@article{3039, abstract = {During the development of multicellular organisms, organogenesis and pattern formation depend on formative divisions to specify and maintain pools of stem cells. In higher plants, these activities are essential to shape the final root architecture because the functioning of root apical meristems and the de novo formation of lateral roots entirely rely on it. We used transcript profiling on sorted pericycle cells undergoing lateral root initiation to identify the receptor-like kinase ACR4 of Arabidopsis as a key factor both in promoting formative cell divisions in the pericycle and in constraining the number of these divisions once organogenesis has been started. In the root tip meristem, ACR4 shows a similar action by controlling cell proliferation activity in the columella cell lineage. Thus, ACR4 function reveals a common mechanism of formative cell division control in the main root tip meristem and during lateral root initiation.}, author = {De Smet, Ive and Vassileva, Valya and De Rybel, Bert and Levesque, Mitchell P and Grunewald, Wim and Van Damme, Daniël and Van Noorden, Giel and Naudts, Mirande and Van Isterdael, Gert and De Clercq, Rebecca and Wang, Jean Y and Meuli, Nicholas and Vanneste, Steffen and Jirí Friml and Hilson, Pierre and Jürgens, Gerd and Ingram, Gwyneth C and Inzé, Dirk and Benfey, Philip N and Beeckman, Tom}, journal = {Science}, number = {5901}, pages = {594 -- 597}, publisher = {American Association for the Advancement of Science}, title = {{Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root}}, doi = {10.1126/science.1160158}, volume = {322}, year = {2008}, } @article{3040, abstract = {The polar, sub-cellular localization of PIN auxin efflux carriers determines the direction of intercellular auxin flow, thus defining the spatial aspect of auxin signalling. Dynamic, transcytosis-like relocalizations of PIN proteins occur in response to external and internal signals, integrating these signals into changes in auxin distribution. Here, we examine the cellular and molecular mechanisms of polar PIN delivery and transcytosis. The mechanisms of the ARF-GEF-dependent polar targeting and transcytosis are well conserved and show little variations among diverse Arabidopsis ecotypes consistent with their fundamental importance in regulating plant development. At the cellular level, we refine previous findings on the role of the actin cytoskeleton in apical and basal PIN targeting, and identify a previously unknown role for microtubules, specifically in basal targeting. PIN protein delivery to different sides of the cell is mediated by ARF-dependent trafficking with a previously unknown complex level of distinct ARF-GEF vesicle trafficking regulators. Our data suggest that alternative recruitment of PIN proteins by these distinct pathways can account for cell type- and cargo-specific aspects of polar targeting, as well as for polarity changes in response to different signals. The resulting dynamic PIN positioning to different sides of cells defines a three-dimensional pattern of auxin fluxes within plant tissues.}, author = {Kleine-Vehn, Jürgen and Łangowski, Łukasz and Wiśniewska, Justyna and Dhonukshe, Pankaj and Brewer, Philip B and Jirí Friml}, journal = {Molecular Plant}, number = {6}, pages = {1056 -- 1066}, publisher = {Oxford University Press}, title = {{Cellular and molecular requirements for polar PIN targeting and transcytosis in plants}}, doi = {10.1093/mp/ssn062}, volume = {1}, year = {2008}, } @article{3041, abstract = {The rate, polarity, and symmetry of the flow of the plant hormone auxin are determined by the polar cellular localization of PIN-FORMED (PIN) auxin efflux carriers. Flavonoids, a class of secondary plant metabolites, have been suspected to modulate auxin transport and tropic responses. Nevertheless, the identity of specific flavonoid compounds involved and their molecular function and targets in vivo are essentially unknown. Here we show that the root elongation zone of agravitropic pin2/eir1/wav6/agr1 has an altered pattern and amount of flavonol glycosides. Application of nanomolar concentrations of flavonols to pin2 roots is sufficient to partially restore root gravitropism. By employing a quantitative cell biological approach, we demonstrate that flavonoids partially restore the formation of lateral auxin gradients in the absence of PIN2. Chemical complementation by flavonoids correlates with an asymmetric distribution of the PIN1 protein. pin2 complementation probably does not result from inhibition of auxin efflux, as supply of the auxin transport inhibitor N-1-naphthylphthalamic acid failed to restore pin2 gravitropism. We propose that flavonoids promote asymmetric PIN shifts during gravity stimulation, thus redirecting basipetal auxin streams necessary for root bending. © 2008 by The American Society for Biochemistry and Molecular Biology, Inc.}, author = {Santelia, Diana and Henrichs, Sina and Vincenzetti, Vincent and Sauer, Michael and Bigler, Laurent and Klein, Markus B and Bailly, Aurélien and Lee, Yuree and Jirí Friml and Geisler, Markus and Martinoia, Enrico}, journal = {Journal of Biological Chemistry}, number = {45}, pages = {31218 -- 31226}, publisher = {American Society for Biochemistry and Molecular Biology}, title = {{Flavonoids redirect PIN mediated polar auxin fluxes during root gravitropic responses}}, doi = { 10.1074/jbc.M710122200}, volume = {283}, year = {2008}, } @article{3042, abstract = {All eukaryotic cells present at the cell surface a specific set of plasma membrane proteins that modulate responses to internal and external cues and whose activity is also regulated by protein degradation. We characterized the lytic vacuole-dependent degradation of membrane proteins in Arabidopsis thaliana by means of in vivo visualization of vacuolar targeting combined with quantitative protein analysis. We show that the vacuolar targeting pathway is used by multiple cargos including PIN-FORMED (PIN) efflux carriers for the phytohormone auxin. In vivo visualization of PIN2 vacuolar targeting revealed its differential degradation in response to environmental signals, such as gravity. In contrast to polar PIN delivery to the basal plasma membrane, which depends on the vesicle trafficking regulator ARF-GEF GNOM, PIN sorting to the lytic vacuolar pathway requires additional brefeldin A-sensitive ARF-GEF activity. Furthermore, we identified putative retromer components SORTING NEXIN1 (SNX1) and VACUOLAR PROTEIN SORTING29 (VPS29) as important factors in this pathway and propose that the retromer complex acts to retrieve PIN proteins from a late/pre-vacuolar compartment back to the recycling pathways. Our data suggest that ARF GEF- and retromer-dependent processes regulate PIN sorting to the vacuole in an antagonistic manner and illustrate instrumentalization of this mechanism for fine-tuning the auxin fluxes during gravitropic response.}, author = {Kleine-Vehn, Jürgen and Leitner, Johannes and Zwiewka, Marta and Sauer, Michael and Abas, Lindy and Luschnig, Christian and Jirí Friml}, journal = {PNAS}, number = {46}, pages = {17812 -- 17817}, publisher = {National Academy of Sciences}, title = {{Differential degradation of PIN2 auxin efflux carrier by retromer dependent vacuolar targeting}}, doi = {10.1073/pnas.0808073105}, volume = {105}, year = {2008}, } @article{3043, abstract = {Plant development is characterized by a profound phenotypic plasticity that often involves redefining of the developmental fate and polarity of cells within differentiated tissues. The plant hormone auxin and its directional intercellular transport play a major role in these processes because they provide positional information and link cell polarity with tissue patterning. This plant-specific mechanism of transport-dependent auxin gradients depends on subcellular dynamics of auxin transport components, in particular on endocytic recycling and polar targeting. Recent insights into these cellular processes in plants have revealed important parallels to yeast and animal systems, including clathrin-dependent endocytosis, retromer function, and transcytosis, but have also emphasized unique features of plant cells such as diversity of polar targeting pathways; integration of environmental signals into subcellular trafficking; and the link between endocytosis, cell polarity, and cell fate specification. We review these advances and focus on the translation of the subcellular dynamics to the regulation of whole-plant development.}, author = {Kleine Vehn, Jürgen and Friml, Jirí}, journal = {Annual Review of Cell and Developmental Biology}, pages = {447 -- 473}, publisher = {Annual Reviews}, title = {{Polar targeting and endocytic recycling in auxin-dependent plant development}}, doi = {10.1146/annurev.cellbio.24.110707.175254}, volume = {24}, year = {2008}, } @article{3044, abstract = {The signalling molecule auxin controls plant morphogenesis via its activity gradients, which are produced by intercellular auxin transport. Cellular auxin efflux is the rate-limiting step in this process and depends on PIN and phosphoglycoprotein (PGP) auxin transporters. Mutual roles for these proteins in auxin transport are unclear, as is the significance of their interactions for plant development. Here, we have analysed the importance of the functional interaction between PIN- and PGP-dependent auxin transport in development. We show by analysis of inducible overexpression lines that PINs and PGPs define distinct auxin transport mechanisms: both mediate auxin efflux but they play diverse developmental roles. Components of both systems are expressed during embryogenesis, organogenesis and tropisms, and they interact genetically in both synergistic and antagonistic fashions. A concerted action of PIN- and PGP-dependent efflux systems is required for asymmetric auxin distribution during these processes. We propose a model in which PGP-mediated efflux controls auxin levels in auxin channel-forming cells and, thus, auxin availability for PIN-dependent vectorial auxin movement.}, author = {Mravec, Jozef and Kubeš, Martin and Bielach, Agnieszka and Gaykova, Vassilena and Petrášek, Jan and Skůpa, Petr and Chand, Suresh and Eva Benková and Zažímalová, Eva and Jirí Friml}, journal = {Development}, number = {20}, pages = {3345 -- 3354}, publisher = {Company of Biologists}, title = {{Interaction of PIN and PGP transport mechanisms in auxin distribution-dependent development}}, doi = {10.1242/dev.021071}, volume = {135}, year = {2008}, } @article{3045, abstract = {Dynamically polarized membrane proteins define different cell boundaries and have an important role in intercellular communication - a vital feature of multicellular development. Efflux carriers for the signalling molecule auxin from the PIN family are landmarks of cell polarity in plants and have a crucial involvement in auxin distribution-dependent development including embryo patterning, organogenesis and tropisms. Polar PIN localization determines the direction of intercellular auxin flow, yet the mechanisms generating PIN polarity remain unclear. Here we identify an endocytosis-dependent mechanism of PIN polarity generation and analyse its developmental implications. Real-time PIN tracking showed that after synthesis, PINs are initially delivered to the plasma membrane in a non-polar manner and their polarity is established by subsequent endocytic recycling. Interference with PIN endocytosis either by auxin or by manipulation of the Arabidopsis Rab5 GTPase pathway prevents PIN polarization. Failure of PIN polarization transiently alters asymmetric auxin distribution during embryogenesis and increases the local auxin response in apical embryo regions. This results in ectopic expression of auxin pathway-associated root-forming master regulators in embryonic leaves and promotes homeotic transformation of leaves to roots. Our results indicate a two-step mechanism for the generation of PIN polar localization and the essential role of endocytosis in this process. It also highlights the link between endocytosis-dependent polarity of individual cells and auxin distribution-dependent cell fate establishment for multicellular patterning.}, author = {Dhonukshe, Pankaj and Tanaka, Hirokazu and Goh, Tatsuaki and Ebine, Kazuo and Mähönen, Ari Pekka and Prasad, Kalika and Blilou, Ikram and Geldner, Niko and Xu, Jian and Uemura, Tomohiro and Chory, Joanne and Ueda, Takashi and Nakano, Akihiko and Scheres, Ben and Jirí Friml}, journal = {Nature}, number = {7224}, pages = {962 -- 966}, publisher = {Nature Publishing Group}, title = {{Generation of cell polarity in plants links endocytosis auxin distribution and cell fate decisions}}, doi = {10.1038/nature07409}, volume = {456}, year = {2008}, } @inproceedings{3194, abstract = {We consider the problem of optimizing multilabel MRFs, which is in general NP-hard and ubiquitous in low-level computer vision. One approach for its solution is to formulate it as an integer linear programming and relax the integrality constraints. The approach we consider in this paper is to first convert the multi-label MRF into an equivalent binary-label MRF and then to relax it. The resulting relaxation can be efficiently solved using a maximum flow algorithm. Its solution provides us with a partially optimal labelling of the binary variables. This partial labelling is then easily transferred to the multi-label problem. We study the theoretical properties of the new relaxation and compare it with the standard one. Specifically, we compare tightness, and characterize a subclass of problems where the two relaxations coincide. We propose several combined algorithms based on the technique and demonstrate their performance on challenging computer vision problems.}, author = {Kohli, Pushmeet and Shekhovtsov, Alexander and Rother, Carsten and Vladimir Kolmogorov and Torr, Philip H}, pages = {480 -- 487}, publisher = {Omnipress}, title = {{On partial optimality in multi label MRFs}}, doi = {10.1145/1390156.1390217}, year = {2008}, } @inproceedings{3195, abstract = {Graph cut is a popular technique for interactive image segmentation. However, it has certain shortcomings. In particular, graph cut has problems with segmenting thin elongated objects due to the ldquoshrinking biasrdquo. To overcome this problem, we propose to impose an additional connectivity prior, which is a very natural assumption about objects. We formulate several versions of the connectivity constraint and show that the corresponding optimization problems are all NP-hard. For some of these versions we propose two optimization algorithms: (i) a practical heuristic technique which we call DijkstraGC, and (ii) a slow method based on problem decomposition which provides a lower bound on the problem. We use the second technique to verify that for some practical examples DijkstraGC is able to find the global minimum.}, author = {Vicente, Sara and Vladimir Kolmogorov and Rother, Carsten}, publisher = {IEEE}, title = {{Graph cut based image segmentation with connectivity priors}}, doi = {10.1109/CVPR.2008.4587440}, year = {2008}, } @article{3196, abstract = {Among the most exciting advances in early vision has been the development of efficient energy minimization algorithms for pixel-labeling tasks such as depth or texture computation. It has been known for decades that such problems can be elegantly expressed as Markov random fields, yet the resulting energy minimization problems have been widely viewed as intractable. Algorithms such as graph cuts and loopy belief propagation (LBP) have proven to be very powerful: For example, such methods form the basis for almost all the top-performing stereo methods. However, the trade-offs among different energy minimization algorithms are still not well understood. In this paper, we describe a set of energy minimization benchmarks and use them to compare the solution quality and runtime of several common energy minimization algorithms. We investigate three promising methods-graph cuts, LBP, and tree-reweighted message passing-in addition to the well-known older iterated conditional mode (ICM) algorithm. Our benchmark problems are drawn from published energy functions used for stereo, image stitching, interactive segmentation, and denoising. We also provide a general-purpose software interface that allows vision researchers to easily switch between optimization methods. The benchmarks, code, images, and results are available at http://vision.middlebury.edu/MRF/.}, author = {Szeliski, Richard S and Zabih, Ramin and Scharstein, Daniel and Veksler, Olga and Vladimir Kolmogorov and Agarwala, Aseem and Tappen, Marshall F and Rother, Carsten}, journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence}, number = {6}, pages = {1068 -- 1080}, publisher = {IEEE}, title = {{A comparative study of energy minimization methods for Markov random fields with smoothness-based priors}}, doi = {10.1109/TPAMI.2007.70844}, volume = {30}, year = {2008}, } @inproceedings{3198, abstract = {In this paper we present a new approach for establishing correspondences between sparse image features related by an unknown non-rigid mapping and corrupted by clutter and occlusion, such as points extracted from a pair of images containing a human figure in distinct poses. We formulate this matching task as an energy minimization problem by defining a complex objective function of the appearance and the spatial arrangement of the features. Optimization of this energy is an instance of graph matching, which is in general a NP-hard problem. We describe a novel graph matching optimization technique, which we refer to as dual decomposition (DD), and demonstrate on a variety of examples that this method outperforms existing graph matching algorithms. In the majority of our examples DD is able to find the global minimum within a minute. The ability to globally optimize the objective allows us to accurately learn the parameters of our matching model from training examples. We show on several matching tasks that our learned model yields results superior to those of state-of-the-art methods. }, author = {Torresani, Lorenzo and Vladimir Kolmogorov and Rother, Carsten}, pages = {596 -- 609}, publisher = {Springer}, title = {{Feature correspondence via graph matching: Models and global optimization}}, doi = {10.1007/978-3-540-88688-4_44}, volume = {5303}, year = {2008}, } @inproceedings{3224, abstract = {We propose a new mode of operation, enciphered CBC, for domain extension of length-preserving functions (like block ciphers), which is a variation on the popular CBC mode of operation. Our new mode is twice slower than CBC, but has many (property-preserving) properties not enjoyed by CBC and other known modes. Most notably, it yields the first constant-rate Variable Input Length (VIL) MAC from any length preserving Fixed Input Length (FIL) MAC. This answers the question of Dodis and Puniya from Eurocrypt 2007. Further, our mode is a secure domain extender for PRFs (with basically the same security as encrypted CBC). This provides a hedge against the security of the block cipher: if the block cipher is pseudorandom, one gets a VIL-PRF, while if it is "only" unpredictable, one "at least" gets a VIL-MAC. Additionally, our mode yields a VIL random oracle (and, hence, a collision-resistant hash function) when instantiated with length-preserving random functions, or even random permutations (which can be queried from both sides). This means that one does not have to re-key the block cipher during the computation, which was critically used in most previous constructions (analyzed in the ideal cipher model). }, author = {Dodis, Yevgeniy and Krzysztof Pietrzak and Puniya, Prashant}, pages = {198 -- 219}, publisher = {Springer}, title = {{A new mode of operation for block ciphers and length preserving MACs}}, doi = {10.1007/978-3-540-78967-3_12}, volume = {4965}, year = {2008}, } @inproceedings{3225, abstract = {A robust multi-property combiner for a set of security properties merges two hash functions such that the resulting function satisfies each of the properties which at least one of the two starting functions has. Fischlin and Lehmann (TCC 2008) recently constructed a combiner which simultaneously preserves collision-resistance, target collision-resistance, message authentication, pseudorandomness and indifferentiability from a random oracle (IRO). Their combiner produces outputs of 5n bits, where n denotes the output length of the underlying hash functions. In this paper we propose improved combiners with shorter outputs. By sacrificing the indifferentiability from random oracles we obtain a combiner which preserves all of the other aforementioned properties but with output length 2n only. This matches a lower bound for black-box combiners for collision-resistance as the only property, showing that the other properties can be achieved without penalizing the length of the hash values. We then propose a combiner which also preserves the IRO property, slightly increasing the output length to 2n + ω(logn). Finally, we show that a twist on our combiners also makes them robust for one-wayness (but at the price of a fixed input length). }, author = {Fischlin, Marc and Lehmann, Anja and Krzysztof Pietrzak}, number = {PART 2}, pages = {655 -- 666}, publisher = {Springer}, title = {{Robust multi property combiners for hash functions revisited}}, doi = {10.1007/978-3-540-70583-3_53}, volume = {5126}, year = {2008}, } @inproceedings{3226, abstract = {A family of functions is weakly pseudorandom if a random member of the family is indistinguishable from a uniform random function when queried on random inputs. We point out a subtle ambiguity in the definition of weak PRFs: there are natural weak PRFs whose security breaks down if the randomness used to sample the inputs is revealed. To capture this ambiguity we distinguish between public-coin and secret-coin weak PRFs. We show that the existence of a secret-coin weak PRF which is not also a public-coin weak PRF implies the existence of two pass key-agreement (i.e. public-key encryption). So in Minicrypt, i.e. under the assumption that one-way functions exist but public-key cryptography does not, the notion of public- and secret-coin weak PRFs coincide. Previous to this paper all positive cryptographic statements known to hold exclusively in Minicrypt concerned the adaptive security of constructions using non-adaptively secure components. Weak PRFs give rise to a new set of statements having this property. As another example we consider the problem of range extension for weak PRFs. We show that in Minicrypt one can beat the best possible range expansion factor (using a fixed number of distinct keys) for a very general class of constructions (in particular, this class contains all constructions that are known today). }, author = {Krzysztof Pietrzak and Sjödin, Johan}, number = {PART 2}, pages = {423 -- 436}, publisher = {Springer}, title = {{Weak pseudorandom functions in minicrypt}}, doi = {10.1007/978-3-540-70583-3_35}, volume = {5126}, year = {2008}, } @article{3227, abstract = {Large amount of data management can cause a lot of troubles which can be solved by dedicated computer system. To facilitate management of measurement data which are gathered in Institute of Power Engineering - Insulation Department a special system called Elektrowiz® was developed. It allows storing measurement results which concern partial discharges in insulation of turbo- and hydrogenerators in power stations. Multilayer architecture of the system allows reaching gathered data independently on user localization. There are possible different access methods to the system and dependency on current requirements data exploration can be realized with read-only or edit rights.}, author = {Zubielik, Piotr and Nadaczny, Jerzy and Krzysztof Pietrzak and Lawenda, Marcin}, journal = {Przeglad Elektrotechniczny}, number = {10}, pages = {239 -- 242}, publisher = {SIGMA-NOT}, title = {{Elektrowiz – system of measurement data management}}, volume = {84}, year = {2008}, } @inproceedings{3228, abstract = { A black-box combiner for collision resistant hash functions (CRHF) is a construction which given black-box access to two hash functions is collision resistant if at least one of the components is collision resistant. In this paper we prove a lower bound on the output length of black-box combiners for CRHFs. The bound we prove is basically tight as it is achieved by a recent construction of Canetti et al [Crypto'07]. The best previously known lower bounds only ruled out a very restricted class of combiners having a very strong security reduction: the reduction was required to output collisions for both underlying candidate hash-functions given a single collision for the combiner (Canetti et al [Crypto'07] building on Boneh and Boyen [Crypto'06] and Pietrzak [Eurocrypt'07]). Our proof uses a lemma similar to the elegant "reconstruction lemma" of Gennaro and Trevisan [FOCS'00], which states that any function which is not one-way is compressible (and thus uniformly random function must be one-way). In a similar vein we show that a function which is not collision resistant is compressible. We also borrow ideas from recent work by Haitner et al. [FOCS'07], who show that one can prove the reconstruction lemma even relative to some very powerful oracles (in our case this will be an exponential time collision-finding oracle). © 2008 Springer-Verlag Berlin Heidelberg.}, author = {Krzysztof Pietrzak}, pages = {413 -- 432}, publisher = {Springer}, title = {{Compression from collisions or why CRHF combiners have a long output}}, doi = {10.1007/978-3-540-85174-5_23}, volume = {5157}, year = {2008}, } @inproceedings{3229, abstract = {We construct a stream-cipher S whose implementation is secure even if a bounded amount of arbitrary (adversarially chosen) information on the internal state ofS is leaked during computation. This captures all possible side-channel attacks on S where the amount of information leaked in a given period is bounded, but overall can be arbitrary large. The only other assumption we make on the implementation of S is that only data that is accessed during computation leaks information. The stream-cipher S generates its output in chunks K1, K2, . . . and arbitrary but bounded information leakage is modeled by allowing the adversary to adaptively chose a function fl : {0,1}* rarr {0, 1}lambda before Kl is computed, she then gets fl(taul) where taul is the internal state ofS that is accessed during the computation of Kg. One notion of security we prove for S is that Kg is indistinguishable from random when given K1,..., K1-1,f1(tau1 ),..., fl-1(taul-1) and also the complete internal state of S after Kg has been computed (i.e. S is forward-secure). The construction is based on alternating extraction (used in the intrusion-resilient secret-sharing scheme from FOCS'07). We move this concept to the computational setting by proving a lemma that states that the output of any PRG has high HILLpseudoentropy (i.e. is indistinguishable from some distribution with high min-entropy) even if arbitrary information about the seed is leaked. The amount of leakage lambda that we can tolerate in each step depends on the strength of the underlying PRG, it is at least logarithmic, but can be as large as a constant fraction of the internal state of S if the PRG is exponentially hard.}, author = {Dziembowski, Stefan and Krzysztof Pietrzak}, pages = {293 -- 302}, publisher = {IEEE}, title = {{Leakage resilient cryptography}}, doi = {10.1109/FOCS.2008.56}, year = {2008}, } @article{3291, abstract = {The filamentous fungus Aspergillus fumigatus is responsible for a lethal disease called Invasive Aspergillosis that affects immunocompromised patients. This disease, like other human fungal diseases, is generally treated by compounds targeting the primary fungal cell membrane sterol. Recently, glucan synthesis inhibitors were added to the limited antifungal arsenal and encouraged the search for novel targets in cell wall biosynthesis. Although galactomannan is a major component of the A. fumigatus cell wall and extracellular matrix, the biosynthesis and role of galactomannan are currently unknown. By a targeted gene deletion approach, we demonstrate that UDP-galactopyranose mutase, a key enzyme of galactofuranose metabolism, controls the biosynthesis of galactomannan and galactofuranose containing glycoconjugates. The glfA deletion mutant generated in this study is devoid of galactofuranose and displays attenuated virulence in a low-dose mouse model of invasive aspergillosis that likely reflects the impaired growth of the mutant at mammalian body temperature. Furthermore, the absence of galactofuranose results in a thinner cell wall that correlates with an increased susceptibility to several antifungal agents. The UDP-galactopyranose mutase thus appears to be an appealing adjunct therapeutic target in combination with other drugs against A. fumigatus. Its absence from mammalian cells indeed offers a considerable advantage to achieve therapeutic selectivity. }, author = {Philipp Schmalhorst and Krappmann, Sven and Vervecken, Wouter and Rohde, Manfred and Müller, Meike and Braus, Gerhard H. and Contreras, Roland and Braun, Armin and Bakker, Hans and Routier, Françoise H}, journal = {Eukaryotic Cell}, number = {8}, pages = {1268 -- 1277}, publisher = {American Society for Microbiology}, title = {{Contribution of galactofuranose to the virulence of the opportunistic pathogen Aspergillus fumigatus}}, doi = {10.1128/EC.00065-08}, volume = {7}, year = {2008}, } @article{3307, abstract = {A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small.}, author = {Green, Richard E and Malaspinas, Anna-Sapfo and Krause, Johannes and Briggs, Adrian W and Johnson, Philip L and Caroline Uhler and Meyer, Matthias and Good, Jeffrey M and Maricic, Tomislav and Stenzel, Udo and Prüfer, Kay and Siebauer, Michael F and Burbano, Hernän A and Ronan, Michael T and Rothberg, Jonathan M and Egholm, Michael and Rudan, Pavao and Brajković, Dejana and Kućan, Željko and Gušić, Ivan and Wikström, Mårten K and Laakkonen, Liisa J and Kelso, Janet F and Slatkin, Montgomery and Pääbo, Svante H}, journal = {Cell}, pages = {416 -- 426}, publisher = {Cell Press}, title = {{A complete neandertal mitochondrial genome sequence determined by highhhroughput sequencing}}, doi = {10.1016/j.cell.2008.06.021}, volume = {134}, year = {2008}, } @article{3409, abstract = {With the introduction of single-molecule force spectroscopy (SMFS) it has become possible to directly access the interactions of various molecular systems. A bottleneck in conventional SMFS is collecting the large amount of data required for statistically meaningful analysis. Currently, atomic force microscopy (AFM)-based SMFS requires the user to tediously 'fish' for single molecules. In addition, most experimental and environmental conditions must be manually adjusted. Here, we developed a fully automated single-molecule force spectroscope. The instrument is able to perform SMFS while monitoring and regulating experimental conditions such as buffer composition and temperature. Cantilever alignment and calibration can also be automatically performed during experiments. This, combined with in-line data analysis, enables the instrument, once set up, to perform complete SMFS experiments autonomously.}, author = {Struckmeier, Jens and Wahl, Reiner and Leuschner, Mirko and Nunes, Joao and Harald Janovjak and Geisler, Ulrich and Hofmann, Gerd and Jähnke, Torsten and Mueller, Daniel J}, journal = {Nanotechnology}, number = {38}, publisher = {IOP Publishing Ltd.}, title = {{Fully automated single-molecule force spectroscopy for screening applications}}, doi = {10.1088/0957-4484/19/38/384020}, volume = {19}, year = {2008}, }