@article{9458, abstract = {Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.}, author = {Huff, Jason T. and Zilberman, Daniel}, issn = {1097-4172}, journal = {Cell}, number = {6}, pages = {1286--1297}, publisher = {Elsevier}, title = {{Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes}}, doi = {10.1016/j.cell.2014.01.029}, volume = {156}, year = {2014}, } @article{9479, abstract = {Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction.}, author = {Mérai, Zsuzsanna and Chumak, Nina and García-Aguilar, Marcelina and Hsieh, Tzung-Fu and Nishimura, Toshiro and Schoft, Vera K. and Bindics, János and Ślusarz, Lucyna and Arnoux, Stéphanie and Opravil, Susanne and Mechtler, Karl and Zilberman, Daniel and Fischer, Robert L. and Tamaru, Hisashi}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {45}, pages = {16166--16171}, publisher = {National Academy of Sciences}, title = {{The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes}}, doi = {10.1073/pnas.1418564111}, volume = {111}, year = {2014}, } @article{9519, abstract = {Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression.}, author = {Kim, M. Yvonne and Zilberman, Daniel}, issn = {1878-4372}, journal = {Trends in Plant Science}, number = {5}, pages = {320--326}, publisher = {Elsevier}, title = {{DNA methylation as a system of plant genomic immunity}}, doi = {10.1016/j.tplants.2014.01.014}, volume = {19}, year = {2014}, } @article{9594, abstract = {Let d≥3 be a fixed integer. We give an asympotic formula for the expected number of spanning trees in a uniformly random d-regular graph with n vertices. (The asymptotics are as n→∞, restricted to even n if d is odd.) We also obtain the asymptotic distribution of the number of spanning trees in a uniformly random cubic graph, and conjecture that the corresponding result holds for arbitrary (fixed) d. Numerical evidence is presented which supports our conjecture.}, author = {Greenhill, Catherine and Kwan, Matthew Alan and Wind, David}, issn = {1077-8926}, journal = {The Electronic Journal of Combinatorics}, number = {1}, publisher = {The Electronic Journal of Combinatorics}, title = {{On the number of spanning trees in random regular graphs}}, doi = {10.37236/3752}, volume = {21}, year = {2014}, } @article{96, abstract = {Multielectron spin qubits are demonstrated, and performance examined by comparing coherent exchange oscillations in coupled single-electron and multielectron quantum dots, measured in the same device. Fast (>1 GHz) exchange oscillations with a quality factor Q∼15 are found for the multielectron case, compared to Q∼2 for the single-electron case, the latter consistent with experiments in the literature. A model of dephasing that includes voltage and hyperfine noise is developed that is in good agreement with both single- and multielectron data, though in both cases additional exchange-independent dephasing is needed to obtain quantitative agreement across a broad parameter range.}, author = {Higginbotham, Andrew P and Kuemmeth, Ferdinand and Hanson, Micah and Gossard, Arthur and Marcus, Charles}, journal = {APS Physics, Physical Review Letters}, number = {2}, publisher = {American Physiological Society}, title = {{Coherent operations and screening in multielectron spin qubits}}, doi = {10.1103/PhysRevLett.112.026801}, volume = {112}, year = {2014}, } @article{9655, abstract = {Correlative microscopy incorporates the specificity of fluorescent protein labeling into high-resolution electron micrographs. Several approaches exist for correlative microscopy, most of which have used the green fluorescent protein (GFP) as the label for light microscopy. Here we use chemical tagging and synthetic fluorophores instead, in order to achieve protein-specific labeling, and to perform multicolor imaging. We show that synthetic fluorophores preserve their post-embedding fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is of such quality that the specimen can be prepared with identical protocols for scanning electron microscopy (SEM) and transmission electron microscopy (TEM); this is particularly valuable when singular or otherwise difficult samples are examined. We show that synthetic fluorophores give bright, well-resolved signals in super-resolution light microscopy, enabling us to superimpose light microscopic images with a precision of up to 25 nm in the x–y plane on electron micrographs. To exemplify the preservation quality of our new method we visualize the molecular arrangement of cadherins in adherens junctions of mouse epithelial cells.}, author = {Perkovic, Mario and Kunz, Michael and Endesfelder, Ulrike and Bunse, Stefanie and Wigge, Christoph and Yu, Zhou and Hodirnau, Victor-Valentin and Scheffer, Margot P. and Seybert, Anja and Malkusch, Sebastian and Schuman, Erin M. and Heilemann, Mike and Frangakis, Achilleas S.}, issn = {1047-8477}, journal = {Journal of Structural Biology}, number = {2}, pages = {205--213}, publisher = {Elsevier}, title = {{Correlative light- and electron microscopy with chemical tags}}, doi = {10.1016/j.jsb.2014.03.018}, volume = {186}, year = {2014}, } @article{9662, abstract = {Fractionation of isotopes among distinct molecules or phases is a quantum effect which is often exploited to obtain insights on reaction mechanisms, biochemical, geochemical, and atmospheric phenomena. Accurate evaluation of isotope ratios in atomistic simulations is challenging, because one needs to perform a thermodynamic integration with respect to the isotope mass, along with time-consuming path integral calculations. By re-formulating the problem as a particle exchange in the ring polymer partition function, we derive new estimators giving direct access to the differential partitioning of isotopes, which can simplify the calculations by avoiding thermodynamic integration. We demonstrate the efficiency of these estimators by applying them to investigate the isotope fractionation ratios in the gas-phase Zundel cation, and in a few simple hydrocarbons.}, author = {Cheng, Bingqing and Ceriotti, Michele}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, number = {24}, publisher = {AIP Publishing}, title = {{Direct path integral estimators for isotope fractionation ratios}}, doi = {10.1063/1.4904293}, volume = {141}, year = {2014}, } @article{9686, abstract = {It is well known that ultrasonic vibration can soften metals, and this phenomenon has been widely exploited in industrial applications concerning metal forming and bonding. Recent experiments show that the simultaneous application of oscillatory stresses from audible to ultrasonic frequency ranges can lead to not only softening but also significant dislocation annihilation and subgrain formation in metal samples from the nano- to macro-size range. These findings indicate that the existing understanding of ultrasound softening – that the vibrations either impose additional stress waves to augment the quasi-static applied load, or cause heating of the metal, whereas the metal’s intrinsic deformation resistance or mechanism remains unaltered – is far from complete. To understand the softening and the associated enhanced subgrain formation and dislocation annihilation, a new simulator based on the dynamics of dislocation-density functions is employed. This new simulator considers the flux, production and annihilation, as well as the Taylor and elastic interactions between dislocation densities. Softening during vibrations as well as enhanced cell formation is predicted. The simulations reveal the main mechanism for subcell formation under oscillatory loadings to be the enhanced elimination of statistically stored dislocations (SSDs) by the oscillatory stress, leaving behind geometrically necessary dislocations with low Schmid factors which then form the subgrain walls. The oscillatory stress helps the depletion of the SSDs, because the chance for them to meet up and annihilate is increased with reversals of dislocation motions. This is the first simulation effort to successfully predict the cell formation phenomenon under vibratory loadings.}, author = {Cheng, Bingqing and Leung, H.S. and Ngan, A.H.W.}, issn = {1478-6443}, journal = {Philosophical Magazine}, number = {16-18}, pages = {1845--1865}, publisher = {Taylor & Francis}, title = {{Strength of metals under vibrations – dislocation-density-function dynamics simulations}}, doi = {10.1080/14786435.2014.897008}, volume = {95}, year = {2014}, } @article{97, abstract = {The distribution of Coulomb blockade peak heights as a function of magnetic field is investigated experimentally in a Ge-Si nanowire quantum dot. Strong spin-orbit coupling in this hole-gas system leads to antilocalization of Coulomb blockade peaks, consistent with theory. In particular, the peak height distribution has its maximum away from zero at zero magnetic field, with an average that decreases with increasing field. Magnetoconductance in the open-wire regime places a bound on the spin-orbit length (lso < 20 nm), consistent with values extracted in the Coulomb blockade regime (lso < 25 nm).}, author = {Higginbotham, Andrew P and Kuemmeth, Ferdinand and Larsen, Thorvald and Fitzpatrick, Mattias and Yao, Jun and Yan, Hao and Lieber, Charles and Marcus, Charles}, journal = {APS Physics, Physical Review Letters}, number = {21}, publisher = {American Physical Society}, title = {{Antilocalization of coulomb blockade in a Ge/Si nanowire}}, doi = {10.1103/PhysRevLett.112.216806}, volume = {112}, year = {2014}, } @misc{9722, author = {Lovrics, Anna and Gao, Yu and Juhász, Bianka and Bock, István and Byrne, Helen M. and Dinnyés, András and Kovács, Krisztián}, publisher = {Public Library of Science}, title = {{Transition probability between TF expression states when Dbx2 inhibits Nkx2.2}}, doi = {10.1371/journal.pone.0111430.s006}, year = {2014}, } @misc{9739, author = {Chatterjee, Krishnendu and Pavlogiannis, Andreas and Adlam, Ben and Novak, Martin}, publisher = {Public Library of Science}, title = {{Detailed proofs for “The time scale of evolutionary innovation”}}, doi = {10.1371/journal.pcbi.1003818.s001}, year = {2014}, } @misc{9740, abstract = {The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens.}, author = {Konrad, Matthias and Grasse, Anna V and Tragust, Simon and Cremer, Sylvia}, publisher = {Dryad}, title = {{Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host}}, doi = {10.5061/dryad.vm0vc}, year = {2014}, } @misc{9741, abstract = {In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments.}, author = {Lagator, Mato and Colegrave, Nick and Neve, Paul}, publisher = {Dryad}, title = {{Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses}}, doi = {10.5061/dryad.85dn7}, year = {2014}, } @misc{9747, abstract = {Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment.}, author = {Lagator, Mato and Morgan, Andrew and Neve, Paul and Colegrave, Nick}, publisher = {Dryad}, title = {{Data from: Role of sex and migration in adaptation to sink environments}}, doi = {10.5061/dryad.s42n1}, year = {2014}, } @misc{9752, abstract = {Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible.}, author = {Simmons, Kristina and Prentice, Jason and Tkačik, Gašper and Homann, Jan and Yee, Heather and Palmer, Stephanie and Nelson, Philip and Balasubramanian, Vijay}, publisher = {Dryad}, title = {{Data from: Transformation of stimulus correlations by the retina}}, doi = {10.5061/dryad.246qg}, year = {2014}, } @misc{9753, abstract = {Background: The brood of ants and other social insects is highly susceptible to pathogens, particularly those that penetrate the soft larval and pupal cuticle. We here test whether the presence of a pupal cocoon, which occurs in some ant species but not in others, affects the sanitary brood care and fungal infection patterns after exposure to the entomopathogenic fungus Metarhizium brunneum. We use a) a comparative approach analysing four species with either naked or cocooned pupae and b) a within-species analysis of a single ant species, in which both pupal types co-exist in the same colony. Results: We found that the presence of a cocoon did not compromise fungal pathogen detection by the ants and that species with cocooned pupae increased brood grooming after pathogen exposure. All tested ant species further removed brood from their nests, which was predominantly expressed towards larvae and naked pupae treated with the live fungal pathogen. In contrast, cocooned pupae exposed to live fungus were not removed at higher rates than cocooned pupae exposed to dead fungus or a sham control. Consistent with this, exposure to the live fungus caused high numbers of infections and fungal outgrowth in larvae and naked pupae, but not in cocooned pupae. Moreover, the ants consistently removed the brood prior to fungal outgrowth, ensuring a clean brood chamber. Conclusion: Our study suggests that the pupal cocoon has a protective effect against fungal infection, causing an adaptive change in sanitary behaviours by the ants. It further demonstrates that brood removal - originally described for honeybees as “hygienic behaviour” – is a widespread sanitary behaviour in ants, which likely has important implications on disease dynamics in social insect colonies.}, author = {Tragust, Simon and Ugelvig, Line V and Chapuisat, Michel and Heinze, Jürgen and Cremer, Sylvia}, publisher = {Dryad}, title = {{Data from: Pupal cocoons affect sanitary brood care and limit fungal infections in ant colonies}}, doi = {10.5061/dryad.nc0gc}, year = {2014}, } @article{977, abstract = {We propose a method for detecting many-body localization (MBL) in disordered spin systems. The method involves pulsed coherent spin manipulations that probe the dephasing of a given spin due to its entanglement with a set of distant spins. It allows one to distinguish the MBL phase from a noninteracting localized phase and a delocalized phase. In particular, we show that for a properly chosen pulse sequence the MBL phase exhibits a characteristic power-law decay reflecting its slow growth of entanglement. We find that this power-law decay is robust with respect to thermal and disorder averaging, provide numerical simulations supporting our results, and discuss possible experimental realizations in solid-state and cold-atom systems.}, author = {Maksym Serbyn and Knap, Michael J and Gopalakrishnan, Sarang and Papić, Zlatko and Yao, Norman Y and Laumann, Chris R and Abanin, Dmitry A and Lukin, Mikhail D and Demler, Eugene A}, journal = {Physical Review Letters}, number = {14}, publisher = {American Physical Society}, title = {{Interferometric probes of many-body localization}}, doi = {10.1103/PhysRevLett.113.147204}, volume = {113}, year = {2014}, } @article{978, abstract = {The newly discovered topological crystalline insulators feature a complex band structure involving multiple Dirac cones, and are potentially highly tunable by external electric field, temperature or strain. Theoretically, it has been predicted that the various Dirac cones, which are offset in energy and momentum, might harbour vastly different orbital character. However, their orbital texture, which is of immense importance in determining a variety of a materialâ €™ s properties remains elusive. Here, we unveil the orbital texture of Pb 1â ̂'x Sn x Se, a prototypical topological crystalline insulator. By using Fourier-transform scanning tunnelling spectroscopy we measure the interference patterns produced by the scattering of surface-state electrons. We discover that the intensity and energy dependences of the Fourier transforms show distinct characteristics, which can be directly attributed to orbital effects. Our experiments reveal a complex band topology involving two Lifshitz transitions and establish the orbital nature of the Dirac bands, which could provide an alternative pathway towards future quantum applications.}, author = {Zeljkovic, Ilija and Okada, Yoshinori and Huang, Chengyi and Sankar, Raman and Walkup, Daniel and Zhou, Wenwen and Maksym Serbyn and Chou, Fangcheng and Tsai, Wei-Feng and Lin, Hsin and Bansil, Arun and Fu, Liang and Hasan, Md Z and Madhavan, Vidya}, journal = {Nature Physics}, number = {8}, pages = {572 -- 577}, publisher = {Nature Publishing Group}, title = {{Mapping the unconventional orbital texture in topological crystalline insulators}}, doi = {10.1038/nphys3012}, volume = {10}, year = {2014}, } @article{979, abstract = {In the recently discovered topological crystalline insulators SnTe and Pb1-xSnx(Te, Se), crystal symmetry and electronic topology intertwine to create topological surface states with many interesting features including Lifshitz transition, Van-Hove singularity, and fermion mass generation. These surface states are protected by mirror symmetry with respect to the (110) plane. In this work we present a comprehensive study of the effects of different mirror-symmetry-breaking perturbations on the (001) surface band structure. Pristine (001) surface states have four branches of Dirac fermions at low energy. We show that ferroelectric-type structural distortion generates a mass and gaps out some or all of these Dirac points, while strain shifts Dirac points in the Brillouin zone. An in-plane magnetic field leaves the surface state gapless, but introduces asymmetry between Dirac points. Finally, an out-of-plane magnetic field leads to discrete Landau levels. We show that the Landau level spectrum has an unusual pattern of degeneracy and interesting features due to the unique underlying band structure. This suggests that Landau level spectroscopy can detect and distinguish between different mechanisms of symmetry breaking in topological crystalline insulators.}, author = {Maksym Serbyn and Fu, Liang}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {3}, publisher = {American Physical Society}, title = {{Symmetry breaking and Landau quantization in topological crystalline insulators}}, doi = {10.1103/PhysRevB.90.035402}, volume = {90}, year = {2014}, } @article{98, abstract = {Relaxation and dephasing of hole spins are measured in a gate-defined Ge/Si nanowire double quantum dot using a fast pulsed-gate method and dispersive readout. An inhomogeneous dephasing time T2* ∼ 0.18 μs exceeds corresponding measurements in III-V semiconductors by more than an order of magnitude, as expected for predominately nuclear-spin-free materials. Dephasing is observed to be exponential in time, indicating the presence of a broadband noise source, rather than Gaussian, previously seen in systems with nuclear-spin-dominated dephasing.}, author = {Higginbotham, Andrew P and Larsen, Thorvald and Yao, Jun and Yan, Hao and Lieber, Charles and Marcus, Charles and Kuemmeth, Ferdinand}, journal = {Nano Letters}, number = {6}, pages = {3582 -- 3586}, publisher = {American Chemical Society}, title = {{Hole spin coherence in a Ge/Si heterostructure nanowire}}, doi = {10.1021/nl501242b}, volume = {14}, year = {2014}, }