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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 at the Centre for Nanotechnology and Smart Materials (CeNTI) here in northern Portugal. One of the aims of my work is to achieve enrichment of all types of  bacteria present in a sample. This task is then what I set about at CeNTI. The strategy to achieve bacterial enrichment, involves the use of a protein called collagen which some bacteria are known to stick to. 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

As mentioned earlier, collagen is able to enrich many species of 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  first-step enrichment of the sample. This pre-enriched sample will make it easier to identify the specific bacteria present in sample at a later stage. Similar to collagen, there are a vast number of ligands which bind to bacterial bio-receptors. 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. If the ligand in sufficient quantity is used into a diagnostic platform, it is an innovative strategy in diagnosing the disease or illness a patient suffers 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 high specificity to bacterial species/strains . For example, a fragment of single stranded DNA (ssDNA) can bind to bacterial attachment sites with remarkable specificity and sensitivity. These ssDNA molecules are also called aptamers.

I am working with the adhesins of human pathogenic bacteria such as E.coli which widely cause gastrointestinal infections and M. catarrhalis which causes upper respiratory infections, to name a couple. I want to find ways to identify these adhesins (and subsequently the corresponding pathogens) if they are present in 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.


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 a process in the lab called Systematic Evolution of Ligands by Exponential Enrichment or SELEX, for short. Using SELEX, aptamers can be raised against virtually any target including bacterial adhesins . I am selecting aptamers by SELEX for bacterial adhesins already at the Sustainable Bioprocesses and Bioproducts Lab in the University of Minho where I will be 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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