A 3D model of synaptic architecture. ”We used an integrative approach, combining quantitative immunoblotting and mass spectrometry to determine protein numbers; electron microscopy to measure organelle numbers, sizes, and positions; and super-resolution fluorescence microscopy to localize the proteins. Using these data, we generated a three-dimensional model of an “average” synapse, displaying 300,000 proteins in atomic detail.” Via.
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.
Wow! New Biovisions animation does a great job of representing the crowdedness of the cell and realistic molecular dynamics. Most animations portray events as directed.
from “fantastic fungi, the forbidden fruit” by louis schwartzberg, a documentary about mycologist paul stamets. “the task that we face today is to understand the language in nature. my mission is to discover the language of the fungal networks that communicate with the ecosystem. i believe that nature is intelligent. the fact that we lack the language skills to communicate with nature does not impugn the concept that nature is intelligent; it speaks to the inadequacy of our skill set for communication,” paul says. “i believe nature is a force for good. good is not only a concept, it is a spirit. and hopefully this spirit of goodness will survive.”
mycelium infuses all landscapes, it holds soils together. it’s extremely tenacious. it holds up to 30,000 times its mass. we have now discovered that there is a multi directional transfer of nutrients between plants, mitigated by the mycelium. in a single cubic inch of soil, there can be more than eight miles of these cells. the mycelium, in the right conditions, produces a mushroom that bursts through with such ferocity it can break asphalt.
we’re more closely related to fungi than we are to any other kingdom. we share in common the same pathogens. fungi don’t like to rot from bacteria, and so our best antibiotics come from fungi. i”ve been a scanning electron microscopist for many years, and when i’m staring at the mycelium, i realize that they are microfiltration membranes. we exhale carbon dioxide, so does mycelium. it inhales oxygen, just like we do. but these are essentially externalized stomachs and lungs. and i present to you a concept that these are extended neurological membranes.
most of you may not know that fungi were the first organisms to come to land. they came to land 1.3 billion years ago, and plants followed several hundred million years later. the mycelium produced oxalic acids, pockmarking rock and grabbing calcium and other minerals and forming calcium oxalates. this makes the rocks crumble, and is the first step in the generation of soil.
now, we’ve had several extinction events (and our currently in the sixth), and 65 million years ago we had an asteroid impact, and a huge amount of debris was jettisoned into the atmosphere. sunlight was cut off, and fungi inherited the earth. those organisms that paired with fungi were rewarded, because fungi do not need light. fungi use radiation as a source of energy, much like plants use light. so, the prospect of fungi existing on other planets elsewhere, i think, is a forgone conclusion.