Week 6 Preclass

Something from “Nothing.” Why do molecules move? How do patterns grow?

Please read and consider the below before start of class on Monday. The questions given are only study questions not homework to be graded. Talk about it all with your classmates, friends, or TAs, as you like.

Preclass for Monday

Introduction - Diffusion Happens

Welcome to the first pre-class material for Diffusion and Patterning. The examples here will prepare you (and provide you with a mindset and a feeling) before the the class towards the following goals:

Goal-1: You will be able to recognize that diffusion is everywhere in biology and beyond.

Goal-2: You will be able to describe the mechanism behind diffusion (microscopically and macroscopically). Stated differently, you will be able to describe what does it mean that diffusion happens.

Goal-3: You will be able to describe the role and application of diffusion in engineering living matter.

Let’s briefly learn about application of diffusion in engineering living matter with an interesting example of Blinking Squares …

Case-1: Blinking Squares

We’ve uploaded two videos to Canvas of some blinking squares. Please see w6_preclass_video_1.mov, which shows 500 blinking squares. Each square is about 100μm x 100μm and there are 25 μm gaps between each square. Each square contains about 5,000 bacterial cells. You may remember this video from class (Day 9: April 24) during the analysis and design of the genetic systems lecture earlier in the quarter.

NOTE: if you have a hard time finding or playing the video upload to Canvas, you can find it in the original paper in the Supplementary Material (Sup Movie 1). You can also use the paper as a reference in answering the questions below.

Q.1. What do you observe?

Q.2. How long does it take for all the squares to synchronize (i.e., blink ON/OFF all together)?

Q.3. What is the simplest mechanism you can imagine that would cause all the squares to synchronize their blinking?

Q.4. Can the squares synchronize their blinking together without an external signal? If yes how would that signal synchronize the squares together?

Q.5. Can autonomous agents synchronize their behavior, and if so how?

Case-2: Blinking Square

We’ve also uploaded a second video to Canvas, titled w6_preclass_video_2.mov, which depicts single blinking square (100μm x1 00μm) containing about approximately 5,000 cells. Please watch it.

NOTE: if you have a hard time finding or playing the video upload to Canvas, you can find it in the original paper. You can also use the paper as a reference in answering the questions below.

Q.6. What do you observe?

Q.7. What is the simplest mechanism you canimagine that would cause the square to synchronize its blinking?

Q.8. Watching cells inside the square do you see a different brightness levels within each cell- how uniformed is the distribution of fluorescentproteins inside each individual cell in the square?

Optional reading-1: A synchronized quorum of genetic clocks

Optional reading-2: A sensing array of radically coupled genetic biopixels

What Is Diffusion

Diffusion is everywhere in living matter and beyond. We encounter diffusion routinely in our daily lives.

Diffusion is a spontaneous net movement of matter (e.g., molecules, atoms) from regions of high concentration to a region of low concentration. Stated differently, diffusion is a transfer of mass that causes the distribution of molecules, or atoms to be more uniform in space as time evolves.

Q.9. Can you think about everyday examples of diffusion in your life?

Is this Diffusion?

Take a look at the following video

Q.10. Is this diffusion? why or why not? How can you tell?

Optional reading-3: Life at Low Reynolds_Number

Additional Resource

Entropy Explained link-1

Khan Academy videos:

Diffusion - Membranes and transport link-2
Diffusion and osmosis membranes and transport link-3
Fick’s law of diffusion and respiratory system physiology link-4

Preclass for Wednesday: Dancing Droplets

Note: To prepare for Wednesday’s class, you can attend Physics of Dancing Droplets tutorial (video recording is available at this link and slides are on Canvas), or read the following pre-class material.

To get started please spend ~5 minutes watching these two videos:

Dancing Droplets

Briefly examine:

Here is what we will do in class together on Wednesday

Goal our practical goal is to gain experience programing the behavior of simple systems in space and time.

We ask,

What rule did you observe (or read) about - which droplets chase which?
Why does the sharpie marker create a physical barrier and how do the droplets respond to it?
To what extent were you able to realize increasingly autonomous behavior?
How would you use autonomous behaviors (with droplets or cells) to generate pattersn?

To explore these concepts we are challenging you to realize three types of behaviors that illustrate the three modes of patterning.

First, a pattern that you control directly by your own hand marking a path.

Second, a pattern that you control somewhat indirectly, by using spontaneous physical processes to create an external coordinate system.

Third, a pattern that you initiate but that otherwise entirely controls itself via its own autogeneration of a coordinate system.

MATERIALS & METHODS

Materials (you have recieved):

3 cleaned glass slides (side with a black dot is cleaned),
4 colored solutions,
4 transfer pipettes

You will also need a sharpie marker.

We have prepared the following solutions of propylene glycol and water (% v/v)

30% (Purple), 15% (Teal), 5% (Orange), 2.5% (Pink).

A few notes on the glass slides and cleanliness:

To preserve the cleanliness of the slides and help the activity work properly, please do not touch the slide surface with your hands. Hold the slide from the side. Glass slides have been cleaned with a Plasma cleaning machine; this makes the glass slides both incredibly clean and hydrophilic.

Now, practice by playing with making droplets dance:

Place the slide on the paper work surface, with the marked treated side facing UP.
Place small volumes (< 10 μL) of varying solutions of propylene glycol and colored water onto the slides using pipettes (use one pipette per color).
Observe. The droplets should start moving.
To gain additional controls over the system, you can draw on the slides with sharpie markers. Ask questions or ask for help as needed!

When you feel ready…

Three Challenge

Challenge 1.( ~ 5-7 minutes)

Can you get one droplet to chase another along a curved path between two points? (Hint: Sharpie)

Challenge 2. (~ 10-12 minutes)

Can you get one droplet to follow a defined path withoutusing the black sharpie, only by placing other droplets in the field? How few “control” droplets can you use?

Challenge 3. (All remaining time)

By only placing droplets in a confined initial region, can you get a droplet to eject and follow a defined path (again, all without placing any droplets elsewhere in the field)?

Note: Take pictures to help you answer the problem set questions.

QUESTIONS

Part of these questions will also appear on PSET:

— If you have two different droplets why do they chase each other? What other behaviors have you observed?

— Why does the sharpie marker create a physical barrier and how do the droplets respond to it?

— To what extent were you able to realize increasingly autonomous behavior?

— How good do we have to become at implementing these different frames of reference in order to engineer living matter?

— Extra: Make your own dancing droplet video (30 to 60 seconds) with your own choice of background music.

Preclass for Friday:

We ended class on Monday with an initial consideration of diffusion, introducing the idea that spontaneous diffusion of systems comprised of more than one molecule can temporarily result in non-trivial spatial patterns (e.g., a bullseye).

Next we used simple rules to create a complex pattern with droplets.

On Friday, we will build on both ideas.E.g,. how can state (i.e., memory) be used to capture and make permanent fleeting patterns? How can patterns build upon patterns?

We’ll start by drawing again upon the preclass from Monday(i.e., the bacterial blinking oscillators) and end by working through a challenge of how to program the growth an arm-like structure.

Please ponder how cells can act… I.e., the various primary functions that cells can “execute” or carry out. By combining spontaneous physical processes starting from diffusion with programmed cellular functions, both natural and engineered biological systems can realize non-trivial behaviors over both space and time. More specifically:

(1) Cells can grow and divide.

I.e., one cell can become two and so on. Cell Division - Exponential

(2) Cells can move.

I.e., cell migration can result in significant changes in shape and form. Don’t believe See a brand new movie of an immune cell moving inside the ear of a fish… Immune Cell Migration in the Zebrafish Inner Ear

Or, a slime mold swarming on a plate and growing a stalk… Swarming

(3) Cells can communicate with each other.

I.e., cells can send chemical messages between and among each other. E.g., here’s a type of “pulse” in gene expression generated across many cells during development of a tail-like structure… Wave of gene expression in an embryo

(4) Cells canchange state.

I.e., one type of cell can become another type of cell, in response to signals or even spontaneously.E.g., here are bacterial cells infected with virus realizing different cell-fate outcomes. Bacteriophage lambda lysis and lysogeny

(5) Cells can undergo programmed cell death

I.e., cells can die. Apoptosis

Taken together these functions can be used to realize incredible outcomes.E.g., watch this old-time movie of a frog egg becoming a frog.

The Development of a Frog

Question: How many of the five mechanisms introduced above can you observe or infer in the formation of a frog?

Additional video, if you have time watch Marvels of Bacterial Behavior

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