Akanksha Yadav @akankshay58@qoto.org

So very cool!
---
RT @CellRaiser_
MinDE circuits produce a unique signal that acts like a “cellular radio”, emitting frequency-barcoded data that can spectrally separate single cells or sub-cellular compartments using digital signal processing tools like FFTs, FIR filters, or wavelets with a single fluorophore.
https://twitter.com/CellRaiser_/status/1592909960157237249

‘The functions of an engineer’ from Nature 1900 issue, an address by Sir William Henry Preece, on being an engineer, printing, engineering/tackling bacteria!
https://www.nature.com/articles/061374b0

Also from earlier this week based on similar tx design for epilespy,

---
RT @akankshay58
Not at all an expert, but a fascinating data point that makes a case for 🧬 therapy because it's neat and it works!
'a strategy that self-selects neurons that are pathologically overactive and down-regulates their excitability in a closed loop'
🔴⏫activity->IEG-K+ channel->🟢📉 https://twitter.com/LignaniLab_UCL/status/1588231473072459781
https://twitter.com/akankshay58/status/1588295055688708097

Always cool to see such modalities work out in vivo!
From @JunoThera -
Activation-inducible CAR expression enables precise control over engineered CAR T cell function https://www.biorxiv.org/content/10.1101/2022.11.08.515608v1
design: 'CAR construct integrated downstream of a T cell activation-dependent promoter'

#DNAnanotech #preprint
4 DNA origami structures (helix-bundles and ring) used as scaffolds to initiate assembly of CCMV^ (virus) coat protein, takeaways -
- capsid shape, size control
- DNA encapsulation (nuclease resistant)
- tubular origami structure preferred, negative curvature not well tolerated

*imagining 🪆*
^CCMV's reversible assembly process is well characterized, pH/ionic strength control --> formation of hexagonal sheets, tubes

Building on prior work (from the same lab) 2014,
https://pubs.acs.org/doi/abs/10.1021/nl500677j

DNA origami directed virus capsid polymorphism @biorxivpreprint https://biorxiv.org/content/10.1101/2022.11.07.515152v1

Unrelated (or not), also appending an ode to the thought of a connection my brain made while reading the above with the following figure from https://www.nature.com/articles/s41592-020-0869-x
5/n

Steps involved -
- rolling circle amplification of DNA -> concatemers on flowcell
- imaging 🐙 ie 'avidite': a dye labeled polymer with multiple, identical nucleotide attached -> binds multiple nucleotides across DNA copies
- washing with 🐙 intact -> detection
- remove 🐙 (since held by non-covalent interaction)
- extend 1 base with polymerase + unlabeled, blocked nucleotide
- remove block, repeat

Undiscussed but personally curious about 🐙 design.
4/n

Avidity in this context implies the cumulative strength of multiple base pair interactions as opposed to single base pair binding events that SBS relies on.

Stronger interaction means lower substrate concentration needed and longer residence time ➡️ enables imaging without bond formation

Some nice biochemical characterization summarized in the figure below from the paper to crunch kinetic rates from -
3/n

Practically needs micromolar amounts of enzyme + substrate ie nucleotides conjugated to fluorescent dye (detection) + blocking group (1 base at a time)

Avidity sequencing chemically decouples detection from polymerase extension allowing separate optimizations of each step. That helped reduce working concentration of the new reagents.

The idea of decoupling was also pursued by BGI using antibodies in 2020,
https://www.biorxiv.org/content/10.1101/2020.02.19.953307v1
2/n

Fascinating chemistry based on the concept of 'avidity' for sequencing from Element Biosciences described in this recent @biorxivpreprint

It fundamentally differs from sequencing by synthesis (SBS) technology as used in NGS by Illumina, hence it tickled my fancy to write a 🧵:
https://www.biorxiv.org/content/10.1101/2022.11.03.514117v1

Sequencing by synthesis works by sequential incorporation (catalyzed by polymerase) and detection of synthetic nucleotides.
1/n

#introduction #biology #biotech #science #academic
Hi all!

I am Akanksha, currently working as a research tech at HHMI Janelia Research Campus, engineering bioluminescent proteins for functional imaging.

My research interests lie at the interface of chemistry, biology, and engineering 🔬. 'A tool developer' describes me best - in the dry lab, I was working on a systems biology project involving detecting hard-to-find nucleotide changes with certain effects from human transcriptome datasets. Transitioning to a wet lab, I have been engineering proteins for various applications.

Being an avid learner, I spend a lot of time reading articles from across various sub-disciplines in bioscience and biotech. I'm happiest when brainstorming ideas in molecular/synthetic biology or new tools that don't exist with a near-perfect cup of coffee☕ ! Always happy to connect over a crazy idea!

Cheers!