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Timothy Saunders

@timesaunders.bsky.social
1.7K followers 189 following 53 posts

Professor at Warwick Medical School interested in how complex shape emerges during embryo development. Will work on anything that can be imaged live :)

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Timothy Saunders @timesaunders.bsky.social · 27/03/2025
Major pet conference peeve - speakers not speaking to time. It shortens breaks, reduces chances to engage ECRs and sets a bad precedent. Typically the bigger the name, the worse the timing.
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Cell Press @cellpress.bsky.social · 12/03/2025
Cells “speed date” to find their perfect neighbors when forming tissues. This marks a pivotal step in creating functional organs, like in this early heart development illustrated in a fly larvae. Learn more: www.cell.com/biophysj/ful... @timesaunders.bsky.social @biophysj.bsky.social
Fly embyro with cells labeled to show heart formation. The heart (cyan) forms from two distant regions of the embryo (far left). These regions migrate to the embryo midline, where they fuse into a tube to make the first heart structure (far right). Precise alignment and pairing of these cells are crucial for proper heart development.
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Campàs Lab @campaslab.bsky.social · 13/03/2025
👀 Looking for a Master Program in Physics of Life? Preferably free? Maybe in a collaborative and interdisciplinary environment? Check this out👇🏻
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Timothy Saunders @timesaunders.bsky.social · 13/03/2025
Of course, biology likes to be complicated. The above work generally takes the microtubule interaction between nuclei to be repulsive - but this doesn’t have to be the case (www.nature.com/articles/s41...). Future work will hopefully reveal how general these principles are.
nature.com
Nuclear speed and cycle length co-vary with local density during syncytial blastoderm formation in a cricket - Nature Communications
Early in insect embryo development, many nuclei share one large cell, travel varied paths and self-organize into a single layer. Donoughe et al. illuminate this process with live-imaging, modeling, an...
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Timothy Saunders @timesaunders.bsky.social · 13/03/2025
With Ivo Telley, we have looked at packing of nuclei in ex vivo systems (journals.biologists.com/dev/article/..., elifesciences.org/articles/90541). It’s exciting to see how quantitative measurements reveal deeper insight into how biological systems reliably generate complex form from simple rules.
journals.biologists.com
Aster repulsion drives short-ranged ordering in the Drosophila syncytial blastoderm
Summary: The multinucleated embryo of the fruit fly D. melanogaster distributes nuclei with the help of centrosome-organised microtubule asters, with ordering dynamically adapting to synchronous nucle...
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Timothy Saunders @timesaunders.bsky.social · 13/03/2025
Such topological behaviour has also been shown to potentially play a role in cell extrusion (www.nature.com/articles/nat...). I wrote a short commentary on this, which is hopefully accessible for the more general audience (www.nature.com/articles/s41...).
nature.com
Topological defects in epithelia govern cell death and extrusion - Nature
By modelling epithelial cells as active nematic liquid crystals, stresses induced at the sites of topological defects are found to be the primary drivers of extrusion and cell death.
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Timothy Saunders @timesaunders.bsky.social · 13/03/2025
There’s been exciting work recently linking ideas from topology to biological systems. This has ranged from bird flocking (www.pnas.org/doi/full/10....), to gene networks (www.pnas.org/doi/full/10....), and now how nuclei pack in the Drosophila blastocyst (www.nature.com/articles/s41...).
pnas.org
Geometry of gene regulatory dynamics | PNAS
Embryonic development leads to the reproducible and ordered appearance of complexity from egg to adult. The successive differentiation of different...
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Timothy Saunders @timesaunders.bsky.social · 12/03/2025
Enjoyed doing this interview. Hope it's helpful for a more general audience.
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Timothy Saunders @timesaunders.bsky.social · 12/03/2025
Latest lab paper is out :) eur01.safelinks.protection.outlook.com?url=https%3A... With Sham Tlili, we show that a surprisingly simple equilibrium physics model can explain the highly dynamic process of cell matching in the heart.
eur01.safelinks.protection.outlook.com
ScienceDirect.com | Science, health and medical journals, full text articles and books.
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Zebrafish Rock! 🎃 @zebrafishrock.bsky.social · 21/01/2025
#ZebrafishMeeting featuring @nicolettapetridou.bsky.social & @rashmi-priya.bsky.social
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Timothy Saunders @timesaunders.bsky.social · 16/12/2024
Read about my amazing PhD student Ryan. Many thanks to CoB for hosting him for 3 months
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Timothy Saunders @timesaunders.bsky.social · 13/12/2024
A wonderful day. Thanks so much for the invitation
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Timothy Saunders @timesaunders.bsky.social · 20/11/2024
Hi Joachim. Can you add me - we do optogenetics ( elifesciences.org/articles/26258), laser ablation (www.cell.com/current-biol... and any quantitative tools we can use in fish and flies.
elifesciences.org
Decoding temporal interpretation of the morphogen Bicoid in the early Drosophila embryo
Cell fates endowed by higher Bicoid concentration require input for longer duration, demonstrating a temporally non-linear morphogen-mediated pattern formation.
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Rodrigo Fernandez-Gonzalez @rodrigofg.bsky.social · 19/11/2024
Since I have so many new friends 😄, I thought I'd advertise this. Together with @pritiagarwal.bsky.social and Lance Davidson, we run a Developmental Mechanics seminar series on Zoom (originally started by Ronen Zaidel-Bar). This coming Thursday, we have our last session for 2024. Join us!!
Dev Mech 2024-25 logo
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
Just discovering how clunky Bluesky is for this :(
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
Our collaborators - the Weil lab - primarily focused on the first question. They revealed that localisation of bicoid mRNA localisation to P bodies inhibits translation. Chemically releasing bicoid from the P bodies resulted in translation in the oocyte…
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
We generated a Bicoid::Suntag reporter line. Importantly, this could address two important questions: (i) is bicoid translated in the oocyte, and if not, what is regulating this process?; (ii) where and when is bicoid translated in the embryo? (20)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
We were motivated by the development of SunTag (PMID: 25307933), especially its application to the living Drosophila embryo by the Mounia lab (PMID: 33927056). (19)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
It has remained an open question as to precisely when and where bicoid mRNA is translated. If bicoid mRNA is not translated in the oocyte, what is the mechanism? This motivated us to revisit the “S” part of the SDD model. (18/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
These direct measures of motion reveal that the “diffusive” part of the SDD model needs adaptation (e.g., spatial and temporal change), but Bicoid does move through the embryo sufficiently fast to generate a gradient. (18/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
With Thorsten Wohland, we used FCS at multiple locations and time points on Bicoid. We demonstrated different rates of diffusivity in the anterior and posterior regions (PMID: 38345326). (17/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
However, these measurements were essentially averaging over the whole system – what is happening with Bicoid at more local (e.g., within a nuclear domain) scales? (16/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
While all the models proposed can generate an exponentially-decaying profile, they all made different predictions for how old Bicoid would be at different locations. Only the SDD model was consistent with the overall behaviour of the protein age. (15/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
During my post-doc and into my own lab we developed a Bicoid-timer reporter. By tagging Bicoid with two fluorescent proteins with different folding rates, we could effectively measure the age (i.e., ratio of the two fluorophore signals) of Bicoid at different locations (PMID: 30181144). (14/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
Fluorescence correlation spectroscopy (FCS) of Bicoid::eGFP revealed that the dynamics were more complicated than inferred from FRAP. In particular, an effective diffusion coefficient of around 7um2s-1 (PMID: 20712981). This measurement was more in line with expectations from the SDD model. (13/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
The Gregor lab optimised fluorescent in situ hybridisation (PMID: 21390295) to reveal “>90% of all bicoid mRNA is continuously present within the anterior 20%.” They also concluded that Bicoid is rapidly removed in nuclear cycle 14, after patterning is set. (12/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
Therefore, we see that up to 2010 there were still major questions regarding pretty much every part of how the Bicoid gradient formed, and this cast major doubts over the validity of the SDD model. (11/22).
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
Tweetorial continued -unable to post more on the previous one: (ii) Bicoid could be produced in the oocyte, leading to early distribution of Bicoid (PMID: 28296637). (iii) Bicoid may not need to be degraded;dilution by nuclei could be sufficient to generate a gradient (PMID: 18001703) (10/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
Therefore, we see that up to 2010 there were still major questions regarding pretty much every part of how the Bicoid gradient formed, and this cast major doubts over the validity of the SDD model. (11/22).
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
(ii) Bicoid could be produced in the oocyte, leading to early distribution of Bicoid (PMID: 28296637). (iii) If the diffusivity is small enough, then Bicoid may not need to be degraded; dilution by nuclei would be sufficient to generate a gradient on the relevant time scales (PMID: 18001703) (10/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
(ii) Bicoid could be produced in the oocyte, leading to early distribution of Bicoid (PMID: 28296637). (iii) If the diffusivity is small enough, then Bicoid may not need to be degraded; dilution by nuclei would be sufficient to generate a gradient on relevant time scales (PMID: 18001703) (10/22).
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
Therefore, we see that up to 2010 there were still major questions regarding pretty much every part of how the Bicoid gradient formed, and this cast major doubts over the validity of the SDD model. (10/22).
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
(ii) Bicoid could be produced in the oocyte, leading to early distribution of Bicoid (PMID: 28296637). (iii) If the diffusivity is small enough, then Bicoid may not need to be degraded; dilution by nuclei would be sufficient to generate a gradient on the relevant time scales (PMID: 18001703) (9/22).
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
These results (and others I apologise for not covering) led to new models for how the Bicoid gradient forms. (i) There could be a gradient of bicoid mRNA, and consequently more local production of Bicoid. This model removes the need for large diffusion, consistent with FRAP. (9/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
FRAP measurements estimated a (relatively) small diffusion constant around 0.5um2s-1. Further, the noise in the Bicoid gradient (around 10% variability) was much higher than the variability in position of downstream gene boundaries. (8/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
They constructed a Bicoid::eGFP line that rescued the bicoidE1 mutant, demonstrating the Bicoid::eGFP protein was still functional as a morphogen. Their work threw up a number of surprising results. (7/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
The original experiments on Bicoid were largely of fixed embryos. In 2007, Thomas Gregor, at the time in Eric Wieschaus’ lab, published seminal back-to-back papers revealing the dynamics of Bicoid in living embryos (PMID: 17632062, 17632061). (6/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
Bicoid antibody staining revealed the gradient was close to exponential. Downstream target genes, such as hunchback, are expressed with astonishing levels of accuracy (PMID: 11845210). How does a noisy biochemical gradient result in such precise patterning? (5/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
For this model to work requires bicoid mRNA to be localised to the anterior pole (PMID: 2901954). bicoid mRNA should not be translated in the oocyte and needs to maintain its localisation during oogenesis (PMID: 18639459). Further, bicoid mRNA needs to be removed post-patterning. (4/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
How does the gradient form? The Source, Diffusion, Degradation (SDD) model proposed localised Bicoid production to the anterior domain, with Bicoid then diffusing through the embryo, and degradation regulating total protein number, enabling it to reach a steady-state when patterning occurs. (3/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
Bicoid was the first morphogen discovered (PMID: 3383244) and has lots of work over 30+ years on how the gradient forms. Bicoid is a transcription factor that determines spatial patterning due to concentration-dependence of its readout in the early Drosophila embryo (PMID: 2911348, 9753673). (2/22)
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
Our new focuses on translation of Bicoid during early Drosophila development (www.biorxiv.org/content/10.1...). We answer precisely when and where bicoid mRNA is translated. This helps us build an improved model of gradient formation. But, before going into results, first some background… (1/22)
biorxiv.org
Regulation of bicoid mRNA throughout oogenesis and early embryogenesis impacts protein gradient formation
The transcription factor Bicoid (Bcd) establishes patterning in the early Drosophila blastocyst through its graded concentration along the anterior-posterior (AP) axis. bcd mRNA is maternally deposite...
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Timothy Saunders @timesaunders.bsky.social · 17/11/2024
One thing I really liked about SciTwitter were the “tweetorials” on the latest papers – these really helped get a grip on new work, and also opened up potential research avenues that I would have otherwise missed. In this vein, I am about to try something similar here on BlueSky.
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Timothy Saunders @timesaunders.bsky.social · 08/11/2024
Amazed by the sudden increase in activity here following a certain event. Hopefully a strong community can build
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Timothy Saunders @timesaunders.bsky.social · 02/06/2024
A quick reminder that if you're n=2 SEM is meaningless. SEM is not a "trick" to make your error bars look smaller.
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Timothy Saunders @timesaunders.bsky.social · 16/05/2024
Really excited to have the Warwick-Cambridge Meeting on quantitative cell biology today at Warwick. warwick.ac.uk/fac/sci/med/....
warwick.ac.uk
warwick-cambridge_quantitative_cell
This two-day meeting will focus on Quantitative Cell and Developmental Biology. We will bring expertise from across scales, combining people working on subcellular cell biology through to tissue scale...
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Timothy Saunders @timesaunders.bsky.social · 16/04/2024
BSDB 2024. As usual, such a fun and welcoming meeting
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Timothy Saunders @timesaunders.bsky.social · 04/03/2024
We show that in the drosophila early embryo, microtubule asters interact through an effective pushing interaction
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Timothy Saunders @timesaunders.bsky.social · 04/03/2024
We utilise Ivo's great explant system to make clean and quantitative measurements. This is backed up by theoretical modelling of the aster interactions with boundaries and each other.
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Timothy Saunders @timesaunders.bsky.social · 04/03/2024
Many thanks to HFSP for funding most of this work. And Jorge and Sham who did so much to bring it all together.
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