@article{871, abstract = {BACKGROUND: Gene duplications have a major role in the evolution of new biological functions. Theoretical studies often assume that a duplication per se is selectively neutral and that, following a duplication, one of the gene copies is freed from purifying (stabilizing) selection, which creates the potential for evolution of a new function. RESULTS: In search of systematic evidence of accelerated evolution after duplication, we used data from 26 bacterial, six archaeal, and seven eukaryotic genomes to compare the mode and strength of selection acting on recently duplicated genes (paralogs) and on similarly diverged, unduplicated orthologous genes in different species. We find that the ratio of nonsynonymous to synonymous substitutions (Kn/Ks) in most paralogous pairs is <<1 and that paralogs typically evolve at similar rates, without significant asymmetry, indicating that both paralogs produced by a duplication are subject to purifying selection. This selection is, however, substantially weaker than the purifying selection affecting unduplicated orthologs that have diverged to the same extent as the analyzed paralogs. Most of the recently duplicated genes appear to be involved in various forms of environmental response; in particular, many of them encode membrane and secreted proteins. CONCLUSIONS: The results of this analysis indicate that recently duplicated paralogs evolve faster than orthologs with the same level of divergence and similar functions, but apparently do not experience a phase of neutral evolution. We hypothesize that gene duplications that persist in an evolving lineage are beneficial from the time of their origin, due primarily to a protein dosage effect in response to variable environmental conditions; duplications are likely to give rise to new functions at a later phase of their evolution once a higher level of divergence is reached.}, author = {Kondrashov, Fyodor and Rogozin, Igor and Wolf, Yuri and Koonin, Eugene}, issn = {1465-6906}, journal = {Genome Biology}, number = {2}, publisher = {BioMed Central}, title = {{Selection in the evolution of gene duplications }}, doi = {10.1186/gb-2002-3-2-research0008}, volume = {3}, year = {2002}, } @article{885, abstract = {We study fitness landscape in the space of protein sequences by relating sets of human pathogenic missense mutations in 32 proteins to amino acid substitutions that occurred in the course of evolution of these proteins. On average, ≈10% of deviations of a nonhuman protein from its human ortholog are compensated pathogenic deviations (CPDs), i.e., are caused by an amino acid substitution that, at this site, would be pathogenic to humans. Normal functioning of a CPD-containing protein must be caused by other, compensatory deviations of the nonhuman species from humans. Together, a CPD and the corresponding compensatory deviation form a Dobzhansky-Muller incompatibility that can be visualized as the corner on a fitness ridge. Thus, proteins evolve along fitness ridges which contain only ≈10 steps between sucessive corners. The fraction of CPDs among all deviations of a protein from its human ortholog does not increase with the evolutionary distance between the proteins, indicating that subtitutions that carry evolving proteins around these corners occur in rapid succession, driven by positive selection. Data on fitness of interspecies hybrids suggest that the compensatory change that makes a CPD fit usually occurs within the same protein. Data on protein structures and on cooccurrence of amino acids at different sites of multiple orthologous proteins often make it possible to provisionally identify the substitution that compensates a partiCUlar CPD.}, author = {Kondrashov, Alexey and Sunyaev, Shamil and Kondrashov, Fyodor}, issn = {0027-8424}, journal = {PNAS}, number = {23}, pages = {14878 -- 14883}, publisher = {National Academy of Sciences}, title = {{Dobzhansky-Muller incompatibilities in protein evolution}}, doi = {10.1073/pnas.232565499}, volume = {99}, year = {2002}, } @inproceedings{2340, abstract = {Recent experimental breakthroughs in the treatment of dilute Bose gases have renewed interest in their quantum mechanical description, respectively in approximations to it. The ground state properties of dilute Bose gases confined in external potentials and interacting via repulsive short range forces are usually described by means of the Gross-Pitaevskii energy functional. In joint work with Elliott H. Lieb and Jakob Yngvason its status as an approximation for the quantum mechanical many-body ground state problem has recently been rigorously clarified. We present a summary of this work, for both the two-and three-dimensional case. }, author = {Seiringer, Robert}, editor = {Demuth, Michael and Schultze, Bert}, isbn = {9783034894838}, location = {Clausthal, Germany}, pages = {307 -- 314}, publisher = {Birkhäuser}, title = {{Bosons in a trap: Asymptotic exactness of the Gross-Pitaevskii ground state energy formula}}, doi = {10.1007/978-3-0348-8231-6}, volume = {126}, year = {2001}, } @article{2341, abstract = {We study the ground state properties of an atom with nuclear charge Z and N bosonic "electrons" in the presence of a homogeneous magnetic field B. We investigate the mean field limit N→∞ with N / Z fixed, and identify three different asymptotic regions, according to B≪Z2,B∼Z2,andB≫Z2 . In Region 1 standard Hartree theory is applicable. Region 3 is described by a one-dimensional functional, which is identical to the so-called Hyper-Strong functional introduced by Lieb, Solovej and Yngvason for atoms with fermionic electrons in the region B≫Z3 ; i.e., for very strong magnetic fields the ground state properties of atoms are independent of statistics. For Region 2 we introduce a general magnetic Hartree functional, which is studied in detail. It is shown that in the special case of an atom it can be restricted to the subspace of zero angular momentum parallel to the magnetic field, which simplifies the theory considerably. The functional reproduces the energy and the one-particle reduced density matrix for the full N-particle ground state to leading order in N, and it implies the description of the other regions as limiting cases.}, author = {Baumgartner, Bernhard and Seiringer, Robert}, issn = {1424-0637}, journal = {Annales Henri Poincare}, number = {1}, pages = {41 -- 76}, publisher = {Birkhäuser}, title = {{Atoms with bosonic "electrons" in strong magnetic fields}}, doi = {10.1007/PL00001032}, volume = {2}, year = {2001}, } @article{2345, abstract = {We give upper bounds for the number of spin-1/2 particles that can be bound to a nucleus of charge Z in the presence of a magnetic field B, including the spin-field coupling. We use Lieb's strategy, which is known to yield Nc < 2Z + 1 for magnetic fields that go to zero at infinity, ignoring the spin-field interaction. For particles with fermionic statistics in a homogeneous magnetic field our upper bound has an additional term of the order of Z × min {(B/Z3)2/5, 1 + | 1n(B/Z3)|2}.}, author = {Seiringer, Robert}, issn = {0305-4470}, journal = {Journal of Physics A: Mathematical and General}, number = {9}, pages = {1943 -- 1948}, publisher = {IOP Publishing Ltd.}, title = {{On the maximal ionization of atoms in strong magnetic fields}}, doi = {10.1088/0305-4470/34/9/311}, volume = {34}, year = {2001}, } @article{2346, abstract = {By means of a generalization of the Fefferman - de la Llave decomposition we derive a general lower bound on the interaction energy of one-dimensional quantum systems. We apply this result to a specific class of lowest Landau band wave functions.}, author = {Hainzl, Christian and Seiringer, Robert}, issn = {0377-9017}, journal = {Letters in Mathematical Physics}, number = {2}, pages = {133 -- 142}, publisher = {Springer}, title = {{Bounds on one-dimensional exchange energies with application to lowest Landau band quantum mechanics}}, doi = {10.1023/A:1010951905548}, volume = {55}, year = {2001}, } @article{2347, abstract = {We consider the ground state properties of an inhomogeneous two-dimensional Bose gas with a repulsive, short range pair interaction and an external confining potential. In the limit when the particle number N is large but ρ̅a 2 is small, where ρ̅ is the average particle density and a the scattering length, the ground state energy and density are rigorously shown to be given to leading order by a Gross–Pitaevskii (GP) energy functional with a coupling constant g~1/|1n(ρ̅a 2)|. In contrast to the 3D case the coupling constant depends on N through the mean density. The GP energy per particle depends only on Ng. In 2D this parameter is typically so large that the gradient term in the GP energy functional is negligible and the simpler description by a Thomas–Fermi type functional is adequate.}, author = {Lieb, Élliott and Seiringer, Robert and Yngvason, Jakob}, issn = {0010-3616}, journal = {Communications in Mathematical Physics}, number = {1}, pages = {17 -- 31}, publisher = {Springer}, title = {{A rigorous derivation of the Gross-Pitaevskii energy functional for a two-dimensional Bose gas}}, doi = {10.1007/s002200100533}, volume = {224}, year = {2001}, } @article{2348, abstract = {This paper concerns the asymptotic ground state properties of heavy atoms in strong, homogeneous magnetic fields. In the limit when the nuclear charge Z tends to ∞ with the magnetic field B satisfying B ≫ Z4/3 all the electrons are confined to the lowest Landau band. We consider here an energy functional, whose variable is a sequence of one-dimensional density matrices corresponding to different angular momentum functions in the lowest Landau band. We study this functional in detail and derive various interesting properties, which are compared with the density matrix (DM) theory introduced by Lieb, Solovej and Yngvason. In contrast to the DM theory the variable perpendicular to the field is replaced by the discrete angular momentum quantum numbers. Hence we call the new functional a discrete density matrix (DDM) functional. We relate this DDM theory to the lowest Landau band quantum mechanics and show that it reproduces correctly the ground state energy apart from errors due to the indirect part of the Coulomb interaction energy.}, author = {Hainzl, Christian and Seiringer, Robert}, issn = {0010-3616}, journal = {Communications in Mathematical Physics}, number = {1}, pages = {229 -- 248}, publisher = {Springer}, title = {{A discrete density matrix theory for atoms in strong magnetic fields}}, doi = {10.1007/s002200100373}, volume = {217}, year = {2001}, } @article{2610, abstract = {To study the role of mGlu7 receptors (mGluR7), we used homologous recombination to generate mice lacking this metabotropic receptor subtype (mGluR7 -/-). After the serendipitous discovery of a sensory stimulus-evoked epileptic phenotype, we tested two convulsant drugs, pentylenetetrazole (PTZ) and bicuculline. In animals aged 12 weeks and older, subthreshold doses of these drugs induced seizures in mGluR7 -/-, but not in mGluR7 +/-, mice. PTZ-induced seizures were inhibited by three standard anticonvulsant drugs, but not by the group III selective mGluR agonist (R,S)-4-phosphonophenylglycine (PPG). Consistent with the lack of signs of epileptic activity in the absence of specific stimuli, mGluR7 -/- mice showed no major changes in synaptic properties in two slice preparations. However, slightly increased excitability was evident in hippocampal slices. In addition, there was slower recovery from frequency facilitation in cortical slices, suggesting a role for mGluR7 as a frequency-dependent regulator in presynaptic terminals. Our findings suggest that mGluR7 receptors have a unique role in regulating neuronal excitability and that these receptors may be a novel target for the development of anticonvulsant drugs.}, author = {Sansig, Gilles and Bushell, Trevor and Clarke, Vernon and Rozov, Andrei and Burnashev, Nail and Portet, Chantal and Gasparini, Fabrizio and Schmutz, Markus and Klebs, Klaus and Shigemoto, Ryuichi and Flor, Peter and Kühn, Rainer and Knoepfel, Thomas and Schroeder, Markus and Hampson, David and Collett, Valerie and Zhang, Congxiao and Duvoisin, Robert and Collingridge, Graham and Van Der Putten, Herman}, issn = {0270-6474}, journal = {Journal of Neuroscience}, number = {22}, pages = {8734 -- 8745}, publisher = {Society for Neuroscience}, title = {{Increased seizure susceptibility in mice lacking metabotropic glutamate receptor 7}}, doi = {10.1523/JNEUROSCI.21-22-08734.2001}, volume = {21}, year = {2001}, } @article{2734, abstract = {In this paper we describe an intrinsically geometric way of producing magnetic fields on S3 and R3 for which the corresponding Dirac operators have a non-trivial kernel. In many cases we are able to compute the dimension of the kernel. In particular we can give examples where the kernel has any given dimension. This generalizes the examples of Loss and Yau [1].}, author = {Erdös, László and Solovej, Jan}, issn = {0129-055X}, journal = {Reviews in Mathematical Physics}, number = {10}, pages = {1247 -- 1280}, publisher = {World Scientific Publishing}, title = {{The kernel of Dirac operators on S3 and R3}}, doi = {10.1142/S0129055X01000983}, volume = {13}, year = {2001}, } @article{2735, abstract = {We establish the exact low-energy asymptotics of the integrated density of states (Lifschitz tail) in a homogeneous magnetic field and Poissonian impurities with a repulsive single-site potential of Gaussian decay. It has been known that the Gaussian potential tail discriminates between the so-called “classical” and “quantum” regimes, and precise asymptotics are known in these cases. For the borderline case, the coexistence of the classical and quantum regimes was conjectured. Here we settle this last remaining open case to complete the full picture of the magnetic Lifschitz tails.}, author = {Erdös, László}, issn = {0044-3719}, journal = {Probability Theory and Related Fields}, number = {2}, pages = {219 -- 236}, publisher = {Springer}, title = {{Lifschitz tail in a magnetic field: Coexistence of classical and quantum behavior in the borderline case}}, doi = {10.1007/PL00008803}, volume = {121}, year = {2001}, } @article{2736, abstract = {We consider the time evolution of N bosonic particles interacting via a mean field Coulomb potential. Suppose the initial state is a product wavefunction. We show that at any finite time the correlation functions factorize in the limit N → ∞. Furthermore, the limiting one particle density matrix satisfies the nonlinear Hartree equation. The key ingredients are the uniqueness of the BBGKY hierarchy for the correlation functions and a new apriori estimate for the many-body Schrödinger equations.}, author = {Erdös, László and Yau, Horng}, issn = {1095-0761}, journal = {Advances in Theoretical and Mathematical Physics}, number = {6}, pages = {1169 -- 1205}, publisher = {International Press}, title = {{Derivation of the nonlinear Schrödinger equation from a many body Coulomb system}}, doi = {10.48550/arXiv.math-ph/0111042}, volume = {5}, year = {2001}, } @article{2981, abstract = {Plants contain a novel unique subfamily of Rho GTPases, vital components of cellular signalling networks. Here we report a general role for some members of this family in polarized plant growth processes. We show that Arabidopsis AtRop4 and AtRop6 encode functional GTPases with similar intrinsic GTP hydrolysis rates. We localized AtRop proteins in root meristem cells to the cross-wall and cell plate membranes. Polar localization of AtRops in trichoblasts specifies the growth sites for emerging root hairs. These sites were visible before budding and elongation of the Arabidopsis root hair when AtRops accumulated at their tips. Expression of constitutively active AtRop4 and AtRop6 mutant proteins in root hairs of transgenic Arabidopsis plants abolished polarized growth and delocalized the tip-focused Ca2+ gradient. Polar localization of AtRops was inhibited by brefeldin A, but not by other drugs such as latrunculin B, cytochalasin D or caffeine. Our results demonstrate a general function of AtRop GTPases in tip growth and in polar diffuse growth.}, author = {Molendijk, Arthur and Bischoff, Friedrich and Rajendrakumar, Chadalavada and Friml, Jirí and Braun, Markus and Gilroy, Simon and Palme, Klaus}, issn = {0261-4189}, journal = {EMBO Journal}, number = {11}, pages = {2779 -- 2788}, publisher = {Wiley-Blackwell}, title = {{Arabidopsis thaliana Rop GTPases are localized to tips of root hairs and control polar growth}}, doi = {10.1093/emboj/20.11.2779}, volume = {20}, year = {2001}, } @article{2982, abstract = {Polar auxin transport is crucial for the regulation of auxin action and required for some light-regulated responses during plant development. We have found that two mutants of Arabidopsis - doc1, which displays altered expression of light-regulated genes, and tir3, known for its reduced auxin transport - have similar defects and define mutations in a single gene that we have renamed BIG. BIG is very similar to the Drosophila gene Calossin/Pushover, a member of a gene family also present in Caenorhabditis elegans and human genomes. The protein encoded by BIG is extraordinary in size, 560 kD, and contains several putative Zn-finger domains. Expression-profiling experiments indicate that altered expression of multiple light-regulated genes in doc1 mutants can be suppressed by elevated levels of auxin caused by overexpression of an auxin biosynthetic gene, suggesting that normal auxin distribution is required to maintain low-level expression of these genes in the dark. Double mutants of tir3 with the auxin mutants pin1, pid, and axr1 display severe defects in auxin-dependent growth of the inflorescence. Chemical inhibitors of auxin transport change the intracellular localization of the auxin efflux carrier PIN1 in doc1/tir3 mutants, supporting the idea that BIG is required for normal auxin efflux.}, author = {Gil, Pedro and Dewey, Elizabeth and Friml, Jirí and Zhao, Yunde and Snowden, Kimberley and Putterill, Jo and Palme, Klaus and Estelle, Mark and Chory, Joanne}, issn = {0890-9369}, journal = {Genes and Development}, number = {15}, pages = {1985 -- 1997}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{BIG: A calossin-like protein required for polar auxin transport in Arabidopsis}}, doi = {10.1101/gad.905201}, volume = {15}, year = {2001}, } @article{2984, abstract = {Auxins represent an important class of plant hormone that regulate plant development. Plants use specialized carrier proteins to transport the auxin indole-3-acetic acid (IAA) to target tissues. To date, efflux carrier-mediated polar auxin transport has been assumed to represent the sole mode of long distance IAA movement. Localization of the auxin permease AUX1 in the Arabidopsis root apex has revealed a novel phloem-based IAA transport pathway. AUX1, asymmetrically localized to the plasma membrane of root protophloem cells, is proposed to promote the acropetal, post-phloem movement of auxin to the root apex. MS analysis shows that IAA accumulation in aux1 mutant root apices is impaired, consistent with an AUX1 phloem unloading function. AUX1 localization to columella and lateral root cap tissues of the Arabidopsis root apex reveals that the auxin permease regulates a second IAA transport pathway. Expression studies using an auxin-regulated reporter suggest that AUX1 is necessary for root gravitropism by facilitating basipetal auxin transport to distal elongation zone tissues.}, author = {Swarup, Ranjan and Friml, Jirí and Marchant, Alan and Ljung, Karin and Sandberg, Göran and Palme, Klaus and Bennett, Malcolm}, issn = {Genes and Development}, journal = {Genes and Development}, number = {20}, pages = {2648 -- 2653}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{Localization of the auxin permease AUX1 suggests two functionally distinct hormone transport pathways operate in the Arabidopsis root apex}}, doi = {10.1101/gad.210501}, volume = {15}, year = {2001}, } @article{1452, abstract = {In this Note we present pairs of hyperkähler orbifolds which satisfy two different versions of mirror symmetry. On the one hand, we show that their Hodge numbers (or more precisely, stringy E-polynomials) are equal. On the other hand, we show that they satisfy the prescription of Strominger, Yau, and Zaslow (which in the present case goes back to Bershadsky, Johansen, Sadov and Vafa): that a Calabi-Yau and its mirror should fiber over the same real manifold, with special Lagrangian fibers which are tori dual to each other. Our examples arise as moduli spaces of local systems on a curve with structure group SL(n); the mirror is the corresponding space with structure group PGL(n). The special Lagrangian tori come from an algebraically completely integrable Hamiltonian system: the Hitchin system.}, author = {Hausel, Tamas and Thaddeus, Michael}, issn = {0764-4442}, journal = {Comptes Rendus de l'Academie des Sciences - Series I: Mathematics}, number = {4}, pages = {313 -- 318}, publisher = {Elsevier}, title = {{Examples of mirror partners arising from integrable systems}}, doi = {10.1016/S0764-4442(01)02057-2}, volume = {333}, year = {2001}, } @article{1453, abstract = {In this Letter we exhibit a one-parameter family of new Taub-NUT instantons parameterized by a half-line. The endpoint of the half-line will be the reducible Yang-Mills instanton corresponding to the Eguchi-Hanson-Gibbons L2 harmonic 2-form, while at an inner point we recover the Pope-Yuille instanton constructed as a projection of the Levi-Civitá connection onto the positive su(2)+ ⊂ so(4) subalgebra. Our method imitates the Jackiw-Nohl-Rebbi construction originally designed for flat R4. That is we find a one-parameter family of harmonic functions on the Taub-NUT space with a point singularity, rescale the metric and project the obtained Levi-Civitá connection onto the other negative su(2)- ⊂ so(4) part. Our solutions will possess the full U(2) symmetry, and thus provide more solutions to the recently proposed U(2) symmetric ansatz of Kim and Yoon.}, author = {Etesi, Gábor and Hausel, Tamas}, issn = {0370-2693}, journal = {Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics}, number = {1-2}, pages = {189 -- 199}, publisher = {Elsevier}, title = {{Geometric construction of new Yang-Mills instantons over Taub-NUT space}}, doi = {10.1016/S0370-2693(01)00821-8}, volume = {514}, year = {2001}, } @article{1454, abstract = {We address the problem of finding Abelian instantons of finite energy on the Euclidean Schwarzschild manifold. This amounts to construct self-dual L2 harmonic 2-forms on the space. Gibbons found a non-topological L2 harmonic form in the Taub-NUT metric, leading to Abelian instantons with continuous energy. We imitate his construction in the case of the Euclidean Schwarzschild manifold and find a non-topological self-dual L2 harmonic 2-form on it. We show how this gives rise to Abelian instantons and identify them with SU(2)-instantons of Pontryagin number 2n2 found by Charap and Duff in 1977. Using results of Dodziuk and Hitchin we also calculate the full L2 harmonic space for the Euclidean Schwarzschild manifold.}, author = {Etesi, Gábor and Hausel, Tamas}, issn = {0393-0440}, journal = {Journal of Geometry and Physics}, number = {1-2}, pages = {126 -- 136}, publisher = {Elsevier}, title = {{Geometric interpretation of Schwarzschild instantons}}, doi = {10.1016/S0393-0440(00)00040-1}, volume = {37}, year = {2001}, } @inproceedings{18736, abstract = {Empirical studies of the first generation of stars and quasars will likely become feasible within the next decade in several different wavelength bands. Microwave anisotropy experiments, such as MAP or Planck, will set constraints on the ionization history of the intergalactic medium due to these sources. In the infrared, the Next Generation Space Telescope (NGST) will be able to directly detect sub-galactic objects at redshifts z>10. In the optical, data from the Hubble Deep Field already places a constraint on the abundance of high-redshift quasars. However, the epoch of the first quasars might be first probed in X-ray bands, by instruments such as the Chandra X-ray Observatory (CXO) and the X-ray Multi-mirror Mission (XMM). In a 500 Ksec integration, CXO reaches a sensitivity of 2x10-16 erg/s cm^2. Based on simple hierarchical CDM models, we find that at this flux threshold approx. 100 quasars might be detectable from redshifts z>5, and approx. 1 quasar at z=10, in each 17x17 arcmin field. Measurement of the power spectrum of the unresolved soft X-ray background will further constrain models of faint, high-redshift quasars.}, author = {Haiman, Zoltán}, booktitle = {AIP Conference Proceedings}, issn = {0094-243X}, location = {Bologna, Italy}, number = {1}, pages = {140--149}, publisher = {AIP Publishing}, title = {{Probing the cosmic dark age in X-rays}}, doi = {10.1063/1.1434627}, volume = {599}, year = {2001}, } @article{18743, abstract = {Over the coming decade, the observational samples available for studies of cluster abundance evolution will increase from tens to hundreds, or possibly to thousands, of clusters. Here we assess the power of future surveys to determine cosmological parameters. We quantify the statistical differences among cosmologies, including the effects of the cosmic equation of state parameter w, in mock cluster catalogs simulating a 12 deg^2 Sunyaev-Zel’dovich Effect (SZE) survey and a deep 10^4 deg^2 X-ray survey. The constraints from clusters are complementary to those from studies of high-redshift Supernovae (SNe), CMB anisotropies, or counts of high-redshift galaxies. Our results indicate that a statistical uncertainty of a few percent on both Ωm and w can be reached when cluster surveys are used in combination with any of these other datasets.}, author = {Haiman, Zoltán}, issn = {0094-243X}, journal = {AIP Conference Proceedings}, location = {Austin, TX, United States}, number = {1}, pages = {303--309}, publisher = {AIP}, title = {{Clusters in the precision cosmology era}}, doi = {10.1063/1.1419569}, volume = {586}, year = {2001}, }