By Grant Jacobs 13/05/2018 2


Here’s a great video of HIV infection animated, showing molecular life at play –

Molecular life is fascinating stuff. Complex molecules getting around making life happen. I’ve been following it for 30+ years and it continues to amaze me. It’s a realm where chemistry and physics merge to become life.

In this case, an HIV infection taking place.

There’s a narrated version on the Science of HIV animations page. I’ve told my version* of the story at the end of this post; see the section What’s happening in the video? below.

All that science!

The video gives an idea of the rich collection of details scientists use to draw a (mental) picture how life works. Here we’re seeing it visualised. One thing that might not be obvious is just how much work is. Each of the molecular structures and what they do is the result of years, sometimes decades, of work by teams of scientists.

I won’t estimate the time involved, but it’d comfortably be millennia of person years if we count all the people involved.

It also takes a lot work to make these realistic, complex animations.

Animation is another approach to science communication. If it’s to be realistic, a thorough knowledge of molecular life as well as the software used to make the models is needed. In that way it’s a truly cross-disciplinary approach to communication. Science and visualisation meeting art and communication.

This work is a collaboration of members of the CHEETAH consortium and the NIGMS Specialized Centers for HIV/AIDS-Related Structural Biology.

Doing it for a living

I’ve written about molecular animation before, in Animating our DNA. I love the notion of working making molecular animations, especially that it blends a deep knowledge of the science and creative communication, but I privately I wondered how you could make a living out of it.** It blends computational biology (my field; I originally worked on molecular structures) and science communication (something I now also do). Looking at the Chan Zuckerberg Initiative twitter account I see on April 20th they announced funding for,

85 one-year projects that will focus on developing an open set of computational tools, algorithms, visualization methods and benchmark datasets for scientists working on the [human cell atlas project].

It seems a few might be lucky to be paid to work on creative science tools. (At least for a while!) It looks an interesting initiative,*** one of several they fund. All the best for those given the opportunity!

What’s happening in the video?

We first see a virus enclosed inside a membrane envelope floating in our bloodstream.

It bumps into a cell, gets trapped on the surface, then engulfed into the cell via an invagination process. The virus particle is transported into the interior of the cell, and starts to reads it’s RNA genome to make double-stranded DNA.

Our genes are stored in double-stranded DNA. HIV viruses store their genes in single-stranded RNA. They have to convert them to double-stranded DNA so that they can get our cells to read their genes. Basically they’re being little parasites, poking their DNA into our cells, and getting our cells to do the work.

Our DNA is kept inside the nucleus, a sort of safe storage unit. Access in and out of the nucleus takes place at nuclear pores.

The virus particle reaches a nuclear pore, and the virus DNA is drawn into the nucleus. The viral DNA is drawn to our DNA, and merges with it (recombines with it) to become part of the genome of that cell.

At some point the viral genes lying in the cell’s DNA are read, creating an RNA copy of these genes. That’s a complex process involving a lot of molecules. The viral RNA is moved back to a nuclear pore to outside the nucleus.

Once outside the nucleus, the viral RNA is formed into loop (lariats). These RNA loops are read to form the proteins that make up viral particles.

The virus RNA is taken to the surface of the cell and blebs out of the cell surrounded by a membrane.

Each infected cell can make many copies of the virus. Once outside the cell, a new virus particle continues to assemble.

We’ve seen one virus replicate to make many copies of itself. Each can infect other cells.

Other articles on Code for life

Animating our DNA (In which I show some earlier animations, and ruminate about my own encounters with visualising molecular life.)

Coiling bacterial DNA (A pictorial essay on how a chain of proteins hold bacterial DNA in a compacted spiral.)

The scale of cellular life and compacting chromosomes (This little animation gives some idea of the different sizes of the stuff that makes up life.)

Loops to tie a knot in proteins? (How proteins fold is an interest from my Ph.D. student days. A few proteins do more than just collapse on themselves in folding: they also tie knots, threading the chain through itself.)

Finding platypus venom (Researchers cleverly did not extract the venom, but created possible venom proteins by comparing the platypus genome with known venomous proteins and expressing the genes that matched.)

Map shows New Zealand with lowest death rate on earth in 1856, over 11 in 1000 dying (Science history is great stuff. The current death rate is roughly 7 per 1,000.)

Footnotes

Originally seen from the tweet by the Chan Zuckerberg Initiative twitter account, and the Observations blog at Scientific American blogs.

In addition to the animation there are illustrations.

* I’ve written this myself from the un-narrated video essentially from the top of my head, as it were. Their narration will likely be more complete! I’d add the times each event happens in the video, but I think it’d make the text messy to read.

** I did propose to a museum working on this sort of thing as part of a job application, with the idea of displaying it in a planetarium projection system. I liked the idea that a planetarium could not only look out to the stars, but also look in to our internal universe. There’s a vast amount of stuff going on inside us that are probably best presented to non-scientists visually.

** Unfortunately their description reads ambiguously to me. It appears to be an announcement of projects have been funded, rather than a call for applications. (I’m going by the responses to the tweet, with people acknowledging support/collaboration, rather than the website or tweets.)

Featured image

The image is a crop still from the animation, showing HIV ‘sliced’ open.


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