Review
Cell Biology
Puja Agrawal, Sridhar Rao
Summary: Cell fate decisions rely on gene expression changes mediated by regulatory elements like enhancers and CTCF binding sites. These elements play crucial roles in early mammalian development and impact cell-type specific gene expression.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Yiran Meng, Joana Carrelha, Roy Drissen, Xiying Ren, Bowen Zhang, Adriana Gambardella, Simona Valletta, Supat Thongjuea, Sten Eirik Jacobsen, Claus Nerlov
Summary: The lymphoid fate in haematopoietic stem cells is determined through epigenetic programming rather than transcriptional control, which also influences the differentiation pathways of platelets with distinct kinetics.
NATURE CELL BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Dongwei Li, Xiaodong Shu, Ping Zhu, Duanqing Pei
Summary: Recent research has shown that chromatin dynamics are closely linked to cell fate control, with a binary off/on switch occurring during iPSC reprogramming. This implies that similar mechanisms may also be present in normal development, suggesting potential for further approaches to directing cell fate changes.
Review
Cell Biology
Li Sun, Xiuling Fu, Gang Ma, Andrew P. Hutchins
Summary: During embryonic development, epigenetic information on DNA and histones undergoes rearrangement, with mechanisms not fully understood. As embryos transition from totipotency to pluripotency, there are dynamic changes in epigenetic marks.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Kushagra Pandey, Hamim Zafar
Summary: MARGARET is a method for inferring single-cell trajectories and fate mapping, which can reconstruct complex cell-state manifolds and quantify fate plasticity. Evaluation on multiple datasets from different domains demonstrates that MARGARET outperforms other methods and has been successfully applied to study hematopoiesis, embryoid body differentiation, and colon differentiation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Physical
Thorsten Prustel, Martin Meier-Schellersheim
Summary: This study focused on computational models of reaction-diffusion systems commonly found in cellular signaling pathways, and introduced an approach that allows for the reconstruction of entire molecular trajectories after a simulated time step, avoiding the need for inefficient draws from non-standard distributions. This method enables highly accurate stochastic simulations for system sizes that would be prohibitively costly to simulate with conventional Green's function based methods.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biology
Runxiang Qiu, Jun Wu, Brian Gudenas, Paul A. Northcott, Robert J. Wechsler-Reya, Qiang Lu
Summary: The study shows that targeting Kif20a can inhibit early cell cycle exit and premature neuronal differentiation of cerebellar granule neuron progenitors, suppressing tumor formation in medulloblastoma models. This suggests a potential novel avenue for developing anti-proliferation treatment for malignant brain tumors.
COMMUNICATIONS BIOLOGY
(2021)
Article
Cell & Tissue Engineering
Baojiang Wu, Yunxia Li, Bojiang Li, Baojing Zhang, Yanqiu Wang, Lin Li, Junpeng Gao, Yuting Fu, Shudong Li, Chen Chen, M. Azim Surani, Fuchou Tang, Xihe Li, Siqin Bao
Summary: The study demonstrates that only LIF in the medium is sufficient for adapting 2i/L-ESCs to embryonic stem cells (ESCs) in a hypermethylated state (L-ESCs). L-ESCs are close to 2i/L-ESCs and in a stable state between naive and primed pluripotency, with an important role of DNA methyltransferases (DNMTs) in LIF-dependent mouse ESC adaptation and self-renewal.
Article
Cell Biology
Sophia J. Hafner, Martin D. Jansson, Kubra Altinel, Kasper L. Andersen, Zehra Abay-Norgaard, Patrice Menard, Martin Fontenas, Daniel M. Sorensen, David M. Gay, Frederic S. Arendrup, Disa Tehler, Nicolai Krogh, Henrik Nielsen, Matthew L. Kraushar, Agnete Kirkeby, Anders H. Lund
Summary: Translational regulation plays a crucial role in pluripotency maintenance and cell differentiation. This study reveals ribosome heterogeneity through rRNA 2'-O-methylation during early development and differentiation, indicating a direct role for ribosomes in regulating translation during cell fate acquisition.
DEVELOPMENTAL CELL
(2023)
Article
Chemistry, Physical
Tetsuro Nagai, Akira Yoshimori, Susumu Okazaki
Summary: This study investigates a series of new Monte Carlo transition probabilities that can simulate molecular trajectories satisfying the diffusion equation. The results show good agreement with the numerical solution. The method is useful for studying long-distance transport of molecules in heterogeneous systems and many-particle dynamics.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Yi Hao, Xiang Li, Ke Qin, Yujie Shi, Yanwen He, Che Zhang, Bo Cheng, Xiwen Zhang, Guangyu Hu, Shuyu Liang, Qi Tang, Xing Chen
Summary: The O-GlcNAc modification is found to affect the self-renewal and differentiation of embryonic stem cells (ESCs), and the core pluripotency transcription factor NANOG is regulated by this modification. During neuronal lineage differentiation, the O-GlcNAc modification decreases, and suppressing O-GlcNAcylation can upregulate neuron-related genes, thus influencing the fate determination of ESCs.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Immunology
Yoon-A Kang, Hyojung Paik, Si Yi Zhang, Jonathan J. Chen, Oakley C. Olson, Carl A. Mitchell, Amelie Collins, James W. Swann, Matthew R. Warr, Rong Fan, Emmanuelle Passegue
Summary: The study reveals the existence of a secretory subset of myeloid-biased multipotent progenitors, MPP3, that plays a crucial role in myeloid lineage differentiation and cytokine production. These cells serve as a reservoir for rapid production of granulocyte/macrophage progenitors and contribute to the amplification of myeloid cell production in stress and disease conditions.
JOURNAL OF EXPERIMENTAL MEDICINE
(2023)
Article
Biotechnology & Applied Microbiology
Chen Li, Maria C. Virgilio, Kathleen L. Collins, Joshua D. Welch
Summary: This paper introduces a model called MultiVelo, which extends the RNA velocity framework using differential equations to incorporate epigenomic data. The model improves the accuracy of cell fate prediction by estimating the temporal relationship between chromatin accessibility and gene expression. The study reveals different classes of genes and cell states, and identifies time lags between transcription factor expression and binding site accessibility, as well as disease-associated SNP accessibility and linked gene expression.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Masaki Kinoshita, Meng Amy Li, Michael Barber, William Mansfield, Sabine Dietmann, Austin Smith
Summary: Genome remethylation is crucial for mammalian development, with a study showing that deficiencies in Dnmt3a and Dnmt3b lead to ES cells developing into trophoblast cells due to failed suppression of Ascl2. Regulating the expression of Ascl2 can impact the transdifferentiation and contribution of ES cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Oncology
Hwa-Ryung Song, Han-Kyu Kim, Seung-Gook Kim, Hyung-Jin Lim, Hyun-Yi Kim, Myung-Kwan Han
Summary: Leukemia inhibitory factor (LIF) is a stem cell growth factor that influences protein phosphorylation via various pathways, with the present study revealing its modulation of nucleotide metabolism-associated protein phosphorylation levels in mouse embryonic stem cells (mESCs).
MOLECULAR MEDICINE REPORTS
(2021)
Article
Engineering, Chemical
Milad Abolhasani, Eugenia Kumacheva, Axel Guenther
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2015)
Article
Biochemical Research Methods
Ali Oskooei, Axel Guenther
Article
Biochemical Research Methods
Sanjesh Yasotharan, Sascha Pinto, John G. Sled, Steffen-Sebastian Bolz, Axel Guenther
Article
Biophysics
K. Middleton, S. Al-Dujaili, X. Mei, A. Guenther, L. You
JOURNAL OF BIOMECHANICS
(2017)
Article
Biochemical Research Methods
Navid Hakimi, Richard Cheng, Lian Leng, Mohammad Sotoudehfar, Phoenix Qing Ba, Nazihah Bakhtyar, Saeid Amini-Nik, Marc G. Jeschke, Axel Guenther
Review
Chemistry, Multidisciplinary
Milad Abolhasani, Axel Guenther, Eugenia Kumacheva
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2014)
Article
Engineering, Electrical & Electronic
Ritu Raj Singh, Lian Leng, Axel Guenther, Roman Genov
IEEE JOURNAL OF SOLID-STATE CIRCUITS
(2012)
Article
Engineering, Biomedical
Meisam Honarvar Nazari, Hamed Mazhab-Jafari, Lian Leng, Axel Guenther, Roman Genov
IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS
(2013)
Article
Chemistry, Multidisciplinary
Gabriella Lestari, Milad Abolhasani, Darla Bennett, Preston Chase, Axel Guenther, Eugenia Kumacheva
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2014)
Article
Chemistry, Multidisciplinary
Dan Voicu, Milad Abolhasani, Rachelle Choueiri, Gabriella Lestari, Caroline Seiler, Gabriel Menard, Jesse Greener, Axel Guenther, Douglas W. Stephan, Eugenia Kumacheva
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2014)
Article
Biochemical Research Methods
Ali Oskooei, Milad Abolhasani, Axel Guenther
Article
Biochemical Research Methods
Milad Abolhasani, Ali Oskooei, Anna Klinkova, Eugenia Kumacheva, Axel Guenther
Article
Materials Science, Biomaterials
Shashi Malladi, David Miranda-Nieves, Lian Leng, Stephanie J. Grainger, Constantine Tarabanis, Alexander P. Nesmith, Revanth Kosaraju, Carolyn A. Haller, Kevin Kit Parker, Elliot L. Chaikof, Axel Guenther
ACS BIOMATERIALS SCIENCE & ENGINEERING
(2020)
Article
Chemistry, Multidisciplinary
Renee M. Ripken, Jeffery A. Wood, Stefan Schlautmann, Axel Gunther, Han J. G. E. Gardeniers, Severine Le Gac
Summary: Guiding bubble nucleation in a microfluidic device can optimize the performance of multiphase catalytic microreactors. Experimental results show that the presence of bubbles has a significant impact on transport phenomena and reaction conversion within the reactor.
REACTION CHEMISTRY & ENGINEERING
(2021)
Article
Engineering, Biomedical
Richard Y. Cheng, Gertraud Eylert, Jean-Michel Gariepy, Sijin He, Hasan Ahmad, Yizhou Gao, Stefania Priore, Navid Hakimi, Marc G. Jeschke, Axel Gunther