New technique sheds light on human neural networks

New technique sheds light on human neural networks

A new technique, developed by researchers in the Quantitative Light Imaging Laboratory at the Beckman Institute at the University of Illinois, provides a method to noninvasively measure human neural networks in order to characterize how they form.

Using spatial light interference microscopy (SLIM) techniques developed by Gabriel Popescu, director of the lab, the researchers were able to show for the first time how human embryonic stem cell-derived neurons within a network grow, organize spatially, and dynamically transport materials to one another.

"Because our method is label-free, we've imaged these type of neurons differentiating and maturing from neuron progenitor cells over 12 days without damage," said Popescu. "I think this (technique) is pretty much the only way you can monitor for such a long time."

Scientific Reports recently published their paper on the topic, "Label-Free Characterization of Emerging Human Neuronal Networks."

Using time-lapse measurement, the researchers are able to watch the changes over time. "We've been looking at the neurons every 10 minutes for 24 hours to see how the spatial organization and mass transport dynamics change," said Taewoo Kim, one of the lead authors on the paper.

The SLIM technique measures the optical path length shift distribution, or the effective length of the path that light follows through the sample. "The light going through the neuron itself will be in a sense slower than the light going through the media around the neuron," explains Kim. Accounting for that difference allows the researchers to see cell activity—how the cells are moving, forming neural clusters, and then connecting with other cells within the cluster or with other clusters of cells.

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Using spatial light interference microscopy (SLIM) techniques developed by Gabriel Popescu, director of the Quantitative Light Imaging Laboratory at the Beckman Institute at the University of Illinois, researchers were able to show for the first time how human embryonic stem cell derived neurons within a network grow, organize spatially, and dynamically transport materials to one another. (Time-lapse video). Credit: Gabriel Popescu, director of the Quantitative Light Imaging Laboratory at the Beckman Institute at the University of Illinois

"Individual neurons act like they are getting on Facebook," explains Popescu. "In our movies you can see how they extend these arms, these processes, and begin forming new connections, establishing a network." Like many users of Facebook, once some connections have been made, the neurons divert attention from looking for more connections and begin to communicate with one another—exchanging materials and information. According to the researchers, the communication process begins after about 10 hours; for the first 10 hours the studies show that the main neuronal activity is dedicated to creating mass in the form of neural extensions or neurites, which allows them to extend their reach.

"Since SLIM allows us to simultaneously measure several fundamental properties of these neural networks as they form, we were able to for the first time understand and characterize the link between changes that occur across a broad range of different spatial and temporal scales. This is impossible to do with any other existing technology" explains Mustafa Mir, a lead author on the study.

The researchers used untreated cells and cells that were treated with lithium chloride, which delays neurite growth. This allowed them to compare the mass of both the treated and , and showed that the main growth of cells is during the connection phase, where dendrites are being extended within and between clusters.

"When we first compared the data from the treated and untreated samples, the potential of this technique to answer important questions in neuroscience and developmental biology became clear. Many diseases result in subtle changes in how neural networks organize and behave, and now we have a tool to study these changes in a practical manner," said Mir.

The work is done in conjunction with a science and technology center sponsored by the National Science Foundation, Emergent Behaviors of Integrated Cellular Systems (EBICS), which is a multi-institutional effort led by MIT, Georgia Tech and the University of Illinois. The Illinois site is led by Rashid Bashir, from the Beckman 3D Micro- and Nanosystems Group and head of the Illinois Department of Bioengineering.

EBICS is examining the way that complex systems and patterns rise out of relatively simple interactions with a goal of building living, multi-cellular machines that solve real-world problems in health, security and the environment.

"Through this center in the past four years, we've developed a number of tools trying to understand emergence, trying to define what emergence means," said Popescu. "This paper is a clear example of our progress toward defining and quantifying this important and universal phenomena.

"We developed these methods based on SLIM to understand at what scale the cells get organized, they become predictable. We quantify emergence versus spatial and temporal scales at which order occurs. The formation of a neuron network is a beautiful example of how emergence occurs. You deploy the cells that have nothing to do with one another—they are completely independent. Then, in less than 24 hours they start to talk to one another—operate more as an ensemble, an organized group, rather than as individuals. Using SLIM we can attest that, although structurally, individual cells do not change much over short time scales, it is their arrangement in space and their collective behavior in time that evolves quickly."

Popescu hopes that his work will help in building machines that can help with health-related questions, including Alzheimer's, memory-related conditions, and aging. The first step is to identify the deterministic behavior of the and discover treatments that enhance this predictable behavior.

"I think we have a set of good tools to both structurally and dynamically tell the difference when cells are functioning in various modes now. The plan is to control the predictable part, such as material transport in neurons or beating in heart cells, and hopefully get the cells to accomplish small tasks," said Popescu.

"Although in this study we have used SLIM to examine , the technology showcased here can be applied to a wide variety of biological systems, this is only the tip of the iceberg," said Mir.

"SLIM technology holds tremendous promise for imaging not only cell-based networks, but also whole slices of brain tissue, where the connections laid down during development are preserved and natural functionalities are expressed," said Martha Gillette, a neuroscientist in the Neurotech Group at the Beckman Institute and collaborator on the study. "Heterogeneities among of functionally specialized brain regions are emerging as key contributors to healthy versus diseased states. The ability to analyze individual within a multicellular micro-environment that preserves the native structural and functional complexity of the brain is a major challenge that can be addressed using SLIM."

SLIM is currently being installed in the Microscopy Suite at the Beckman Institute in order to allow other researchers access to this imaging technique.

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JVK
1 / 5 (1) Mar 25, 2014
RE: "...can help with health-related questions, including Alzheimer's, memory-related conditions, and aging. The first step is to identify the deterministic behavior of the neural cells and discover treatments that enhance this predictable behavior."

How does this research help those with diseases and disorders attributed to mutations? Why isn't the money being spent on research that follows the path of what's been learned from evolutionary theory? Experimental evidence complicates everything. Everyone knows that brain pathology -- like brain development -- is due to beneficial mutations. No wait, only evolutionary theorists know that -- everyone else knows better than that, so... never mind.
RealScience
5 / 5 (1) Mar 28, 2014
How does this research help those with diseases and disorders attributed to mutations? ...
Experimental evidence complicates everything. Everyone knows that brain pathology -- like brain development -- is due to beneficial mutations. No wait, only evolutionary theorists know that -- everyone else knows better than that...


You sounds confused, JVK, so I'll explain it for you.

This research provides a technique for watching and measuring neurons connect into neural networks. It can be applied to see how such networks typically grow, and how the growth differs in various pathologies.

Experimental evidence shows that mutations such as those in FOXP2 (after hominids and the chimpanzee lineage split) are beneficial, while others, such as Fragile-X mutation in the FMR1 gene cause brain pathologies. Experimental evidence thus confirms mainstream thinking that mutations can be either harmful or beneficial. It is only those clinging to failed hypotheses who think otherwise.
JVK
1 / 5 (1) Mar 28, 2014
FoxP2 links ecological adaptation in songbirds to human language development sans any ridiculous theories that involve mutations in any vertebrate species. Didn't you get the memo?

Or is the problem that you think everything that is actually an ecological adaptation must be a mutation? If so, I'm willing to bet you are the idiot minion of an uninformed biology teacher who taught you to believe in a ridiculous theory and ignore biological facts. That would explain why you think I am confused. But thanks for your concern. Now, please examine the facts:

miR-9 and miR-140-5p Target FoxP2 and Are Regulated as a Function of the Social Context of Singing Behavior in Zebra Finches

http://www.jneuro...abstract

RealScience
5 / 5 (1) Mar 28, 2014
Didn't you get the memo?

You apparently didn't get the memo on the evolutionary history of FOXP2. You might want to go back a decade and start catching up with: http://www.ncbi.n...12192408

Or is the problem that you think everything that is actually an ecological adaptation must be a mutation?

Of course not. As I have told you before, I agree that nutrients and epigenetics play important roles in adaptation, and in the short term (up to thousands of generations) their role is more important than mutations. However in the long term (hundreds of thousands to millions of generations), I think that mutations play an important role.

Your mistake is in thinking that a role for nutrition, epigenetics etc. EXCLUDES a role for mutations, and then ignoring experimental evidence that contradicts your thinking so that you fail to see and correct your mistake.
JVK
1 / 5 (1) Mar 28, 2014
Do you that food odors cause mutations in songbirds?

Food rewards modulate the activity of song neurons in Bengalese finches
http://dx.doi.org...jn.12457

Do you think that mutations cause natural selection for vocalizations in some vertebrates that have mutated into other vertebrates with nutrient-dependent pheromone-controlled physiology of reproduction?

Songbird chemosignals: volatile compounds in preen gland secretions vary among individuals, sexes, and populations

http://beheco.oxf...21/3/608

Is there a model in the idiot minion world that suggests that? No, wait -- I just realized, you're don't realize that molecular evolution of FOXP2 did not begin in primates.
RealScience
5 / 5 (1) Mar 28, 2014
Do you that food odors cause mutations in songbirds?

No, I don't think that food odors cause mutations in songbirds.
Do YOU think that food odors cause mutations (DNA sequence changes) in songbirds?

I just realized, you're don't realize that molecular evolution of FOXP2 did not begin in primates.

Then you jumped to yet another mistaken conclusion.

I could jump to a similar conclusion like this:
The article I cited starts with mice, so JVK must think that I think that's where FOXP2 arose.
Therefore JVK must think that mice are primates.
And JVK's link included birds and higher vertebrates in general as having FOXP2. Since JVK knows I read the article, JVK must think the birds are primates too.

See how silly jumping to conclusions is? My guess is that EVEN YOU know the difference between primates and birds. Am I right?
JVK
1 / 5 (1) Mar 28, 2014
All idiot minions who believe what they were taught about mutations and evolution are welcome to respond to the details of cause and effect in my 2012 published work. RealScience has become a RealPain-in-the-ass. There is only one model that incorporates the conserved molecular mechanisms of cause and effect. It excludes any role of mutations and replaces a ridiculous theory with experimental evidence of ecological adaptations.

http://www.socioa...38/20758

Conclusion: "Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000)."

RealScience
5 / 5 (1) Mar 28, 2014
Since your model "excludes any role of mutations", then any role for mutations proves your model wrong. All it takes is one counter example, and there are numerous counter-examples in nature (e.g., sickle-cell alleles) as well as experimental results (e.g., Lenski).

As for "a RealPain-in-the-ass", you are the one who keeps spamming this message board with your anti-mutations pseudo-science that has already been shown to be wrong.

If you cut the insults, and stop ignoring evidence (challenging evidence is part of science, but ignoring it is pseudo-science), we might be able to have a civil discussion about how silly many scientists are to ignore pheromones and underestimate epigenetics.

But as long as you keep posting non-science, I'll keep showing your comments to be wrong.
JVK
1 / 5 (1) Mar 28, 2014
"The initial demonstration that miRNA-related genetic variants can affect disease phenotype was given by Abelson et al. (2005), who found that a mutation in miR-189 binding site of SLITRK1 gene was associated with Tourette's syndrome. Since then, several studies have identified associations between polymorphisms, mainly SNPs, influencing miRNA function and different human disorders, going from PD to multiple forms of cancer (Sethupathy and Collins, 2008)." http://www.fronti...14.00075

For someone who desperately wants mutations to somehow be involved in evolution, your inabilty to cite any current literature that tells what mutation was beneficial and how its benefit was fixed in the organized genome of any species is a pitiful example of your ignorance. Sickle cell hemoglobin and Lenski's experiments provide examples of nutrient-dependent ecological adaptations.
RealScience
5 / 5 (1) Mar 29, 2014
In Lenski the genomes have been SEQUENCED, so we KNOW that there were sequence changes (mutations). And by thawing samples frozen at various points, we get EXPERIMENTAL EVIDENCE that these changes are beneficial and selected FOR.

As for whether these mutations (DNA sequence changes) are nutrient-dependent and pheromone controlled, you have not shown any experimental evidence that they are, and also not offered a detailed molecular explanation of HOW these changes are made under pheromone control.

Furthermore you have not answered why if these sequence changes were nutrient-dependent and pheromone controlled it took tens of thousands of generations before they appeared in just one population. In contrast that timeline fits the classic quasi-random mutations theory.

Stop ignoring experimental evidence. Discard the part of your theory that has been shown to be wrong, and you might actually do something useful again in science.
JVK
1 / 5 (1) Mar 29, 2014
Experimental evidence never comes from studies that only address population genetics.

Only an idiot minion of an ignorant biology teacher who knows nothing about biologically based cause and effect attributes it to beneficial mutations.

Mutations perturb protein folding, which is how they contribute to diseases and disorders in individuals.

The perturbed protein folding in individuals does not benefit the individuals or the species.

Nutrient-dependent pheromone-controlled ecological adaptations benefit individuals which is why they are manifested in every species -- not just E. coli.

You're not very bright, are you? I've told you this so many times that it should have sunk in long before now -- and I've published a series of journal articles since 1996 on molecular epigenetics that have helped the biological facts sink into everyone except the most uninformed / ridiculous theorists. Find some intelligent people to discuss facts with, and quit making a fool of yourself here.
RealScience
5 / 5 (1) Mar 29, 2014
Experimental evidence never comes from studies that only address population genetics.

Wrong. Experimental evidence on the nature of population genetics can come from studies that only addressed population genetics. For example, experiments on population genetics, dating back to Mendel, show that traits are inherited.

Furthermore Lenski also sequenced the bacteria and found out what changes, were responsible for the ability to use citrate, and how, on a molecular level, they enabled that use.

Find some intelligent people to discuss facts with...

So you are admitting that you are NOT an intelligent person?
No wonder discussing facts with you has so little impact on your lack of comprehension...
JVK
1 / 5 (1) Mar 29, 2014
"... taken together these observations make the dynamic equilibrium of the noncanonical DNA structure an attractive target for small molecule control of gene expression." -- try to find out where this came from. I'm done providing links to anonymous fools and idiot minions who have no understanding of biologically based cause and effect.

What I have detailed in my forthcoming review is small molecule control of gene expression.

I shut off further notifications on this thread. If anyone has any intelligent comments to add, you can comment on my blog posts at Pheromones.com under the "Science" section.
anonymous_9001
5 / 5 (2) Mar 29, 2014
What I have detailed in my forthcoming review is small molecule control of gene expression.


Key word: EXPRESSION

Changes in expression don't have anything to do with sequence changes. Nobody is challenging your model of expression, but your model has yet to account for or describe how SEQUENCE changes occur.
RealScience
5 / 5 (1) Mar 29, 2014
*9001 - JVK doesn't understand the difference.

I even explained it to him:

Gene expression is reading a gene, so reading 'pray' three times instead of reading it twice would be a change in how often it is expressed.

Changing a gene's nucleotide sequence changes the way a gene is spelled, like changing the 'r' to an 'l' so that 'pray' gets changed to 'play'.

So the difference between the difference between changing a gene's nucleotide sequence and changing how often it is expressed is the same as the difference between changing 'pray' to 'play' and reading 'pray' three times instead of twice.

But in spite of the difference being so simple and basic, JVK ADMITS that he doesn't understand the difference between changing a gene's nucleotide sequence and changing how often a gene is expressed without using 'quantum physics'.

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