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Virtual discovery of melatonin receptor ligands to modulate circadian rhythms 期刊论文
NATURE, 2020, 579 (7800) : 609-+
作者:  Huang, Weijiao;  Masureel, Matthieu;  Qu, Qianhui;  Janetzko, John;  Inoue, Asuka;  Kato, Hideaki E.;  Robertson, Michael J.;  Nguyen, Khanh C.;  Glenn, Jeffrey S.;  Skiniotis, Georgios;  Kobilka, Brian K.
收藏  |  浏览/下载:39/0  |  提交时间:2020/07/03

The neuromodulator melatonin synchronizes circadian rhythms and related physiological functions through the actions of two G-protein-coupled receptors: MT1 and MT2. Circadian release of melatonin at night from the pineal gland activates melatonin receptors in the suprachiasmatic nucleus of the hypothalamus, synchronizing the physiology and behaviour of animals to the light-dark cycle(1-4). The two receptors are established drug targets for aligning circadian phase to this cycle in disorders of sleep(5,6) and depression(1-4,7-9). Despite their importance, few in vivo active MT1-selective ligands have been reported(2,8,10-12), hampering both the understanding of circadian biology and the development of targeted therapeutics. Here we docked more than 150 million virtual molecules to an MT1 crystal structure, prioritizing structural fit and chemical novelty. Of these compounds, 38 high-ranking molecules were synthesized and tested, revealing ligands with potencies ranging from 470 picomolar to 6 micromolar. Structure-based optimization led to two selective MT1 inverse agonists-which were topologically unrelated to previously explored chemotypes-that acted as inverse agonists in a mouse model of circadian re-entrainment. Notably, we found that these MT1-selective inverse agonists advanced the phase of the mouse circadian clock by 1.3-1.5 h when given at subjective dusk, an agonist-like effect that was eliminated in MT1- but not in MT2-knockout mice. This study illustrates the opportunities for modulating melatonin receptor biology through MT1-selective ligands and for the discovery of previously undescribed, in vivo active chemotypes from structure-based screens of diverse, ultralarge libraries. A computational screen of an ultra-large virtual library against the structure of the melatonin receptor found nanomolar ligands, and ultimately two selective MT1 inverse agonists that induced phase advancement of the mouse circadian clock when given at subjective dusk.


  
Microbiome analyses of blood and tissues suggest cancer diagnostic approach 期刊论文
NATURE, 2020, 579 (7800) : 567-+
作者:  Shao, Zhengping;  Flynn, Ryan A.;  Crowe, Jennifer L.;  Zhu, Yimeng;  Liang, Jialiang;  Jiang, Wenxia;  Aryan, Fardin;  Aoude, Patrick;  Bertozzi, Carolyn R.;  Estes, Verna M.;  Lee, Brian J.;  Bhagat, Govind;  Zha, Shan;  Calo, Eliezer
收藏  |  浏览/下载:83/0  |  提交时间:2020/07/03

Microbial nucleic acids are detected in samples of tissues and blood from more than 10,000 patients with cancer, and machine learning is used to show that these can be used to discriminate between and among different types of cancer, suggesting a new microbiome-based diagnostic approach.


Systematic characterization of the cancer microbiome provides the opportunity to develop techniques that exploit non-human, microorganism-derived molecules in the diagnosis of a major human disease. Following recent demonstrations that some types of cancer show substantial microbial contributions(1-10), we re-examined whole-genome and whole-transcriptome sequencing studies in The Cancer Genome Atlas(11) (TCGA) of 33 types of cancer from treatment-naive patients (a total of 18,116 samples) for microbial reads, and found unique microbial signatures in tissue and blood within and between most major types of cancer. These TCGA blood signatures remained predictive when applied to patients with stage Ia-IIc cancer and cancers lacking any genomic alterations currently measured on two commercial-grade cell-free tumour DNA platforms, despite the use of very stringent decontamination analyses that discarded up to 92.3% of total sequence data. In addition, we could discriminate among samples from healthy, cancer-free individuals (n = 69) and those from patients with multiple types of cancer (prostate, lung, and melanoma  100 samples in total) solely using plasma-derived, cell-free microbial nucleic acids. This potential microbiome-based oncology diagnostic tool warrants further exploration.


  
Gene expression and cell identity controlled by anaphase-promoting complex 期刊论文
NATURE, 2020
作者:  Filacchione, Gianrico;  Capaccioni, Fabrizio;  Ciarniello, Mauro;  Raponi, Andrea;  Rinaldi, Giovanna;  De Sanctis, Maria Cristina;  Bockelee-Morvan, Dominique;  Erard, Stephane;  Arnold, Gabriele;  Mennella, Vito;  Formisano, Michelangelo;  Longobardo, Andrea;  Mottola, Stefano
收藏  |  浏览/下载:20/0  |  提交时间:2020/07/03

Metazoan development requires the robust proliferation of progenitor cells, the identities of which are established by tightly controlled transcriptional networks(1). As gene expression is globally inhibited during mitosis, the transcriptional programs that define cell identity must be restarted in each cell cycle(2-5) but how this is accomplished is poorly understood. Here we identify a ubiquitin-dependent mechanism that integrates gene expression with cell division to preserve cell identity. We found that WDR5 and TBP, which bind active interphase promoters(6,7), recruit the anaphase-promoting complex (APC/C) to specific transcription start sites during mitosis. This allows APC/C to decorate histones with ubiquitin chains branched at Lys11 and Lys48 (K11/K48-branched ubiquitin chains) that recruit p97 (also known as VCP) and the proteasome, which ensures the rapid expression of pluripotency genes in the next cell cycle. Mitotic exit and the re-initiation of transcription are thus controlled by a single regulator (APC/C), which provides a robust mechanism for maintaining cell identity throughout cell division.


WDR5 and TBP recruit anaphase-promoting complex to specific transcription start sites in mitosis, initiating a ubiquitin-dependent mechanism that preserves cell identity by linking gene expression and cell division.


  
Last appearance of Homo erectus at Ngandong, Java, 117,000-108,000 years ago 期刊论文
NATURE, 2020, 577 (7790) : 381-+
作者:  Haldane, Andy
收藏  |  浏览/下载:44/0  |  提交时间:2020/04/16

Homo erectus is the founding early hominin species of Island Southeast Asia, and reached Java (Indonesia) more than 1.5 million years ago(1,2). Twelve H. erectus calvaria (skull caps) and two tibiae (lower leg bones) were discovered from a bone bed located about 20 m above the Solo River at Ngandong (Central Java) between 1931 and 1933(3,4), and are of the youngest, most-advanced form of H. erectus(5-8). Despite the importance of the Ngandong fossils, the relationship between the fossils, terrace fill and ages have been heavily debated(9-14). Here, to resolve the age of the Ngandong evidence, we use Bayesian modelling of 52 radiometric age estimates to establish-to our knowledg-the first robust chronology at regional, valley and local scales. We used uranium-series dating of speleothems to constrain regional landscape evolution  luminescence, (40)argon/(39)argon (Ar-40/Ar-39) and uranium-series dating to constrain the sequence of terrace evolution  and applied uranium-series and uranium series-electron-spin resonance (US-ESR) dating to non-human fossils to directly date our re-excavation of Ngandong(5,15). We show that at least by 500 thousand years ago (ka) the Solo River was diverted into the Kendeng Hills, and that it formed the Solo terrace sequence between 316 and 31 ka and the Ngandong terrace between about 140 and 92 ka. Non-human fossils recovered during the re-excavation of Ngandong date to between 109 and 106 ka (uranium-series minimum)(16) and 134 and 118 ka (US-ESR), with modelled ages of 117 to 108 thousand years (kyr) for the H. erectus bone bed, which accumulated during flood conditions(3,17). These results negate the extreme ages that have been proposed for the site and solidify Ngandong as the last known occurrence of this long-lived species.


  
Re-emergence of North Atlantic subsurface ocean temperature anomalies in a seasonal forecast system 期刊论文
CLIMATE DYNAMICS, 2019, 53: 4799-4820
作者:  Grist, Jeremy P.;  Sinha, Bablu;  Hewitt, Helene. T.;  Duchez, Aurelie;  MacLachlan, Craig;  Hyder, Patrick;  Josey, Simon A.;  Hirschi, Joel J. -M.;  Blaker, Adam T.;  New, Adrian. L.;  Scaife, Adam A.;  Roberts, Chris D.
收藏  |  浏览/下载:19/0  |  提交时间:2019/11/27
Seasonal forecasting  Climate model  Re-emergence  
Re-caching behaviour of rodents improves seed dispersal effectiveness: Evidence from seedling establishment 期刊论文
FOREST ECOLOGY AND MANAGEMENT, 2019, 444: 207-213
作者:  Wang, Zhenyu;  Wang, Bo;  Yi, Xianfeng;  Yan, Chuan;  Zhang, Zhibin;  Cao, Lin
收藏  |  浏览/下载:18/0  |  提交时间:2019/11/27
Long-distance dispersal  Re-caching  Rodents  Scatter hoarding  Seed dispersal  Seedling establishment  
Deep soil flipping increases carbon stocks of New Zealand grasslands 期刊论文
GLOBAL CHANGE BIOLOGY, 2019, 25 (7) : 2296-2309
作者:  Schiedung, Marcus;  Tregurtha, Craig S.;  Beare, Michael H.;  Thomas, Steve M.;  Don, Axel
收藏  |  浏览/下载:15/0  |  提交时间:2019/11/27
carbon burial  carbon sequestration  carbon stocks  chronosequence  grassland  re-sampling  soil organic carbon  subsoil  
Visions for small-scale renewable energy production on Finnish farms - A Delphi study on the opportunities for new business 期刊论文
ENERGY POLICY, 2019, 129: 939-948
作者:  Rikkonen, Pasi;  Tapio, Petri;  Rintamaki, Heidi
收藏  |  浏览/下载:32/0  |  提交时间:2019/11/26
Business opportunities  Delphi method  Future images  Renewable energy (RE)  
How essential of the balance between large and small scale features to reproduce precipitation during a sudden sharp turn from drought to flood 期刊论文
CLIMATE DYNAMICS, 2019, 52: 5013-5029
作者:  Ma, Yuanyuan;  Yang, Yi;  Wang, Chenghai
收藏  |  浏览/下载:13/0  |  提交时间:2019/11/26
Sudden turn from drought to flood  Conventional continuous simulation  Grid nudging  Spectral nudging  Re-initialization  
Management implications of tree growth patterns in miombo woodlands of Zambia 期刊论文
FOREST ECOLOGY AND MANAGEMENT, 2019, 436: 105-116
作者:  Chidumayo, E. N.
收藏  |  浏览/下载:17/0  |  提交时间:2019/04/09
Basal area  Diameter increment  Dry and wet miombo  Growth models  Permanent sample plots  Re-growth