ALBERT

Description: Bellamya aeruginosa is a widely distributed Chinese freshwater snail that is heavily harvested, and its natural habitats are under severe threat due to fragmentation and loss. We were interested whether the large geographic distances between populations and habitat fragmentation have led to population differentiation and reduced genetic diversity in the species. To estimate the genetic diversity and population structure of B. aeruginosa , 277 individuals from 12 populations throughout its distribution range across China were sampled: two populations were sampled from the Yellow River system, eight populations from the Yangtze River system, and two populations from isolated plateau lakes. We used seven microsatellite loci and mitochondrial cytochrome oxidase I sequences to estimate population genetic parameters and test for demographic fluctuations. Our results showed that (1) the genetic diversity of B. aeruginosa was high for both markers in most of the studied populations and effective population sizes appear to be large, (2) only very low and mostly nonsignificant levels of genetic differentiation existed among the 12 populations, gene flow was generally high, and (3) relatively weak geographic structure was detected despite large geographic distances between populations. Further, no isolation by linear or stream distance was found among populations within the Yangtze River system and no signs of population bottlenecks were detected. Gene flow occurred even between far distant populations, possibly as a result of passive dispersal during flooding events, zoochoric dispersal, and/or anthropogenic translocations explaining the lack of stronger differentiation across large geographic distances. The high genetic diversity of B. aeruginosa and the weak population differentiation are likely the results of strong gene flow facilitated by passive dispersal and large population sizes suggesting that the species currently is not of conservation concern. High levels of intra-population genetic diversity and low inter-population differentiation was found in Bellamya aeruginosa in China. Population sizes were intermediate to large and levels of gene flow were high suggesting that both gene flow and population size help to maintain high genetic variation. Gene flow occurred even between far distant populations, likely as a result of passive dispersal during flooding events, zoochoric dispersal and possibly anthropogenic translocations.

Description: DNA methylation is essential for normal development and has been implicated in many pathologies including cancer. Our knowledge about the genome-wide distribution of DNA methylation, how it changes during cellular differentiation and how it relates to histone methylation and other chromatin modifications in mammals remains limited. Here we report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput reduced representation bisulphite sequencing and single-molecule-based sequencing, we generated DNA methylation maps covering most CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for mouse embryonic stem cells, embryonic-stem-cell-derived and primary neural cells, and eight other primary tissues. Several key findings emerge from the data. First, DNA methylation patterns are better correlated with histone methylation patterns than with the underlying genome sequence context. Second, methylation of CpGs are dynamic epigenetic marks that undergo extensive changes during cellular differentiation, particularly in regulatory regions outside of core promoters. Third, analysis of embryonic-stem-cell-derived and primary cells reveals that 'weak' CpG islands associated with a specific set of developmentally regulated genes undergo aberrant hypermethylation during extended proliferation in vitro, in a pattern reminiscent of that reported in some primary tumours. More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896277/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896277/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meissner, Alexander -- Mikkelsen, Tarjei S -- Gu, Hongcang -- Wernig, Marius -- Hanna, Jacob -- Sivachenko, Andrey -- Zhang, Xiaolan -- Bernstein, Bradley E -- Nusbaum, Chad -- Jaffe, David B -- Gnirke, Andreas -- Jaenisch, Rudolf -- Lander, Eric S -- R01 HG004401/HG/NHGRI NIH HHS/ -- R01 HG004401-02/HG/NHGRI NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- U54 HG003067-04/HG/NHGRI NIH HHS/ -- U54 HG003067-06/HG/NHGRI NIH HHS/ -- England -- Nature. 2008 Aug 7;454(7205):766-70. doi: 10.1038/nature07107. Epub 2008 Jul 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18600261" target="_blank"〉PubMed〈/a〉

Description: CRM1 (also known as XPO1 and exportin 1) mediates nuclear export of hundreds of proteins through the recognition of the leucine-rich nuclear export signal (LR-NES). Here we present the 2.9 A structure of CRM1 bound to snurportin 1 (SNUPN). Snurportin 1 binds CRM1 in a bipartite manner by means of an amino-terminal LR-NES and its nucleotide-binding domain. The LR-NES is a combined alpha-helical-extended structure that occupies a hydrophobic groove between two CRM1 outer helices. The LR-NES interface explains the consensus hydrophobic pattern, preference for intervening electronegative residues and inhibition by leptomycin B. The second nuclear export signal epitope is a basic surface on the snurportin 1 nucleotide-binding domain, which binds an acidic patch on CRM1 adjacent to the LR-NES site. Multipartite recognition of individually weak nuclear export signal epitopes may be common to CRM1 substrates, enhancing CRM1 binding beyond the generally low affinity LR-NES. Similar energetic construction is also used in multipartite nuclear localization signals to provide broad substrate specificity and rapid evolution in nuclear transport.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3437623/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3437623/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dong, Xiuhua -- Biswas, Anindita -- Suel, Katherine E -- Jackson, Laurie K -- Martinez, Rita -- Gu, Hongmei -- Chook, Yuh Min -- 5-T32-GM008297/GM/NIGMS NIH HHS/ -- R01 GM069909/GM/NIGMS NIH HHS/ -- R01GM069909/GM/NIGMS NIH HHS/ -- R01GM069909-03S1/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Apr 30;458(7242):1136-41. doi: 10.1038/nature07975. Epub 2009 Apr 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park, Dallas, Texas 75390-9041, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19339969" target="_blank"〉PubMed〈/a〉

Description: Pluripotent stem cells provide a powerful system to dissect the underlying molecular dynamics that regulate cell fate changes during mammalian development. Here we report the integrative analysis of genome-wide binding data for 38 transcription factors with extensive epigenome and transcriptional data across the differentiation of human embryonic stem cells to the three germ layers. We describe core regulatory dynamics and show the lineage-specific behaviour of selected factors. In addition to the orchestrated remodelling of the chromatin landscape, we find that the binding of several transcription factors is strongly associated with specific loss of DNA methylation in one germ layer, and in many cases a reciprocal gain in the other layers. Taken together, our work shows context-dependent rewiring of transcription factor binding, downstream signalling effectors, and the epigenome during human embryonic stem cell differentiation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499331/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499331/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tsankov, Alexander M -- Gu, Hongcang -- Akopian, Veronika -- Ziller, Michael J -- Donaghey, Julie -- Amit, Ido -- Gnirke, Andreas -- Meissner, Alexander -- 5F32DK095537/DK/NIDDK NIH HHS/ -- P01 GM099117/GM/NIGMS NIH HHS/ -- P01GM099117/GM/NIGMS NIH HHS/ -- P50HG006193/HG/NHGRI NIH HHS/ -- U01 ES017155/ES/NIEHS NIH HHS/ -- U01ES017155/ES/NIEHS NIH HHS/ -- England -- Nature. 2015 Feb 19;518(7539):344-9. doi: 10.1038/nature14233.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA. ; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. ; 1] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA [2] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA. ; 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Immunology, Weizmann Institute, Rehovot, 76100 Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25693565" target="_blank"〉PubMed〈/a〉

Description: Models derived from human pluripotent stem cells that accurately recapitulate neural development in vitro and allow for the generation of specific neuronal subtypes are of major interest to the stem cell and biomedical community. Notch signalling, particularly through the Notch effector HES5, is a major pathway critical for the onset and maintenance of neural progenitor cells in the embryonic and adult nervous system. Here we report the transcriptional and epigenomic analysis of six consecutive neural progenitor cell stages derived from a HES5::eGFP reporter human embryonic stem cell line. Using this system, we aimed to model cell-fate decisions including specification, expansion and patterning during the ontogeny of cortical neural stem and progenitor cells. In order to dissect regulatory mechanisms that orchestrate the stage-specific differentiation process, we developed a computational framework to infer key regulators of each cell-state transition based on the progressive remodelling of the epigenetic landscape and then validated these through a pooled short hairpin RNA screen. We were also able to refine our previous observations on epigenetic priming at transcription factor binding sites and suggest here that they are mediated by combinations of core and stage-specific factors. Taken together, we demonstrate the utility of our system and outline a general framework, not limited to the context of the neural lineage, to dissect regulatory circuits of differentiation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4336237/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4336237/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ziller, Michael J -- Edri, Reuven -- Yaffe, Yakey -- Donaghey, Julie -- Pop, Ramona -- Mallard, William -- Issner, Robbyn -- Gifford, Casey A -- Goren, Alon -- Xing, Jeffrey -- Gu, Hongcang -- Cacchiarelli, Davide -- Tsankov, Alexander M -- Epstein, Charles -- Rinn, John L -- Mikkelsen, Tarjei S -- Kohlbacher, Oliver -- Gnirke, Andreas -- Bernstein, Bradley E -- Elkabetz, Yechiel -- Meissner, Alexander -- F32 DK095537/DK/NIDDK NIH HHS/ -- HG006911/HG/NHGRI NIH HHS/ -- P01 GM099117/GM/NIGMS NIH HHS/ -- P01GM099117/GM/NIGMS NIH HHS/ -- U01 ES017155/ES/NIEHS NIH HHS/ -- U01ES017155/ES/NIEHS NIH HHS/ -- U54 HG006991/HG/NHGRI NIH HHS/ -- England -- Nature. 2015 Feb 19;518(7539):355-9. doi: 10.1038/nature13990. Epub 2014 Dec 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA. ; Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Ramat Aviv 6997801, Israel. ; 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA. ; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA. ; 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA [3] Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA. ; Applied Bioinformatics, Center for Bioinformatics and Quantitative Biology Center, University of Tubingen, Tubingen 72076, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25533951" target="_blank"〉PubMed〈/a〉

Description: DNA methylation is a defining feature of mammalian cellular identity and is essential for normal development. Most cell types, except germ cells and pre-implantation embryos, display relatively stable DNA methylation patterns, with 70-80% of all CpGs being methylated. Despite recent advances, we still have a limited understanding of when, where and how many CpGs participate in genomic regulation. Here we report the in-depth analysis of 42 whole-genome bisulphite sequencing data sets across 30 diverse human cell and tissue types. We observe dynamic regulation for only 21.8% of autosomal CpGs within a normal developmental context, most of which are distal to transcription start sites. These dynamic CpGs co-localize with gene regulatory elements, particularly enhancers and transcription-factor-binding sites, which allow identification of key lineage-specific regulators. In addition, differentially methylated regions (DMRs) often contain single nucleotide polymorphisms associated with cell-type-related diseases as determined by genome-wide association studies. The results also highlight the general inefficiency of whole-genome bisulphite sequencing, as 70-80% of the sequencing reads across these data sets provided little or no relevant information about CpG methylation. To demonstrate further the utility of our DMR set, we use it to classify unknown samples and identify representative signature regions that recapitulate major DNA methylation dynamics. In summary, although in theory every CpG can change its methylation state, our results suggest that only a fraction does so as part of coordinated regulatory programs. Therefore, our selected DMRs can serve as a starting point to guide new, more effective reduced representation approaches to capture the most informative fraction of CpGs, as well as further pinpoint putative regulatory elements.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3821869/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3821869/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ziller, Michael J -- Gu, Hongcang -- Muller, Fabian -- Donaghey, Julie -- Tsai, Linus T-Y -- Kohlbacher, Oliver -- De Jager, Philip L -- Rosen, Evan D -- Bennett, David A -- Bernstein, Bradley E -- Gnirke, Andreas -- Meissner, Alexander -- ES017690/ES/NIEHS NIH HHS/ -- P01 GM099117/GM/NIGMS NIH HHS/ -- P01GM099117/GM/NIGMS NIH HHS/ -- P30AG10161/AG/NIA NIH HHS/ -- R01 AG017917/AG/NIA NIH HHS/ -- R01AG15819/AG/NIA NIH HHS/ -- R01AG17917/AG/NIA NIH HHS/ -- R01AG36042/AG/NIA NIH HHS/ -- U01 ES017155/ES/NIEHS NIH HHS/ -- U01ES017155/ES/NIEHS NIH HHS/ -- England -- Nature. 2013 Aug 22;500(7463):477-81. doi: 10.1038/nature12433. Epub 2013 Aug 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23925113" target="_blank"〉PubMed〈/a〉

Description: Hitherto, rings have been found exclusively around the four giant planets in the Solar System. Rings are natural laboratories in which to study dynamical processes analogous to those that take place during the formation of planetary systems and galaxies. Their presence also tells us about the origin and evolution of the body they encircle. Here we report observations of a multichord stellar occultation that revealed the presence of a ring system around (10199) Chariklo, which is a Centaur--that is, one of a class of small objects orbiting primarily between Jupiter and Neptune--with an equivalent radius of 124 +/- 9 kilometres (ref. 2). There are two dense rings, with respective widths of about 7 and 3 kilometres, optical depths of 0.4 and 0.06, and orbital radii of 391 and 405 kilometres. The present orientation of the ring is consistent with an edge-on geometry in 2008, which provides a simple explanation for the dimming of the Chariklo system between 1997 and 2008, and for the gradual disappearance of ice and other absorption features in its spectrum over the same period. This implies that the rings are partly composed of water ice. They may be the remnants of a debris disk, possibly confined by embedded, kilometre-sized satellites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Braga-Ribas, F -- Sicardy, B -- Ortiz, J L -- Snodgrass, C -- Roques, F -- Vieira-Martins, R -- Camargo, J I B -- Assafin, M -- Duffard, R -- Jehin, E -- Pollock, J -- Leiva, R -- Emilio, M -- Machado, D I -- Colazo, C -- Lellouch, E -- Skottfelt, J -- Gillon, M -- Ligier, N -- Maquet, L -- Benedetti-Rossi, G -- Ramos Gomes, A Jr -- Kervella, P -- Monteiro, H -- Sfair, R -- El Moutamid, M -- Tancredi, G -- Spagnotto, J -- Maury, A -- Morales, N -- Gil-Hutton, R -- Roland, S -- Ceretta, A -- Gu, S-h -- Wang, X-b -- Harpsoe, K -- Rabus, M -- Manfroid, J -- Opitom, C -- Vanzi, L -- Mehret, L -- Lorenzini, L -- Schneiter, E M -- Melia, R -- Lecacheux, J -- Colas, F -- Vachier, F -- Widemann, T -- Almenares, L -- Sandness, R G -- Char, F -- Perez, V -- Lemos, P -- Martinez, N -- Jorgensen, U G -- Dominik, M -- Roig, F -- Reichart, D E -- LaCluyze, A P -- Haislip, J B -- Ivarsen, K M -- Moore, J P -- Frank, N R -- Lambas, D G -- England -- Nature. 2014 Apr 3;508(7494):72-5. doi: 10.1038/nature13155. Epub 2014 Mar 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Observatorio Nacional/MCTI, Rua General Jose Cristino 77, CEP 20921-400 Rio de Janeiro, RJ, Brazil. ; LESIA, Observatoire de Paris, CNRS UMR 8109, Universite Pierre et Marie Curie, Universite Paris-Diderot, 5 place Jules Janssen, F-92195 Meudon Cedex, France. ; Instituto de Astrofisica de Andalucia, CSIC, Apartado 3004, 18080 Granada, Spain. ; Max Planck Institute for Solar System Research, Justus-von-Liebig-Weg 3, 37077 Gottingen, Germany. ; 1] Observatorio Nacional/MCTI, Rua General Jose Cristino 77, CEP 20921-400 Rio de Janeiro, RJ, Brazil [2] Observatorio do Valongo/UFRJ, Ladeira Pedro Antonio 43, CEP 20.080-090 Rio de Janeiro, RJ, Brazil [3] Observatoire de Paris, IMCCE, UPMC, CNRS, 77 Avenue Denfert-Rochereau, 75014 Paris, France. ; Observatorio do Valongo/UFRJ, Ladeira Pedro Antonio 43, CEP 20.080-090 Rio de Janeiro, RJ, Brazil. ; Institut d'Astrophysique de l'Universite de Liege, Allee du 6 Aout 17, B-4000 Liege, Belgium. ; Physics and Astronomy Department, Appalachian State University, Boone, North Carolina 28608, USA. ; Instituto de Astrofisica, Facultad de Fisica, Pontificia Universidad Catolica de Chile, Avenida Vicuna Mackenna 4860, Santiago 7820436, Chile. ; Universidade Estadual de Ponta Grossa, O.A. - DEGEO, Avenida Carlos Cavalcanti 4748, Ponta Grossa 84030-900, PR, Brazil. ; 1] Polo Astronomico Casimiro Montenegro Filho/FPTI-BR, Avenida Tancredo Neves 6731, CEP 85867-900, Foz do Iguacu, PR, Brazil [2] Universidade Estadual do Oeste do Parana (Unioeste), Avenda Tarquinio Joslin dos Santos, 1300, CEP 85870-650, Foz do Iguacu, PR, Brazil. ; 1] Ministerio de Educacion de la Provincia de Cordoba, Santa Rosa 751, Cordoba 5000, Argentina [2] Observatorio Astronomico, Universidad Nacional de Cordoba, Laprida 854, Cordoba 5000, Argentina. ; 1] Niels Bohr Institute, University of Copenhagen, Juliane Maries vej 30, 2100 Copenhagen, Denmark [2] Centre for Star and Planet Formation, Geological Museum, Oster Voldgade 5, 1350 Copenhagen, Denmark. ; Instituto de Fisica e Quimica, Avenida BPS 1303, CEP 37500-903, Itajuba, MG, Brazil. ; UNESP - Universidade Estadual Paulista, Avenida Ariberto Pereira da Cunha, 333, CEP 12516-410 Guaratingueta, SP, Brazil. ; 1] LESIA, Observatoire de Paris, CNRS UMR 8109, Universite Pierre et Marie Curie, Universite Paris-Diderot, 5 place Jules Janssen, F-92195 Meudon Cedex, France [2] Observatoire de Paris, IMCCE, UPMC, CNRS, 77 Avenue Denfert-Rochereau, 75014 Paris, France. ; 1] Observatorio Astronomico Los Molinos, DICYT, MEC, 12400 Montevideo, Uruguay [2] Departamento de Astronomia, Facultad Ciencias, Universidad de la Republica, 11300 Montevideo, Uruguay. ; Observatorio El Catalejo, Mussio 255, Santa Rosa, La Pampa 6300, Argentina. ; San Pedro de Atacama Celestial Explorations, Casilla 21, San Pedro de Atacama 1410000, Chile. ; Complejo Astronomico El Leoncito (CASLEO) and San Juan National University, Avenida Espana 1512 sur, J5402DSP, San Juan, Argentina. ; Observatorio Astronomico Los Molinos, DICYT, MEC, 12400 Montevideo, Uruguay. ; 1] Departamento de Astronomia, Facultad Ciencias, Universidad de la Republica, 11300 Montevideo, Uruguay [2] Observatorio del IPA, Consejo de Formacion en Educacion, 11800 Montevideo, Uruguay. ; 1] Yunnan Observatories, Chinese Academy of Sciences, Kunming 650011, China [2] Key Laboratory for the Structure and Evolution of Celestial Objects, Chinese Academy of Sciences, Kunming 650011, China. ; 1] Instituto de Astrofisica, Facultad de Fisica, Pontificia Universidad Catolica de Chile, Avenida Vicuna Mackenna 4860, Santiago 7820436, Chile [2] Max Planck Institute for Astronomy, Konigstuhl 17, 69117 Heidelberg, Germany. ; Department of Electrical Engineering and Center of Astro-Engineering, Pontificia Universidad Catolica de Chile, Avenida Vicuna Mackenna 4860, Santiago 7820436, Chile. ; Polo Astronomico Casimiro Montenegro Filho/FPTI-BR, Avenida Tancredo Neves 6731, CEP 85867-900, Foz do Iguacu, PR, Brazil. ; 1] Observatorio Astronomico, Universidad Nacional de Cordoba, Laprida 854, Cordoba 5000, Argentina [2] Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Cordoba 5000, Argentina [3] Instituto de Astronomia Teorica y Experimental IATE-CONICET, Cordoba 5000, Argentina [4] Facultad de Ciencias Exactas, Fisicas y Naturales, Universidad Nacional de Cordoba (UNC), Cordoba 5000, Argentina. ; Observatorio Astronomico, Universidad Nacional de Cordoba, Laprida 854, Cordoba 5000, Argentina. ; Observatoire de Paris, IMCCE, UPMC, CNRS, 77 Avenue Denfert-Rochereau, 75014 Paris, France. ; Unidad de Astronomia, Facultad de Ciencias Basicas, Universidad de Antofagasta, Avenida Angamos 601, Antofagasta, Region II, Chile. ; Departamento de Astronomia, Facultad Ciencias, Universidad de la Republica, 11300 Montevideo, Uruguay. ; Scottish Universities Physics Alliance, University of St Andrews, School of Physics and Astronomy, North Haugh, St Andrews KY16 9SS, UK. ; Department of Physics and Astronomy, University of North Carolina - Chapel Hill, North Carolina 27599, USA. ; 1] Observatorio Astronomico, Universidad Nacional de Cordoba, Laprida 854, Cordoba 5000, Argentina [2] Instituto de Astronomia Teorica y Experimental IATE-CONICET, Cordoba 5000, Argentina.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24670644" target="_blank"〉PubMed〈/a〉

Description: DNA methylation is highly dynamic during mammalian embryogenesis. It is broadly accepted that the paternal genome is actively depleted of 5-methylcytosine at fertilization, followed by passive loss that reaches a minimum at the blastocyst stage. However, this model is based on limited data, and so far no base-resolution maps exist to support and refine it. Here we generate genome-scale DNA methylation maps in mouse gametes and from the zygote through post-implantation. We find that the oocyte already exhibits global hypomethylation, particularly at specific families of long interspersed element 1 and long terminal repeat retroelements, which are disparately methylated between gametes and have lower methylation values in the zygote than in sperm. Surprisingly, the oocyte contributes a unique set of differentially methylated regions (DMRs)--including many CpG island promoters--that are maintained in the early embryo but are lost upon specification and absent from somatic cells. In contrast, sperm-contributed DMRs are largely intergenic and become hypermethylated after the blastocyst stage. Our data provide a genome-scale, base-resolution timeline of DNA methylation in the pre-specified embryo, when this epigenetic modification is most dynamic, before returning to the canonical somatic pattern.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3331945/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3331945/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, Zachary D -- Chan, Michelle M -- Mikkelsen, Tarjei S -- Gu, Hongcang -- Gnirke, Andreas -- Regev, Aviv -- Meissner, Alexander -- 1P50HG006193-01/HG/NHGRI NIH HHS/ -- 5DP1OD003958/OD/NIH HHS/ -- 5RC1AA019317/AA/NIAAA NIH HHS/ -- DP1 CA174427/CA/NCI NIH HHS/ -- DP1 OD003958/OD/NIH HHS/ -- DP1 OD003958-04/OD/NIH HHS/ -- P01GM099117/GM/NIGMS NIH HHS/ -- P50 HG006193/HG/NHGRI NIH HHS/ -- P50 HG006193-01/HG/NHGRI NIH HHS/ -- U01ES017155/ES/NIEHS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Mar 28;484(7394):339-44. doi: 10.1038/nature10960.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22456710" target="_blank"〉PubMed〈/a〉

Description: Our ability to synthesize nanometre-scale chemical species, such as nanoparticles with desired shapes and compositions, offers the exciting prospect of generating new functional materials and devices by combining them in a controlled fashion into larger structures. Self-assembly can achieve this task efficiently, but may be subject to thermodynamic and kinetic limitations: reactants, intermediates and products may collide with each other throughout the assembly time course to produce non-target species instead of target species. An alternative approach to nanoscale assembly uses information-containing molecules such as DNA to control interactions and thereby minimize unwanted cross-talk between different components. In principle, this method should allow the stepwise and programmed construction of target products by linking individually selected nanoscale components-much as an automobile is built on an assembly line. Here we demonstrate that a nanoscale assembly line can be realized by the judicious combination of three known DNA-based modules: a DNA origami tile that provides a framework and track for the assembly process, cassettes containing three independently controlled two-state DNA machines that serve as programmable cargo-donating devices and are attached in series to the tile, and a DNA walker that can move on the track from device to device and collect cargo. As the walker traverses the pathway prescribed by the origami tile track, it sequentially encounters the three DNA devices, each of which can be independently switched between an 'ON' state, allowing its cargo to be transferred to the walker, and an 'OFF' state, in which no transfer occurs. We use three different types of gold nanoparticle species as cargo and show that the experimental system does indeed allow the controlled fabrication of the eight different products that can be obtained with three two-state devices.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872101/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872101/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gu, Hongzhou -- Chao, Jie -- Xiao, Shou-Jun -- Seeman, Nadrian C -- GM-29544/GM/NIGMS NIH HHS/ -- R37 GM029554-26/GM/NIGMS NIH HHS/ -- R37 GM029554-27/GM/NIGMS NIH HHS/ -- R37 GM029554-28/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 May 13;465(7295):202-5. doi: 10.1038/nature09026.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, New York University, New York, New York 10003, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20463734" target="_blank"〉PubMed〈/a〉