Publications by Andrew Charles Oates

Open-source microscope add-on for structured illumination microscopy

Theo Lasser, Matthias Lütolf, Aleksandra Radenovic, Andrew Charles Oates, Georg Fantner, John McKinney, Nathan Cyprien Arsène Ronceray, Olivier François Venzin, Antonius Chrisnandy, Prabhu Prasad Swain

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

Andrew Charles Oates, Mahmut Selman Sakar, Ece Özelçi, 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

Andrew Charles Oates, Petr Strnad, Laurel Ann Rohde, Daniele Soroldoni, 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

Andrew Charles Oates, Marko Popovic, 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

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

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

Andrew Charles Oates, Georg Fantner

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