Team:MADRID UCM/Description

DESCRIPTION – iGem Madrid

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DESCRIPTION

Inspiration

Among the challenges that must be faced, the fight against deadly diseases seems a crucial point to address. Nowadays we have good levels of disease detection, but, although these technologies are solid and have huge potential, they still remain far from the scope of some areas of our planet. Unfortunately, these areas are often the most affected by epidemics and infectious diseases, preventable with an early detection system.

Our team directly addresses the challenge of applying a series of innovative technologies to the development of a practical, affordable and easy-to-use platform for the detection of water-related diseases in developing areas.

In addition to our main focus on creating an easy and accurate biological detection methodology, this kind of technology can help to optimize the sensing platforms in developing countries, saving money, time and the need of highly specialized human resources.

The Problem of Cholera

Cholera outbreaks are a major concern for public health in developing countries. Microbial contamination of the water used domestically makes dealing with the prevalence of this disease difficult. Early detection of the presence of cholera in household drinking water is crucial in the fight against the spread of the disease.
But the damage caused by cholera covers a wider area than just the health sphere: cholera outbreaks make populations dependent on foreign help and medicines. This dependence is a harsh strike to the autonomy and self-development of those populations. Just as cholera’s problems are not only physical but also socio-political, so must the solutions be.
placa+azul

The Problem of current Sensing Methods

Currently, cholera is mainly sensed via detection of the pathogen’s genetic material: Polymerase Chain Reaction (PCR) and Loop Mediated Isothermal Amplification (LAMP) are the main DNA identification techniques. Although they are relatively simple and sensitive, they can only be performed by specialized individuals following multiple-step procedures.
This has driven the development of some Rapid Diagnosis Tests (RDTs), able to identify cholera in patients or environmental samples within reduced infrastructures. The vast majority of them are based on antibodies, using Lateral Flow Immunochromatography (LFA) assays. However, their rate of false positives can be up to 40%, and they only aim to detect cholera in patients already showing symptoms, instead of detecting the pathogen in environmental samples such as water or food.

Why Aptamers?

We have bet on aptamers as the solution for the shortcomings that appear when analyzing current sensing methodologies. These resilient particles are short single-stranded deoxyribonucleic acid (DNA) molecules that can be designed to bind specifically to a target molecule.
Their nature, DNA or RNA, gives them a set of extremely useful characteristics
They are capable of resisting higher temperatures than other molecules, as well as extreme levels of pH or other harsh conditions
They are among the most cost-effective molecules to produce at this point in time
They are among the easiest molecules to manage in a wet lab
Maybe the most interesting feature they present is their tertiary structure, which allows highly specific binding to a target, as accurately as if they were two jigsaw pieces.
Aptamers are turning upside-down several biotechnology areas, gradually replacing the current golden-standard antibodies for four main reasons:
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Aptamers are, nowadays, the most cost-effective molecules to produce, as are all DNA molecules.
Aptamers are more stable than antibodies, and therefore can endure less favourable conditions.
Aptamers are more versatile than other molecules, as they can be engineered to bind along an extended target range which includes proteins, cell surfaces, etc. It is also possible to alter them or introduce modifications, so the improvement of their affinity, which facilitates the inclusion of the aptamer in the sensing method, is relatively uncomplicated.
Aptamer production does not involve experimenting with animals. Their development protocols are exclusively in vitro

Dive into our project

Disease

Disease selection & marker expression
The starting point of the development cycle of the new sensor. This step entailed the selection of the target disease (cholera), the study of its pathogenic agent, the choice of its protein marker and, finally, the expression of this marker in another lab bacteria (E.coli), completely safe thanks to our negative gram membrane display system.

After this, this synthetic biological platform (named Escherichia cholira in our proof of concept) went on to the next step: the RoboSELEX.

Keep going to learn more about the building of this platform!

RoboSELEX

RoboSELEX
The second step of the process and central part of our technology. In this stage, we developed the molecules that support the detection of the specific pathogenic agents: aptamers.

Our goal for this year has been the automation of the whole aptamer-selection process (or SELEX) in order to both increase its reproducibility and facilitate the scaling of the pathogenic agents that it is able to detect.

In our vision “Robots making aptamers” we imagine a room full of pipetting robots working full-time constantly discovering new aptamers, so we can scale up our detection system and sense more and more diseases.

Dive into this part of the project under the RoboSELEX section in “Our Technology”!

Characterization

Characterization
Immediately after the end of the SELEX process, a series of aptamers was generated. We knew that they were specific to our protein, but how could we discover to what extent?

To dig into the qualities of the aptamers and obtain necessary variables such as the affinity constant, we developed several automatic characterization protocols.

Discover how we did this under the “Aptamer Characterization” section.

folding

3D Folding & Computational improvement
Understanding the three-dimensional structure of aptamers is key for understanding the mechanisms that underlie their working principle.

Determining structural characteristics as the region where an aptamer and its ligand match can help us to direct further improvements in the most accurate way. This simplifies the SELEX process, as it stops being random, and improves efficacy.

In the course of this year, we took a number of folding algorithms from previous teams and rewrote the folding process. We did this by applying cutting-edge AI techniques for algorithm development, which created a faster and more efficient folding.

Do you want to know more about this process? Have a look at the “Aptamer Folding” section!

HP

Sensor design & implementation
An aptamer is only a molecule. To develop the best hardware that can embrace the aptamer and raise it to its maximum potential, we have carried out a series of activities aimed at better understanding the needs of the population at hand and including them in the development of the sensor.

In this way, the development of the sensor has been intimately linked with our Human Practices, making this entanglement one of the main features of our project. We have based our work on the tangible effect it has on real human lives, by ensuring an interdisciplinary approach that accounts for all aspects of the subject at hand.

To this end, we made our fieldwork in Yaoundé, Cameroon a central part of the project; there, we worked together with local scientists and health workers to tackle the problem of cholera directly, rather than just withdrawing to the lab.

We believe it is essential to not limit science to Western hegemonic knowledge, which recreates colonial patterns of thought, and this community-based fieldwork has allowed us to situate our work amidst - not against - local forms of knowledge. As such, those affected by cholera are just as much part of the project as we are, and will in the future be able to use our protocols in an independent, self-sufficient way.

The sensors

The sensors
An aptamer is only a molecule. To develop the best hardware that can embrace the aptamer and raise it to its maximum potential, we have carried out a series of activities aimed at better understanding the needs of the population at hand and including them in the development of the sensor.

In this way, the development of the sensor has been intimately linked with our Human Practices, making this entanglement one of the main features of our project. We have based our work on the tangible effect it has on real human lives, by ensuring an interdisciplinary approach that accounts for all aspects of the subject at hand.

To this end, we made our fieldwork in Yaoundé, Cameroon a central part of the project; there, we worked together with local scientists and health workers to tackle the problem of cholera directly, rather than just withdrawing to the lab.

We believe it is essential to not limit science to Western hegemonic knowledge, which recreates colonial patterns of thought, and this community-based fieldwork has allowed us to situate our work amidst - not against - local forms of knowledge. As such, those affected by cholera are just as much part of the project as we are, and will in the future be able to use our protocols in an independent, self-sufficient way.