Viruses IRL

Using models from the educational portal of the RCSB Protein Data Bank (PDB), we will explore virus symmetry through paper origami. Paper origami, the art of folding papers into specific shapes, sizes, and forms, is a great tool for visualizing and modeling the shapes of viruses.

Data visualization, also known as “dataviz,” is the graphical representation of information derived from data. Dataviz is particularly useful in the age of “big” data — large and complex datasets that are too unruly for traditional methods of analysis. By showcasing the patterns and outliers through visual means, we can more easily generate conclusions and actions that best address the questions surrounding these datasets. In this video, Rockefeller graduate fellow takes us through the basics of dataviz, and how it relates to the SARS-CoV-2 pandemic.

Close your eyes and picture something alive. Perhaps you’re envisioning a person or a pet dog? Now, picture something that is not alive. Maybe, this time you’re thinking of a rock or a lightbulb.

Seems obvious which of your conjured images are alive and which are not alive, right?

Can you describe what makes something alive?

Will those characteristics of being alive still apply to a barnacle, a flower, or the E.coli that gives you food poisoning?

It turns out that describing the characteristics of living things requires us to dig a bit deeper than behaviors and features of an organism. As scientists we need to really think about the processes that all living things can do. However, even once we’ve done that, we can still run into trouble. This is because even scientists don’t all agree on what behaviors making something alive.

Review some fundamental characteristics of living things. Challenge yourself to apply them to viruses (or not!). Then, think about why it even matters to classify a virus as a living thing or an inanimate object.

What makes something alive? What must it be able to do? Write down a list of the most essential elements. Check your list by seeing if it works to describe a wide variety of living things and excludes a wide variety of non-living things.

Describe viruses based on your set of criteria. Does this suggest they are alive or not?

What about a parasite? Or an obligate symbiote (an animal that MUST live in connection with another)?

Now let’s learn a bit more about viruses…

Relatively recently, scientists were surprised to discover viruses so large they are the same size as some bacteria. Might this large size give them the features of other living things? Read this article about giant viruses and see what you think!

Scientists are also puzzled by viruses that infect other viruses. Can a nonliving thing invade another nonliving thing or should we reframe what we think of as being alive? Read more about virophage and make up your own mind.

Did anything in the articles change your mind? Do you want to modify your list of what makes something alive or adjust your understanding of viruses in some way?

The “Open Data” movement — or the call for making valuable information free and accessible to anyone without restriction or limitation — enables everyday citizens to innovate in order to serve the needs of their communities. However, as we tinker and explore with public data sets, particularly when creating visuals to communicate these data, we must uphold stringent best practices to avoid spreading misinformation or promoting misinterpretation (learn more about this in Data Visualization and Covid-19). In the next sections, Rockefeller graduate student Caitlin Gilbert will take you through the steps of finding and preparing open COVID-19 data to make a thematic map showing virus spread in NYC using Shiny, a package in the free software environment R.

ELISA works like a puzzle, where specific molecules lock together, a bit like puzzle pieces (though actually a bit more wiggly, like if puzzle pieces could shake hands or like this teacher with a unique handshake for each student). In this activity, cut out the puzzle pieces and assemble them just right to model the pieces of an ELISA.

Then, read more in the subsequent sections to learn more about the ELISA technique, antibodies, and more!

qPCR—quantitative PCR (polymerase chain reaction), sometimes also called real-time PCR—is a method for detecting nucleotide sequences (in this case, signatures of viral genomes) through a quick and often quantitative method.

We can simulate the detection of a virus by this method using many of the components scientists have used to design and implement tests for SARS-CoV2 since its discovery in December 2019. Viruses like SARS-CoV2 with genomes stored as RNA, the test has an added step for reverse-transcription of the RNA to DNA and these tests are then often referred to as RT-PCR. The entire process is summarized in the following infographic, which is also available for download in the Save & Share menu.

In the subsequent steps of the activity, we will 1) explore a key component of the specificity of PCR in general, 2) model the RT-PCR test for SARS-CoV2 in silico, and 3) model the added component that can make these tests quantitative and reasonably fast, making them a gold standard for virus identification in an infection.