@HeadsInOcean
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Biologist in @SOlab_Tokyo my current GPS location @UTokyo_RCAST
Tokyo, Japan
Joined January 2021
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A part of my PhD is airing on internet now. Do check it out. And stay tuned for more updates. Yay!
Microfluidic Core-Shell Encapsulation Enables Scalable Generation of Apical-Out Intestinal Spheroids
ift.tt/ukOnRml
#biorxiv_bioE
Pooja Shukla retweeted
Genes for genetic painting in flowers now available on Addgene!: addgene.org/browse/article/2…
Incredibly proud to share this innovative research where I had the pleasure to contribute. Happy reading!
Excited to share our latest work pubs.acs.org/doi/10.1021/acs…
We developed Emulsion-Templated Gel Embedding (ETE), a microfluidics-free method for generating uniform cell-containing hydrogel microcapsules using simple vortex-based emulsification and standard laboratory equipment.
This is really cool (and wild):
Scientists simulated a complete living cell for the first time. Every molecule, every reaction, from DNA replication to cell division.
The paper (Luthey-Schulten et al., Cell 2026, doi.org/10.1016/j.cell.2026.…), just out today, used JCVI-Syn3A — a synthetic minimal bacterium with fewer than 500 genes. A 3D+time simulation of the full 105-minute cell cycle: DNA replication, protein translation, metabolism, division. Every gene, protein, RNA, and chemical reaction tracked through physical space.
It took years to build. Multiple GPUs. Six days of compute time per run.
And this is the simplest possible cell.
A human cell has ~20,000 genes. It lives in tissue. It interacts with neighbors. It differentiates. It responds to drugs in ways that depend on context we haven't fully measured.
Mechanistic simulation of the minimal cell costs 6 GPU-days for 105 minutes of biology. You cannot scale that to human cells. The complexity isn't 40x harder. It's exponentially harder.
This is why the field pivoted to data-driven models. You can't hand-encode the regulatory wiring of a human hepatocyte. But you can learn it — if you have the right perturbation data collected across enough diverse biological contexts.
The two approaches aren't competing. Papers like this generate the ground truth that future ML models need for validation. But the path to a clinically useful virtual cell runs through foundation models, not through scaling up mechanistic simulation.
Amazing work!
Looking forward to exciting science and learning! Grateful to my lab @soLab_tokyo and Takeda Foundation for this opportunity.
Yay! Catch me at the poster no. L027.T to know how you can fit your intestines in a tube!!
I've got u-fluidics, hydrogels, cells, and lots of anecdotes to discuss how we've made them.
Looking forward
@MicroTas2025 #Microfluidics
Back at #MicroTAS2025!
Catch our fantastic folks presenting posters on method development, microphysiological systems, and flow cytometry — all happening Nov 4 at the Adelaide Convention Centre. Don’t miss it.
Pooja Shukla retweeted
This is amazing - a periodic table showing every element and how it’s used.
Chemistry really is everywhere. 🔬✨
What’s your favorite element?
Pooja Shukla retweeted
Professor Ramamurthy Shankar. BTech from IIT Madras in the late 60s. Then a PhD from Berkeley. Now a professor at Yale. Here is his style :) nitter.cf/Rainmaker1973/status/1…
This is genuinely groundbreaking stuff. Education for all in its truest sense. Amazing 👏 – at Shibuya-ku, Tokyo
Breaking the Language Barrier, as inclusivity meets innovation at @iitmadras, enabling AI-powered translation of classroom lectures in 11 Indian languages, ensuring that every student can learn in the language they are most comfortable with.
This initiative, combined with mentorship support in regional languages, opens new doors for learning and growth.
We were honored to have the Hon’ble Minister of Education, Shri @dpradhanbjp ji, who appreciated our efforts to make education more accessible and equitable for all.
@EduMinOfIndia
#iitmadras #educationforall #Nep
Pooja Shukla retweeted
आप सभी को गणेश चतुर्थी की ढेरों शुभकामनाएं। श्रद्धा और भक्ति से भरा यह पावन अवसर हर किसी के लिए शुभकारी हो। भगवान गजानन से प्रार्थना है कि वे अपने सभी भक्तों को सुख, शांति और उत्तम स्वास्थ्य का आशीर्वाद दें। गणपति बाप्पा मोरया!
This is so beautiful and closely resonates with what I do!!❤️
Happy Ganesh Chaturthi. What's better than the ultimate Supreme representing the work..😭❤️ – at Shibuya-ku, Tokyo
Happy Ganesha Chaturthi and cheers to the possibility of Alternative to Animal Models
#organoids
#organonchip
#microfulidics
#biomimicking
Pooja Shukla retweeted
Does Parkinson's start in the kidney? New research from Wuhan recently published in Nature Neuroscience suggests a surprising twist: the kidneys, in some cases, may seed toxic α-synuclein and the protein may actually travel to the brain. Could a kidney-to-brain pathway could help explain why chronic kidney disease raises Parkinson’s risk. Let's not go too far on this data yet.
Key Points:
- We’ve long known about gut to brain spread and now the kidney emerges as another possible origin site.
- These findings may unlock new strategies for early detection and therapies aimed at clearing α-synuclein before it reaches the brain.
- Pathologic α-synuclein deposits were found in the kidneys of folks w/ Parkinson’s disease, dementia with Lewy bodies, and chronic kidney disease.
- In animal models, α-synuclein injected into the kidney spread along renal nerve pathways into the brain.
- It also resulted in PD-like motor symptoms.
My take: Parkinson's is a whole body disease and the proteins can thus be found all over. These findings do not surprise me, however I would be cautious about over-interpreting them. Here are 5 points that stuck w/ me. 1- Parkinson’s may not start in the brain, in some cases the kidney could be a surprising origin site for the disease. 2- Toxic Parkinson’s proteins can build up in the kidney, especially when kidney function is impaired. 3- Proteins may travel along nerve highways directly to the brain. 4- Does this paper explain why people w/ kidney disease face higher risks of developing Parkinson’s? Maybe? 5- Could we target α-synuclein in the blood or kidney? Maybe?
nature.com/articles/s41593-0… @ParkinsonDotOrg #parkinson @FixelInstitute @Nature
