Show some details of Viruses

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.

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.