Open Project

Life Dynamics

We are developing automated aquariums with a new type of model organism for aging biology—small crustaceans, Daphnia. And we propose to use them to collect data on the effectiveness of geroprotectors. The project implies complete openness and teamwork: the assembled data will become public. The scientific director of the project is Leonid Peshkin, Harvard Medical School.
Our installation will allow conducting a large amount of research in a short time. Standardization of protocols and, as a result, reproducibility of outcomes is also essential for us. With the help of the Life Dynamics system, it will be possible to obtain valuable data in life extension: activity levels of various compounds, their combinations, and therapeutic schemes.

In the future, neural network models trained on the obtained data will create a universal tool for the virtual screening of drugs for their ability to prolong life.

All the obtained data will be collected in a universal open database and made available to the international community.
Such a platform will accelerate the discovery of target drugs for many human diseases caused by aging, such as degenerative and metabolic disorders. It is also easy to imagine further applications in bio-surveillance and toxicology. The platform will also have a far-reaching impact on the democratization of research and provide new tools for teaching and disseminating scientific knowledge.
Leonid Peshkin, author of the project
Harvard Medical School
Our goal is to test geroprotectors and their combinations and contribute to the development of automated experiments with animals.
The social task of the project is also essential: we want to involve a large number of people and organizations in life extension, providing an opportunity to conduct experiments remotely.
Live points on the graph
Daphnia specifically and very actively move in water, which makes it possible to predict the action of the tested molecule and regularly perform automated counting and tracking of organisms.
The video shows Daphnia in an aquarium and their periodic characteristic "jumps."

Phototaxis - a movement to light is observed in Daphnia. When the top of the aquarium is illuminated, the Daphnia begin to move upwards. Here we see young individuals, but in the process of aging, the light signal begins to be ignored. The reason for this phenomenon is not yet apparent (do not see? no strength to swim?).
We have already learned to count Daphnia automatically. The next stage is the implementation of tracking organisms, determination of movement speeds, health status, and bio-age, verification of a model for predicting the activity of a substance by a series of videos. All this will reduce the time of the experiment several times.
Why did we choose Daphnia?
Daphnia is well-studied freshwater crustaceans, widely used in toxicological tests due to its permeability to small molecules.
Save time
The average lifespan of Daphnia is about 60 days, which is convenient. Moreover, there is a chance to make the duration of the experiment even shorter by implementing our new approaches in data analysis. But to speak with confidence about the accuracy of the latter method, it is necessary to conduct several preliminary studies.
Save money
A 1-liter aquarium can comfortably accommodate 100 Daphnia. For comparison, there would be only one fish in the same volume. In addition, very low test substance concentrations are sufficient for Daphnia (vital for checking newly developed chemicals, which, as a rule, are very expensive). A crowd of cheap Daphnia in a weak solution and compact conditions makes the work very economical.
Convenient to dose the drug
Since we know precisely the volume of the aquarium, we can control the concentration of the drug in the study. We can also control the time of drug exposure. When working with worms and flies, there is no such level of control. In addition, the testing of drugs on worms requires concentrations exceeding the physiological doses for humans by 100 times, which is extremely expensive. Flies mostly eat like larva, and it is impossible to control the amount of consumed drug.
Complete genome
The size of the Daphnia genome is relatively small—only 250 Mb (250 million base pairs). It is among the five most thoroughly sequenced and assembled genomes among all organisms, including humans. Consequently, it is possible to test various gene editing variants and do the transcriptomic analysis of the Daphnia organism.
Other advantages
Clonal. Many descendants. Transparent. Visible macrophages.
Aging model
Firstly, Daphnia does ages (the probability of their death increases with age). Secondly, at least one mechanism associated with aging in Daphnia intersects with other model organisms and even, probably, with humans: a moderate reduction in calories prolongs their life.
Convenient to evaluate the results
It is enough for us to observe the phenotype of Daphnia, namely, the nature of their movement (there is no need to dissect them and measure the indicators chemically). This provides opportunities for automation (using video cameras and image recognition) and scaling: many aquariums are in the hands of completely different teams.
... and also
It's also a new idea, a new model organism for aging research, which has not been tried before. An organism that is ideally suited for a quick check of various drugs and their combinations is one of the primary tasks in prolonging human life.
Translation into clinical practice
Transferring the result to humans
Daphnia has many genes and cell types homologous to humans. Unlike the same C.elegans worms, Daphnia still has internal organs, and individual tissues of these organs under a microscope are visually indistinguishable from, for example, mice. Daphnia reacts to medications used for humans.

Transferring the results obtained on laboratory animals is not unique to Daphnia and is typical for the pharmaceutical industry in principle. Any preclinical studies are carried out on animals or cell cultures. There are many types of such laboratory animals. For example, geroprotectors have often been tested on flies, worms, and mice, and a similar question arises for all these animals.

Moreover, it seems to us that Daphnia have a potential competitive advantage here (see the table above).
By the way, there is an excellent article from Sarah Konstantin: Why Drugs that Work in Mice Don't Work In Humans.
What has already been done
The engineering scheme of the modular system of aquariums with the selection of the most suitable materials;
A computer vision algorithm has been created that counts the number of Daphnia in a recording with 10% intervals;
The nutrition of Daphnia and their maintenance under normal conditions has been studied;
The system of non-toxic gluing of aquarium parts;
The pipeline of the algorithm that predicts the action of a geroprotector based on longitudinal data from surveys of moving organisms;
The optimal geometry of the Daphnia section has been developed. This allows for effective shooting of moving organisms, purification of water from offspring and corpses, as well as water aeration.
Two types of setting
We are working on the two types of setting: a fully automated and simplified one
Automated
Fully automated system with a large number of cassettes: pairs of control and experimental groups.

Here one can see not only a diagram of the experimental setup but also an interaction system for users to order research remotely.

Simpified
Soon you will be able to order a non-automated but suitable for conducting independent research nonetheless version of the setting.

There is no automated supply of the test substance in a simplified system. But it does have an automatic tracking and counting algorithm.
Our project has tasks for biologists, engineers, and programmers. We would also be grateful for any financial or media support as well as for the first experiment requests.
Anastasia Velikanova, project manager in Russia
Skoltech PhD student, Life Science
Urgent tasks
For programmers
- Tracking of organisms
- Predicting algorithms for molecules' activity
- Network architecture
- Application for the experiment r
emote ordering
For engineers
- Development of a phytoplankton feeding system
- Compaction of the system
- Selection of optimal pumps

For biologists
- Development of a protocol for obtaining dry Daphnia eggs
- Development of a protocol for obtaining males
- Breeding optimization
- Carrying out the first experiments within the system

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