Genetic effect estimates for loci detected in quantitative trait locus (QTL) mapping experiments depend upon two factors. First, they are parameterizations of the genotypic values determined by the model of genetic ef...Genetic effect estimates for loci detected in quantitative trait locus (QTL) mapping experiments depend upon two factors. First, they are parameterizations of the genotypic values determined by the model of genetic effects. Second, they are consequently also affected by the regression method used to estimate the genotypic values from the observed marker genotypes and phenotypes. There are two common causes for marker-genotype data to be incomplete in those experiments—missing marker-genotypes and within-interval mapping. Different regression methods tend to differ in how this missing information is represented and handled. In this communication we explain why the estimates of genetic effects of QTL obtained using standard regression methods are not coherent with the model of genetic effects and indeed show intrinsic inconsistencies when there is incomeplete genotype information. We then describe the interval mapping by imputations (IMI) regression method and prove that it overcomes those problems. A numerical example is used to illustrate the use of IMI and the consequences of using current methods of choice. IMI enables researchers to obtain estimates of genetic effects that are coherent with the model of genetic effects used, despite incomplete genotype information. Furthermore, because IMI allows orthogonal estimation of genetic effects, it shows potential performance advantages for being implemented in QTL mapping tools.展开更多
The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many.It was one of the arguments for building X-ray free-electron lasers.According to theory,the...The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many.It was one of the arguments for building X-ray free-electron lasers.According to theory,the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier,and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes.This was first demonstrated on biological samples a decade ago on the giant mimivirus.Since then,a large collaboration has been pushing the limit of the smallest sample that can be imaged.The ability to capture snapshots on the timescale of atomic vibrations,while keeping the sample at room temperature,may allow probing the entire conformational phase space of macromolecules.Here we show the first observation of an X-ray diffraction pattern from a single protein,that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays,and demonstrate that the concept of diffraction before destruction extends to single proteins.From the pattern,it is possible to determine the approximate orientation of the protein.Our experiment demonstrates the feasibility of ultrafast imaging of single proteins,opening the way to single-molecule time-resolved studies on the femtosecond timescale.展开更多
基金CN was funded by The Graduate School in Mathematics and Computing(FMB),SwedenOC was funded by a EURYI Award and a Future Research Leaders grant from SSFJAC was funded by an“Isidro Parga Pondal”contract from the autonomous administration Xunta de Galicia and by research projects BFU2009-11988 and BFU2010-20003 form the Spanish Ministry of Science and Innovation.
文摘Genetic effect estimates for loci detected in quantitative trait locus (QTL) mapping experiments depend upon two factors. First, they are parameterizations of the genotypic values determined by the model of genetic effects. Second, they are consequently also affected by the regression method used to estimate the genotypic values from the observed marker genotypes and phenotypes. There are two common causes for marker-genotype data to be incomplete in those experiments—missing marker-genotypes and within-interval mapping. Different regression methods tend to differ in how this missing information is represented and handled. In this communication we explain why the estimates of genetic effects of QTL obtained using standard regression methods are not coherent with the model of genetic effects and indeed show intrinsic inconsistencies when there is incomeplete genotype information. We then describe the interval mapping by imputations (IMI) regression method and prove that it overcomes those problems. A numerical example is used to illustrate the use of IMI and the consequences of using current methods of choice. IMI enables researchers to obtain estimates of genetic effects that are coherent with the model of genetic effects used, despite incomplete genotype information. Furthermore, because IMI allows orthogonal estimation of genetic effects, it shows potential performance advantages for being implemented in QTL mapping tools.
基金supported by the Universität Hamburg and DFG grant numbers(INST 152/772-1|152/774-1|152/775-1|152/776-1|152/777-1 FUGG)We acknowledge the support of funding from:Cluster of Excellence‘CUI:Advanced Imaging of Matter’of the Deutsche Forschungsgemeinschaft(DFG)-EXC 2056-project ID 390715994+7 种基金ERC-2013-CoG COMOTION 614507NFR 240770Fellowship from the Joachim Herz Stiftung(P.L.X.)P.L.X.and H.N.C.acknowledge support from the Human Frontiers Science Program(RGP0010/2017)J.H.acknowledges support from the European Development Fund:Structural dynamics of biomolecular systems(ELIBIO)(CZ.02.1.01/0.0/0.0/15_003/0000447)EMBO long-term fellowship(ALTF 356-2018)awarded to L.E.F.the Röntgen-Ångström Cluster(2015-06107 and 2019-06092)the Swedish Research Council(2017-05336,2018-00234 and 2019-03935)the Swedish Foundation for Strategic Research(ITM17-0455).
文摘The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many.It was one of the arguments for building X-ray free-electron lasers.According to theory,the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier,and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes.This was first demonstrated on biological samples a decade ago on the giant mimivirus.Since then,a large collaboration has been pushing the limit of the smallest sample that can be imaged.The ability to capture snapshots on the timescale of atomic vibrations,while keeping the sample at room temperature,may allow probing the entire conformational phase space of macromolecules.Here we show the first observation of an X-ray diffraction pattern from a single protein,that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays,and demonstrate that the concept of diffraction before destruction extends to single proteins.From the pattern,it is possible to determine the approximate orientation of the protein.Our experiment demonstrates the feasibility of ultrafast imaging of single proteins,opening the way to single-molecule time-resolved studies on the femtosecond timescale.
