Literature DB >> 29229492

Programming Morphogenesis through Systems and Synthetic Biology.

Jeremy J Velazquez1, Emily Su2, Patrick Cahan3, Mo R Ebrahimkhani4.   

Abstract

Mammalian tissue development is an intricate, spatiotemporal process of self-organization that emerges from gene regulatory networks of differentiating stem cells. A major goal in stem cell biology is to gain a sufficient understanding of gene regulatory networks and cell-cell interactions to enable the reliable and robust engineering of morphogenesis. Here, we review advances in synthetic biology, single cell genomics, and multiscale modeling, which, when synthesized, provide a framework to achieve the ambitious goal of programming morphogenesis in complex tissues and organoids.
Copyright © 2017 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  multicellular systems; organoids; single cell genomics; stem cell self-organization; synthetic biology; systems biology

Mesh:

Year:  2017        PMID: 29229492      PMCID: PMC6589336          DOI: 10.1016/j.tibtech.2017.11.003

Source DB:  PubMed          Journal:  Trends Biotechnol        ISSN: 0167-7799            Impact factor:   19.536


  91 in total

Review 1.  Modeling transcriptional regulatory networks.

Authors:  Hamid Bolouri; Eric H Davidson
Journal:  Bioessays       Date:  2002-12       Impact factor: 4.345

2.  Analysis of gene expression in single live neurons.

Authors:  J Eberwine; H Yeh; K Miyashiro; Y Cao; S Nair; R Finnell; M Zettel; P Coleman
Journal:  Proc Natl Acad Sci U S A       Date:  1992-04-01       Impact factor: 11.205

3.  A synthetic multicellular system for programmed pattern formation.

Authors:  Subhayu Basu; Yoram Gerchman; Cynthia H Collins; Frances H Arnold; Ron Weiss
Journal:  Nature       Date:  2005-04-28       Impact factor: 49.962

Review 4.  Cell death in development: shaping the embryo.

Authors:  Carlos Penaloza; Lin Lin; Richard A Lockshin; Zahra Zakeri
Journal:  Histochem Cell Biol       Date:  2006-07-01       Impact factor: 4.304

5.  Multi-cell agent-based simulation of the microvasculature to study the dynamics of circulating inflammatory cell trafficking.

Authors:  Alexander M Bailey; Bryan C Thorne; Shayn M Peirce
Journal:  Ann Biomed Eng       Date:  2007-04-10       Impact factor: 3.934

6.  Endogenous microRNA can be broadly exploited to regulate transgene expression according to tissue, lineage and differentiation state.

Authors:  Brian D Brown; Bernhard Gentner; Alessio Cantore; Silvia Colleoni; Mario Amendola; Anna Zingale; Alessia Baccarini; Giovanna Lazzari; Cesare Galli; Luigi Naldini
Journal:  Nat Biotechnol       Date:  2007-11-16       Impact factor: 54.908

7.  Construction of an artificial intercellular communication network using the nitric oxide signaling elements in mammalian cells.

Authors:  Wei-Dong Wang; Zheng-Tang Chen; Bao-Guo Kang; Rong Li
Journal:  Exp Cell Res       Date:  2007-12-05       Impact factor: 3.905

8.  Isolation of rare circulating tumour cells in cancer patients by microchip technology.

Authors:  Sunitha Nagrath; Lecia V Sequist; Shyamala Maheswaran; Daphne W Bell; Daniel Irimia; Lindsey Ulkus; Matthew R Smith; Eunice L Kwak; Subba Digumarthy; Alona Muzikansky; Paula Ryan; Ulysses J Balis; Ronald G Tompkins; Daniel A Haber; Mehmet Toner
Journal:  Nature       Date:  2007-12-20       Impact factor: 49.962

Review 9.  Mammalian synthetic biology: engineering of sophisticated gene networks.

Authors:  David Greber; Martin Fussenegger
Journal:  J Biotechnol       Date:  2007-05-24       Impact factor: 3.307

10.  Imaging individual mRNA molecules using multiple singly labeled probes.

Authors:  Arjun Raj; Patrick van den Bogaard; Scott A Rifkin; Alexander van Oudenaarden; Sanjay Tyagi
Journal:  Nat Methods       Date:  2008-09-21       Impact factor: 28.547

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  11 in total

Review 1.  The Cognitive Lens: a primer on conceptual tools for analysing information processing in developmental and regenerative morphogenesis.

Authors:  Santosh Manicka; Michael Levin
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2019-06-10       Impact factor: 6.237

Review 2.  Synthetic development: building mammalian multicellular structures with artificial genetic programs.

Authors:  Marco Santorelli; Calvin Lam; Leonardo Morsut
Journal:  Curr Opin Biotechnol       Date:  2019-05-23       Impact factor: 9.740

Review 3.  Mathematical Modelling in Plant Synthetic Biology.

Authors:  Anna Deneer; Christian Fleck
Journal:  Methods Mol Biol       Date:  2022

4.  Self-organizing hair peg-like structures from dissociated skin progenitor cells: New insights for human hair follicle organoid engineering and Turing patterning in an asymmetric morphogenetic field.

Authors:  Erin L Weber; Thomas E Woolley; Chao-Yuan Yeh; Kuang-Ling Ou; Philip K Maini; Cheng-Ming Chuong
Journal:  Exp Dermatol       Date:  2019-04       Impact factor: 3.960

5.  Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids.

Authors:  Jeremy J Velazquez; Ryan LeGraw; Farzaneh Moghadam; Yuqi Tan; Jacquelyn Kilbourne; Joseph C Maggiore; Joshua Hislop; Silvia Liu; Davy Cats; Susana M Chuva de Sousa Lopes; Christopher Plaisier; Patrick Cahan; Samira Kiani; Mo R Ebrahimkhani
Journal:  Cell Syst       Date:  2020-12-07       Impact factor: 10.304

Review 6.  Human biomimetic liver microphysiology systems in drug development and precision medicine.

Authors:  Albert Gough; Alejandro Soto-Gutierrez; Lawrence Vernetti; Mo R Ebrahimkhani; Andrew M Stern; D Lansing Taylor
Journal:  Nat Rev Gastroenterol Hepatol       Date:  2020-12-17       Impact factor: 73.082

7.  Perspective: The promise of multi-cellular engineered living systems.

Authors:  Roger D Kamm; Rashid Bashir; Natasha Arora; Roy D Dar; Martha U Gillette; Linda G Griffith; Melissa L Kemp; Kathy Kinlaw; Michael Levin; Adam C Martin; Todd C McDevitt; Robert M Nerem; Mark J Powers; Taher A Saif; James Sharpe; Shuichi Takayama; Shoji Takeuchi; Ron Weiss; Kaiming Ye; Hannah G Yevick; Muhammad H Zaman
Journal:  APL Bioeng       Date:  2018-10-11

8.  Multi-scale cellular engineering: From molecules to organ-on-a-chip.

Authors:  Ngan F Huang; Ovijit Chaudhuri; Patrick Cahan; Aijun Wang; Adam J Engler; Yingxiao Wang; Sanjay Kumar; Ali Khademhosseini; Song Li
Journal:  APL Bioeng       Date:  2020-03-03

Review 9.  Synthetic living machines: A new window on life.

Authors:  Mo R Ebrahimkhani; Michael Levin
Journal:  iScience       Date:  2021-05-04

10.  Toward Engineering Biosystems With Emergent Collective Functions.

Authors:  Thomas E Gorochowski; Sabine Hauert; Jan-Ulrich Kreft; Lucia Marucci; Namid R Stillman; T-Y Dora Tang; Lucia Bandiera; Vittorio Bartoli; Daniel O R Dixon; Alex J H Fedorec; Harold Fellermann; Alexander G Fletcher; Tim Foster; Luca Giuggioli; Antoni Matyjaszkiewicz; Scott McCormick; Sandra Montes Olivas; Jonathan Naylor; Ana Rubio Denniss; Daniel Ward
Journal:  Front Bioeng Biotechnol       Date:  2020-06-26
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