Deans' stroke musings: Probing the connectivity of neural circuits at single-neuron resolution using high-throughput DNA sequencing

Changing stroke rehab and research worldwide now.Time is Brain! trillions and trillions of neurons that DIE each day because there are NO effective hyperacute therapies besides tPA(only 12% effective). I have 523 posts on hyperacute therapy, enough for researchers to spend decades proving them out. These are my personal ideas and blog on stroke rehabilitation and stroke research. Do not attempt any of these without checking with your medical provider. Unless you join me in agitating, when you need these therapies they won't be there.

What this blog is for:

My blog is not to help survivors recover, it is to have the 10 million yearly stroke survivors light fires underneath their doctors, stroke hospitals and stroke researchers to get stroke solved. 100% recovery. The stroke medical world is completely failing at that goal, they don't even have it as a goal. Shortly after getting out of the hospital and getting NO information on the process or protocols of stroke rehabilitation and recovery I started searching on the internet and found that no other survivor received useful information. This is an attempt to cover all stroke rehabilitation information that should be readily available to survivors so they can talk with informed knowledge to their medical staff. It lays out what needs to be done to get stroke survivors closer to 100% recovery. It's quite disgusting that this information is not available from every stroke association and doctors group.

Monday, January 2, 2012

Probing the connectivity of neural circuits at single-neuron resolution using high-throughput DNA sequencing

We need this as a base if we are ever to understand enough about the brain to fix things after they go wrong.
http://precedings.nature.com/documents/6452/version/1

Abstract:: There is growing excitement in determining the complete connectivity diagram of the brain—the “connectome”. So far, the complete connectome has been established for only one organism, C. elegans, with 302 neurons connected by about 7000 synapses—and even this was a heroic task, requiring over 50 person-years of labor. Like all current approaches, this reconstruction was based on microscopy. Unfortunately, microscopy is poorly suited to the study of neural connectivity because brains are macroscopic structures, whereas synapses are microscopic. Nevertheless, there are several large-scale projects underway to scale up high-throughput microscopic approaches to the connectome.
Here we present a completely novel method for determining the brain’s wiring diagram based on high-throughput DNA sequencing technology, which has not previously been applied in the context of neural connectivity. The appeal of using sequencing is that it is getting faster and cheaper exponentially: it will soon be routine to sequence an entire human genome (~3B nucleotides) within one day for $1000.
Our approach has three main components. First, we express a unique sequence of nucleotides—a DNA “barcode”—in individual neurons. A barcode consisting of a random string of even 30 nucleotides can uniquely label 10^{18} neurons, far more than the number of neurons in a mouse brain (fewer than 100 million). Second, we use a specially engineered transsynaptic virus to transport “host” barcodes from one neuron to synaptically coupled partners; after transsynaptic spread, each neuron contains copies of “invader” barcodes from other synaptically coupled neurons, as well its own “host” barcode. Third, we join pairs of host and invader barcodes into single pieces of DNA suitable for high-throughput sequencing.
Modern sequencing technology could in principle yield the connectivity diagram of the entire mouse brain. Similar approaches can be applied to Drosophila and C. elegans.