biovisions

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Inner Life of a Cell | Protein Packing (NT TImes)

Two years ago, BioVisions and Xvivo set out to upgrade their animations by capturing some of the messy complexity of protein movements. They wanted to cram a virtual cell with proteins at a more realistic density, and then have them jitter and collide

In this movie, we enter a neuron by diving through a channel on its surface. Once inside, we’re instantly surrounded by a swarm of molecules. We push through the crowd until we reach a proteasome, a barrel-shaped molecule that shreds damaged proteins so their components can be used to make new proteins.

Once more we see a vesicle being hauled by kinesin. But in this version, the kinesin doesn’t look like a molecule out for a stroll. Its movements are barely constrained randomness.

Every now and then, a tiny molecule loaded with fuel binds to one of the kinesin “feet.” It delivers a jolt of energy, causing that foot to leap off the molecular cable and flail wildly, pulling hard on the foot that’s still anchored. Eventually, the gyrating foot stumbles into contact again with the cable, locking on once more — and advancing the vesicle a tiny step forward.

This updated movie offers a better way to picture our most intricate inner workings. For one thing, it helps us to understand why we become sick. A number of diseases, such as Alzheimer’s and Parkinson’s, are caused when defective proteins clamp onto other proteins, creating toxic clumps.

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When biology is taught, it can look very static.

It seems, on paper, that things in a cell follow a logical order; we can trace the path of carbohydrates, for example, through glycolysis and the citric acid cycle, the latter fueling the reduction of high-energy electron carriers to generate ATP through the churning of the electron transport chain’s proton pump. Proteins looked rigid, trapped in complex three-dimensional structures, and everything in the cell appears as neat little capsules within the cellular membrane: Organised. Logical. Functional.

Not so, say Alain Viel and Robert. A. Lue.

The Harvard University professors of Molecular and Cell Biology pioneered the BioVisions project - an aim to get Harvard undergraduates to understand the chaotic complexity of the cellular environment. To do this, they developed extraordinarily precise animations; a far cry from the typical narrative explanations in science documentaries, these are accurate down to the smallest protein subunit.

The ultimate goal of the BioVisions project can be summarised by ’to see is to begin to understand.’ Biology is constantly innovating, and new and more powerful ways to communicate it are becoming increasingly necessary as the discipline becomes ever more microscopic. The very act of observing and recording data lies at the foundation of all the natural sciences - and molecular biology is no exception.

So sit back, relax, and take a tour of the mitochondria: The cell’s ATP pump. See what you can spot in the animation; ATP is the glowing orange molecule, for example, and ADP is the burnt orange one.

All video credit goes to Harvard University and the BioVisions project.

OK, so yesterday I promised a special treat for those of you who love the now-famous Inner Life of the Cell video.  Here it is!  The Harvard University team behind that video has created a new animation highlighting the powerhouse of the cell, the mitochondria.  If you thought the last one was complicated, it’s got nothing on this one.

The little prokaryotic endosymbionts that we call the mitochondria are a biological world unto themselves, participating in unique biochemistry that takes place nowhere else in the cell.  You’ll see redox, ATP synthesis, ion gradients … enjoy.

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A few years ago, Harvard’s BioVisions group put out some really amazing videos, including The Inner Life of the Cell embedded here. Unfortunately, for all their intricate and true-to-life visual detail, there isn’t narration to describe the things you’re seeing. I’m going to work through this video and their others, but for now just enjoy! (My favorite is the motor protein featured starting at 3:40.)

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I legitimately think this is one of the coolest videos ever. It really is amazing to almost actually see those things that I’ve been learning about for the past many years. And yes, I’m aware of how nerdy I sound at the moment :)

(and I really wish I knew how play that on the piano, so pretty)

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Powering the Cell: Mitochondria (by XVIVO Scientific Animation)

Together Harvard University and XVIVO developed this 3D animation journey for Harvard’s undergraduate Molecular and Cellular Biology students about the microscopic world of mitochondria. The animation highlights the creation of Adenosine Triphosphate (ATP) – mobile molecules which store chemical energy derived from the breakdown of carbon-based food. ATP molecules act as a kind of currency, imparting chemical energy to power all the functional components of cellular activity. This piece is the second in a series of award winning animations XVIVO is creating for Harvard’s educational website BioVisions at Harvard. The first program, Inner Life of the Cell, received international acclaim and can be seen both on our website and the BioVisions site.