--- _id: '9483' abstract: - lang: eng text: Imprinted genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon that occurs in flowering plants and mammals. Flowering plant imprinted gene expression has been described primarily in endosperm, a terminal nutritive tissue consumed by the embryo during seed development or after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated by differences in cytosine DNA methylation between the paternal and maternal genomes as well as by Polycomb group proteins. Currently, only 11 imprinted A. thaliana genes are known. Here, we use extensive sequencing of cDNA libraries to identify 9 paternally expressed and 34 maternally expressed imprinted genes in A. thaliana endosperm that are regulated by the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1, and/or the core Polycomb group protein FIE. These genes encode transcription factors, proteins involved in hormone signaling, components of the ubiquitin protein degradation pathway, regulators of histone and DNA methylation, and small RNA pathway proteins. We also identify maternally expressed genes that may be regulated by unknown mechanisms or deposited from maternal tissues. We did not detect any imprinted genes in the embryo. Our results show that imprinted gene expression is an extensive mechanistically complex phenomenon that likely affects multiple aspects of seed development. article_processing_charge: No article_type: original author: - first_name: Tzung-Fu full_name: Hsieh, Tzung-Fu last_name: Hsieh - first_name: Juhyun full_name: Shin, Juhyun last_name: Shin - first_name: Rie full_name: Uzawa, Rie last_name: Uzawa - first_name: Pedro full_name: Silva, Pedro last_name: Silva - first_name: Stephanie full_name: Cohen, Stephanie last_name: Cohen - first_name: Matthew J. full_name: Bauer, Matthew J. last_name: Bauer - first_name: Meryl full_name: Hashimoto, Meryl last_name: Hashimoto - first_name: Ryan C. full_name: Kirkbride, Ryan C. last_name: Kirkbride - first_name: John J. full_name: Harada, John J. last_name: Harada - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Robert L. full_name: Fischer, Robert L. last_name: Fischer citation: ama: Hsieh T-F, Shin J, Uzawa R, et al. Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 2011;108(5):1755-1762. doi:10.1073/pnas.1019273108 apa: Hsieh, T.-F., Shin, J., Uzawa, R., Silva, P., Cohen, S., Bauer, M. J., … Fischer, R. L. (2011). Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1019273108 chicago: Hsieh, Tzung-Fu, Juhyun Shin, Rie Uzawa, Pedro Silva, Stephanie Cohen, Matthew J. Bauer, Meryl Hashimoto, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2011. https://doi.org/10.1073/pnas.1019273108. ieee: T.-F. Hsieh et al., “Regulation of imprinted gene expression in Arabidopsis endosperm,” Proceedings of the National Academy of Sciences, vol. 108, no. 5. National Academy of Sciences, pp. 1755–1762, 2011. ista: Hsieh T-F, Shin J, Uzawa R, Silva P, Cohen S, Bauer MJ, Hashimoto M, Kirkbride RC, Harada JJ, Zilberman D, Fischer RL. 2011. Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 108(5), 1755–1762. mla: Hsieh, Tzung-Fu, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” Proceedings of the National Academy of Sciences, vol. 108, no. 5, National Academy of Sciences, 2011, pp. 1755–62, doi:10.1073/pnas.1019273108. short: T.-F. Hsieh, J. Shin, R. Uzawa, P. Silva, S. Cohen, M.J. Bauer, M. Hashimoto, R.C. Kirkbride, J.J. Harada, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 108 (2011) 1755–1762. date_created: 2021-06-07T07:40:38Z date_published: 2011-02-01T00:00:00Z date_updated: 2021-12-14T08:33:49Z day: '01' department: - _id: DaZi doi: 10.1073/pnas.1019273108 extern: '1' external_id: pmid: - '21257907' intvolume: ' 108' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.1019273108 month: '02' oa: 1 oa_version: Published Version page: 1755-1762 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Regulation of imprinted gene expression in Arabidopsis endosperm type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 108 year: '2011' ... --- _id: '967' abstract: - lang: eng text: Motivated by recent experiments on the material Ba3NiSb 2O9, we consider a spin-one quantum antiferromagnet on a triangular lattice with the Heisenberg bilinear and biquadratic exchange interactions and a single-ion anisotropy. Using a fermionic "triplon" representation for spins, we study the phase diagram within mean-field theory. In addition to a fully gapped spin-liquid ground state, we find a state where one gapless triplon mode with a Fermi surface coexists with d+id topological pairing of the other triplons. Despite the existence of a Fermi surface, this ground state has fully gapped bulk spin excitations. Such a state has linear in-temperature specific heat and constant in-plane spin susceptibility, with an unusually high Wilson ratio. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Todadri full_name: Senthil, Todadri S last_name: Senthil - first_name: Patrick full_name: Lee, Patrick last_name: Lee citation: ama: Serbyn M, Senthil T, Lee P. Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 2011;84(18). doi:10.1103/PhysRevB.84.180403 apa: Serbyn, M., Senthil, T., & Lee, P. (2011). Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.84.180403 chicago: Serbyn, Maksym, Todadri Senthil, and Patrick Lee. “Exotic S=1 Spin-Liquid State with Fermionic Excitations on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevB.84.180403. ieee: M. Serbyn, T. Senthil, and P. Lee, “Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice,” Physical Review B - Condensed Matter and Materials Physics, vol. 84, no. 18. American Physical Society, 2011. ista: Serbyn M, Senthil T, Lee P. 2011. Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice. Physical Review B - Condensed Matter and Materials Physics. 84(18). mla: Serbyn, Maksym, et al. “Exotic S=1 Spin-Liquid State with Fermionic Excitations on the Triangular Lattice.” Physical Review B - Condensed Matter and Materials Physics, vol. 84, no. 18, American Physical Society, 2011, doi:10.1103/PhysRevB.84.180403. short: M. Serbyn, T. Senthil, P. Lee, Physical Review B - Condensed Matter and Materials Physics 84 (2011). date_created: 2018-12-11T11:49:27Z date_published: 2011-11-03T00:00:00Z date_updated: 2021-01-12T08:22:18Z day: '03' doi: 10.1103/PhysRevB.84.180403 extern: 1 intvolume: ' 84' issue: '18' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1108.3070 month: '11' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6432' quality_controlled: 0 status: public title: Exotic S=1 spin-liquid state with fermionic excitations on the triangular lattice type: journal_article volume: 84 year: '2011' ... --- _id: '969' abstract: - lang: eng text: We investigate the isotope effect on the London penetration depth of a superconductor which measures n S/m*, the ratio of superfluid density to effective mass. We use a simplified model of electrons weakly coupled to a single phonon frequency ω E, but assume that the energy gap Δ does not have any isotope effect. Nevertheless, we find an isotope effect for n S/m* which is significant if Δ is sufficiently large that it becomes comparable to ω E, a regime of interest to high-T c cuprate superconductors and possibly other families of unconventional superconductors with relatively high T c. Our model is too simple to describe the cuprates and it gives the wrong sign of the isotope effect when compared with experiment, but it is a proof of principle that the isotope effect exists for n S/m* in materials where the pairing gap and T c are not of phonon origin and have no isotope effect. author: - first_name: Maksym full_name: Maksym Serbyn id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Patrick full_name: Lee, Patrick last_name: Lee citation: ama: Serbyn M, Lee P. Isotope effect on the superfluid density in conventional and high-temperature superconductors. Physical Review B - Condensed Matter and Materials Physics. 2011;83(2). doi:10.1103/PhysRevB.83.024506 apa: Serbyn, M., & Lee, P. (2011). Isotope effect on the superfluid density in conventional and high-temperature superconductors. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.83.024506 chicago: Serbyn, Maksym, and Patrick Lee. “Isotope Effect on the Superfluid Density in Conventional and High-Temperature Superconductors.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2011. https://doi.org/10.1103/PhysRevB.83.024506. ieee: M. Serbyn and P. Lee, “Isotope effect on the superfluid density in conventional and high-temperature superconductors,” Physical Review B - Condensed Matter and Materials Physics, vol. 83, no. 2. American Physical Society, 2011. ista: Serbyn M, Lee P. 2011. Isotope effect on the superfluid density in conventional and high-temperature superconductors. Physical Review B - Condensed Matter and Materials Physics. 83(2). mla: Serbyn, Maksym, and Patrick Lee. “Isotope Effect on the Superfluid Density in Conventional and High-Temperature Superconductors.” Physical Review B - Condensed Matter and Materials Physics, vol. 83, no. 2, American Physical Society, 2011, doi:10.1103/PhysRevB.83.024506. short: M. Serbyn, P. Lee, Physical Review B - Condensed Matter and Materials Physics 83 (2011). date_created: 2018-12-11T11:49:28Z date_published: 2011-01-19T00:00:00Z date_updated: 2021-01-12T08:22:19Z day: '19' doi: 10.1103/PhysRevB.83.024506 extern: 1 intvolume: ' 83' issue: '2' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1009.2429 month: '01' oa: 1 publication: Physical Review B - Condensed Matter and Materials Physics publication_status: published publisher: American Physical Society publist_id: '6434' quality_controlled: 0 status: public title: Isotope effect on the superfluid density in conventional and high-temperature superconductors type: journal_article volume: 83 year: '2011' ... --- _id: '8471' abstract: - lang: eng text: Despite the importance of protein fibrils in the context of conformational diseases, information on their structure is still sparse. Hydrogen/deuterium exchange measurements of backbone amide protons allow the identification hydrogen-bonding patterns and reveal pertinent information on the amyloid β-sheet architecture. However, they provide only little information on the identity of residues exposed to solvent or buried inside the fibril core. NMR spectroscopy is a potent method for identifying solvent-accessible residues in proteins via observation of polarization transfer between chemically exchanging side-chain protons and water protons. We show here that the combined use of highly deuterated samples and fast magic-angle spinning greatly attenuates unwanted spin diffusion and allows identification of polarization exchange with the solvent in a site-specific manner. We apply this measurement protocol to HET-s(218–289) prion fibrils under different conditions (including physiological pH, where protofibrils assemble together into thicker fibrils) and demonstrate that each protofibril of HET-s(218–289), is surrounded by water, thus excluding the existence of extended dry interfibril contacts. We also show that exchangeable side-chain protons inside the hydrophobic core of HET-s(218–289) do not exchange over time intervals of weeks to months. The experiments proposed in this study can provide insight into the detailed structural features of amyloid fibrils in general. article_processing_charge: No article_type: original author: - first_name: Hélène full_name: Van Melckebeke, Hélène last_name: Van Melckebeke - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Julia full_name: Gath, Julia last_name: Gath - first_name: Christian full_name: Wasmer, Christian last_name: Wasmer - first_name: René full_name: Verel, René last_name: Verel - first_name: Adam full_name: Lange, Adam last_name: Lange - first_name: Beat H. full_name: Meier, Beat H. last_name: Meier - first_name: Anja full_name: Böckmann, Anja last_name: Böckmann citation: ama: Van Melckebeke H, Schanda P, Gath J, et al. Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR. Journal of Molecular Biology. 2011;405(3):765-772. doi:10.1016/j.jmb.2010.11.004 apa: Van Melckebeke, H., Schanda, P., Gath, J., Wasmer, C., Verel, R., Lange, A., … Böckmann, A. (2011). Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2010.11.004 chicago: Van Melckebeke, Hélène, Paul Schanda, Julia Gath, Christian Wasmer, René Verel, Adam Lange, Beat H. Meier, and Anja Böckmann. “Probing Water Accessibility in HET-s(218–289) Amyloid Fibrils by Solid-State NMR.” Journal of Molecular Biology. Elsevier, 2011. https://doi.org/10.1016/j.jmb.2010.11.004. ieee: H. Van Melckebeke et al., “Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR,” Journal of Molecular Biology, vol. 405, no. 3. Elsevier, pp. 765–772, 2011. ista: Van Melckebeke H, Schanda P, Gath J, Wasmer C, Verel R, Lange A, Meier BH, Böckmann A. 2011. Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR. Journal of Molecular Biology. 405(3), 765–772. mla: Van Melckebeke, Hélène, et al. “Probing Water Accessibility in HET-s(218–289) Amyloid Fibrils by Solid-State NMR.” Journal of Molecular Biology, vol. 405, no. 3, Elsevier, 2011, pp. 765–72, doi:10.1016/j.jmb.2010.11.004. short: H. Van Melckebeke, P. Schanda, J. Gath, C. Wasmer, R. Verel, A. Lange, B.H. Meier, A. Böckmann, Journal of Molecular Biology 405 (2011) 765–772. date_created: 2020-09-18T10:11:03Z date_published: 2011-01-21T00:00:00Z date_updated: 2021-01-12T08:19:30Z day: '21' doi: 10.1016/j.jmb.2010.11.004 extern: '1' intvolume: ' 405' issue: '3' language: - iso: eng month: '01' oa_version: None page: 765-772 publication: Journal of Molecular Biology publication_identifier: issn: - 0022-2836 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 405 year: '2011' ... --- _id: '8505' abstract: - lang: eng text: The classical principle of least action says that orbits of mechanical systems extremize action; an important subclass are those orbits that minimize action. In this paper we utilize this principle along with Aubry-Mather theory to construct (Birkhoff) regions of instability for a certain three-body problem, given by a Hamiltonian system of 2 degrees of freedom. We believe that these methods can be applied to construct instability regions for a variety of Hamiltonian systems with 2 degrees of freedom. The Hamiltonian model we consider describes dynamics of a Sun-Jupiter-comet system, and under some simplifying assumptions, we show the existence of instabilities for the orbit of the comet. In particular, we show that a comet which starts close to an orbit in the shape of an ellipse of eccentricity e=0.66 can increase in eccentricity up to e=0.96. In the sequels to this paper, we extend the result to beyond e=1 and show the existence of ejection orbits. Such orbits are initially well within the range of our solar system. This might give an indication of why most objects rotating around the Sun in our solar system have relatively low eccentricity. article_processing_charge: No article_type: original author: - first_name: Joseph full_name: Galante, Joseph last_name: Galante - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: Galante J, Kaloshin V. Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action. Duke Mathematical Journal. 2011;159(2):275-327. doi:10.1215/00127094-1415878 apa: Galante, J., & Kaloshin, V. (2011). Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/00127094-1415878 chicago: Galante, Joseph, and Vadim Kaloshin. “Destruction of Invariant Curves in the Restricted Circular Planar Three-Body Problem by Using Comparison of Action.” Duke Mathematical Journal. Duke University Press, 2011. https://doi.org/10.1215/00127094-1415878. ieee: J. Galante and V. Kaloshin, “Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action,” Duke Mathematical Journal, vol. 159, no. 2. Duke University Press, pp. 275–327, 2011. ista: Galante J, Kaloshin V. 2011. Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action. Duke Mathematical Journal. 159(2), 275–327. mla: Galante, Joseph, and Vadim Kaloshin. “Destruction of Invariant Curves in the Restricted Circular Planar Three-Body Problem by Using Comparison of Action.” Duke Mathematical Journal, vol. 159, no. 2, Duke University Press, 2011, pp. 275–327, doi:10.1215/00127094-1415878. short: J. Galante, V. Kaloshin, Duke Mathematical Journal 159 (2011) 275–327. date_created: 2020-09-18T10:47:41Z date_published: 2011-08-04T00:00:00Z date_updated: 2021-01-12T08:19:45Z day: '04' doi: 10.1215/00127094-1415878 extern: '1' intvolume: ' 159' issue: '2' keyword: - General Mathematics language: - iso: eng month: '08' oa_version: None page: 275-327 publication: Duke Mathematical Journal publication_identifier: issn: - 0012-7094 publication_status: published publisher: Duke University Press quality_controlled: '1' status: public title: Destruction of invariant curves in the restricted circular planar three-body problem by using comparison of action type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 159 year: '2011' ...