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Fragments of DNA can help diagnose an infection

The role of collagen in a diagnostic pathway 

During a major part of my first year of research, I was working at labs in CENTI here in northern Portugal. One of the aims of my work is to enrich bacteria from a sample, and that is the task I was working on at Centi. To achieve bacterial enrichment, the strategy is to use collagen to bind bacteria. This approach is also being used elsewhere in the ViBrANT network, like by Juan, who described his work in a recent post.

But what is collagen? And why is it a preferred bio-receptor? Collagen is the main structural protein of the extracellular matrix (ECM) in the human body and the most abundant protein in mammals. ECM components like collagen, are attractive targets for adherence and invasion by various human pathogenic bacteria.

Therefore, because bacterial pathogens readily bind to collagen, the idea is to coat collagen onto magnetic nanoparticles (MNPs) and the bacteria present in an infected blood sample, for example, will bind to this collagen. By recovering the bacteria from the MNPs, we can have the bacteria in an enriched form! Samples in this enriched form are useful, because they can enhance downstream processing in diagnostics for identifying the infection-causing bacteria. Therefore, this work can have useful application in diagnosis of infectious diseases. However, this is just the first part!

Ligands to identify bacteria

While collagen is able to enrich bacteria in general, for a successful diagnostic platform, it is necessary to discriminate between the different species of bacteria present in the sample. So the purpose of collagen in my work is to enrich the sample, since this enriched sample will make it possible to identify the specific bacteria present in sample at a later stage. Just like collagen, there are a vast number of ligands which bind bacteria. But unlike collagen, there exist biological molecules or ligands which are able to bind to specific species of bacteria or even specific strains within a species. This is very useful, because if a ligand is able to recognize a specific pathogen, it can be used to identify that pathogen from a patient’s sample. So by incorporating the ligand into a diagnostic device, it is possible to identify the disease or illness the patient is suffering from.

A suitable biomolecule which can double up as a ligand with great specificity which comes to mind are – antibodies. This is because antibodies, by their very nature and function, target specific pathogens. However, nowadays very many types of ligands have been used or developed which display specificity against bacteria . For example, a fragment of single stranded DNA is known to bind to bacteria with great specificity and stability. These ssDNA molecules are also called aptamers.

I am working with the adhesins of human pathogenic bacteria such as E.coli which widely causes gastrointestinal infections and M. catarrhalis which causes upper respiratory infections, to name a few. I want to find ways to identify these adhesins (and subsequently the corresponding pathogens) from samples. So I am now focused on discovering aptamers against these adhesins. I will develop aptamers for each adhesin which binds specifically only to that adhesin. Once the aptamer is developed, it can be coated on a surface or a biosensor for detection of the pathogen and subsequent diagnosis of the infection.

SELEX

But all this begs the question.. How do I develop an aptamer with specificity to the adhesins I’m working with? For this I will be using SELEX (Systematic Evolution of Ligands by Exponential Enrichment) because virtually aptamers
can be raised against any target using this method. Selection of aptamers by SELEX is already underway by me at the Sustainable Bioprocesses and Bioproducts Lab at the University of Minho where I will conducting this part of my research.

As Christmas is fast approaching, I leave you with some images of the cheerful Christmas lights here in the city of Braga. And wish you all a Merry and joyous Christmas!

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