Computer systems have played an increasingly important role in our lives during the COVID-19 pandemic of the last months. Be it using digital technology to work from home, to teach an online class, or to communicate with our loved ones whilst in ‘voluntary’ lockdown. It is, therefore, unsurprising that computer tools also played a key part in the studying of the pandemic itself. Bioinforma­tics is a scientific field that applies computer science techniques to investigate molecular biology phenomena, such as the virus that causes COVID-19 – known as SARS-CoV-2 (quite a mouthful!).

Viruses on their own are not ‘alive’ in the strict sense of the word, they rely on other organisms (e.g. humans) to thrive. Viruses have special molecules that contain an ‘instruction set’ (either DNA or RNA molecules) that can hijack a cell and force it to produce many copies of the virus. Sometimes when new viral molecules are being produced, this instruction set mutates serendipitously, and this gives rise to variants of the virus which may (or may not) be more infectious and cause greater damage to the host.

Computer tools are being used to help design laboratory tests to detect SARS-CoV-2. We want to be able to detect this virus specifically, so we need to design accurate tests that minimise false positive and false negative results. Bioinformatics techniques are used to design these tests based on the specific instruction set of SARS-CoV-2. If the virus changes substantially over time, new tests have to be designed.

Computers are also used to annotate the instructions set of the virus. Some of these instructions (quite literally a code), are similar to the instructions found in other viruses. If we know what the instructions do in other viruses, perhaps we can make an educated guess regarding the function of the same instruction in SARS-CoV-2. This process is known as ‘genome annotation’ and helps us to understand how the virus behaves.

The virus’ instruction set produces other molecules called proteins. Proteins are responsible for a myriad of functions, such as allowing the virus to enter the host cell. Bioinformatics techniques help us build 3D models of these proteins, and enable us to learn about their structure and function. These 3D models are especially important to design drugs that interact with these proteins and stop them from carrying out their function. Bioinformatics can also help us identify suitable targets for which it is possible to design medicines that can help block or attenuate the severe effects of SARS-CoV-2 infections. TargetID (Novel Drug Targets for Infectious Diseases; COV.RD.2020-11) is one such research project coordinated by Dr Stephanie Bezzina Wettinger at the University of Malta. It is funded through the MCST COVID-19 R&D Fund 2020 jointly administered by MCST and Malta Enterprise.

The development and refinement of bioinformatics techniques during the COVID-19 pandemic has heralded many important discoveries, and partially enabled the swift development of a vaccine.

Dr Jean-Paul Ebejer and Dr Rosienne Farrugia are senior lecturers at the University of Malta. They collaborate closely on various bioinformatics, genomics, and molecular biology projects.

Did you know?

• The film Swordfish (2001) has a 30-second explosion scene that cost $5 million, required 180 cameras, and took three days to shoot and eight months to complete in post-production. The script just said “KABOOM!”

•  Naturally balding men have just as many hairs as before. They have simply shrunk to the extent that they are invisible to the naked eye.

• The capital city of the Dutch island of Saba (in the Caribbean) is ‘The Bottom’.

• After a Russian cat was found abandoned at a waste plant last month, the cat was promoted to become the Ulyanovsk region’s honorary deputy in charge of wildlife protection.

For more trivia see: www.um.edu.mt/think

Sound bites

• Chemists at Scripps Research have made a discovery that supports a surprising new view of how life originated on our planet. In a study published in the chemistry journal Angewandte Chemie, they demonstrated that a simple compound called diamidophosphate (DAP), which was plausibly present on Earth before life arose, could have chemically knitted together tiny DNA building blocks called deoxynucleosides into strands of primordial DNA. The finding is the latest in a series of discoveries, over the past several years, pointing to the possibility that DNA and its close chemical cousin RNA arose together as products of similar chemical reactions, and that the first self-replicating molecules ‒ the first life forms on Earth ‒ were mixes of the two.

https://www.sciencedaily.com/releases/2020/12/201228095428.htm

• Mussels, oysters and scallops have the highest levels of microplastic contamination among seafood, a new study reveals. The research ‒ led by researchers at Hull York Medi­cal School and the University of Hull ‒ looked at more than 50 studies between 2014 and 2020 to investigate the levels of microplastic contamination globally in fish and shellfish. Scientists are still trying to understand the health implications for humans consuming fish and shellfish contaminated with these tiny particles of waste plastic, which finds its way into waterways and oceans through waste mismanagement. Study author Evangelos Danopoulos, a postgraduate student at Hull York Medical School, said: “No-one yet fully understands the full impact of microplastics on the human body, but early evidence from other studies suggest they do cause harm.”

https://www.sciencedaily.com/releases/2020/12/201223091547.htm

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