Manipulation of Living Cells & Dead Ones

There are many methods for manipulating living cells and pieces of dead ones. The method of choice is entirely context dependent.

Thanks to Paul for sending me this lovely diagram!
Thanks to Paul for sending me this lovely diagram!

Optical tweezers are highly concentrated laser beams which are used to attract and repel microscale and nanoscale objects in order to precisely move them. This method basically uses high powered photons to punch the cell around $\rightarrow$ manipulate its momentum.

 

Electrophoresis works on things that are charged. ABEL is a form of electrophoresis which requires active feedback. Electrophoresis implements the principle of electro-osmotic flow: flowing a mixed solution through porous material (gel electrophoresis) or capillaries (for capillary electrophoresis) to separate and purify the contents according to their electrophoretic mobility (a function of their molecular weight and charge). I won’t go into sequencing techniques in this post.

Note: For analyzing DNA or proteins with gel or capillary electrophoresis, you likely lysed your cell [killed it brutally] to extract the object of interest.  

 Image Source: Gel Electrophoresis
Image Source: Agarose Gel Electrophoresis

PAGE is a vertical electrophoretic technique used to uniformly move relatively small objects (lower molecular weight DNA, proteins., etc.). PAGE results in “smeared” bands compared to those resultant from agarose gel (due to the smaller pore size of polyacrylamide).

Image Source: PAGE Setup
Image Source: PAGE Setup

Cells have a non-uniform charge distribution. The solution holding the cells for observation often forms a counter-ion cloud which can shield and neutralize the charge of the cell. To avoid such complications, we use dielectrophoresis: an electrophoretic technique that works for all dielectric materials.

Dielectrophoresis

There are a variety of electrode geometries. As a general principle: the geometries are less complex for things on the order of cell size, (easy to trap), and more complex for smaller objects.

Chemical or Microfluidic Immobilization

Acoustic Trapping with Microfluidics

Electrorotation

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Image Source

Other options include flowing cells through confocal microscopes, or magnetically manipulating cells using magnelles. Anything that generates a force reliably can be used as a trapping device!

Keep in mind that trapping the specimen is only half of the battle. The consequent imaging techniques are far more beautiful and complex.

Neuroprosthetic Sensing Hardware

Diving Into Neuroprosthetics

For the past 7 months, I explored the improvement of current assistive mobility devices.

Last month, with the freedom provided by the $100K Thiel fellowship, I realized that I had the opportunity to work on projects with higher technical risk.

This understanding lead me to dive into neuroprosthetic research, driven by the goal of understanding the human brain and processing coupled with the goal to create neuroprosthetics with the control and dexterity comparable to natural movements and lifetime usability.

I started with the convergence analysis of common decoder algorithms.

As I examined decoder optimizations to deal with the noisy data sets collected from most sensor arrays, I realized that the low resolution sensing methods currently employed are a barrier to implementing optimally functional and elegant algorithmic solutions.

With respect to accurate sensing for accurate neuroprosthetics, optical recording seems to be the superior alternative to an electrode array. Reading through the publications of the Synthetic Neurobiology Group at MIT sparked a crazy idea.

Neuroprosthetic Application of Sensing Hardware 

Using accurate 3D images which capture the state of a sparse set of synapses to train control signal classifiers to automatically learn the structural connections that create natural movement is a huge leap to achieving the goal of optimally functional prosthetics.

Accurate sensing extends far beyond prosthetics by advancing medical imaging for diagnosis, monitoring and research!

Proposal

tl;dr Place sensors in synapses to identify the 3D coordinates of firing synapses. 

Semi-permanent localized deposition of florescent voltage sensor to neuromuscular junction

$\Rightarrow$ monitoring myocyte activity with a compact infared light field microscope with CMOS to record.












Technical Q&A

What are the florescent options? || How do we attach the voltage sensor?

Continue reading Neuroprosthetic Sensing Hardware

Reframing the Gluten Scanner

A lesson that every scientist (or any person in a fast-paced creative field) learns: be glad when we find out that our research idea has already been done.The situation can be re-framed as follows:

  1. It’s awesome that there are others working just as hard as you to better the world.
  2. Reassurance that you’re not idiotic.
  3. You can now devote your precious time to developing your other projects.
I learned this lesson in 2011. After proving myself competent by assisting others in the robotics lab, I was encouraged to pursue an independent research project.
I excitedly came up with a list of ideas, then progressively descended into disappointment.
In the crowded lab, I said aloud, “It seems that every project I come up with has either already been proposed or wouldn’t be funded”.
To which the senior engineer in the lab (whom had not spoken to me before) responded, “Welcome to science!”.

One of the main projects that I’ve been working on is a gluten scanner.

The scanner allows those with food allergies to avoid accidentally poisoning themselves. This is done in one of two ways:

Raman Spectroscopy Method

  • Identify the minima and maxima on the absorption spectrum of a given protein (currently gluten) with a 1D array of IR / Vis lasers and an Avalanche photodiode Si(c).
  • Perform differential data analysis to determine if the food is contaminated.

This scanner would be able to analyse the food ~>1cm in depth without effecting the food, whereas (if desired) taking a small sample out of the food at an opportune sampling point allows for deeper results.

Originally planning on taking spectroscopic approach, I found that it was incredibly noisy (see below) to detect gluten in a vinegar solution [gluten is insoluble in water], let alone amongst protein rich food!

Thank you, Sunnyvale Biocurious, for training Paul on the spectrophotometer!

Realizing the specificity of the antigen-binding sites on antibodies, I came up with the following biomarker approach to significantly increase the accuracy of my device.

Biomarker Method

Gluten is a protein composite of gliadin and glutenin (stuck together with a starch). G12 and A1 are antibodies that bind to gliadin (a highly immunotoxic 33-mer peptide).

Although A1 has a higher sensitivity to gluten (0.33ppm) than G12 (0.5ppm), most Celiac patients have a 20ppm poisoning threshold (far below both thresholds). G12 is far less expensive, and thus the better option for regular consumer use if you aren’t willing to synthesize your own antibodies in bulk.

Anti-gliadin antibodies can be paired with a colorimetric assay to form a biomarker-based detector in the form of: a toothpick-sized detector to poke into food || the gluten-detecting equivalent of litmus strips.

G12       (Image credit: PDB)

In the past few days, I found that there are a set of devices, GlutenTox, which use my planned approach. Since this realization, I’ve also come across 6sensorlabs, and the TellSpec.

It seems to me that these solutions are not cost-effective enough to be sustainable for daily use. This is likely because antibodies are expensive unless you bulk synthesize them.

What is Bra-ket Notation?

Bra-ket notation is concise and useful.

A wavefunction is represented by a ket $|\psi\rangle$.
The complex conjugate of  wave function is written as a bra $\langle\psi|$.

The complex conjugate of a variable is found by swapping the sign of the imaginary part of said variable’s complex number, in other words: reflecting z across the real axis. For example,
$$z = x + iy$$
$$z^* = x – iy$$

A bra on the left and a ket on the right implies integration over dt.
$$\langle\psi|\psi\rangle \equiv \int\psi^*\psi dt$$

Similarly
$$\langle\psi|\hat{X}|\psi\rangle \equiv \int\psi^*\hat{X}\psi dt$$

My brief tutorial covered the basic usages of bra-ket notation in a quantum mechanical context; bra-ket notation is also used elsewhere.