Journal Articles
Pluripotency, Differentiation, and Reprogramming: A Gene Expression Dynamics Model with Epigenetic Feedback Regulation
by Tadashi Miyamoto, Chikara Furusawa, Kunihiko Kaneko
Embryonic stem cells exhibit pluripotency: they can differentiate into all types of somatic cells. Pluripotent genes such as Oct4 and Nanog are activated in the pluripotent state, and their expression decreases during cell differentiation. Inversely, expression of differentiation genes such as Gata6 and Gata4 is promoted during differentiation. The gene regulatory network controlling the expression of these genes has been described, and slower-scale epigenetic modifications have been uncovered. Although the differentiation of pluripotent stem cells is normally irreversible, reprogramming of cells can be experimentally manipulated to regain pluripotency via overexpression of certain genes. Despite these experimental advances, the dynamics and mechanisms of differentiation and reprogramming are not yet fully understood. Based on recent experimental findings, we constructed a simple gene regulatory network including pluripotent and differentiation genes, and we demonstrated the existence of pluripotent and differentiated states from the resultant dynamical-systems model. Two differentiation mechanisms, interaction-induced switching from an expression oscillatory state and noise-assisted transition between bistable stationary states, were tested in the model. The former was found to be relevant to the differentiation process. We also introduced variables representing epigenetic modifications, which controlled the threshold for gene expression. By assuming positive feedback between expression levels and the epigenetic variables, we observed differentiation in expression dynamics. Additionally, with numerical reprogramming experiments for differentiated cells, we showed that pluripotency was recovered in cells by imposing overexpression of two pluripotent genes and external factors to control expression of differentiation genes. Interestingly, these factors were consistent with the four Yamanaka factors, Oct4, Sox2, Klf4, and Myc, which were necessary for the establishment of induced pluripotent stem cells. These results, based on a gene regulatory network and expression dynamics, contribute to our wider understanding of pluripotency, differentiation, and reprogramming of cells, and they provide a fresh viewpoint on robustness and control during development.What Makes the Photocatalytic CO2 Reduction on N-Doped Ta2O5 Efficient: Insights from Nonadiabatic Molecular Dynamics
Valence Band Modification and High Thermoelectric Performance in SnTe Heavily Alloyed with MnTe
Rhodium-Catalyzed Asymmetric 1,4-Addition of α,β-Unsaturated Imino Esters Using Chiral Bicyclic Bridgehead Phosphoramidite Ligands
Electrochemistry at a Metal Nanoparticle on a Tunneling Film: A Steady-State Model of Current Densities at a Tunneling Ultramicroelectrode
Ultrathin Black Phosphorus Nanosheets for Efficient Singlet Oxygen Generation
Structural Organization of Insulin Fibrils Based on Polarized Raman Spectroscopy: Evaluation of Existing Models
Iron(II) Active Species in Iron–Bisphosphine Catalyzed Kumada and Suzuki–Miyaura Cross-Couplings of Phenyl Nucleophiles and Secondary Alkyl Halides
Proton-Coupled Electron Transfer in the Reduction of Arenes by SmI2–Water Complexes
Search for a Symmetrical C–F–C Fluoronium Ion in Solution: Kinetic Isotope Effects, Synthetic Labeling, and Computational, Solvent, and Rate Studies
Catalytic Kinetic Resolution of Disubstituted Piperidines by Enantioselective Acylation: Synthetic Utility and Mechanistic Insights
Corrigendum: Lanosterol reverses protein aggregation in cataracts
Corrigendum: Lanosterol reverses protein aggregation in cataracts
Nature 526, 7574 (2015). doi:10.1038/nature15253
Authors: Ling Zhao, Xiang-Jun Chen, Jie Zhu, Yi-Bo Xi, Xu Yang, Li-Dan Hu, Hong Ouyang, Sherrina H. Patel, Xin Jin, Danni Lin, Frances Wu, Ken Flagg, Huimin Cai, Gen Li, Guiqun Cao, Ying Lin, Daniel Chen, Cindy Wen, Christopher Chung, Yandong Wang, Austin Qiu, Emily Yeh, Wenqiu Wang, Xun Hu, Seanna Grob, Ruben Abagyan, Zhiguang Su, Harry Christianto Tjondro, Xi-Juan Zhao, Hongrong Luo, Rui Hou, J. Jefferson P. Perry, Weiwei Gao, Igor Kozak, David Granet, Yingrui Li, Xiaodong Sun, Jun Wang, Liangfang Zhang, Yizhi Liu, Yong-Bin Yan & Kang Zhang
Nature523, 607–611 (2015); doi:10.1038/nature14650In this Letter, author Yong-Bin Yan was incorrectly associated with affiliation number 5 (Department of Ophthalmology, Xijing Hospital) instead of affiliation number 4 (State Key Laboratory of Membrane Biology, School of Life Sciences,
Erratum: Genetic diversity and evolutionary dynamics of Ebola virus in Sierra Leone
Erratum: Genetic diversity and evolutionary dynamics of Ebola virus in Sierra Leone
Nature 526, 7574 (2015). doi:10.1038/nature15255
Authors: Yi-Gang Tong, Wei-Feng Shi, Di Liu, Jun Qian, Long Liang, Xiao-Chen Bo, Jun Liu, Hong-Guang Ren, Hang Fan, Ming Ni, Yang Sun, Yuan Jin, Yue Teng, Zhen Li, David Kargbo, Foday Dafae, Alex Kanu, Cheng-Chao Chen, Zhi-Heng Lan, Hui Jiang, Yang Luo, Hui-Jun Lu, Xiao-Guang Zhang, Fan Yang, Yi Hu, Yu-Xi Cao, Yong-Qiang Deng, Hao-Xiang Su, Yu Sun, Wen-Sen Liu, Zhuang Wang, Cheng-Yu Wang, Zhao-Yang Bu, Zhen-Dong Guo, Liu-Bo Zhang, Wei-Min Nie, Chang-Qing Bai, Chun-Hua Sun, Xiao-Ping An, Pei-Song Xu, Xiang-Li-Lan Zhang, Yong Huang, Zhi-Qiang Mi, Dong Yu, Hong-Wu Yao, Yong Feng, Zhi-Ping Xia, Xue-Xing Zheng, Song-Tao Yang, Bing Lu, Jia-Fu Jiang, Brima Kargbo, Fu-Chu He, George F. Gao & Wu-Chun Cao
Nature524, 93–96 (2015); doi:10.1038/nature14490This Letter should have contained an associated Creative Commons statement in the Author Information section. In addition, the Fig. 3c legend should have stated that the bar chart was adapted, with permission, from
FDA vulnerability revealed
FDA vulnerability revealed
Nature 524, 7566 (2015). doi:10.1038/524387a
A politically charged advisory committee meeting may have tipped the scales in favour of a mildly effective female libido drug.
We must build resilience into our communities
We must build resilience into our communities
Nature 524, 7566 (2015). http://www.nature.com/doifinder/10.1038/524389a
Author: Erwann Michel-Kerjan
Innovative approaches can better equip society to deal with natural disasters and other shocks, says Erwann Michel-Kerjan.
Animal behaviour: Hummingbirds sip using mini pumps
Animal behaviour: Hummingbirds sip using mini pumps
Nature 524, 7566 (2015). doi:10.1038/524390a
Hummingbirds draw nectar into their bills using long tongues that act like tiny pumps.It was long thought that liquid travels passively up the birds' tongues without suction. But Alejandro Rico-Guevara and his colleagues at the University of Connecticut in Storrs found a different mechanism
Chemistry: Better catalyst for carbon conversion
Chemistry: Better catalyst for carbon conversion
Nature 524, 7566 (2015). doi:10.1038/524390b
A porous, crystalline compound can speed up the conversion of carbon dioxide to carbon monoxide in water.Omar Yaghi and Christopher Chang at the University of California, Berkeley, and their colleagues used structures called covalent organic frameworks (COFs) — grid-like arrangements of carbon, nitrogen and
Animal behaviour: Stinging cells help jellyfish to mate
Animal behaviour: Stinging cells help jellyfish to mate
Nature 524, 7566 (2015). doi:10.1038/524390c
Some box jellyfish display elaborate mating behaviours and even use their toxic stinging cells to ensure successful fertilization.Many jellyfish reproduce using external fertilization, but in a few box jellyfish, fertilization can occur internally. In one species (Copula sivickisi; pictured), the male
Astrophysics: Dark-energy search narrows
Astrophysics: Dark-energy search narrows
Nature 524, 7566 (2015). doi:10.1038/524390d
Two groups have tightened the limits on the search for elusive dark matter and dark energy, the mysterious force accelerating the expansion of the Universe.Physicists have proposed that dark energy could come from a 'chameleon' field: a force that would act in the low
