@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{11109, abstract = {The nuclear envelope (NE) provides a selective barrier between the nuclear interior and the cytoplasm and constitutes a central component of intracellular architecture. During mitosis in metazoa, the NE breaks down leading to the complete mixing of the nuclear content with the cytosol. Interestingly, many NE components actively participate in mitotic progression. After chromosome segregation, the NE is reassembled around decondensing chromatin and the nuclear compartment is reestablished in the daughter cells. Here, we summarize recent progress in deciphering the molecular mechanisms underlying NE dynamics during cell division.}, author = {Kutay, Ulrike and HETZER, Martin W}, issn = {0955-0674}, journal = {Current Opinion in Cell Biology}, keywords = {Cell Biology}, number = {6}, pages = {669--677}, publisher = {Elsevier}, title = {{Reorganization of the nuclear envelope during open mitosis}}, doi = {10.1016/j.ceb.2008.09.010}, volume = {20}, year = {2008}, } @article{11110, abstract = {Nuclear pore complexes are large aqueous channels that penetrate the nuclear envelope, thereby connecting the nuclear interior with the cytoplasm. Until recently, these macromolecular complexes were viewed as static structures, the only function of which was to control the molecular trafficking between the two compartments. It has now become evident that this simplistic scenario is inaccurate and that nuclear pore complexes are highly dynamic multiprotein assemblies involved in diverse cellular processes ranging from the organization of the cytoskeleton to gene expression. In this review, we discuss the most recent developments in the nuclear-pore-complex field, focusing on the assembly, disassembly, maintenance and function of this macromolecular structure.}, author = {D’Angelo, Maximiliano A. and HETZER, Martin W}, issn = {0962-8924}, journal = {Trends in Cell Biology}, keywords = {Cell Biology}, number = {10}, pages = {456--466}, publisher = {Elsevier}, title = {{Structure, dynamics and function of nuclear pore complexes}}, doi = {10.1016/j.tcb.2008.07.009}, volume = {18}, year = {2008}, } @article{11111, abstract = {During mitosis in metazoans, segregated chromosomes become enclosed by the nuclear envelope (NE), a double membrane that is continuous with the endoplasmic reticulum (ER). Recent in vitro data suggest that NE formation occurs by chromatin-mediated reorganization of the tubular ER; however, the basic principles of such a membrane-reshaping process remain uncharacterized. Here, we present a quantitative analysis of nuclear membrane assembly in mammalian cells using time-lapse microscopy. From the initial recruitment of ER tubules to chromatin, the formation of a membrane-enclosed, transport-competent nucleus occurs within ∼12 min. Overexpression of the ER tubule-forming proteins reticulon 3, reticulon 4, and DP1 inhibits NE formation and nuclear expansion, whereas their knockdown accelerates nuclear assembly. This suggests that the transition from membrane tubules to sheets is rate-limiting for nuclear assembly. Our results provide evidence that ER-shaping proteins are directly involved in the reconstruction of the nuclear compartment and that morphological restructuring of the ER is the principal mechanism of NE formation in vivo.}, author = {Anderson, Daniel J. and HETZER, Martin W}, issn = {1540-8140}, journal = {Journal of Cell Biology}, keywords = {Cell Biology}, number = {5}, pages = {911--924}, publisher = {Rockefeller University Press}, title = {{Reshaping of the endoplasmic reticulum limits the rate for nuclear envelope formation}}, doi = {10.1083/jcb.200805140}, volume = {182}, year = {2008}, } @article{11112, abstract = {The nuclear envelope is a double-layered membrane that encloses the nuclear genome and transcriptional machinery. In dividing cells of metazoa, the nucleus completely disassembles during mitosis, creating the need to re-establish the nuclear compartment at the end of each cell division. Given the crucial role of the nuclear envelope in gene regulation and cellular organization, it is not surprising that its biogenesis and organization have become active research areas. We will review recent insights into nuclear membrane dynamics during the cell cycle.}, author = {Anderson, Daniel J and HETZER, Martin W}, issn = {0955-0674}, journal = {Current Opinion in Cell Biology}, keywords = {Cell Biology}, number = {4}, pages = {386--392}, publisher = {Elsevier}, title = {{The life cycle of the metazoan nuclear envelope}}, doi = {10.1016/j.ceb.2008.03.016}, volume = {20}, year = {2008}, } @article{11113, abstract = {The nuclear envelope (NE), a double membrane enclosing the nucleus of eukaryotic cells, controls the flow of information between the nucleoplasm and the cytoplasm and provides a scaffold for the organization of chromatin and the cytoskeleton. In dividing metazoan cells, the NE breaks down at the onset of mitosis and then reforms around segregated chromosomes to generate the daughter nuclei. Recent data from intact cells and cell-free nuclear assembly systems suggest that the endoplasmic reticulum (ER) is the source of membrane for NE assembly. At the end of mitosis, ER membrane tubules are targeted to chromatin via tubule ends and reorganized into flat nuclear membrane sheets by specific DNA-binding membrane proteins. In contrast to previous models, which proposed vesicle fusion to be the principal mechanism of NE formation, these new studies suggest that the nuclear membrane forms by the chromatin-mediated reshaping of the ER.}, author = {Anderson, Daniel J. and HETZER, Martin W}, issn = {1477-9137}, journal = {Journal of Cell Science}, keywords = {Cell Biology}, number = {2}, pages = {137--142}, publisher = {The Company of Biologists}, title = {{Shaping the endoplasmic reticulum into the nuclear envelope}}, doi = {10.1242/jcs.005777}, volume = {121}, year = {2008}, } @article{11114, abstract = {We present a miniaturized pull-down method for the detection of protein-protein interactions using standard affinity chromatography reagents. Binding events between different proteins, which are color-coded with quantum dots (QDs), are visualized on single affinity chromatography beads by fluorescence microscopy. The use of QDs for single molecule detection allows the simultaneous analysis of multiple protein-protein binding events and reduces the amount of time and material needed to perform a pull-down experiment.}, author = {Schulte, Roberta and Talamas, Jessica and Doucet, Christine and HETZER, Martin W}, issn = {1932-6203}, journal = {PLoS ONE}, keywords = {Multidisciplinary}, number = {4}, publisher = {Public Library of Science}, title = {{Single bead affinity detection (SINBAD) for the analysis of protein-protein interactions}}, doi = {10.1371/journal.pone.0002061}, volume = {3}, year = {2008}, } @article{844, abstract = {Mutation rate varies greatly between nucleotide sites of the human genome and depends both on the global genomic location and the local sequence context of a site. In particular, CpG context elevates the mutation rate by an order of magnitude. Mutations also vary widely in their effect on the molecular function, phenotype, and fitness. Independence of the probability of occurrence of a new mutation's effect has been a fundamental premise in genetics. However, highly mutable contexts may be preserved by negative selection at important sites but destroyed by mutation at sites under no selection. Thus, there may be a positive correlation between the rate of mutations at a nucleotide site and the magnitude of their effect on fitness. We studied the impact of CpG context on the rate of human-chimpanzee divergence and on intrahuman nucleotide diversity at non-synonymous coding sites. We compared nucleotides that occupy identical positions within codons of identical amino acids and only differ by being within versus outside CpG context. Nucleotides within CpG context are under a stronger negative selection, as revealed by their lower, proportionally to the mutation rate, rate of evolution and nucleotide diversity. In particular, the probability of fixation of a non-synonymous transition at a CpG site is two times lower than at a CpG site. Thus, sites with different mutation rates are not necessarily selectively equivalent. This suggests that the mutation rate may complement sequence conservation as a characteristic predictive of functional importance of nucleotide sites.}, author = {Schmidt, Steffen and Gerasimova, Anna and Fyodor Kondrashov and Adzuhbei, Ivan A and Kondrashov, Alexey S and Sunyaev, Shamil R}, journal = {PLoS Genetics}, number = {11}, publisher = {Public Library of Science}, title = {{Hypermutable non-synonymous sites are under stronger negative selection}}, doi = {10.1371/journal.pgen.1000281}, volume = {4}, year = {2008}, } @article{8480, abstract = {The KIX domain of the transcription co-activator CBP is a three-helix bundle protein that folds via rapid accumulation of an intermediate state, followed by a slower folding phase. Recent NMR relaxation dispersion studies revealed the presence of a low-populated (excited) state of KIX that exists in equilibrium with the natively folded form under non-denaturing conditions, and likely represents the equilibrium analog of the folding intermediate. Here, we combine amide hydrogen/deuterium exchange measurements using rapid NMR data acquisition techniques with backbone 15N and 13C relaxation dispersion experiments to further investigate the equilibrium folding of the KIX domain. Residual structure within the folding intermediate is detected by both methods, and their combination enables reliable quantification of the amount of persistent residual structure. Three well-defined folding subunits are found, which display variable stability and correspond closely to the individual helices in the native state. While two of the three helices (α2 and α3) are partially formed in the folding intermediate (to ∼ 50% and ∼ 80%, respectively, at 20 °C), the third helix is disordered. The observed helical content within the excited state exceeds the helical propensities predicted for the corresponding peptide regions, suggesting that the two helices are weakly mutually stabilized, while methyl 13C relaxation dispersion data indicate that a defined packing arrangement is unlikely. Temperature-dependent experiments reveal that the largest enthalpy and entropy changes along the folding reaction occur during the final transition from the intermediate to the native state. Our experimental data are consistent with a folding mechanism where helices α2 and α3 form rapidly, although to different extents, while helix α1 consolidates only as folding proceeds to complete the native state-structure.}, author = {Schanda, Paul and Brutscher, Bernhard and Konrat, Robert and Tollinger, Martin}, issn = {0022-2836}, journal = {Journal of Molecular Biology}, keywords = {Molecular Biology}, number = {4}, pages = {726--741}, publisher = {Elsevier}, title = {{Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy}}, doi = {10.1016/j.jmb.2008.05.040}, volume = {380}, year = {2008}, } @article{8481, abstract = {The copK gene is localized on the pMOL30 plasmid of Cupriavidus metallidurans CH34 within the complex cop cluster of genes, for which 21 genes have been identified. The expression of the corresponding periplasmic CopK protein is strongly upregulated in the presence of copper, leading to a high periplasmic accumulation. The structure and metal-binding properties of CopK were investigated by NMR and mass spectrometry. The protein is dimeric in the apo state with a dissociation constant in the range of 10- 5 M estimated from analytical ultracentrifugation. Mass spectrometry revealed that CopK has two high-affinity Cu(I)-binding sites per monomer with different Cu(I) affinities. Binding of Cu(II) was observed but appeared to be non-specific. The solution structure of apo-CopK revealed an all-β fold formed of two β-sheets in perpendicular orientation with an unstructured C-terminal tail. The dimer interface is formed by the surface of the C-terminal β-sheet. Binding of the first Cu(I)-ion induces a major structural modification involving dissociation of the dimeric apo-protein. Backbone chemical shifts determined for the 1Cu(I)-bound form confirm the conservation of the N-terminal β-sheet, while the last strand of the C-terminal sheet appears in slow conformational exchange. We hypothesize that the partial disruption of the C-terminal β-sheet is related to dimer dissociation. NH-exchange data acquired on the apo-protein are consistent with a lower thermodynamic stability of the C-terminal sheet. CopK contains seven methionine residues, five of which appear highly conserved. Chemical shift data suggest implication of two or three methionines (Met54, Met38, Met28) in the first Cu(I) site. Addition of a second Cu(I) ion further increases protein plasticity. Comparison of the structural and metal-binding properties of CopK with other periplasmic copper-binding proteins reveals two conserved features within these functionally related proteins: the all-β fold and the methionine-rich Cu(I)-binding site.}, author = {Bersch, Beate and Favier, Adrien and Schanda, Paul and van Aelst, Sébastien and Vallaeys, Tatiana and Covès, Jacques and Mergeay, Max and Wattiez, Ruddy}, issn = {0022-2836}, journal = {Journal of Molecular Biology}, keywords = {Molecular Biology}, number = {2}, pages = {386--403}, publisher = {Elsevier}, title = {{Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge}}, doi = {10.1016/j.jmb.2008.05.017}, volume = {380}, year = {2008}, } @article{8482, abstract = {The SOFAST-HMQC experiment [P. Schanda, B. Brutscher, Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds, J. Am. Chem. Soc. 127 (2005) 8014–8015] allows recording two-dimensional correlation spectra of macromolecules such as proteins in only a few seconds acquisition time. To achieve the highest possible sensitivity, SOFAST-HMQC experiments are preferably performed on high-field NMR spectrometers equipped with cryogenically cooled probes. The duty cycle of over 80% in fast-pulsing SOFAST-HMQC experiments, however, may cause problems when using a cryogenic probe. Here we introduce SE-IPAP-SOFAST-HMQC, a new pulse sequence that provides comparable sensitivity to standard SOFAST-HMQC, while avoiding heteronuclear decoupling during 1H detection, and thus significantly reducing the radiofrequency load of the probe during the experiment. The experiment is also attractive for fast and sensitive measurement of heteronuclear one-bond spin coupling constants.}, author = {Kern, Thomas and Schanda, Paul and Brutscher, Bernhard}, issn = {1090-7807}, journal = {Journal of Magnetic Resonance}, keywords = {Nuclear and High Energy Physics, Biophysics, Biochemistry, Condensed Matter Physics}, number = {2}, pages = {333--338}, publisher = {Elsevier}, title = {{Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load}}, doi = {10.1016/j.jmr.2007.11.015}, volume = {190}, year = {2008}, } @article{8509, abstract = {The goal of this paper is to present to nonspecialists what is perhaps the simplest possible geometrical picture explaining the mechanism of Arnold diffusion. We choose to speak of a specific model—that of geometric rays in a periodic optical medium. This model is equivalent to that of a particle in a periodic potential in ${\mathbb R}^{n}$ with energy prescribed and to the geodesic flow in a Riemannian metric on ${\mathbb R}^{n} $.}, author = {Kaloshin, Vadim and Levi, Mark}, issn = {0036-1445}, journal = {SIAM Review}, keywords = {Theoretical Computer Science, Applied Mathematics, Computational Mathematics}, number = {4}, pages = {702--720}, publisher = {Society for Industrial & Applied Mathematics}, title = {{Geometry of Arnold diffusion}}, doi = {10.1137/070703235}, volume = {50}, year = {2008}, } @article{8510, abstract = {In this paper, using the ideas of Bessi and Mather, we present a simple mechanical system exhibiting Arnold diffusion. This system of a particle in a small periodic potential can be also interpreted as ray propagation in a periodic optical medium with a near-constant index of refraction. Arnold diffusion in this context manifests itself as an arbitrary finite change of direction for nearly constant index of refraction.}, author = {Kaloshin, Vadim and Levi, Mark}, issn = {0273-0979}, journal = {Bulletin of the American Mathematical Society}, keywords = {Applied Mathematics, General Mathematics}, number = {3}, pages = {409--427}, publisher = {American Mathematical Society}, title = {{An example of Arnold diffusion for near-integrable Hamiltonians}}, doi = {10.1090/s0273-0979-08-01211-1}, volume = {45}, year = {2008}, } @article{895, abstract = {Background. The arginine vasopressin V1a receptor (V1aR) modulates social cognition and behavior in a wide variety of species. Variation in a repetitive microsatellite element in the 5′ flanking region of the V1aR gene (AVPR1A) in rodents has been associated with variation in brain V1aR expression and in social behavior. In humans, the 5′ flanking region of AVPR1A contains a tandem duplication of two ∼350 bp, microsatellite-containing elements located approximately 3.5 kb upstream of the transcription start site. The first block, referred to as DupA, contains a polymorphic (GT) 25microsatellite; the second block, DupB, has a complex (CT) 4-(TT)-(CT)8-(GT)24polymorphic motif, known as RS3. Polymorphisms in RS3 have been associated with variation in sociobehavioral traits in humans, including autism spectrum disorders. Thus, evolution of these regions may have contributed to variation in social behavior in primates. We examined the structure of these regions in six ape, six monkey, and one prosimian species. Results. Both tandem repeat blocks are present upstream of the AVPR1A coding region in five of the ape species we investigated, while monkeys have only one copy of this region. As in humans, the microsatellites within DupA and DupB are polymorphic in many primate species. Furthermore, both single (lacking DupB) and duplicated alleles (containing both DupA and DupB) are present in chimpanzee (Pan troglodytes) populations with allele frequencies of 0.795 and 0.205 for the single and duplicated alleles, respectively, based on the analysis of 47 wild-caught individuals. Finally, a phylogenetic reconstruction suggests two alternate evolutionary histories for this locus. Conclusion. There is no obvious relationship between the presence of the RS3 duplication and social organization in primates. However, polymorphisms identified in some species may be useful in future genetic association studies. In particular, the presence of both single and duplicated alleles in chimpanzees provides a unique opportunity to assess the functional role of this duplication in contributing to variation in social behavior in primates. While our initial studies show no signs of directional selection on this locus in chimps, pharmacological and genetic association studies support a potential role for this region in influencing V1aR expression and social behavior.}, author = {Donaldson, Zoe R and Fyodor Kondrashov and Putnam, Andrea S and Bai, Yaohui and Stoinski, Tara S and Hammock, Elizabeth A and Young, Larry}, journal = {BMC Evolutionary Biology}, number = {1}, publisher = {BioMed Central}, title = {{Evolution of a behavior-linked microsatellite-containing element in the 5′ flanking region of the primate AVPR1A gene}}, doi = {10.1186/1471-2148-8-180}, volume = {8}, year = {2008}, }