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The mutational landscape of normal human endometrial epithelium 期刊论文
NATURE, 2020, 580 (7805) : 640-+
作者:  Rogelj, Joeri;  Forster, Piers M.;  Kriegler, Elmar;  Smith, Christopher J.;  Seferian, Roland
收藏  |  浏览/下载:13/0  |  提交时间:2020/07/03

All normal somatic cells are thought to acquire mutations, but understanding of the rates, patterns, causes and consequences of somatic mutations in normal cells is limited. The uterine endometrium adopts multiple physiological states over a lifetime and is lined by a gland-forming epithelium(1,2). Here, using whole-genome sequencing, we show that normal human endometrial glands are clonal cell populations with total mutation burdens that increase at about 29 base substitutions per year and that are many-fold lower than those of endometrial cancers. Normal endometrial glands frequently carry '  driver'  mutations in cancer genes, the burden of which increases with age and decreases with parity. Cell clones with drivers often originate during the first decades of life and subsequently progressively colonize the epithelial lining of the endometrium. Our results show that mutational landscapes differ markedly between normal tissues-perhaps shaped by differences in their structure and physiology-and indicate that the procession of neoplastic change that leads to endometrial cancer is initiated early in life.


Whole-genome sequencing of normal human endometrial glands shows that most are clonal cell populations and frequently carry cancer driver mutations that occur early in life, and that parity has a protective effect.


  
Intensive farming drives long-term shifts in avian community composition 期刊论文
NATURE, 2020, 579 (7799) : 393-+
作者:  Oh, Eugene;  Mark, Kevin G.;  Mocciaro, Annamaria;  Watson, Edmond R.;  Prabu, J. Rajan;  Cha, Denny D.;  Kampmann, Martin;  Gamarra, Nathan;  Zhou, Coral Y.;  Rape, Michael
收藏  |  浏览/下载:15/0  |  提交时间:2020/05/13

Variation in vegetation and climate affects the long-term changes in bird communities in intensive-agriculture habitats, but not in diversified-agriculture or natural-forest habitats, by changing the local colonization and extinction rates.


Agricultural practices constitute both the greatest cause of biodiversity loss and the greatest opportunity for conservation(1,2), given the shrinking scope of protected areas in many regions. Recent studies have documented the high levels of biodiversity-across many taxa and biomes-that agricultural landscapes can support over the short term(1,3,4). However, little is known about the long-term effects of alternative agricultural practices on ecological communities(4,5) Here we document changes in bird communities in intensive-agriculture, diversified-agriculture and natural-forest habitats in 4 regions of Costa Rica over a period of 18 years. Long-term directional shifts in bird communities were evident in intensive- and diversified-agricultural habitats, but were strongest in intensive-agricultural habitats, where the number of endemic and International Union for Conservation of Nature (IUCN) Red List species fell over time. All major guilds, including those involved in pest control, pollination and seed dispersal, were affected. Bird communities in intensive-agricultural habitats proved more susceptible to changes in climate, with hotter and drier periods associated with greater changes in community composition in these settings. These findings demonstrate that diversified agriculture can help to alleviate the long-term loss of biodiversity outside natural protected areas(1).


  
Parental-to-embryo switch of chromosome organization in early embryogenesis 期刊论文
NATURE, 2020: 142-+
作者:  Kim, Eugene;  Kerssemakers, Jacob;  Shaltiel, Indra A.;  Haering, Christian H.;  Dekker, Cees
收藏  |  浏览/下载:18/0  |  提交时间:2020/07/03

Single-cell allelic HiC analysis, combined with allelic gene expression and chromatin states, reveals parent-of-origin-specific dynamics of chromosome organization and gene expression during mouse preimplantation development.


Paternal and maternal epigenomes undergo marked changes after fertilization(1). Recent epigenomic studies have revealed the unusual chromatin landscapes that are present in oocytes, sperm and early preimplantation embryos, including atypical patterns of histone modifications(2-4) and differences in chromosome organization and accessibility, both in gametes(5-8) and after fertilization(5,8-10). However, these studies have led to very different conclusions: the global absence of local topological-associated domains (TADs) in gametes and their appearance in the embryo(8,9) versus the pre-existence of TADs and loops in the zygote(5,11). The questions of whether parental structures can be inherited in the newly formed embryo and how these structures might relate to allele-specific gene regulation remain open. Here we map genomic interactions for each parental genome (including the X chromosome), using an optimized single-cell high-throughput chromosome conformation capture (HiC) protocol(12,13), during preimplantation in the mouse. We integrate chromosome organization with allelic expression states and chromatin marks, and reveal that higher-order chromatin structure after fertilization coincides with an allele-specific enrichment of methylation of histone H3 at lysine 27. These early parental-specific domains correlate with gene repression and participate in parentally biased gene expression-including in recently described, transiently imprinted loci(14). We also find TADs that arise in a non-parental-specific manner during a second wave of genome assembly. These de novo domains are associated with active chromatin. Finally, we obtain insights into the relationship between TADs and gene expression by investigating structural changes to the paternal X chromosome before and during X chromosome inactivation in preimplantation female embryos(15). We find that TADs are lost as genes become silenced on the paternal X chromosome but linger in regions that escape X chromosome inactivation. These findings demonstrate the complex dynamics of three-dimensional genome organization and gene expression during early development.


  
Construction of a human cell landscape at single-cell level 期刊论文
NATURE, 2020, 581 (7808) : 303-+
作者:  Han, Yan;  Reyes, Alexis A.;  Malik, Sara;  He, Yuan
收藏  |  浏览/下载:11/0  |  提交时间:2020/07/03

Single-cell analysis is a valuable tool for dissecting cellular heterogeneity in complex systems(1). However, a comprehensive single-cell atlas has not been achieved for humans. Here we use single-cell mRNA sequencing to determine the cell-type composition of all major human organs and construct a scheme for the human cell landscape (HCL). We have uncovered a single-cell hierarchy for many tissues that have not been well characterized. We established a '  single-cell HCL analysis'  pipeline that helps to define human cell identity. Finally, we performed a single-cell comparative analysis of landscapes from human and mouse to identify conserved genetic networks. We found that stem and progenitor cells exhibit strong transcriptomic stochasticity, whereas differentiated cells are more distinct. Our results provide a useful resource for the study of human biology.


Single-cell RNA sequencing is used to generate a dataset covering all major human organs in both adult and fetal stages, enabling comparison with similar datasets for mouse tissues.


  
Bird response to woody pastoral management of ancient chestnut orchards: A case study from the southern Alps 期刊论文
FOREST ECOLOGY AND MANAGEMENT, 2019, 453
作者:  Morelli, Federico;  Python, Anita;  Pezzatti, Gianni Boris;  Moretti, Marco
收藏  |  浏览/下载:12/0  |  提交时间:2020/02/17
Chestnut groves  Forest management  Indicator species  Resilience to disturbance  Species diversity  Woody pastoral landscapes  
Human-carnivore relations: conflicts, tolerance and coexistence in the American West 期刊论文
ENVIRONMENTAL RESEARCH LETTERS, 2019, 14 (12)
作者:  Exposito-Granados, Monica;  Castro, Antonio J.;  Lozano, Jorge;  Aznar-Sanchez, Jose A.;  Carter, Neil H.;  Requena-Mullor, Juan M.;  Malo, Aurelio F.;  Olszanska, Agnieszka;  Morales-Reyes, Zebensui;  Moleon, Marcos;  Sanchez-Zapata, Jose A.;  Cortes-Avizanda, Ainara;  Fischer, Joern;  Martin-Lopez, Berta
收藏  |  浏览/下载:11/0  |  提交时间:2020/02/17
ecosystem services  human-wildlife interactions  multi-use landscapes  shared landscapes  socio-ecological systems  
Shared landscapes increase condominium unit selling price in a high-density city 期刊论文
LANDSCAPE AND URBAN PLANNING, 2019, 192
作者:  Belcher, Richard N.;  Suen, Ester;  Menz, Sacha;  Schroepfer, Thomas
收藏  |  浏览/下载:9/0  |  提交时间:2020/02/17
Urban planning  Urban landscapes  Ecosystem service valuation  High-density  Hedonic pricing  Tropical vegetation  
Riparian forest recovery following a decade of cattle exclusion in the Colombian Andes 期刊论文
FOREST ECOLOGY AND MANAGEMENT, 2019, 452
作者:  Calle, Alicia;  Holl, Karen D.
收藏  |  浏览/下载:7/0  |  提交时间:2019/11/27
Forest and landscape restoration  Forest recovery  Human-managed landscapes  Silvopastoral systems  Tropical forest  
Primary forest distribution and representation in a Central European landscape: Results of a large-scale field-based census 期刊论文
FOREST ECOLOGY AND MANAGEMENT, 2019, 449
作者:  Mikolas, Martin;  Ujhazy, Karol;  Jasik, Marian;  Wiezik, Michal;  Gallay, Igor;  Polak, Pavol;  Vysoky, Juraj;  Ciliak, Marek;  Meigs, Garrett W.;  Svoboda, Miroslav;  Trotsiuk, Volodymyr;  Keeton, William S.
收藏  |  浏览/下载:20/0  |  提交时间:2019/11/27
Forest landscapes  Ecosystem functions  Biodiversity  Habitat loss  Fragmentation  Reserve design  
Drivers of mammal richness, diversity and occurrence in heterogeneous landscapes composed by plantation forests and natural environments 期刊论文
FOREST ECOLOGY AND MANAGEMENT, 2019, 449
作者:  Pina, Tony E. N.;  Carvalho, William D.;  Rosalino, Luis Miguel C.;  Hilario, Renato R.
收藏  |  浏览/下载:5/0  |  提交时间:2019/11/27
Landscape composition  Landscape structure  Camera trap  Conservation  Anthropogenic landscapes  Brazilian Amazon