Eyal Karzbrun

Eyal Karzbrun
University of California, Santa Barbara | UCSB · Kavli Institute for Theoretical Physics

PHD
Postdoctoral Fellow KITP UCSB

About

22
Publications
3,578
Reads
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1,012
Citations
Additional affiliations
January 2018 - present
University of California, Santa Barbara
Position
  • PostDoc Position
December 2014 - January 2018
Weizmann Institute of Science
Position
  • PostDoc Position
January 2011 - September 2014
Weizmann Institute of Science
Position
  • PhD Student
Education
April 2009 - September 2014
Weizmann Institute of Science
Field of study
  • Biophysics
September 2006 - April 2009
Weizmann Institute of Science
Field of study
  • Physics
September 2003 - September 2006
Hebrew University of Jerusalem
Field of study
  • Physics

Publications

Publications (22)
Preprint
The emergence of different cell types and the role of the epigenome in regulating transcription is a key yet understudied event during human gastrulation. Investigating these questions remain infeasible due to the lack of availability of embryos at these stages of development. Further, human gastrulation is marked by dynamic changes in cell states...
Article
Full-text available
Understanding human organ formation is a scientific challenge with far-reaching medical implications1,2. Three-dimensional stem-cell cultures have provided insights into human cell differentiation3,4. However, current approaches use scaffold-free stem-cell aggregates, which develop non-reproducible tissue shapes and variable cell-fate patterns. Thi...
Preprint
Neural tube morphogenesis is the first step in the formation of the nervous system, and tube defects are among the highest rate birth defects. However, it is not possible to study the dynamics of organ formation in humans. Animals differ from humans in key aspects, and in particular in the development of the nervous system. Conventional organoids a...
Preprint
Understanding how human embryos develop their shape is a fundamental question in physics of life with strong medical implications. However, it is not possible to study the dynamics of organ formation in humans. Animals differ from humans in key aspects, and in particular in the development of the nervous system. Conventional organoids are unreprodu...
Chapter
Nucleokinesis, literally the movement of the nucleus, may or may not be coupled with cellular motility. In this chapter, we present our point of view on the moving nucleus. We depict the structure of the nucleus, discuss how the chromatin is organized within the nucleus, highlight nuclear substructure, and describe the molecules that anchor it to t...
Chapter
Organoids are three-dimensional cell cultures derived from mammalian stem cells that recapitulate key aspects of embryonic organ development and morphogenesis. In particular, brain organoids are cell cultures designed to mimic aspects of embryonic brain development. These systems exhibit remarkable self-organization of shape and cell fate. Brain or...
Article
Full-text available
Brain organoids have recently emerged as a three-dimensional tissue culture platform to study the principles of neurodevelopment and morphogenesis. Importantly, brain organoids can be derived from human stem cells, and thus offer a model system for early human brain development and human specific disorders. However, there are still major difference...
Article
Brain organoids are an emerging technique for studying human neurodevelopment in vitro, with biomedical implications. However, three‐dimensional tissue culture poses several challenges, including lack of nutrient exchange at the organoid core and limited imaging accessibility of whole organoids. Here we present a method for culturing organoids in a...
Article
Full-text available
Human brain wrinkling has been implicated in neurodevelopmental disorders and yet its origins remain unknown. Polymer gel models suggest that wrinkling emerges spontaneously due to compression forces arising during differential swelling, but these ideas have not been tested in a living system. Here, we report the appearance of surface wrinkles duri...
Article
Full-text available
Understanding how biochemical networks lead to large-scale nonequilibrium self-organization and pattern formation in life is a major challenge, with important implications for the design of programmable synthetic systems. Here, we assembled cell-free genetic oscillators in a spatially distributed system of on-chip DNA compartments as artificial cel...
Article
Autism Spectrum Disorders (ASD) encompass a group of neurodevelopmental diseases that demonstrate strong heritability, however the inheritance is not simple and many genes have been associated with these disorders. ASD is regarded as a neurodevelopmental disorder, and abnormalities at different developmental stages are part of the disease etiology....
Article
Living systems employ front propagation and spatiotemporal patterns encoded in biochemical reactions for communication, self-organization and computation1, 2, 3, 4. Emulating such dynamics in minimal systems is important for understanding physical principles in living cells5, 6, 7, 8 and in vitro9, 10, 11, 12, 13, 14. Here, we report a one-dimensio...
Article
Full-text available
The assembly of artificial cells capable of executing synthetic DNA programs has been an important goal for basic research and biotechnology. We assembled two-dimensional DNA compartments fabricated in silicon as artificial cells capable of metabolism, programmable protein synthesis, and communication. Metabolism is maintained by continuous diffusi...
Article
The expression of genes in a cell in response to external signals or internal programs occurs within an environment that is compartmentalized and dense. Reconstituting gene expression in man-made systems is relevant for the basic understanding of gene regulation, as well as for the development of applications in bio- and nanotechnology. DNA polymer...
Article
We designed a new integration scheme for artificial biological systems into solid materials. Inspired by the spatial patterns in morphogenesis and by microelectronics, we developed a biochip on which the protein synthesis and assembly is carried out in spatially segregated micro-compartments.
Article
Full-text available
Cell-free gene expression in localized DNA brushes on a biochip has been shown to depend on gene density and orientation, suggesting that brushes form compartments with partitioned conditions. At high density, the interplay of DNA entropic elasticity, electrostatics, and excluded volume interactions leads to collective conformations that affect the...
Article
To study dense double-stranded DNA (dsDNA) polymer phases, we fabricated continuous density gradients of binding sites for assembly on a photochemical interface and measured both dsDNA occupancy and extension using evanescent fluorescence. Despite the abundance of available binding sites, the dsDNA density saturates after occupation of only a fract...
Article
A complete gene expression reaction is reconstituted in a cell-free system comprising the entire endogenous transcription, translation, as well as mRNA and protein degradation machinery of E. coli. In dissecting the major reaction steps, we derive a coarse-grained enzymatic description of biosynthesis and degradation, from which ten relevant rate c...
Article
Full-text available
We study the low-energy effective action on confining strings (in the fundamental representation) in SU(N) gauge theories in D space-time dimensions. We write this action in terms of the physical transverse fluctuations of the string. We show that for any D, the four-derivative terms in the effective action must exactly match the ones in the Nambu-...

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