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APS-DBIO

@ApsDbio

Apr 15, 2021 • 11 tweets • 4 min read • Read on X

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@taekjip

@taekjip is taking over @ApsDbio today to run a tweetorial titled 'single is good but a couple is better'.

Single molecule methods are allowing direct detection of subpopulations & dynamics, and correlation between multiple observables, with rapidly rising popularity. Technical milestones in single molecule fluorescence can be seen here.

Many flavors of single molecule methods. (1) fluorescence (2) mechanical (3) electrical & (4) in silico. All four have been honored by Nobel prizes in physics, chemistry and physiology.

For example, the ability to detect single fluorophores is crucial to super-resolution microscopy and single molecule long-read sequencing via zero mode waveguide. See this cool discovery of actin rings in neurons.

Optical traps can also reveal how flexible DNA is and how quickly it relaxes.

But, going beyond one molecule, one fluorophore or one flavor of single molecule methods can be rewarding. Hence, single is good but a couple is better. As a reminder, you are not fully vaccinated until you get your second shot!

Single molecule FRET uses dipole-dipole interaction between two fluorophores of different color to infer their relative distance. If you know where in the protein the labels are attached, you can deduce conformational dynamics. See this illustration by Harold Kim.

Moving from a single optical trap to dual optical traps can dramatically improve precision, even allowing us to detect single base pair steps by an RNA polymerase.

Combining optical trap with single molecule fluorescence can reveal correlation between multiple observables, for example ATP binding and myosin powerstroke as shown here.

You can even combine ultrahigh resolution dual optical traps with single molecule FRET. See this illustration of ‘fleezers’ by Matt Comstock.

Now a question for you. Can we do something equivalent in single cell studies? Study interaction between two cells in high throughput for example. Regardless, Iet's celebrate single molecule biophysics but better things are ahead when we form a couple. 10/10

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More from @ApsDbio

APS-DBIO

@ApsDbio

Oct 7, 2021

@v_madhu

Hello and welcome to this week’s #DBIOTweetorial by Prof. Madhusudhan Venkadesan @v_madhu. Let’s go!

Feet and fins are quite different in their anatomy. But both have to be stiff enough to withstand the forces of propulsion. Are there deeper connections between them?

Paper: dx.doi.org/10.1038/nature…
Video:

All land vertebrates, or tetrapods, evolved from aquatic ancestors over 370 million years ago. So we and all land vertebrates are fish, in a manner of speaking!

Limbs evolved from fins, but the earliest tetrapod probably used a fin to move on land.

Ref: jstor.org/stable/j.ctt16…

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APS-DBIO

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Aug 5, 2021

@wbialek

Hello, it's a gorgeous Thursday! Time for a #DBIOTweetorial. A special edition this week — an inaugural *Editweetorial* by your host today, Prof. Bill Bialek @wbialek. #DBIOEditweetorial

Biological systems are complicated. If we try to make “realistic” models we are led into a forest of parameters. If we are going to have a theoretical physicist’s understanding of life, we have to find principles that cut through this complexity.

Maybe a #DBIOEditweetorial provides just enough space to summarize different strategies in the search for principles. Links are to papers that illustrate these ideas, and of course are just a sampling. Please respond with your own favorites.

Read 12 tweets

APS-DBIO

@ApsDbio

Jun 17, 2021

@goleylab

Have you seen images of bacteria and wondered, “How do they form such strange shapes?” or “Why do they all look so different?” Join us for today's #DBIOTweetorial as we dive into how and why bacteria adopt the shapes they do! #EngageDBIO @goleylab @jordanmbarrows

As Kevin Young eloquently put it, “To be brutally honest, few people care that bacteria have different shapes. Which is a shame, because the bacteria seem to care very much.” Check out how diverse bacterial shapes can be! tinyurl.com/6d93vce4 tinyurl.com/uvbtwvs3

Bacterial shape is largely determined by the peptidoglycan (PG) cell wall, a large macromolecule that surrounds cells and provides structure and support. PG is necessary to maintain cell shape - cells burst when treated with drugs that target PG!
tinyurl.com/m4dys6hb

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APS-DBIO

@ApsDbio

Jun 10, 2021

@NatashaMhatre

Are the screaming BroodX cicadas driving you nuts? Wonder how such tiny insects even make such a racket? You’ve come to the right place! I study how insects make and hear sound. By the end of this I hope I can show what biophysical marvels they are! #DBIOTweetorial @NatashaMhatre

@drussellpsu

So what is sound? It’s a disturbance in a medium, generated by a moving object. In this cool gif, by @drussellpsu, you can you see a grey bar moving back and forth within a pipe. The air in the pipe is pushed around, and the disturbance within it (sound) travels through the air.

So anything that moves makes a sound?

Yup, pretty much! The world is full of it: the wind shakes leaves, they rustle; tires vibrate because of friction, and they rumble.

But how ‘loud’ the sound is depends on quite a few things!

frontiersin.org/articles/10.33…

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APS-DBIO

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Jun 3, 2021

@gibbological

It's #DBIOtweetorial time, with your host @gibbological from @isbsci. Today, you'll get some facts about the ~10^13 microbes that call your gut home. By the end, I hope that you'll see yourself as much more than a mere human. You are an ecosystem! #EngageDBIO #microbiome 💩🦠🧑‍🔬

In the womb, we are sterile (obgyn.onlinelibrary.wiley.com/doi/abs/10.111…). At birth, our mothers (and surrounding environment) act as our 'sour-dough starter culture,' inoculating us with hundreds-to-thousands of species. The exact composition of this 'microbiome' is as unique to us as our genome.

Topologically speaking, humans are doughnuts. The entire outside of this doughnut is *covered* in microbes (mostly bacteria). Most of our microbes live in the colon. There are about 3*10^13 human cells and 4*10^13 bacterial cells in the body (doi.org/10.1371/journa…).

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APS-DBIO

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May 27, 2021

@BhamlaLab

It's #DBIOtweetorial time! Your host is Saad Bhamla @BhamlaLab. Today we'll learn about 10 ultrafast movements in organisms - from single cells to multicellular beasts. We hope to get you thinking engg+bio+physics of extreme movements.
#EngageDBIO #UltrafastOrganisms.

Contrary to common perception, cheetahs and falcons are not the fastest animals. Mantis shrimps for example can use a saddle-shaped spring to hammer at ~100,000 m/s^2. This is so blazing fast, it cavitates surrounding fluid. nature.com/articles/42881…

Trap jaw ants use their spring-loaded jaws to jump at faster acceleration of 10^6 m/s^2 in 0.06 ms. Faster than the blink of an eye or a bullet from a gun !! How to build robots at this scale and speed remains an open challenge. pnas.org/content/103/34…