Publications de Andrew Charles Oates

Open-source microscope add-on for structured illumination microscopy

Matthias Lütolf, Theo Lasser, Aleksandra Radenovic, John McKinney, Georg Fantner, Olivier François Venzin, Mélanie Thérèse Marie Hannebelle, Tomas Lukes, Samuel Mendes Leitão, Antonius Chrisnandy, Chiara Toniolo, Andrew Charles Oates, Prabhu Prasad Swain, Nathan Cyprien Arsène Ronceray

Super-resolution techniques expand the abilities of researchers who have the knowledge and resources to either build or purchase a system. This excludes the part of the research community without these capabilities. Here we introduce the openSIM add-on to ...

Nature Portfolio2024

A Robotic Surgery Platform for Automated Tissue Micromanipulation in Zebrafish Embryos

Mahmut Selman Sakar, Ece Özelçi, Andrew Charles Oates, Laurel Ann Rohde, Erfan Etesami

Microsurgical manipulations are key experimental techniques in life science research, particularly in embryology. These techniques are most often performed manually by highly skilled scientists, posing limitations on speed, precision, and reproducibility. ...

2024

Cell-autonomous timing drives the vertebrate segmentation clock's wave pattern

Petr Strnad, Andrew Charles Oates, Daniele Soroldoni, Laurel Ann Rohde, Sundar Ram Naganathan, Arianne Bercowsky Rama

Rhythmic and sequential segmentation of the growing vertebrate body relies on the segmentation clock, a multi-cellular oscillating genetic network. The clock is visible as tissue-level kinematic waves of gene expression that travel through the presomitic m ...

2024

Identification of side effects of COVID-19 drug candidates on embryogenesis using an integrated zebrafish screening platform

Andrew Charles Oates

Drug repurposing is an important strategy in COVID-19 treatment, but many clinically approved compounds have not been extensively studied in the context of embryogenesis, thus limiting their administration during pregnancy. Here we used the zebrafish embry ...

Nature Portfolio2023

Preparation of Single-Somite Explants from Zebrafish Embryos

Andrew Charles Oates, Sundar Ram Naganathan

The body axis of vertebrate embryos is periodically subdivided into 3D multicellular units called somites. While genetic oscillations and molecular prepatterns determine the initial length-scale of somites, mechanical processes have been implicated in sett ...

JOURNAL OF VISUALIZED EXPERIMENTS2022

Left-right symmetry of zebrafish embryos requires somite surface tension

Marko Popovic, Andrew Charles Oates, Sundar Ram Naganathan

The body axis of vertebrate embryos is periodically segmented into bilaterally symmetric pairs of somites(1,2). The anteroposterior length of somites, their position and left-right symmetry are thought to be molecularly determined before somite morphogenes ...

NATURE PORTFOLIO2022

Reaction wavefront theory of notochord segment patterning

Andrew Charles Oates

The vertebrate axis is segmented into repetitive structures, the vertebrae. In fish, these segmented structures are thought to form from the paraxial mesoderm and the adjacent notochord. Recent work revealed an autonomous patterning mechanism in the zebraf ...

FRONTIERS MEDIA SA2022

Deconstructing body axis morphogenesis in zebrafish embryos using robot-assisted tissue micromanipulation

Matthias Rüegg, Mahmut Selman Sakar, Erik Mailand, Ece Özelçi, Andrew Charles Oates

Classic microsurgical techniques, such as those used in the early 1900s by Mangold and Spemann, have been instrumental in advancing our understanding of embryonic development. However, these techniques are highly specialized, leading to issues of inter-ope ...

Nature Research2022

Towards a physical understanding of developmental patterning

Andrew Charles Oates, Jose Negrete Jr

The temporal coordination of events at cellular and tissue scales is essential for the proper development of organisms, and involves cell-intrinsic processes that can be coupled by local cellular signalling and instructed by global signalling, thereby crea ...

NATURE RESEARCH2021

Instruments of change for academic tool development comment

Georg Fantner, Andrew Charles Oates

Scientific progress has always been driven by the ability to build an instrument to answer a specific question. But spreading the news of how to replicate that tool is an evolving art, ripe for an open-source revolution. ...

NATURE RESEARCH2021

From local resynchronization to global pattern recovery in the zebrafish segmentation clock

Andrew Charles Oates

Integrity of rhythmic spatial gene expression patterns in the vertebrate segmentation clock requires local synchronization between neighboring cells by Delta-Notch signaling and its inhibition causes defective segment boundaries. Whether deformation of the ...

2021

Theory of time delayed genetic oscillations with external noisy regulation

Andrew Charles Oates, Laurel Ann Rohde, Jose Negrete Jr

Video Abstract Video Abstract: Theory of time delayed genetic oscillations with external noisy regulation We present a general theory of noisy genetic oscillators with externally regulated production rate and multiplicative noise. The observables that char ...

2021

Patterning and mechanics of somite boundaries in zebrafish embryos

Andrew Charles Oates, Sundar Ram Naganathan

The body axis of vertebrates is subdivided into repetitive compartments called somites, which give rise primarily to the segmented architecture of the musculoskeletal system in the adult body. Somites form in a sequential and rhythmic manner in embryos and ...

2020

Waiting on the Fringe: cell autonomy and signaling delays in segmentation clocks

Andrew Charles Oates

The rhythmic and sequential segmentation of the vertebrate body axis into somites during embryogenesis is governed by a multicellular, oscillatory patterning system called the segmentation clock. Despite many overt similarities between vertebrates, differe ...

2020

What are you synching about? Emerging complexity of Notch signaling in the segmentation clock

Olivier François Venzin, Andrew Charles Oates

The Segmentation clock is a population of cellular genetic oscillators, located in the posterior of the elongating vertebrate embryo, that governs the rhythmic and sequential segmentation of the body axis into somites. Somites are blocks of cells that give ...

ACADEMIC PRESS INC ELSEVIER SCIENCE2020

Detection of mRNA by Whole Mount in situ Hybridization and DNA Extraction for Genotyping of Zebrafish Embryos

Andrew Charles Oates, Rachna Narayanan

In situ hybridization is used to visualize the spatial distribution of gene transcripts in tissues and in embryos, providing important information about disease and development. Current methods involve the use of complementary riboprobes incorporating non- ...

2019

Embryonic lateral inhibition as optical modes: An analytical framework for mesoscopic pattern formation

Andrew Charles Oates, Jose Negrete Jr

Cellular checkerboard patterns are observed at many stages of embryonic development. We study an analytically tractable model for lateral inhibition and show that the steady states are analogous to optical phonons at the Gamma point, which have the wave nu ...

2019

Segmentation of the zebrafish axial skeleton relies on notochord sheath cells and not on the segmentation clock

Andrew Charles Oates, Rachna Narayanan

2018

The Sweetness of Embryonic Elongation and Differentiation

Andrew Charles Oates, Sundar Ram Naganathan

Metabolic pathways play a vital yet poorly understood role in embryogenesis. In this issue of Developmental Cell, Bulusu et al. (2017) and Oginuma et al. (2017) provide insights into the intricate relationship between metabolism and morphogenesis, showing ...

Cell Press - Elsevier2017

Emergence of bilaterally symmetric somites

Andrew Charles Oates, Chen Qian

2017