@article{17785, abstract = {We study the potential of a large future weak-lensing survey to constrain dark energy properties by using both the number counts of detected galaxy clusters (sensitive primarily to density fluctuations on small scales) and tomographic shear-shear correlations (restricted to large scales). We use the Fisher matrix formalism, assume a flat universe and parameterize the equation of state of dark energy by w(a)=w_0+w_a(1-a), to forecast the expected statistical errors from either observable, and from their combination. We show that the covariance between these two observables is small, and argue that therefore they can be regarded as independent constraints. We find that when the number counts and the shear-shear correlations (on angular scales l < 1000) are combined, an LSST (Large Synoptic Survey Telescope)-like survey can yield statistical errors on (Omega_DE, w_0, w_a) as tight as (0.003, 0.03, 0.1). These values are a factor of 2-25 better than using either observable alone. The results are also about a factor of two better than those from combining number counts of galaxy clusters and their power spectrum.}, author = {Fang, Wenjuan and Haiman, Zoltán}, issn = {1550-7998}, journal = {Physical Review D}, number = {4}, publisher = {American Physical Society}, title = {{Constraining dark energy by combining cluster counts and shear-shear correlations in a weak lensing survey}}, doi = {10.1103/physrevd.75.043010}, volume = {75}, year = {2007}, } @article{17791, abstract = {We consider the pumping of the 63.2 μm fine-structure line of neutral O I in the high-redshift intergalactic medium (IGM), in analogy with the Wouthuysen-Field effect for the 21 cm line of cosmic H I. We show that the soft UV background at ~1300 Å can affect the population levels, and if a significant fraction of the IGM volume is filled with "fossil H II regions" containing neutral O I, then this can produce a nonnegligible spectral distortion in the cosmic microwave background (CMB). O I from redshift z is seen in emission at (1 + z)63.2 μm, and in the range 7 < z < 10 produces a mean spectral distortion of the CMB with y = (10^-9 to 3 × 10^-8)(Z/10^-3 Z☉)(IUV), where Z is the mean metallicity of the IGM and IUV is the UV background at 1300 Å in units of 10^-20 ergs s-1 Hz^-1 cm-2 sr^-1. A measurement of this signature can trace the metallicity at the end of the dark ages, prior to the completion of cosmic reionization, and is complementary to cosmological 21 cm studies. While future CMB experiments such as Planck could constrain the metallicity to the 10^-2 Z☉ level, specifically designed experiments could potentially achieve a detection.}, author = {Hernández-Monteagudo, Carlos and Haiman, Zoltán and Jimenez, Raul and Verde, Licia}, issn = {0004-637X}, journal = {The Astrophysical Journal}, number = {2}, pages = {L85--L88}, publisher = {American Astronomical Society}, title = {{Oxygen pumping: Probing intergalactic metals at the epoch of reionization}}, doi = {10.1086/518090}, volume = {660}, year = {2007}, } @article{17793, abstract = {We use the spectra of ~22,000 early-type galaxies, selected from the Sloan Digital Sky Survey, to infer the ages, metallicities, and star formation histories of these galaxies. We find clear evidence of "downsizing," i.e., that galaxies with larger velocity dispersion have older stellar populations. In particular, we find that most early-type galaxies with velocity dispersion exceeding 200 km s-1 formed more than 90% of their current stellar mass at redshift z > 2.5. Therefore, star formation was suppressed around this redshift. We also show that chemical enrichment was rapid, lasting 1-2 Gyr, and find evidence that [Fe/H] is subsolar. We study the robustness of these results by comparing three different approaches: (1) using Lick absorption line indices, (2) fitting a single-burst stellar population model to the whole spectrum (lines and continuum), and (3) reconstructing the star formation and metallicity histories in multiple age bins, providing a method to measure mass-weighted ages and metallicities. We find good agreement between the luminosity-weighted ages and metallicities computed with these three methods.}, author = {Jimenez, Raul and Bernardi, Mariangela and Haiman, Zoltán and Panter, Ben and Heavens, Alan F.}, issn = {0004-637X}, journal = {The Astrophysical Journal}, number = {2}, pages = {947--951}, publisher = {American Astronomical Society}, title = {{The ages, metallicities, and star formation histories of early‐type galaxies in the SDSS}}, doi = {10.1086/521323}, volume = {669}, year = {2007}, } @inproceedings{17795, abstract = {The gravitational waves (GWs) emitted during the coalescence of supermassive black holes (SMBHs) will be detectable with the future Laser Interferometric Space Antenna (LISA). The direction and distance can be determined from the accumulated GW signal with a precision that increases rapidly in the final stages of the inspiral. We find that for M = (105 − 107)M⊙ near z = 1 the angular uncertainty decreases under 1ˆ at least several hours before the plunge, allowing a targeted electromagnetic (EM) observation of the final stages of the merger with a wide field instrument. We then calculate the size of the final, three dimensional error volume. Under the plausible assumption that SMBH-SMBH mergers are accompanied by gas accretion leading to Eddington-limited quasar activity, we find that many cases this error volume will contain at most a single quasar for M = (105 − 107) M⊙ near z = 1. This will allow a straightforward test of the hypothesis that GW events are accompanied by bright quasar activity. The identification and observation of counterparts would allow unprecedented tests of the physics of MBH accretion, such as precision–measurements of the Eddington ratio. They would clarify the role of gas as a catalyst in SMBH coalescences, and would also offer an alternative method to constrain cosmological parameters.}, author = {Kocsis, B. and Frei, Z. and Haiman, Zoltán and Menou, K.}, booktitle = {Proceedings of the 2005 MPE/USM/MPA/ESO Joint Astronomy Conference}, isbn = {9783540747123}, location = {Munich, Germany}, pages = {82--86}, publisher = {Springer Nature}, title = {{Finding the electromagnetic counterparts of standard sirens}}, doi = {10.1007/978-3-540-74713-0_18}, year = {2007}, } @article{7704, abstract = {Gradients of axon guidance molecules instruct the formation of continuous neural maps, such as the retinotopic map in the vertebrate visual system. Here we show that molecular gradients can also instruct the formation of a discrete neural map. In the fly olfactory system, axons of 50 classes of olfactory receptor neurons (ORNs) and dendrites of 50 classes of projection neurons (PNs) form one-to-one connections at discrete units called glomeruli. We provide expression, loss- and gain-of-function data to demonstrate that the levels of transmembrane Semaphorin-1a (Sema-1a), acting cell-autonomously as a receptor or part of a receptor complex, direct the dendritic targeting of PNs along the dorsolateral to ventromedial axis of the antennal lobe. Sema-1a also regulates PN axon targeting in higher olfactory centers. Thus, graded expression of Sema-1a contributes to connection specificity from ORNs to PNs and then to higher brain centers, ensuring proper representation of olfactory information in the brain.}, author = {Komiyama, Takaki and Sweeney, Lora Beatrice Jaeger and Schuldiner, Oren and Garcia, K. Christopher and Luo, Liqun}, issn = {0092-8674}, journal = {Cell}, number = {2}, pages = {399--410}, publisher = {Elsevier}, title = {{Graded expression of semaphorin-1a cell-autonomously directs dendritic targeting of olfactory projection neurons}}, doi = {10.1016/j.cell.2006.12.028}, volume = {128}, year = {2007}, } @article{7705, abstract = {Axon-axon interactions have been implicated in neural circuit assembly, but the underlying mechanisms are poorly understood. Here, we show that in the Drosophila antennal lobe, early-arriving axons of olfactory receptor neurons (ORNs) from the antenna are required for the proper targeting of late-arriving ORN axons from the maxillary palp (MP). Semaphorin-1a is required for targeting of all MP but only half of the antennal ORN classes examined. Sema-1a acts nonautonomously to control ORN axon-axon interactions, in contrast to its cell-autonomous function in olfactory projection neurons. Phenotypic and genetic interaction analyses implicate PlexinA as the Sema-1a receptor in ORN targeting. Sema-1a on antennal ORN axons is required for correct targeting of MP axons within the antennal lobe, while interactions amongst MP axons facilitate their entry into the antennal lobe. We propose that Sema-1a/PlexinA-mediated repulsion provides a mechanism by which early-arriving ORN axons constrain the target choices of late-arriving axons.}, author = {Sweeney, Lora Beatrice Jaeger and Couto, Africa and Chou, Ya-Hui and Berdnik, Daniela and Dickson, Barry J. and Luo, Liqun and Komiyama, Takaki}, issn = {0896-6273}, journal = {Neuron}, number = {2}, pages = {185--200}, publisher = {Elsevier}, title = {{Temporal target restriction of olfactory receptor neurons by semaphorin-1a/plexinA-mediated axon-axon interactions}}, doi = {10.1016/j.neuron.2006.12.022}, volume = {53}, year = {2007}, } @article{7753, abstract = {In many species, females show reduced expression of a trait that is under sexual selection in males, and this expression is thought to be maintained through genetic associations with the male phenotype. However, there is also the potential for the female trait to convey an advantage in intrasexual conflicts over resources. We tested this hypothesis in a feral population of Soay sheep, in which males and females have a polymorphism for horn development, producing either full (normal horned), reduced (scurred) or no (polled, females only) horns. During the lambing period, females who possessed horns were more likely to initiate and win aggressive interactions, independent of age, weight and birthing status. The occurrence of aggression was also context dependent, decreasing over the lambing period and associated with local density. Our results demonstrate that a trait that confers benefits to males during intrasexual competition for mates may also be used by females in intrasexual competition over resources: males use weaponry to gain mates, whereas females use weaponry to gain food.}, author = {Robinson, Matthew Richard and Kruuk, Loeske E.B}, issn = {1744-9561}, journal = {Biology Letters}, number = {6}, pages = {651--654}, publisher = {The Royal Society}, title = {{Function of weaponry in females: The use of horns in intrasexual competition for resources in female Soay sheep}}, doi = {10.1098/rsbl.2007.0278}, volume = {3}, year = {2007}, } @article{7780, abstract = {We used single-channel electrical recordings and Langevin molecular dynamics simulations to explore the electrophoretic translocation of various β-hairpin peptides across the staphylococcal α-hemolysin (αHL) protein pore at single-molecule resolution. The β-hairpin peptides, which varied in their folding properties, corresponded to the C terminal residues of the B1 domain of protein G. The translocation time was strongly dependent on the electric force and was correlated with the folding features of the β-hairpin peptides. Highly unfolded peptides entered the pore in an extended conformation, resulting in fast single-file translocation events. In contrast, the translocation of the folded β-hairpin peptides occurred more slowly. In this case, the β-hairpin peptides traversed the αHL pore in a misfolded or fully folded conformation. This study demonstrates that the interaction between a polypeptide and a β-barrel protein pore is dependent on the folding features of the polypeptide. }, author = {Goodrich, Carl Peter and Kirmizialtin, Serdal and Huyghues-Despointes, Beatrice M. and Zhu, Aiping and Scholtz, J. Martin and Makarov, Dmitrii E. and Movileanu, Liviu}, issn = {1520-6106}, journal = {The Journal of Physical Chemistry B}, number = {13}, pages = {3332--3335}, publisher = {American Chemical Society}, title = {{Single-molecule electrophoresis of β-hairpin peptides by electrical recordings and Langevin dynamics simulations}}, doi = {10.1021/jp071364h}, volume = {111}, year = {2007}, } @article{7781, abstract = {Males are predicted to compete for reproductive opportunities, with sexual selection driving the evolution of large body size and weaponry through the advantage they confer for access to females. Few studies have explored potential trade‐offs of investment in secondary sexual traits between different components of fitness or tested for sexually antagonistic selection pressures. These factors may provide explanations for observed polymorphisms in both form and quality of secondary sexual traits. We report here an analysis of selection on horn phenotype in a feral population of Soay sheep (Ovis aries) on the island of Hirta, St. Kilda, Scotland. Soay sheep display a phenotypic polymorphism for horn type with males growing either normal or reduced (scurred) horns, and females growing either normal, scurred, or no (polled) horns; further variation in size exists within horn morphs. We show that horn phenotype and the size of the trait displayed is subject to different selection pressures in males and females, generating sexually antagonistic selection. Furthermore, there was evidence of a trade‐off between breeding success and longevity in normal‐horned males, with both the normal horn type and larger horn size being associated with greater annual breeding success but reduced longevity. Therefore, selection through lifetime breeding success was not found to act upon horn phenotype in males. In females, a negative association of annual breeding success within the normal‐horned phenotype did not result in a significant difference in lifetime fitness when compared to scurred individuals, as no significant difference in longevity was found. However, increased horn size within this group was negatively associated with breeding success and longevity. Females without horns (polled) suffered reduced longevity and thus reduced lifetime breeding success relative the other horn morphs. Our results therefore suggest that trade‐offs between different components of fitness and antagonistic selection between the sexes may maintain genetic variation for secondary sexual traits within a population.}, author = {Robinson, Matthew Richard and Pilkington, Jill G. and Clutton-Brock, Tim H. and Pemberton, Josephine M. and Kruuk, Loeske E.B.}, issn = {0014-3820}, journal = {Evolution}, number = {10}, pages = {2168--2181}, publisher = {Wiley}, title = {{Live fast, die young: Trade-offs between fitness components and sexually antagonistic selection on weaponry in soay sheep}}, doi = {10.1111/j.0014-3820.2006.tb01854.x}, volume = {60}, year = {2007}, } @article{8027, abstract = {Gating deficits and hallucinatory sensations are prominent symptoms of schizophrenia. Comparing these abnormalities with the failure modes of network models is an interesting way to explore how they arise. We present a network model that can both propagate and gate signals. The model exhibits effects reminiscent of clinically observed pathologies when the balance between excitation and inhibition that it requires is not properly maintained.}, author = {Vogels, Tim P and Abbott, L.}, issn = {0176-3679}, journal = {Pharmacopsychiatry}, number = {S 1}, pages = {S73--S77}, publisher = {Thieme}, title = {{Gating deficits in model networks: A path to schizophrenia?}}, doi = {10.1055/s-2007-992130}, volume = {40}, year = {2007}, } @article{8483, abstract = {Atom-resolved real-time studies of kinetic processes in proteins have been hampered in the past by the lack of experimental techniques that yield sufficient temporal and atomic resolution. Here we present band-selective optimized flip-angle short transient (SOFAST) real-time 2D NMR spectroscopy, a method that allows simultaneous observation of reaction kinetics for a large number of nuclear sites along the polypeptide chain of a protein with an unprecedented time resolution of a few seconds. SOFAST real-time 2D NMR spectroscopy combines fast NMR data acquisition techniques with rapid sample mixing inside the NMR magnet to initiate the kinetic event. We demonstrate the use of SOFAST real-time 2D NMR to monitor the conformational transition of α-lactalbumin from a molten globular to the native state for a large number of amide sites along the polypeptide chain. The kinetic behavior observed for the disappearance of the molten globule and the appearance of the native state is monoexponential and uniform along the polypeptide chain. This observation confirms previous findings that a single transition state ensemble controls folding of α-lactalbumin from the molten globule to the native state. In a second application, the spontaneous unfolding of native ubiquitin under nondenaturing conditions is characterized by amide hydrogen exchange rate constants measured at high pH by using SOFAST real-time 2D NMR. Our data reveal that ubiquitin unfolds in a gradual manner with distinct unfolding regimes.}, author = {Schanda, Paul and Forge, V. and Brutscher, B.}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, keywords = {Multidisciplinary}, number = {27}, pages = {11257--11262}, publisher = {National Academy of Sciences}, title = {{Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy}}, doi = {10.1073/pnas.0702069104}, volume = {104}, year = {2007}, } @article{8484, abstract = {A series of sequential, intra-residue, and bi-directional BEST H–N–CA, H–N–CO, and H–N–CB pulse sequences is presented that extends the BEST concept introduced recently for fast multidimensional protein NMR [Schanda et al., J. Am. Chem. Soc. 128 (2006) 9042] to the complete set of experiments required for sequential resonance assignment. We demonstrate for the protein ubiquitin that 3D BEST H–N–C correlation spectra can be recorded on a 600 MHz NMR spectrometer equipped with a cryogenic probe in only a few minutes of acquisition time with sufficient sensitivity to detect all expected cross peaks.}, author = {Lescop, Ewen and Schanda, Paul and Brutscher, Bernhard}, issn = {1090-7807}, journal = {Journal of Magnetic Resonance}, number = {1}, pages = {163--169}, publisher = {Elsevier}, title = {{A set of BEST triple-resonance experiments for time-optimized protein resonance assignment}}, doi = {10.1016/j.jmr.2007.04.002}, volume = {187}, year = {2007}, } @article{8485, abstract = {High signal to noise is a necessity for the quantification of NMR spectral parameters to be translated into accurate and precise restraints on protein structure and dynamics. An important source of long-range structural information is obtained from 1H–1H residual dipolar couplings (RDCs) measured for weakly aligned molecules. For sensitivity reasons, such measurements are generally performed on highly deuterated protein samples. Here we show that high sensitivity is also obtained for protonated protein samples if the pulse schemes are optimized in terms of longitudinal relaxation efficiency and J-mismatch compensated coherence transfer. The new sensitivity-optimized quantitative J-correlation experiment yields important signal gains reaching factors of 1.5 to 8 for individual correlation peaks when compared to previously proposed pulse schemes.}, author = {Schanda, Paul and Lescop, Ewen and Falge, Mirjam and Sounier, Rémy and Boisbouvier, Jérôme and Brutscher, Bernhard}, issn = {0925-2738}, journal = {Journal of Biomolecular NMR}, keywords = {Spectroscopy, Biochemistry}, pages = {47--55}, publisher = {Springer Nature}, title = {{Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons}}, doi = {10.1007/s10858-006-9138-2}, volume = {38}, year = {2007}, } @article{8486, abstract = {A technique is described that allows reducing acquisition times of multidimensional NMR experiments by extensive spectral folding. The method is simple and has many interesting applications for NMR studies of molecular structure, dynamics, and kinetics.}, author = {Lescop, Ewen and Schanda, Paul and Rasia, Rodolfo and Brutscher, Bernhard}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {10}, pages = {2756--2757}, publisher = {American Chemical Society}, title = {{Automated spectral compression for fast multidimensional NMR and increased time resolution in real-time NMR spectroscopy}}, doi = {10.1021/ja068949u}, volume = {129}, year = {2007}, } @article{8487, abstract = {Following unidirectional biophysical events such as the folding of proteins or the equilibration of binding interactions, requires experimental methods that yield information at both atomic-level resolution and at high repetition rates. Toward this end a number of different approaches enabling the rapid acquisition of 2D NMR spectra have been recently introduced, including spatially encoded “ultrafast” 2D NMR spectroscopy and SOFAST HMQC NMR. Whereas the former accelerates acquisitions by reducing the number of scans that are necessary for completing arbitrary 2D NMR experiments, the latter operates by reducing the delay between consecutive scans while preserving sensitivity. Given the complementarities between these two approaches it seems natural to combine them into a single tool, enabling the acquisition of full 2D protein NMR spectra at high repetition rates. We demonstrate here this capability with the introduction of “ultraSOFAST” HMQC NMR, a spatially encoded and relaxation-optimized approach that can provide 2D protein correlation spectra at ∼1 s repetition rates for samples in the ∼2 mM concentration range. The principles, relative advantages, and current limitations of this new approach are discussed, and its application is exemplified with a study of the fast hydrogen−deuterium exchange characterizing amide sites in Ubiquitin.}, author = {Gal, Maayan and Schanda, Paul and Brutscher, Bernhard and Frydman, Lucio}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {5}, pages = {1372--1377}, publisher = {American Chemical Society}, title = {{UltraSOFAST HMQC NMR and the repetitive acquisition of 2D protein spectra at Hz rates}}, doi = {10.1021/ja066915g}, volume = {129}, year = {2007}, } @article{8511, abstract = {Here we study an amazing phenomenon discovered by Newhouse [S. Newhouse, Non-density of Axiom A(a) on S2, in: Proc. Sympos. Pure Math., vol. 14, Amer. Math. Soc., 1970, pp. 191–202; S. Newhouse, Diffeomorphisms with infinitely many sinks, Topology 13 (1974) 9–18; S. Newhouse, The abundance of wild hyperbolic sets and nonsmooth stable sets of diffeomorphisms, Publ. Math. Inst. Hautes Études Sci. 50 (1979) 101–151]. It turns out that in the space of Cr smooth diffeomorphisms Diffr(M) of a compact surface M there is an open set U such that a Baire generic diffeomorphism f ∈ U has infinitely many coexisting sinks. In this paper we make a step towards understanding “how often does a surface diffeomorphism have infinitely many sinks.” Our main result roughly says that with probability one for any positive D a surface diffeomorphism has only finitely many localized sinks either of cyclicity bounded by D or those whose period is relatively large compared to its cyclicity. It verifies a particular case of Palis’ Conjecture saying that even though diffeomorphisms with infinitely many coexisting sinks are Baire generic, they have probability zero. One of the key points of the proof is an application of Newton Interpolation Polynomials to study the dynamics initiated in [V. Kaloshin, B. Hunt, A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms I, Ann. of Math., in press, 92 pp.; V. Kaloshin, A stretched exponential bound on the rate of growth of the number of periodic points for prevalent diffeomorphisms II, preprint, 85 pp.].}, author = {Gorodetski, A. and Kaloshin, Vadim}, issn = {0001-8708}, journal = {Advances in Mathematics}, keywords = {General Mathematics}, number = {2}, pages = {710--797}, publisher = {Elsevier}, title = {{How often surface diffeomorphisms have infinitely many sinks and hyperbolicity of periodic points near a homoclinic tangency}}, doi = {10.1016/j.aim.2006.03.012}, volume = {208}, year = {2007}, } @article{8512, abstract = {For diffeomorphisms of smooth compact finite-dimensional manifolds, we consider the problem of how fast the number of periodic points with period n grows as a function of n. In many familiar cases (e.g., Anosov systems) the growth is exponential, but arbitrarily fast growth is possible; in fact, the first author has shown that arbitrarily fast growth is topologically (Baire) generic for C2 or smoother diffeomorphisms. In the present work we show that, by contrast, for a measure-theoretic notion of genericity we call “prevalence”, the growth is not much faster than exponential. Specifically, we show that for each ρ,δ>0, there is a prevalent set of C1+ρ (or smoother) diffeomorphisms for which the number of periodic n points is bounded above by exp(Cn1+δ) for some C independent of n. We also obtain a related bound on the decay of hyperbolicity of the periodic points as a function of n, and obtain the same results for 1-dimensional endomorphisms. The contrast between topologically generic and measure-theoretically generic behavior for the growth of the number of periodic points and the decay of their hyperbolicity show this to be a subtle and complex phenomenon, reminiscent of KAM theory. Here in Part I we state our results and describe the methods we use. We complete most of the proof in the 1-dimensional C2-smooth case and outline the remaining steps, deferred to Part II, that are needed to establish the general case. The novel feature of the approach we develop in this paper is the introduction of Newton Interpolation Polynomials as a tool for perturbing trajectories of iterated maps.}, author = {Kaloshin, Vadim and Hunt, Brian}, issn = {0003-486X}, journal = {Annals of Mathematics}, number = {1}, pages = {89--170}, publisher = {Princeton University Press}, title = {{Stretched exponential estimates on growth of the number of periodic points for prevalent diffeomorphisms I}}, doi = {10.4007/annals.2007.165.89}, volume = {165}, year = {2007}, } @article{860, abstract = {We identified a mutation in the CRYGD gene (P23S) of the γ-crystallin gene cluster that is associated with a polymorphic congenital cataract that occurs with frequency of ∼0.3% in a human population. To gain insight into the molecular mechanism of the pathogenesis of γ-crystallin isoforms, we undertook an evolutionary analysis of the available mammalian and newly obtained primate sequences of the γ-crystallin genes. The cataract-associated serine at site 23 corresponds to the ancestral state, since it was found in CRYGD of a lower primate and all the surveyed nonprimate mammals. Crystallin proteins include two structurally similar domains, and substitutions in mammalian CRYGD protein at site 23 of the first domain were always associated with substitutions in the structurally reciprocal sites 109 and 136 of the second domain. These data suggest that the cataractogenic effect of serine at site 23 in the N-terminal domain of CRYGD may be compensated indirectly by amino acid changes in a distal domain. We also found that gene conversion was a factor in the evolution of the γ-crystallin gene cluster throughout different mammalian clades. The high rate of gene conversion observed between the functional CRYGD gene and two primate γ-crystallin pseudogenes (CRYGEP1 and CRYGFP1) coupled with a surprising finding of apparent negative selection in primate pseudogenes suggest a deleterious impact of recently derived pseudogenes involved in gene conversion in the γ-crystallin gene cluster.}, author = {Plotnikova, Olga V and Fyodor Kondrashov and Vlasov, Peter K and Grigorenko, Anastasia P and Ginter, Evgeny K and Rogaev, Evgeny I}, journal = {American Journal of Human Genetics}, number = {1}, pages = {32 -- 43}, publisher = {Cell Press}, title = {{Conversion and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic mutation that reverses the sequence of the human CRYGD gene to an ancestral state}}, doi = {10.1086/518616}, volume = {81}, year = {2007}, } @article{861, abstract = {Background: Mitochondrial tRNAs have been the subject of study for structural biologists interested in their secondary structure characteristics, evolutionary biologists have researched patterns of compensatory and structural evolution and medical studies have been directed towards understanding the basis of human disease. However, an up to date, manually curated database of mitochondrially encoded tRNAs from higher animals is currently not available. Description: We obtained the complete mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated all of the tRNAs based on a multiple alignment of each tRNA gene and secondary structure prediction made independently for each tRNA. The mitochondrial (mt) tRNA sequences and the secondary structure based multiple alignments are freely available as Supplemental Information online. Conclusion: We compiled a manually curated database of mitochondrially encoded tRNAs from tetrapods with completely sequenced genomes. In the course of our work, we reannotated more than 10% of all tetrapod mt-tRNAs and subsequently predicted the secondary structures of 6060 mitochondrial tRNAs. This carefully constructed database can be utilized to enhance our knowledge in several different fields including the evolution of mt-tRNA secondary structure and prediction of pathogenic mt-tRNA mutations. In addition, researchers reporting novel mitochondrial genome sequences should check their tRNA gene annotations against our database to ensure a higher level of fidelity of their annotation.}, author = {Popadin, Konstantin Yu and Mamirova, Leila A and Fyodor Kondrashov}, journal = {BMC Bioinformatics}, publisher = {BioMed Central}, title = {{A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures}}, doi = {10.1186/1471-2105-8-441}, volume = {8}, year = {2007}, } @article{879, abstract = {Having an extra copy of a gene is thought to provide some functional redundancy, which results in a higher rate of evolution in duplicated genes. In this article, we estimate the impact of gene duplication on the selection of tuf paralogs, and we find that in the absence of gene conversion, tuf paralogs have evolved significantly slower than when gene conversion has been a factor in their evolution. Thus, tuf gene copies evolve under a selective pressure that ensures their functional uniformity, and gene conversion reduces selection against amino acid substitutions that affect the function of the encoded protein, EF-Tu.}, author = {Fyodor Kondrashov and Gurbich, Tatiana A and Vlasov, Peter K}, journal = {Trends in Genetics}, number = {5}, pages = {215 -- 218}, publisher = {Elsevier}, title = {{Selection for functional uniformity of tuf duplicates in γ-proteobacteria}}, doi = {10.1016/j.tig.2007.03.002}, volume = {23}, year = {2007}, }