkhäuser}, title = {{Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models}}, doi = {10.1007/s00030-013-0235-0}, volume = {21}, year = {2014}, } @article{1312, abstract = {We derive upper bounds on the waiting time of solutions to the thin-film equation in the regime of weak slippage n ∈ [2, 32\11). In particular, we give sufficient conditions on the initial data for instantaneous forward motion of the free boundary. For n ∈ (2, 32\11), our estimates are sharp, for n = 2, they are sharp up to a logarithmic correction term. Note that the case n = 2 corresponds-with a grain of salt-to the assumption of the Navier slip condition at the fluid-solid interface. We also obtain results in the regime of strong slippage n ∈ (1,2); however, in this regime we expect them not to be optimal. Our method is based on weighted backward entropy estimates, Hardy's inequality and singular weight functions; we deduce a differential inequality which would enforce blowup of the weighted entropy if the contact line were to remain stationary for too long.}, author = {Julian Fischer}, journal = {Archive for Rational Mechanics and Analysis}, number = {3}, pages = {771 -- 818}, publisher = {Springer}, title = {{Upper bounds on waiting times for the Thin-film equation: The case of weak slippage}}, doi = {10.1007/s00205-013-0690-0}, volume = {211}, year = {2014}, } @article{1979, abstract = {NADH-ubiquinone oxidoreductase (complex I) is the first and largest enzyme in the respiratory chain of mitochondria and many bacteria. It couples the transfer of two electrons between NADH and ubiquinone to the translocation of four protons across the membrane. Complex I is an L-shaped assembly formed by the hydrophilic (peripheral) arm, containing all the redox centres performing electron transfer and the membrane arm, containing proton-translocating machinery. Mitochondrial complex I consists of 44 subunits of about 1 MDa in total, whilst the prokaryotic enzyme is simpler and generally consists of 14 conserved “core” subunits. Recently we have determined the first atomic structure of the entire complex I, using the enzyme from Thermus thermophilus (536 kDa, 16 subunits, 9 Fe-S clusters, 64 TM helices). Structure suggests a unique coupling mechanism, with redox energy of electron transfer driving proton translocation via long-range (up to ~200 Å) conformational changes. It resembles a steam engine, with coupling elements (akin to coupling rods) linking parts of this molecular machine.}, author = {Leonid Sazanov}, journal = {Journal of Bioenergetics and Biomembranes}, number = {4}, pages = {247 -- 253}, publisher = {Springer}, title = {{The mechanism of coupling between electron transfer and proton translocation in respiratory complex I}}, doi = {10.1007/s10863-014-9554-z}, volume = {46}, year = {2014}, } @article{1980, abstract = {Non-proton pumping type II NADH dehydrogenase (NDH-2) plays a central role in the respiratory metabolism of bacteria, and in the mitochondria of fungi, plants and protists. The lack of NDH-2 in mammalian mitochondria and its essentiality in important bacterial pathogens suggests these enzymes may represent a potential new drug target to combat microbial pathogens. Here, we report the first crystal structure of a bacterial NDH-2 enzyme at 2.5Å resolution from Caldalkalibacillus thermarum. The NDH-2 structure reveals a homodimeric organization that has a unique dimer interface. NDH-2 is localized to the cytoplasmic membrane by two separated C-terminal membrane-anchoring regions that are essential for membrane localization and FAD binding, but not NDH-2 dimerization. Comparison of bacterial NDH-2 with the yeast NADH dehydrogenase (Ndi1) structure revealed non-overlapping binding sites for quinone and NADH in the bacterial enzyme. The bacterial NDH-2 structure establishes a framework for the structure-based design of small-molecule inhibitors.}, author = {Heikal, Adam and Nakatani, Yoshio and Dunn, Elyse A and Weimar, Marion R and Day, Catherine and Baker, Edward N and Lott, Shaun J and Leonid Sazanov and Cook, Gregory}, journal = {Molecular Microbiology}, number = {5}, pages = {950 -- 964}, publisher = {Wiley-Blackwell}, title = {{Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation}}, doi = {10.1111/mmi.12507}, volume = {91}, year = {2014}, } @article{1989, abstract = {During animal cell division, the cleavage furrow is positioned by microtubules that signal to the actin cortex at the cell midplane. We developed a cell-free system to recapitulate cytokinesis signaling using cytoplasmic extract from Xenopus eggs. Microtubules grew out as asters from artificial centrosomes and met to organize antiparallel overlap zones. These zones blocked the interpenetration of neighboring asters and recruited cytokinesis midzone proteins, including the chromosomal passenger complex (CPC) and centralspindlin. The CPC was transported to overlap zones, which required two motor proteins, Kif4A and a Kif20A paralog. Using supported lipid bilayers to mimic the plasma membrane, we observed the recruitment of cleavage furrow markers, including an active RhoA reporter, at microtubule overlaps. This system opens further approaches to understanding the biophysics of cytokinesis signaling.}, author = {Nguyen, Phuong and Groen, Aaron and Loose, Martin and Ishihara, Keisuke and Wühr, Martin and Field, Christine and Mitchison, Timothy}, journal = {Science}, number = {6206}, pages = {244 -- 247}, publisher = {American Association for the Advancement of Science}, title = {{Spatial organization of cytokinesis signaling reconstituted in a cell-free system}}, doi = {10.1126/science.1256773}, volume = {346}, year = {2014}, }