Author Archives: Jessica Petrochuk

Mice Grown In Vials: Are Humans Next?

For at least a hundred years, researchers have been struggling to answer one question: how does a single cell become a full grown human.

One major barrier to fully understanding this process, was that we could never see it happening before our own eyes. Luckily, a team of biologists led by Dr. Jacob Hanna at the Weizmann Institute of Science had a major breakthrough: mice grown in vials. 

The Problem

In an interview with the New York Times, biologist Dr. Paul Tesar said:

“The holy grail of developmental biology is to understand how a single cell, a fertilized egg, can make all of the specific cell types in the human body and grow into 40 trillion cells. Since the beginning of time, researchers have been trying to develop ways to answer this question.”

Each one of us started the same, as just one cell. In our mothers, one cell became two, then four, which eventually led to us. During these beginning stages of development, we were what researchers call an embryo, or an early-stage animal. Embryos are located in a mother’s uterus, which acts like a house that provides everything needed to grow. 

To see what is going on inside this house, researchers have tried many different tricks including taking pictures, or even removing the uterus fully from animals such as mice to get a better look. What researchers have not been able to do thus far, is watch the embryo grow continuously outside of the mother. This has not only made research in the field difficult, but has restricted the work being done.

The Solution

Although the researchers at Weizmann were not the first to come up with the idea, up until now, mice grown outside of a mother have either not been able to survive, or did not grow correctly. In fact, it took Dr. Hanna and his colleagues 7 years to perfect their technique. 

The entire process consists of two steps. First, the uterus of a recently pregnant mouse is removed. Second, the uterus is transferred to a vial filled with liquid containing all the food it will need. As seen in the video below, the embryo is slowly spun to make sure it does not attach itself to the wall of the vial as that could result in death. 

Mice embryos growing inside spinning vials (Video from MIT Technology Review)

The mice were under constant observation and images, as seen below, were taken and compared to mice developing inside a mother. The two were identical. 

Mice developing over a 5-day period (Image from The New York Times)

Implications

As a result of this breakthrough, researchers will be able to better understand events including birth defects and miscarriages. Additionally, researchers can now easily change the environment that the embryo grows in to see what conditions can affect development. Although it may still be some time until this research is transferred to humans, this breakthrough certainly marks a big step in the right direction.

-Jessica Petrochuk

Protein Folding: Solved

Just as the turmoil of 2020 was coming to a wrap, a scientific breakthrough came about. On November 30th AlphaFold, coming out of Google’s DeepMind, claimed to have solved the protein folding problem using artificial intelligence.

The Problem

From making our DNA to getting rid of waste, proteins are like small machines that perform the majority of work done in cells. In fact, within our bodies there are an estimated 80,000 to 400,000 unique proteins each playing their own role. And, just like the way a building is built determines its use, a protein’s structure decides what tasks it performs. Yet, although it is easy to distinguish an apartment from an office, according to UCONN Health, it can take scientists between a few weeks to a few months to piece together what a protein looks like.

The Game Changer

This is where AlphaFold sneaks in. Although, as seen in the video above, the task was not easy, AlphaFold chose a different approach to this problem: artificial intelligence. 

Nowadays, the word artificial intelligence pops-up everywhere from self-driving cars to artificial voices, but what is most important is how it works and how it can be applied to the protein folding problem.

General scheme for developing an artificial intelligence model.

 

For the computer it all starts with data. As seen in the diagram above, once given data the computer looks for patterns between points. These patterns can then be used to make predictions on new data. Before in their final structure, proteins begin as a simple string of amino acids, or the building blocks of proteins. Given a dataset with the original string paired with the protein in its final form, the computer looks for patterns between the two. Using these patterns it can then predict what a protein might look like from just its string.

The Importance

Just one of the many protein folding predictions generated by AlphaFold’s model.

To the left you can see one prediction Alpha Fold’s model created. In comparison to the time it takes in the lab, this model is able to make a prediction in a mere half an hour with 90% accuracy according to their statement. In fact, it has already helped a biologist named Andrei Lupis with piecing together a protein his team has been stuck on for a decade. In an interview with Nature, Lupis even said: 

This is a game changer, this will change medicine. It will change research. It will change bioengineering. It will change everything.

With this new break-through, not only will scientists save time and money by not having to experimentally determine a protein’s structure, but research will accelerate at a pace never seen before. 

Beyond AlphaFold

While AlphaFold may be a hot-topic, beyond protein folding AI has also been used for a variety of tasks including interpreting MRI images or even predicting climate change. The applications seem to be limitless so make sure to keep an eye out, the next breakthrough could be coming up just around the corner!

Jessica Petrochuk

 

Protein Folding: Solved

Just as the turmoil of 2020 was coming to a wrap, a scientific breakthrough came about. On November 30th, AlphaFold, coming out of DeepMind, claimed to have solved the protein folding problem using artificial intelligence.

The Problem

Proteins perform the majority of work done in our cells from synthesizing DNA to getting rid of waste. Of course, the way a protein functions is largely dependent on its structure. This can include characterizations such as what parts of the protein are exposed versus tucked away. The proteomics field is dedicated to studying these, what is currently estimated to be, 80,000 to 400,000 proteins in our bodies and use two main strategies to determine their structure in the lab: X-ray crystallography and NMR. And yet, even in the midst of these complex protocols and high-tech machinery, a structure can take between a week to a few months to piece together according to UCONN Health.

The Game Changer

This is where AlphaFold sneaks into the picture. AlphaFold chose to take a different approach to this nominal problem: artificial intelligence.

Artificial intelligence has taken the world by storm and has improved the accuracy and efficiency of processes in almost every industry. From self-driving cars to artificial voices the possibilities are endless. 

General scheme for developing an artificial intelligence model.

Put very simply by the diagram above, artificial intelligence, more specifically machine learning, trains a computer to look for patterns within a given dataset. Once trained, this program can use the patterns it learned to make predictions of its own. In the case of AlphaFold, their model was trained off of amino acid sequences and their predetermined structures.

Just one of the many protein folding predictions generated by AlphaFold’s model.

In comparison to the time it takes in the lab, AlphaFold’s model was able to predict protein structure in a mere half an hour with an accuracy of 90% according to their statement. In fact, it has already helped an evolutionary biologist named Andrei Lupis with piecing together a protein his team has been stuck on for a decade. In an interview for nature, Lupis even said: 

“This is a game changer, this will change medicine. It will change research. It will change bioengineering. It will change everything”

Beyond AlphaFold

Of course, while AlphaFold may be a hot-topic, beyond protein folding, AI has also been used for a variety of tasks including interpreting MRI images, predicting climate change, or even sifting through astronomical data. The applications seem to be limitless so make sure to keep an eye out, the next breakthrough could be coming up just around the corner!

Jessica Petrochuk