@article{891, abstract = {Gene duplications and their subsequent divergence play an important part in the evolution of novel gene functions. Several models for the emergence, maintenance and evolution of gene copies have been proposed. However, a clear consensus on how gene duplications are fixed and maintained in genomes is lacking. Here, we present a comprehensive classification of the models that are relevant to all stages of the evolution of gene duplications. Each model predicts a unique combination of evolutionary dynamics and functional properties. Setting out these predictions is an important step towards identifying the main mechanisms that are involved in the evolution of gene duplications.}, author = {Innan, Hideki and Fyodor Kondrashov}, journal = {Nature Reviews Genetics}, number = {2}, pages = {97 -- 108}, publisher = {Nature Publishing Group}, title = {{The evolution of gene duplications: Classifying and distinguishing between models}}, doi = {10.1038/nrg2689}, volume = {11}, year = {2010}, } @article{901, abstract = {Background: Surveying deleterious variation in human populations is crucial for our understanding, diagnosis and potential treatment of human genetic pathologies. A number of recent genome-wide analyses focused on the prevalence of segregating deleterious alleles in the nuclear genome. However, such studies have not been conducted for the mitochondrial genome.Results: We present a systematic survey of polymorphisms in the human mitochondrial genome, including those predicted to be deleterious and those that correspond to known pathogenic mutations. Analyzing 4458 completely sequenced mitochondrial genomes we characterize the genetic diversity of different types of single nucleotide polymorphisms (SNPs) in African (L haplotypes) and non-African (M and N haplotypes) populations. We find that the overall level of polymorphism is higher in the mitochondrial compared to the nuclear genome, although the mitochondrial genome appears to be under stronger selection as indicated by proportionally fewer nonsynonymous than synonymous substitutions. The African mitochondrial genomes show higher heterozygosity, a greater number of polymorphic sites and higher frequencies of polymorphisms for synonymous, benign and damaging polymorphism than non-African genomes. However, African genomes carry significantly fewer SNPs that have been previously characterized as pathogenic compared to non-African genomes.Conclusions: Finding SNPs classified as pathogenic to be the only category of polymorphisms that are more abundant in non-African genomes is best explained by a systematic ascertainment bias that favours the discovery of pathogenic polymorphisms segregating in non-African populations. This further suggests that, contrary to the common disease-common variant hypothesis, pathogenic mutations are largely population-specific and different SNPs may be associated with the same disease in different populations. Therefore, to obtain a comprehensive picture of the deleterious variability in the human population, as well as to improve the diagnostics of individuals carrying African mitochondrial haplotypes, it is necessary to survey different populations independently.Reviewers: This article was reviewed by Dr Mikhail Gelfand, Dr Vasily Ramensky (nominated by Dr Eugene Koonin) and Dr David Rand (nominated by Dr Laurence Hurst).}, author = {Breen, Michael S and Fyodor Kondrashov}, journal = {Biology Direct}, publisher = {BioMed Central}, title = {{Mitochondrial pathogenic mutations are population-specific}}, doi = {10.1186/1745-6150-5-68}, volume = {5}, year = {2010}, } @article{9012, abstract = {In this Letter, we characterize experimentally the diffusiophoretic motion of colloids and λ-DNA toward higher concentration of solutes, using microfluidic technology to build spatially and temporally controlled concentration gradients. We then demonstrate that segregation and spatial patterning of the particles can be achieved from temporal variations of the solute concentration profile. This segregation takes the form of a strong trapping potential, stemming from an osmotically induced rectification mechanism of the solute time-dependent variations. Depending on the spatial and temporal symmetry of the solute signal, localization patterns with various shapes can be achieved. These results highlight the role of solute contrasts in out-of-equilibrium processes occurring in soft matter.}, author = {Palacci, Jérémie A and Abécassis, Benjamin and Cottin-Bizonne, Cécile and Ybert, Christophe and Bocquet, Lydéric}, issn = {10797114}, journal = {Physical Review Letters}, number = {13}, publisher = {American Physical Society}, title = {{Colloidal motility and pattern formation under rectified diffusiophoresis}}, doi = {10.1103/physrevlett.104.138302}, volume = {104}, year = {2010}, } @article{9013, abstract = {In this Letter, we investigate experimentally the nonequilibrium steady state of an active colloidal suspension under gravity field. The active particles are made of chemically powered colloids, showing self propulsion in the presence of an added fuel, here hydrogen peroxide. The active suspension is studied in a dedicated microfluidic device, made of permeable gel microstructures. Both the microdynamics of individual colloids and the global stationary state of the suspension under gravity are measured with optical microscopy. This yields a direct measurement of the effective temperature of the active system as a function of the particle activity, on the basis of the fluctuation-dissipation relationship. Our work is a first step in the experimental exploration of the out-of-equilibrium properties of active colloidal systems.}, author = {Palacci, Jérémie A and Cottin-Bizonne, Cécile and Ybert, Christophe and Bocquet, Lydéric}, issn = {10797114}, journal = {Physical Review Letters}, number = {8}, publisher = {American Physical Society }, title = {{Sedimentation and effective temperature of active colloidal suspensions}}, doi = {10.1103/physrevlett.105.088304}, volume = {105}, year = {2010}, } @article{9145, abstract = {We have found a new way to express the solutions of the RSM (Reynolds Stress Model) equations that allows us to present the turbulent diffusivities for heat, salt and momentum in a way that is considerably simpler and thus easier to implement than in previous work. The RSM provides the dimensionless mixing efficiencies Γα (α stands for heat, salt and momentum). However, to compute the diffusivities, one needs additional information, specifically, the dissipation ε. Since a dynamic equation for the latter that includes the physical processes relevant to the ocean is still not available, one must resort to different sources of information outside the RSM to obtain a complete Mixing Scheme usable in OGCMs. As for the RSM results, we show that the Γα’s are functions of both Ri and Rρ (Richardson number and density ratio representing double diffusion, DD); the Γα are different for heat, salt and momentum; in the case of heat, the traditional value Γh = 0.2 is valid only in the presence of strong shear (when DD is inoperative) while when shear subsides, NATRE data show that Γh can be three times as large, a result that we reproduce. The salt Γs is given in terms of Γh. The momentum Γm has thus far been guessed with different prescriptions while the RSM provides a well defined expression for Γm(Ri, Rρ). Having tested Γh, we then test the momentum Γm by showing that the turbulent Prandtl number Γm/Γh vs. Ri reproduces the available data quite well. As for the dissipation ε, we use different representations, one for the mixed layer (ML), one for the thermocline and one for the ocean’s bottom. For the ML, we adopt a procedure analogous to the one successfully used in PB (planetary boundary layer) studies; for the thermocline, we employ an expression for the variable εN−2 from studies of the internal gravity waves spectra which includes a latitude dependence; for the ocean bottom, we adopt the enhanced bottom diffusivity expression used by previous authors but with a state of the art internal tidal energy formulation and replace the fixed Γα = 0.2 with the RSM result that brings into the problem the Ri, Rρ dependence of the Γα; the unresolved bottom drag, which has thus far been either ignored or modeled with heuristic relations, is modeled using a formalism we previously developed and tested in PBL studies. We carried out several tests without an OGCM. Prandtl and flux Richardson numbers vs. Ri. The RSM model reproduces both types of data satisfactorily. DD and Mixing efficiency Γh(Ri, Rρ). The RSM model reproduces well the NATRE data. Bimodal ε-distribution. NATRE data show that ε(Ri < 1) ≈ 10ε(Ri > 1), which our model reproduces. Heat to salt flux ratio. In the Ri ≫ 1 regime, the RSM predictions reproduce the data satisfactorily. NATRE mass diffusivity. The z-profile of the mass diffusivity reproduces well the measurements at NATRE. The local form of the mixing scheme is algebraic with one cubic equation to solve.}, author = {Canuto, V.M. and Howard, A.M. and Cheng, Y. and Muller, Caroline J and Leboissetier, A. and Jayne, S.R.}, issn = {1463-5003}, journal = {Ocean Modelling}, keywords = {Computer Science (miscellaneous), Geotechnical Engineering and Engineering Geology, Atmospheric Science, Oceanography}, number = {3-4}, pages = {70--91}, publisher = {Elsevier}, title = {{Ocean turbulence, III: New GISS vertical mixing scheme}}, doi = {10.1016/j.ocemod.2010.04.006}, volume = {34}, year = {2010}, } @article{9146, abstract = {The factors governing the rate of change in the amount of atmospheric water vapor are analyzed in simulations of climate change. The global-mean amount of water vapor is estimated to increase at a differential rate of 7.3% K − 1 with respect to global-mean surface air temperature in the multi-model mean. Larger rates of change result if the fractional change is evaluated over a finite change in temperature (e.g., 8.2% K − 1 for a 3 K warming), and rates of change of zonal-mean column water vapor range from 6 to 12% K − 1 depending on latitude. Clausius–Clapeyron scaling is directly evaluated using an invariant distribution of monthly-mean relative humidity, giving a rate of 7.4% K − 1 for global-mean water vapor. There are deviations from Clausius–Clapeyron scaling of zonal-mean column water vapor in the tropics and mid-latitudes, but they largely cancel in the global mean. A purely thermodynamic scaling based on a saturated troposphere gives a higher global rate of 7.9% K − 1. Surface specific humidity increases at a rate of 5.7% K − 1, considerably lower than the rate for global-mean water vapor. Surface specific humidity closely follows Clausius–Clapeyron scaling over ocean. But there are widespread decreases in surface relative humidity over land (by more than 1% K − 1 in many regions), and it is argued that decreases of this magnitude could result from the land/ocean contrast in surface warming.}, author = {O’Gorman, P A and Muller, Caroline J}, issn = {1748-9326}, journal = {Environmental Research Letters}, keywords = {Renewable Energy, Sustainability and the Environment, Public Health, Environmental and Occupational Health, General Environmental Science}, number = {2}, publisher = {IOP Publishing}, title = {{How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?}}, doi = {10.1088/1748-9326/5/2/025207}, volume = {5}, year = {2010}, } @article{920, abstract = {Most eukaryotic cells sense and respond to the mechanical properties of their surroundings. This can strongly influence their collective behavior in embryonic development, tissue function, and wound healing. We use a deformable substrate to measure collective behavior in cell motion due to substrate mediated cell-cell interactions. We quantify spatial and temporal correlations in migration velocity and substrate deformation, and show that cooperative cell-driven patterns of substrate deformation mediate long-distance mechanical coupling between cells and control collective cell migration.}, author = {Angelini, Thomas and Hannezo, Edouard B and Trepat, Xavier and Fredberg, Jeffrey and Weitz, David}, journal = {Physical Review Letters}, number = {16}, publisher = {American Physical Society}, title = {{Cell migration driven by cooperative substrate deformation patterns}}, doi = {10.1103/PhysRevLett.104.168104}, volume = {104}, year = {2010}, } @article{9452, abstract = {Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae and that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes.}, author = {Zemach, Assaf and McDaniel, Ivy E. and Silva, Pedro and Zilberman, Daniel}, issn = {1095-9203}, journal = {Science}, keywords = {Multidisciplinary}, number = {5980}, pages = {916--919}, publisher = {American Association for the Advancement of Science}, title = {{Genome-wide evolutionary analysis of eukaryotic DNA methylation}}, doi = {10.1126/science.1186366}, volume = {328}, year = {2010}, } @article{9485, abstract = {Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops.}, author = {Zemach, Assaf and Kim, M. Yvonne and Silva, Pedro and Rodrigues, Jessica A. and Dotson, Bradley and Brooks, Matthew D. and Zilberman, Daniel}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {43}, pages = {18729--18734}, publisher = {National Academy of Sciences}, title = {{Local DNA hypomethylation activates genes in rice endosperm}}, doi = {10.1073/pnas.1009695107}, volume = {107}, year = {2010}, } @article{9489, abstract = {Cytosine methylation is an ancient process with conserved enzymology but diverse biological functions that include defense against transposable elements and regulation of gene expression. Here we will discuss the evolution and biological significance of eukaryotic DNA methylation, the likely drivers of that evolution, and major remaining mysteries.}, author = {Zemach, Assaf and Zilberman, Daniel}, issn = {1879-0445}, journal = {Current Biology}, number = {17}, pages = {R780--R785}, publisher = {Elsevier}, title = {{Evolution of eukaryotic DNA methylation and the pursuit of safer sex}}, doi = {10.1016/j.cub.2010.07.007}, volume = {20}, year = {2010}, } @misc{9764, author = {Rosas, Ulises and Barton, Nicholas H and Copsey, Lucy and Barbier De Reuille, Pierre and Coen, Enrico}, publisher = {Public Library of Science}, title = {{Heterosis and the drift load}}, doi = {10.1371/journal.pbio.1000429.s003}, year = {2010}, } @article{7078, abstract = {We report resonant ultrasound spectroscopy (RUS), dilatometry/magnetostriction, magnetotransport, magnetization, specific-heat, and 119Sn Mössbauer spectroscopy measurements on SnTe and Sn0.995Cr0.005Te. Hall measurements at T=77 K indicate that our Bridgman-grown single crystals have a p-type carrier concentration of 3.4×1019 cm−3 and that our Cr-doped crystals have an n-type concentration of 5.8×1022 cm−3. Although our SnTe crystals are diamagnetic over the temperature range 2≤T≤1100 K, the Cr-doped crystals are room-temperature ferromagnets with a Curie temperature of 294 K. For each sample type, three-terminal capacitive dilatometry measurements detect a subtle 0.5 μm distortion at Tc≈85 K. Whereas our RUS measurements on SnTe show elastic hardening near the structural transition, pointing to co-elastic behavior, similar measurements on Sn0.995Cr0.005Te show a pronounced softening, pointing to ferroelastic behavior. Effective Debye temperature, θD, values of SnTe obtained from 119Sn Mössbauer studies show a hardening of phonons in the range 60–115 K (θD=162 K) as compared with the 100–300 K range (θD=150 K). In addition, a precursor softening extending over approximately 100 K anticipates this collapse at the critical temperature and quantitative analysis over three decades of its reduced modulus finds ΔC44/C44=A|(T−T0)/T0|−κ with κ=0.50±0.02, a value indicating a three-dimensional softening of phonon branches at a temperature T0∼75 K, considerably below Tc. We suggest that the differences in these two types of elastic behaviors lie in the absence of elastic domain-wall motion in the one case and their nucleation in the other.}, author = {Salje, E. K. H. and Safarik, D. J. and Modic, Kimberly A and Gubernatis, J. E. and Cooley, J. C. and Taylor, R. D. and Mihaila, B. and Saxena, A. and Lookman, T. and Smith, J. L. and Fisher, R. A. and Pasternak, M. and Opeil, C. P. and Siegrist, T. and Littlewood, P. B. and Lashley, J. C.}, issn = {1098-0121}, journal = {Physical Review B}, number = {18}, publisher = {APS}, title = {{Tin telluride: A weakly co-elastic metal}}, doi = {10.1103/physrevb.82.184112}, volume = {82}, year = {2010}, } @article{7079, abstract = {We have observed that reacting Pb:Te:Ag:Se in a 1:1:1.9:1 molar ratio gives rise to what appears to be a predominantly single-phase alloy, which crystallizes in the PbSe cF8 fcc structure. However, further investigation of the structure using energy dispersive x-ray analysis reveals the presence of two phases, PbSe and β-Ag2Te, with identical lattice parameters. The total thermal conductivity of the formed alloy is remarkably low for a crystalline material, κT<0.6W∕mK at 675K, it is reproducible, and in addition, the compound has good mechanical properties.}, author = {Drymiotis, Fivos R. and Drye, Tyler B. and Wang, Yisha and He, Jian and Rhodes, Daniel and Modic, Kimberly A and Cawthorne, Samantha and Zhang, Qiu Run}, issn = {0021-8979}, journal = {Journal of Applied Physics}, number = {3}, publisher = {AIP}, title = {{Structure formation and very low thermal conductivity in Pb:Te:Ag:Se mixtures}}, doi = {10.1063/1.3284946}, volume = {107}, year = {2010}, } @article{7318, abstract = {The decomposition reaction of H2O2 aqueous solutions (H2O2 - H2O + 1/2O2) catalyzed by transition metal oxide powders has been compared with the charging voltage of nonaqueous Li-O2 cells containing the same catalyst. An inverse linear relationship between Ln k (rate constant for the H2O2 decomposition) and the charging voltage has been found, despite differences in media and possible mechanistic differences. The results suggest that the decomposition may be a reliable, useful, and fast screening tool for materials that promote the charging process of the Li-O2 battery and may ultimately give insight into the charging mechanism.}, author = {Giordani, V. and Freunberger, Stefan Alexander and Bruce, P. G. and Tarascon, J.-M. and Larcher, D.}, issn = {1099-0062}, journal = {Electrochemical and Solid-State Letters}, number = {12}, publisher = {The Electrochemical Society}, title = {{H2O2 decomposition reaction as selecting tool for catalysts in Li–O2 cells}}, doi = {10.1149/1.3494045}, volume = {13}, year = {2010}, } @inproceedings{754, abstract = {Most people believe that renaming is easy: simply choose a name at random; if more than one process selects the same name, then try again. We highlight the issues that occur when trying to implement such a scheme and shed new light on the read-write complexity of randomized renaming in an asynchronous environment. At the heart of our new perspective stands an adaptive implementation of a randomized test-and-set object, that has poly-logarithmic step complexity per operation, with high probability. Interestingly, our implementation is anonymous, as it does not require process identifiers. Based on this implementation, we present two new randomized renaming algorithms. The first ensures a tight namespace of n names using O( n log4 n) total steps, with high probability. This significantly improves on the complexity of the best previously known namespace-optimal algorithms. The second algorithm achieves a namespace of size k (1 + ε) using O( k log4 k / log2 (1 + ε) ) total steps, both with high probability, where k is the total contention in the execution. It is the first adaptive randomized renaming algorithm, and it improves on existing deterministic solutions by providing a smaller namespace, and by lowering step complexity.}, author = {Alistarh, Dan-Adrian and Attiya, Hagit and Gilbert, Seth and Giurgiu, Andrei and Guerraoui, Rachid}, pages = {94 -- 108}, publisher = {Springer}, title = {{Fast randomized test-and-set and renaming}}, doi = {10.1007/978-3-642-15763-9_9}, volume = {6343 LNCS}, year = {2010}, } @inproceedings{755, abstract = {Gossip, also known as epidemic dissemination, is becoming an increasingly popular technique in distributed systems. Yet, it has remained a partially open question: how robust are such protocols? We consider a natural extension of the random phone-call model (introduced by Karp et al. [1]), and we analyze two different notions of robustness: the ability to tolerate adaptive failures, and the ability to tolerate oblivious failures. For adaptive failures, we present a new gossip protocol, TrickleGossip, which achieves near-optimal O(n log 3 n) message complexity. To the best of our knowledge, this is the first epidemic-style protocol that can tolerate adaptive failures. We also show a direct relation between resilience and message complexity, demonstrating that gossip protocols which tolerate a large number of adaptive failures need to use a super-linear number of messages with high probability. For oblivious failures, we present a new gossip protocol, CoordinatedGossip, that achieves optimal O(n) message complexity. This protocol makes novel use of the universe reduction technique to limit the message complexity.}, author = {Alistarh, Dan-Adrian and Gilbert, Seth and Guerraoui, Rachid and Zadimoghaddam, Morteza}, number = {PART 2}, pages = {115 -- 126}, publisher = {Springer}, title = {{How efficient can gossip be? (On the cost of resilient information exchange)}}, doi = {10.1007/978-3-642-14162-1_10}, volume = {6199 LNCS}, year = {2010}, } @inproceedings{756, abstract = {This paper studies non-cryptographic authenticated broadcast in radio networks subject to malicious failures. We introduce two protocols that address this problem. The first, NeighborWatchRB, makes use of a novel strategy in which honest devices monitor their neighbors for malicious behavior. Second, we present a more robust variant, MultiPathRB, that tolerates the maximum possible density of malicious devices per region, using an elaborate voting strategy. We also introduce a new proof technique to show that both protocols ensure asymptotically optimal running time. We demonstrate the fault tolerance of our protocols through extensive simulation. Simulations show the practical superiority of the NeighborWatchRB protocol (an advantage hidden in the constants of the asymptotic complexity). The NeighborWatchRB protocol even performs relatively well when compared to the simple, fast epidemic protocols commonly used in the radio setting, protocols that tolerate no malicious faults. We therefore believe that the overhead for ensuring authenticated broadcast is reasonable, especially in applications that use authenticated broadcast only when necessary, such as distributing an authenticated digest.}, author = {Alistarh, Dan-Adrian and Gilbert, Seth and Guerraoui, Rachid and Milošević, Žarko and Newport, Calvin}, pages = {50 -- 59}, publisher = {ACM}, title = {{Securing every bit: Authenticated broadcast in radio networks}}, doi = {10.1145/1810479.1810489}, year = {2010}, } @article{22029, abstract = {We consider two classes of defocusing energy-supercritical nonlinear Schrödinger equations in dimensions d ≥ 5. We prove that if the solution u is a priori bounded in the critical Sobolev space, that is, {mathematical formular} , then u is global and scatters.}, author = {Killip, Rowan and Visan, Monica}, issn = {1532-4133}, journal = {Communications in Partial Differential Equations}, keywords = {critical regularity, Nonlinear Schrödinger equations}, number = {6}, pages = {945--987}, publisher = {Informa UK Limited}, title = {{Energy-supercritical NLS: Critical [Hdot]^s-bounds imply scattering}}, doi = {10.1080/03605301003717084}, volume = {35}, year = {2010}, } @article{22089, abstract = {We consider the focusing energy-critical nonlinear Schr\"odinger equation $iu_t+\Delta u = - |u|^{4\over{d-2}}u$ in dimensions $d\geq 5$. We prove that if a maximal-lifespan solution $u\colon \ I\times {\Bbb R}^d\to {\Bbb C}$ obeys $\sup_{t\in I}\|\nabla u(t)\|_2<\|\nabla W\|_2$, then it is global and scatters both forward and backward in time. Here $W$ denotes the ground state, which is a stationary solution of the equation. In particular, if a solution has both energy and kinetic energy less than those of the ground state $W$ at some point in time, then the solution is global and scatters. We also show that any solution that blows up with bounded kinetic energy must concentrate at least the kinetic energy of the ground state. Similar results were obtained by Kenig and Merle for spherically symmetric initial data and dimensions $d=3,4,5$. }, author = {Killip, Rowan and Visan, Monica}, issn = {1080-6377}, journal = {American Journal of Mathematics}, number = {2}, pages = {361--424}, publisher = {Johns Hopkins University Press}, title = {{The focusing energy-critical nonlinear Schrödinger equation in dimensions five and higher}}, doi = {10.1353/ajm.0.0107}, volume = {132}, year = {2010}, } @article{110, abstract = {In order to better understand magnetic reconnection and particle acceleration in solar flares, we compare the RHESSI hard X-ray (HXR) footpoint motions of three flares with a detailed study of the corresponding topology given by a Magnetic Charge Topology model. We analyze the relationship between the footpoint motions and topological spine lines and find that the examined footpoint sources move along spine lines. We present a three-dimensional topological model in which this movement can be understood. As reconnection proceeds, flux is transferred between the reconnecting domains, causing the separator to move. The movement of the separator\'s chromospheric ends, identified with the HXR footpoints, is along those spine lines on which the separator ends.}, author = {Des Jardins, Angela and Canfield, Richard and Longcope, Dana and Fordyce, Crystal and Waitukaitis, Scott R}, journal = {The Astrophysical Journal}, number = {2}, pages = {1628 -- 1636}, publisher = {IOP Publishing Ltd.}, title = {{Reconnection in three dimensions: The role of spines in three eruptive flares}}, doi = {10.1088/0004-637X/693/2/1628}, volume = {693}, year = {2009}, }