Understanding of Cellular Metabolism

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Better Understanding of Cellular Metabolism With AI   By EPFL

October 6, 2022  Scientists at EPFL, the Swiss Federal Institute of Technology, Lausanne, have developed REKINDLE, a deep learning-based computational framework that replicates dynamic metabolism in cells.

"REKINDLE will allow the research community to reduce computational efforts in generating kinetic models by several orders of magnitude," says EPFL's Ljubisa Miskovic. "It will also help in postulating new hypotheses by integrating biochemical data in these models, elucidating experimental observations, and steering new therapeutic discoveries and biotechnology designs."

Researchers envision the framework optimizing the metabolic network of microbes to generate industrial-scale chemical compounds, as well as unifying the use of kinetic modeling in the scientific community. To that end, EPFL's Subham Choudhury said REKINDLE uses popular Python libraries to promote accessibility and ease of use. ... 

An EPFL framework that leverages deep learning paves the way for the efficient and accurate modeling of metabolic processes. ... 

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Lab Grown Brain Cells Play Pong

Has this gone too far?

Lab-grown brain cells play video game Pong  By Pallab Ghosh  in the BBC, Science correspondent

Researchers have grown brain cells in a lab that have learned to play the 1970s tennis-like video game, Pong,

They say their "mini-brain" can sense and respond to its environment.

Writing in the journal Neuron , Dr Brett Kagan, of the company Cortical Labs, claims to have created the first ''sentient'' lab-grown brain in a dish.

Other experts describe the work as ''exciting'' but say calling the brain cells sentient is going too far.

"We could find no better term to describe the device,'' Dr Kagan says. ''It is able to take in information from an external source, process it and then respond to it in real time." .... ' 

Cell Factory Modeling

Predicting how fast and efficiently enzymes work.

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Algorithm Uncovers Secrets of Cell Factories

By Chalmers University of Technology (Sweden), September 1, 2022

An algorithm developed by researchers at Sweden's Chalmers University of Technology can predict how fast enzymes work based on the sequence of amino acids that make up the enzymes.

The computer model calculates an enzyme's kcat value, which indicates how fast and efficiently an enzyme works, using the order of the amino acids that make up the enzyme, which can be found through open databases.

The model could help researchers identify the most promising enzyme candidates for lab testing, paving the way for the creation of new medicines and biofuels, among other things.

Additionally, the model can determine changes in kcat values in the event of mutations, identify animo acids that hinder an enzyme's efficiency, and predict whether enzymes will produce undesirable metabolites.

Chalmers' Eduard Kerkhoven said, "It is useful in industries where you often want to manufacture a single pure product."  ...

Researchers at Sweden's Chalmers University of Technology have developed a computer model that can predict how fast enzymes work, making it possible to find the most efficient living factories, as well as to study difficult diseases. .... 

From Chalmers University of Technology (Sweden)

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Cell Computations Discovered

 Interesting direction, cell computations.

A Secret Language of Cells? Cell Computations Uncovered

By King Abdullah University of Science and Technology, July 28, 2022

The researchers' model centers on how glial cells cooperate with neurons to fuel the brain and participate in computations.

Scientists at King Abdullah University of Science and Technology (KAUST) in Saudi Arabia and  EPFL's Blue Brain Project in Switzerland have published a theory describing a secret cell language for sharing information about the outside world.

The researchers used a computational model to confirm that metabolic pathways could plausibly encode details about neuromodulators that boost energy consumption. Neuromodulators regulate the exchange of information in the brain, and the researchers' astrocytic energy metabolism model focused on how astrocytes collaborate with neurons to drive the brain and engage in computation.

KAUST's said, "The teams' simulations of neuromodulator-stimulated glucose metabolism in an astrocyte suggest that metabolic pathways could be capable of more information processing than we previously realized," says Pierre Magistretti, director of the KAUST Smart Health Initiative.

From King Abdullah University of Science and Technology

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