About

Sebastian Streichan is associated with the UCSB College of Creative Studies and is involved in teaching courses such as Introduction to Quantitative Developmental Biology. His contact email is streicha@kitp.ucsb.edu. The available information indicates his role in the academic community at UCSB, focusing on developmental biology and related quantitative approaches. No additional biographical details, research focus, background, or key contributions are provided in the page text.

Research topics

• Anatomy
• Biology
• Cell biology
• Biophysics
• Genetics

Selected publications

• Accessible and cost-effective methods for patterning cell monolayers on compliant substrates

  PLoS ONE · 2026-03-18

  articleOpen access

  Micropatterning is a versatile technique for confining single cells and cell monolayers to a particular size or shape. The resulting geometrical confinement is one means of controlling migration, differentiation, and force generation. As such, micropatterning is a valuable tool for studying the principles governing collective cell behavior, tissue morphogenesis, and other questions in mechanobiology. Here, we present two detailed and accessible protocols for micropatterning cell monolayers onto compliant substrates made of a polyacrylamide hydrogel and a polydimethylsiloxane elastomer. These protocols require minimal specialized equipment, making them broadly accessible. We validate the fidelity of our protocols across a range of confinement geometries. Furthermore, we demonstrate an example application of our hydrogel protocol to traction force microscopy, which allows for investigating effects of geometric confinement on cell-generated forces. Together, these protocols provide detailed, reproducible tools to support the widespread application of micropatterning in studies of mechanobiology and collective cell dynamics.

  PublisherDOI

• Topological interactions drive the first fate decision in the Drosophila embryo

  Nature Physics · 2025-02-25 · 3 citations

  articleOpen access
  PublisherOA PDFDOI

• Stationary and germ layer-specific cellular flows shape the zebrafish gastrula

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-12

  preprintOpen accessSenior author

  Abstract During gastrulation, a sequence of complex processes transforms the blastula into a multi-layered embryo. Fixed sample analysis has revealed much about how genetic signaling cascades determine the major body axes and organize cell fate patterns into the germ layers: ectoderm, mesoderm, and endoderm. In toto live imaging of vertebrate development highlights that embryogenesis is a dynamic process that involves on the order of ten thousand cells, but hurdles related to data handling have hampered quantitative analysis. Therefore, our understanding of the rich physical aspects of multilayered tissue reconfigurations remains incomplete. Here, we reveal that modules of stationary and germ-layer-specific tissue flows shape the zebrafish gastrula. We combine in toto live imaging with tissue-specific markers and image analysis to reveal the global shape of the enveloping layer (EVL), epiblast, and mesoderm over time. A user-friendly tissue cartography pipeline based on the Blender 3D software moves into the reference frame of individual tissue layers. We find distinct tissue flow patterns in the enveloping layer (EVL), epiblast, and mesoderm, respectively. The instantaneous tissue flow of these germ layers is organized in a temporal sequence of hours-long, constant flow patterns. This suggests that a sequence of stationary tissue flow modules transports cells to their destination during gastrulation. Mathematical decomposition suggests that epiblast flow is strongly influenced by a superposition of rotational flow in the mesoderm, and divergent flow in the EVL. Molecular and cellular complexity notwithstanding, these results hint at surprisingly, tractable physical processes that underlie vertebrate gastrulation, and set the stage for investigations of how morphogens orchestrate dynamics.

  PublisherOA PDFDOI

• Searching for physical principles of morphogenesis

  Development · 2025-11-01

  articleOpen accessSenior author

  In morphogenesis, biology uses physics to sculpt organs. Understanding this fascinating process requires interdisciplinary collaboration. We highlight recent work in the 'physics of development', with a focus on the interplay between quantitative experiments and mathematical theory. We argue that the role of theory in developmental biology lies in identifying and describing dynamical mechanisms - from the processing of positional information to mechanical pattern formation - independently of their molecular implementation. This level of abstraction provides a structured approach to embrace developmental complexity, but can propose experimental tests to verify its key tenets. We conclude with a sketch of future research perspectives in emerging synthetic morphogenesis systems, which may serve as a platform to distill principles of developmental self-organization.

  PublisherOA PDFDOI

• DynamicAtlas: a morphodynamic atlas for Drosophila development

  Nature Methods · 2025-12-24 · 1 citations

  articleOpen accessSenior author

  Living organisms develop their shape through the interplay of gene expression and mechanics. While atlases of static samples characterize cell fates and gene regulation, understanding dynamic shape changes requires live imaging. Here we present DynamicAtlas: a 'morphodynamic atlas' of live and static datasets from 500 Drosophila melanogaster embryos (wild type and 18 mutants), aligned to a common morphological timeline. Surprisingly, characterizing wild-type surface tissue flows reveals distinct 'morphodynamic modules'-time periods in which the global pattern of motion is stationary-corresponding to key developmental stages. Mutant analysis shows stationary flow patterns depend on genes that break spatial symmetry along the dorsal-ventral axis. Temperature perturbations indicate that morphodynamic modules change in response to accumulated tissue deformation, rather than elapsed time. Extending our approach to the embryonic Drosophila midgut, we find modules in covariant measures of the dynamic three-dimensional surface. DynamicAtlas provides a high-resolution framework for studying shape formation across living systems.

  PublisherDOI

• Basement membrane perforations guide anterior–posterior axis formation

  Nature Communications · 2025-07-22 · 6 citations

  articleOpen access

  Establishment of the anterior-posterior (AP) axis is a critical symmetry-breaking event in mammalian development. In mice, this process involves the directed migration of the distal visceral endoderm (DVE). Here, we use targeted perturbations to demonstrate that asymmetric perforations in the basement membrane guide DVE migration. During implantation, matrix metalloproteinases in extra-embryonic tissues create uneven basement membrane perforations, establishing directional cues for cohesive DVE migration. Using light-sheet microscopy and tissue cartography, we show that migrating DVE deforms surrounding tissues. Physical modeling and live imaging of DVE protrusions indicate that basement membrane perforations orchestrate active force generation within the DVE. Extending these findings to human embryos and stem cell-derived models, we identify basement membranes with enriched perforations near the anterior hypoblast in embryos, suggesting a conserved mechanism for AP axis specification. These findings reveal an unrecognized role of basement membrane remodeling and mechanical heterogeneity in guiding directional tissue migration during mammalian development.

  PublisherOA PDFDOI

• Controlled-environment platform for electrophysiology recordings on organoids with Neuropixels 2.0

  Review of Scientific Instruments · 2025-12-01 · 1 citations

  article

  We present a custom recording platform that enables electrophysiological recordings with Neuropixels 2.0 from human brain and heart organoids by maintaining a stable, physiological environment of 5% CO2, 37 °C, and 95% relative humidity. The platform combines a modular positioning system with real-time camera guidance for precise probe alignment. We validated the system by recording consistent bursting activity in brain organoids over a 110-min period and in heart organoids for up to 11 h.

  PublisherDOI

• Blender tissue cartography: an intuitive tool for the analysis of dynamic 3D microscopy data

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-08 · 5 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Understanding complex, three-dimensional tissues requires volumetric microscopy, but visualization, analysis, and processing of 3D image data can be challenging. Tissue cartography is an emerging method that exploits the sheet-like organization of many biological tissues. Extracting and cartographically projecting curved surfaces from volumetric image data turns 3D into 2D data, which is much easier to visualize, analyze, and computationally process. However, existing tissue cartography tools both require advanced coding expertise and are limited to specific tissue geometries. Here, we create an interactive, visual tool for tissue cartography within Blender, a popular 3D animation environment. blender_tissue_-cartography ( btc ), opens tissue cartography to broad use via a user-friendly graphical interface, while harnessing powerful computer graphics algorithms to process a wide variety of biological shapes. An accompanying Python library allows faithful 3D measurements in 2D cartographic projections and the creation of custom analysis pipelines. btc batch-processes time-lapse data by propagating a cartographic projection from a single key frame to all other frames via surface-to-surface alignment. We demonstrate btc on diverse and complex tissue shapes from Drosophila , stem-cell-based organoids, Arabidopsis , and zebrafish. We believe our tool will open up a powerful set of analysis methods previously only accessible to specialists, enabling quantitative analysis of complex three-dimensional tissues and expanding our understanding of development.

  PublisherDOI

• Learning a conserved mechanism for early neuroectoderm morphogenesis

  PubMed · 2024-05-28 · 1 citations

  articleOpen accessSenior author

  Morphogenesis is the process whereby the body of an organism develops its target shape. The morphogen BMP is known to play a conserved role across bilaterian organisms in determining the dorsoventral (DV) axis. Yet, how BMP governs the spatio-temporal dynamics of cytoskeletal proteins driving morphogenetic flow remains an open question. Here, we use machine learning to mine a morphodynamic atlas of Drosophila development, and construct a mathematical model capable of predicting the coupled dynamics of myosin, E-cadherin, and morphogenetic flow. Mutant analysis shows that BMP sets the initial condition of this dynamical system according to the following signaling cascade: BMP establishes DV pair-rule-gene patterns that set-up an E-cadherin gradient which in turn creates a myosin gradient in the opposite direction through mechanochemical feedbacks. Using neural tube organoids, we argue that BMP, and the signaling cascade it triggers, prime the conserved dynamics of neuroectoderm morphogenesis from fly to humans.

  PublisherOA PDFDOI

• YAP dysregulation triggers hypertrophy by CCN2 secretion and TGFβ uptake in human pluripotent stem cell-derived cardiomyocytes

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-06-03 · 1 citations

  preprintOpen access

  Hypertrophy Cardiomyopathy (HCM) is the most prevalent hereditary cardiovascular disease - affecting >1:500 individuals. Advanced forms of HCM clinically present with hypercontractility, hypertrophy and fibrosis. Several single-point mutations in b-myosin heavy chain (MYH7) have been associated with HCM and increased contractility at the organ level. Different MYH7 mutations have resulted in increased, decreased, or unchanged force production at the molecular level. Yet, how these molecular kinetics link to cell and tissue pathogenesis remains unclear. The Hippo Pathway, specifically its effector molecule YAP, has been demonstrated to be reactivated in pathological hypertrophic growth. We hypothesized that changes in force production (intrinsically or extrinsically) directly alter the homeostatic mechano-signaling of the Hippo pathway through changes in stresses on the nucleus. Using human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), we asked whether homeostatic mechanical signaling through the canonical growth regulator, YAP, is altered 1) by changes in the biomechanics of HCM mutant cardiomyocytes and 2) by alterations in the mechanical environment. We use genetically edited hiPSC-CM with point mutations in MYH7 associated with HCM, and their matched controls, combined with micropatterned traction force microscopy substrates to confirm the hypercontractile phenotype in MYH7 mutants. We next modulate contractility in healthy and disease hiPSC-CMs by treatment with positive and negative inotropic drugs and demonstrate a correlative relationship between contractility and YAP activity. We further demonstrate the activation of YAP in both HCM mutants and healthy hiPSC-CMs treated with contractility modulators is through enhanced nuclear deformation. We conclude that the overactivation of YAP, possibly initiated and driven by hypercontractility, correlates with excessive CCN2 secretion (connective tissue growth factor), enhancing cardiac fibroblast/myofibroblast transition and production of known hypertrophic signaling molecule TGFβ. Our study suggests YAP being an indirect player in the initiation of hypertrophic growth and fibrosis in HCM. Our results provide new insights into HCM progression and bring forth a testbed for therapeutic options in treating HCM.

  PublisherOA PDFDOI

Recent grants

• Tissue flow genetics: using cartography to reveal forces driving morphogenesis

  NIH · $410k · 2017–2020

• Tissue flow genetics: using cartography to reveal forces driving morphogenesis

  NIH · $249k · 2017–2020

• Physics of Living Matter: From Molecule to Embryo

  NIH · $2.3M · 2020–2030

• Tissue flow genetics: using cartography to reveal forces driving morphogenesis

  NIH · $287k · 2016–2018

Frequent coauthors

• Boris I. Shraiman

  Princeton University

  19 shared

• Nicholas Noll

  13 shared

• Noah Mitchell

  11 shared

• Eyal Karzbrun

  Weizmann Institute of Science

  9 shared

• Nikolas H Claussen

  University of California, Santa Barbara

  7 shared

• Vincenzo Vitelli

  University of Chicago

  7 shared

• Dillon Cislo

  Rockefeller University

  7 shared

• Aimal H. Khankhel

  University of California, Santa Barbara

  6 shared

Education

• Vordiplom , Physics

  Humboldt-Universität zu Berlin

  2005