All Categories - Claridge-Chang Lab

Preprint: Getting over ANOVA

2/12/2026

Here's a dirty secret about ANOVA: it tests a null hypothesis that nobody cares about. When you run a one-way ANOVA, you're testing whether "all group means are equal." But even if you reject this hypothesis, you learn nothing about which groups differ, in which direction, or by how much.

So you embark on a second analytical step: multiple two-group comparisons. A modest six-group experiment suddenly requires testing 15 hypotheses. To manage this multiplicity, you apply corrections like Bonferroni, which undermine your statistical power. What you posed as a focused research question has sprawled into a complex web of subsidiary tests, forced by the ANOVA ritual.

Our new preprint, "Getting over ANOVA: Estimation graphics for multi-group comparisons," makes the case for a better approach. Estimation statistics encourages you to compare each test group to a single control, focusing on the effect sizes that actually matter. A six-group experiment focuses attention on just five effect sizes with confidence intervals, showing magnitude and precision directly.

The preprint introduces estimation methods for a range of multi-group designs: repeated-measures experiments, 2×2 factorial designs, binary outcome data, and mini-meta analysis for internal replicates. Each can replace data-analysis practices used in thousands of studies every year.

Read our new preprint here: https://doi.org/10.64898/2026.01.26.701654

Also posted on LinkedIn. #Statistics #OpenScience #DataVisualization #Research

The Word That Wasn't There

1/26/2026

I was writing about serotonin-receiving neurons and reached for "serotonoceptive." The word should exist, but it doesn't.

We have "dopaminergic" for neurons that release dopamine, so why no equivalent for neurons that receive it? Instead, the literature is full of workarounds: "dopamine-sensitive neurons," "neurons expressing dopamine receptors," "dopamine target cells."

A solution was hiding in plain sight: "nociceptive" and "proprioceptive" have been around since Sherrington. Recent papers already use "GABAceptive" and "dopaminoceptive."

So I wrote a short paper proposing we generalize the '-ceptive' suffix. Dopaminergic neurons release dopamine; dopaminoceptive neurons receive it. Simple, systematic, and searchable.

Read the editorial here: https://doi.org/10.5281/zenodo.18373728

First Image of the Actin Nucleus: The Seed That Grows the Cytoskeleton

12/8/2025

For 50 years, biologists have known that cells build their internal scaffolding from actin filaments, but we've never actually seen how filament formation begins. I'm excited to share that our collaborative team has solved this basic mystery about the cytoskeleton.

Using x-ray crystallography, the Robinson group captured the first atomic-resolution structure of an actin nucleus: the three-molecule complex that starts every actin filament. Their secret weapon? Villin protein from Paralvinella sulfincola, a remarkable worm that thrives in scalding deep-sea thermal vents. Collected by submarine, the worm’s naturally stable actin-binding protein proved perfect for crystallization.

The three actin molecules in the nucleus aren't identical: each adopts a different shape, representing different stages of the transformation from individual units to filament building blocks. They also discovered a molecular gate that dynamically opens and closes to allow new actin molecules to join the growing filament.

The structure also illuminates how actin-binding proteins cut filaments: they exploit natural fluctuations to compete for binding sites and destabilize the structure. This principle likely applies to other actin-binding proteins relevant to disease and development, opening new avenues for intervention.

This work was led by the Robinson group, with contributions from the Girguis (marine biology) and Copley (genomics) groups.

Our paper is out now in Science Advances. https://doi.org/10.1126/sciadv.adw6915

Using a long-Stokes-shift dye for two-photon microscopy

12/4/2025

Two colors from one laser: new preprint from my lab about a novel dye application.

Motion artifacts and anatomical orientation can pose challenges to two-photon live imaging. A second color channel helps with both problems—but usually requires a second expensive laser. We found another way. The dye ATTO 490LS is a long-Stokes-shift fluorescent dye that's been around for a decade, but its two-photon properties were unknown. We've now found that 490LS works beautifully with a 920 nm laser, the same wavelength used for GFP and GCaMP imaging. Excite with 920 nm, collect both green and red light with two detectors. One laser, two colors.

Having a stable red marker like 490LS lets you find a region of interest and distinguish real calcium transients from motion-induced changes. We're now working toward HaloTag and other conjugates for in vivo chemogenetic labeling, allowing calcium imaging with a stable reference. Please let us know if you're interested in trying some.

Preprint now on bioRxiv: https://www.biorxiv.org/content/10.1101/2025.11.21.689649v2.full

Work was led by King Yee Cheung, with help from Xianyuan Zhang , Danesha Devini Suresh, Masahiro Fukuda, and the NUS Microscopy Core.

Genome of a thermal-vent worm yields insight into animal heat tolerance

12/4/2025

How do neurons keep working at the thermal limit of animal life?

Our new chromosome-scale genome of the Pompeii worm starts to answer. It has a conservative genome but a finely tuned proteome: expanded globins, anaerobic enzymes, and new sulfur chemistry. These let the worm thrive while grazing on bacteria in hot, dark, oxygen-starved vents at the bottom of the Pacific Ocean.

This new proteome now offers thermostable tools for biochemistry and a window into physiology at extremes.

This amazing project was led by Sami EL HILALI and Richard Copley, with contributions from the Robinson, Hoelz, Martín-Durán, and Jollivet groups.

Read the paper in BMC Biology https://doi.org/10.1186/s12915-025-02369-7

Activation Drift in Kalium Channelrhodopsins

11/11/2025

When KCRs were discovered in 2022, they promised to revolutionize neuronal silencing. Finally we had a light-gated potassium channel that could inhibit neurons in a similar way to endogenous K+ channels. The Spudich, Hegemann, and Deisseroth groups pioneered engineering variants with improved K+ selectivity (WiChR, KALI1, KALI2) each showing progressively better specificity and higher conductance.

But something didn't add up; a report from worms showed, under certain conditions, behavior consistent with undesirable activation. Now, our systematic evaluation in flies and worms shows why: during continuous illumination, many KCRs’ potassium selectivity declines. Indeed, as time wears on and sodium conductance rises, each can shift from acting as an inhibitor to becoming an activator.

This suggests that KCRs have an Achilles heel—but for one exception. Among all variants tested, KCR1-C29D, a single point mutation made by the Hegemann group, outperformed the heavily engineered versions. Across light intensities and durations, C29D maintains stable inhibition, providing reliable silencing.

The TL;DR of the paper:
→ Ion selectivity stability matters more than absolute selectivity
→ Light intensity and illumination duration affect KCR function
→ Sometimes high conductance can be too much of a good thing
→ Sometimes simpler mutations work better than complex engineering

This work bridges the gap between biophysical characterization and applications in neural circuit analysis. It shows why systematic validation remains essential, especially when everyone is excited about a new tool.

🔗 Read more at Advanced Science: https://doi.org/10.1002/advs.202509180

This work was done with collaborators from labs in Würzburg, Leipzig, and Frankfurt, including Shiqiang Gao, who led this important project. Congratulations also to Zhiyi Zhang, and Stanislav Ott from my group whose work established C29D as the best inhibitor.

Synthetic memory inception

11/11/2025

We successfully implanted entirely artificial memories by simultaneously activating sensory neurons and dopaminergic circuits using optogenetics. Even without any natural odors or reinforcements, we could implant new odor memories.
We found that coincident activation of olfactory receptor neurons (ORNs) and dopamine neurons was sufficient to form both aversive and appetitive memories. Complex temporal patterns weren't required: simple rectangular light pulses worked fine.
This study demonstrates that basic co-activation of sensory and neuromodulatory pathways is enough to instruct associative learning.
Our fully optogenetic approach opens new possibilities for dissecting memory mechanisms with unprecedented control over timing and cellular specificity.
Grateful to my co-authors Tayfun Tümkaya, Ph.D., Xianyuan Zhang. Yishan Mai, James Stewart, and the team at Duke-NUS Medical School & A*STAR Singapore.

Read the full paper in iScience: https://doi.org/10.1016/j.isci.2025.113540

Parallel Function of Dopamine Neurons in Acute Behavior

11/11/2025

Our lab identified a previously unknown parallel function of dopamine neurons involved in olfactory memory in Drosophila. While these neurons were known to be crucial for memory formation, we demonstrate they simultaneously drive immediate attraction and aversion behaviors, independent of their memory-related function.

Through optogenetic manipulation, we found that sensory neurons essential for olfactory memory were not required for dopamine-driven immediate responses. We identified two key neuronal populations: a broad network of dopaminergic neurons that influenced behavior through dopamine, glutamate, and octopamine signaling, and a more specific cluster that drove attractive responses. Notably, inhibiting this latter group caused flies to display active avoidance, highlighting its role in ongoing behavioral control.

This work reveals how dopaminergic systems can coherently guide both immediate responses and memory formation, advancing our understanding of the neural circuits underlying learning and behavior.

The study was published in PLOS Biology.

Technical note: Fly KCR construct maps

3/25/2025

We have uploaded the verified vector information for the published Drosophila KCR constructs to Zenodo. Files can be assessed under: https://zenodo.org/records/15074206

The file contains vector maps for the below constructs:

pJFRC7_20xUAS_HcKCR1_AAA_YFP
pJFRC7_20xUAS_HcKCR1_C29D_YFP
pJFRC7_20xUAS_HcKCR1_ET_YFP
pJFRC7_20xUAS_HcKCR1_GS_YFP
pJFRC7_20xUAS_HcKCR2_AAA_YFP
pJFRC7_20xUAS_HcKCR2_ET_YFP
pJFRC7_20xUAS_HcKCR2_GS_YFP
pJFRC7_20xUAS_WiChR_ET_YFP

These were reported in:
Ott, S., Xu, S., Lee, N. et al. Kalium channelrhodopsins effectively inhibit neurons. Nat Commun 15, 3480 (2024). https://doi.org/10.1038/s41467-024-47203-w

Also:
Kalium channelrhodopsins effectively inhibit neurons in the small model animals
Stanislav Ott, Sangyu Xu, Nicole Lee, Ivan Hee Kean Hong, Jonathan Anns, Danesha Devini Suresh, Zhiyi Zhang, Xianyuan Zhang, Raihanah Harion, Weiying Ye, Vaishnavi Chandramouli, Suresh Jesuthasan, Yasunori Saheki, Adam Claridge-Chang
bioRxiv 2024.01.14.575538; doi: https://doi.org/10.1101/2024.01.14.575538

Fly constructs and genetics
UAS-KCR1-ET, UAS-KCR2-ET, UAS-KCR1-GS and UAS-WiChR transgenic lines were generated by de novo synthesis (Genscript) of Drosophila codon-optimized HcKCR insert sequences 43 (Genbank #MZ826861 and #MZ826862) or the WiChR sequence 45 (Genbank #OP710241) as eYFP fusions. After Sanger sequencing verification (Genscript), the fragments were cloned into an pJFRC7-20XUAS-IVS-mCD8::GFP vector (Addgene plasmid # 26220), replacing the mCD8::GFP insert via restriction enzyme digest (XhoI, Xba I). For UAS-KCR1-GS, a 3×GGGGS sequence was used to link the opsin with the fluorophore. For the KCR-ET and WiChR constructs, an AAA linker sequence was used as the starting point, to which two modifications were made: (1) an FCYENEV motif was added to the C terminus of eYFP to boost protein export from the endoplasmic reticulum and prevent potential aggregate formation 51; and (2) a KSRITSEGEYIPLDQIDINV trafficking signal from Kir 2.1 52 was added to the linker at C terminus of the opsin to boost protein expression 10. The KCR1-C29D variant 45 was obtained by site-directed mutagenesis of the KCR1-ET sequence, where the cysteine at position 29 was replaced by aspartic acid (Genscript). The synthesized constructs were injected into flies and targeted to attP1 or attP2 insertion sites on the second or third chromosomes respectively and the transgenic progeny were balanced either over CyO or TM6C (BestGene). Expression was verified by imaging of eYFP fluorescence with a Leica TCS SP8 STED confocal microscope. Opsin transgenic flies were crossed with relevant Gal4 driver lines to produce F1 offspring for use as test subjects. Driver Gal4 lines and UAS-opsin responder lines were each crossed with an otherwise wild-type w1118 line and the F1 progeny (e.g. UAS-KCR1-ET/+ or elav-Gal4/+) were used as control subjects.

New Study Reveals Parallel Function of Dopamine Neurons in Acute Behavior

2/19/2025

Our lab has identified a previously unknown parallel function of dopamine neurons involved in olfactory memory in Drosophila. While these neurons were known to be crucial for memory formation, we demonstrate they simultaneously drive immediate attraction and aversion behaviors, independent of their memory-related function.

Through optogenetic manipulation, we found that sensory neurons essential for olfactory memory were not required for dopamine-driven immediate responses. We identified two key neuronal populations: a broad network of dopaminergic neurons that influenced behavior through dopamine, glutamate, and octopamine signaling, and a more specific cluster that drove attractive responses. Notably, inhibiting this latter group caused flies to display active avoidance, highlighting its role in ongoing behavioral control.

This work reveals how dopaminergic systems can coherently guide both immediate responses and memory formation, advancing our understanding of the neural circuits underlying learning and behavior.

The study was published in PLOS Biology.