Tag Archives: brain cells

The roles mathematics and light play in cellular communication

These are two entirely different types of research but taken together they help build a picture about how the cells in our bodies function.

Cells and light

An April 30, 2018 news item on phys.org describes work on controlling biology with light,

Over the past five years, University of Chicago chemist Bozhi Tian has been figuring out how to control biology with light.

A longterm science goal is devices to serve as the interface between researcher and body—both as a way to understand how cells talk among each other and within themselves, and eventually, as a treatment for brain or nervous system disorders [emphasis mine] by stimulating nerves to fire or limbs to move. Silicon—a versatile, biocompatible material used in both solar panels and surgical implants—is a natural choice.

In a paper published April 30 in Nature Biomedical Engineering, Tian’s team laid out a system of design principles for working with silicon to control biology at three levels—from individual organelles inside cells to tissues to entire limbs. The group has demonstrated each in cells or mice models, including the first time anyone has used light to control behavior without genetic modification.

“We want this to serve as a map, where you can decide which problem you would like to study and immediately find the right material and method to address it,” said Tian, an assistant professor in the Department of Chemistry.

Researchers built this thin layer of silicon lace to modulate neural signals when activated by light. Courtesy of Yuanwen Jiang and Bozhi Tian

An April 30, 2018 University of Chicago news release by Louise Lerner, which originated the news item, describes the work in greater detail,

The scientists’ map lays out best methods to craft silicon devices depending on both the intended task and the scale—ranging from inside a cell to a whole animal.

For example, to affect individual brain cells, silicon can be crafted to respond to light by emitting a tiny ionic current, which encourages neurons to fire. But in order to stimulate limbs, scientists need a system whose signals can travel farther and are stronger—such as a gold-coated silicon material in which light triggers a chemical reaction.

The mechanical properties of the implant are important, too. Say researchers would like to work with a larger piece of the brain, like the cortex, to control motor movement. The brain is a soft, squishy substance, so they’ll need a material that’s similarly soft and flexible, but can bind tightly against the surface. They’d want thin and lacy silicon, say the design principles.

The team favors this method because it doesn’t require genetic modification or a power supply wired in, since the silicon can be fashioned into what are essentially tiny solar panels. (Many other forms of monitoring or interacting with the brain need to have a power supply, and keeping a wire running into a patient is an infection risk.)

They tested the concept in mice and found they could stimulate limb movements by shining light on brain implants. Previous research tested the concept in neurons.

“We don’t have answers to a number of intrinsic questions about biology, such as whether individual mitochondria communicate remotely through bioelectric signals,” said Yuanwen Jiang, the first author on the paper, then a graduate student at UChicago and now a postdoctoral researcher at Stanford. “This set of tools could address such questions as well as pointing the way to potential solutions for nervous system disorders.”

Other UChicago authors were Assoc. Profs. Chin-Tu Chen and Chien-Min Kao, Asst. Prof Xiaoyang, postdoctoral researchers Jaeseok Yi, Yin Fang, Xiang Gao, Jiping Yue, Hsiu-Ming Tsai, Bing Liu and Yin Fang, graduate students Kelliann Koehler, Vishnu Nair, and Edward Sudzilovsky, and undergraduate student George Freyermuth.

Other researchers on the paper hailed from Northwestern University, the University of Illinois at Chicago and Hong Kong Polytechnic University.

The researchers have also made this video illustrating their work,

via Gfycat Tiny silicon nanowires (in blue), activated by light, trigger activity in neurons. (Courtesy Yuanwen Jiang and Bozhi Tian)

Here’s a link to and a citation for the paper,

Rational design of silicon structures for optically controlled multiscale biointerfaces by Yuanwen Jiang, Xiaojian Li, Bing Liu, Jaeseok Yi, Yin Fang, Fengyuan Shi, Xiang Gao, Edward Sudzilovsky, Ramya Parameswaran, Kelliann Koehler, Vishnu Nair, Jiping Yue, KuangHua Guo, Yin Fang, Hsiu-Ming Tsai, George Freyermuth, Raymond C. S. Wong, Chien-Min Kao, Chin-Tu Chen, Alan W. Nicholls, Xiaoyang Wu, Gordon M. G. Shepherd, & Bozhi Tian. Nature Biomedical Engineering (2018) doi:10.1038/s41551-018-0230-1 Published: 30 April 2018

This paper is behind a paywall.

Mathematics and how living cells ‘think’

This May 2, 2018 Queensland University of Technology (QUT; Australia) press release is also on EurekAlert,

How does the ‘brain’ of a living cell work, allowing an organism to function and thrive in changing and unfavourable environments?

Queensland University of Technology (QUT) researcher Dr Robyn Araujo has developed new mathematics to solve a longstanding mystery of how the incredibly complex biological networks within cells can adapt and reset themselves after exposure to a new stimulus.

Her findings, published in Nature Communications, provide a new level of understanding of cellular communication and cellular ‘cognition’, and have potential application in a variety of areas, including new targeted cancer therapies and drug resistance.

Dr Araujo, a lecturer in applied and computational mathematics in QUT’s Science and Engineering Faculty, said that while we know a great deal about gene sequences, we have had extremely limited insight into how the proteins encoded by these genes work together as an integrated network – until now.

“Proteins form unfathomably complex networks of chemical reactions that allow cells to communicate and to ‘think’ – essentially giving the cell a ‘cognitive’ ability, or a ‘brain’,” she said. “It has been a longstanding mystery in science how this cellular ‘brain’ works.

“We could never hope to measure the full complexity of cellular networks – the networks are simply too large and interconnected and their component proteins are too variable.

“But mathematics provides a tool that allows us to explore how these networks might be constructed in order to perform as they do.

“My research is giving us a new way to look at unravelling network complexity in nature.”

Dr Araujo’s work has focused on the widely observed function called perfect adaptation – the ability of a network to reset itself after it has been exposed to a new stimulus.

“An example of perfect adaptation is our sense of smell,” she said. “When exposed to an odour we will smell it initially but after a while it seems to us that the odour has disappeared, even though the chemical, the stimulus, is still present.

“Our sense of smell has exhibited perfect adaptation. This process allows it to remain sensitive to further changes in our environment so that we can detect both very feint and very strong odours.

“This kind of adaptation is essentially what takes place inside living cells all the time. Cells are exposed to signals – hormones, growth factors, and other chemicals – and their proteins will tend to react and respond initially, but then settle down to pre-stimulus levels of activity even though the stimulus is still there.

“I studied all the possible ways a network can be constructed and found that to be capable of this perfect adaptation in a robust way, a network has to satisfy an extremely rigid set of mathematical principles. There are a surprisingly limited number of ways a network could be constructed to perform perfect adaptation.

“Essentially we are now discovering the needles in the haystack in terms of the network constructions that can actually exist in nature.

“It is early days, but this opens the door to being able to modify cell networks with drugs and do it in a more robust and rigorous way. Cancer therapy is a potential area of application, and insights into how proteins work at a cellular level is key.”

Dr Araujo said the published study was the result of more than “five years of relentless effort to solve this incredibly deep mathematical problem”. She began research in this field while at George Mason University in Virginia in the US.

Her mentor at the university’s College of Science and co-author of the Nature Communications paper, Professor Lance Liotta, said the “amazing and surprising” outcome of Dr Araujo’s study is applicable to any living organism or biochemical network of any size.

“The study is a wonderful example of how mathematics can have a profound impact on society and Dr Araujo’s results will provide a set of completely fresh approaches for scientists in a variety of fields,” he said.

“For example, in strategies to overcome cancer drug resistance – why do tumours frequently adapt and grow back after treatment?

“It could also help understanding of how our hormone system, our immune defences, perfectly adapt to frequent challenges and keep us well, and it has future implications for creating new hypotheses about drug addiction and brain neuron signalling adaptation.”

Hre’s a link to and a citation for the paper,

The topological requirements for robust perfect adaptation in networks of any size by Robyn P. Araujo & Lance A. Liotta. Nature Communicationsvolume 9, Article number: 1757 (2018) doi:10.1038/s41467-018-04151-6 Published: 01 May 2018

This paper is open access.

Getting your brain cells to glow in the dark

The extraordinary effort to colonize our brains continues apace with a new sensor from Vanderbilt University. From an Oct. 27, 2016 news item on ScienceDaily,

A new kind of bioluminescent sensor causes individual brain cells to imitate fireflies and glow in the dark.

The probe, which was developed by a team of Vanderbilt scientists, is a genetically modified form of luciferase, the enzyme that a number of other species including fireflies use to produce light. …

The scientists created the technique as a new and improved method for tracking the interactions within large neural networks in the brain.

“For a long time neuroscientists relied on electrical techniques for recording the activity of neurons. These are very good at monitoring individual neurons but are limited to small numbers of neurons. The new wave is to use optical techniques to record the activity of hundreds of neurons at the same time,” said Carl Johnson, Stevenson Professor of Biological Sciences, who headed the effort.

Individual neuron glowing with bioluminescent light produced by a new genetically engineered sensor. (Johnson Lab / Vanderbilt University)

Individual neuron glowing with bioluminescent light produced by a new genetically engineered sensor. (Johnson Lab / Vanderbilt University)

An Oct. 27, 2016 Vanderbilt University news release (also on EurekAlert) by David Salisbury, which originated the news item, explains the work in more detail,

“Most of the efforts in optical recording use fluorescence, but this requires a strong external light source which can cause the tissue to heat up and can interfere with some biological processes, particularly those that are light sensitive,” he [Carl Johnson] said.

Based on their research on bioluminescence in “a scummy little organism, the green alga Chlamydomonas, that nobody cares much about” Johnson and his colleagues realized that if they could combine luminescence with optogenetics – a new biological technique that uses light to control cells, particularly neurons, in living tissue – they could create a powerful new tool for studying brain activity.

“There is an inherent conflict between fluorescent techniques and optogenetics. The light required to produce the fluorescence interferes with the light required to control the cells,” said Johnson. “Luminescence, on the other hand, works in the dark!”

Johnson and his collaborators – Associate Professor Donna Webb, Research Assistant Professor Shuqun Shi, post-doctoral student Jie Yang and doctoral student Derrick Cumberbatch in biological sciences and Professor Danny Winder and postdoctoral student Samuel Centanni in molecular physiology and biophysics – genetically modified a type of luciferase obtained from a luminescent species of shrimp so that it would light up when exposed to calcium ions. Then they hijacked a virus that infects neurons and attached it to their sensor molecule so that the sensors are inserted into the cell interior.

The researchers picked calcium ions because they are involved in neuron activation. Although calcium levels are high in the surrounding area, normally they are very low inside the neurons. However, the internal calcium level spikes briefly when a neuron receives an impulse from one of its neighbors.

They tested their new calcium sensor with one of the optogenetic probes (channelrhodopsin) that causes the calcium ion channels in the neuron’s outer membrane to open, flooding the cell with calcium. Using neurons grown in culture they found that the luminescent enzyme reacted visibly to the influx of calcium produced when the probe was stimulated by brief light flashes of visible light.

To determine how well their sensor works with larger numbers of neurons, they inserted it into brain slices from the mouse hippocampus that contain thousands of neurons. In this case they flooded the slices with an increased concentration of potassium ions, which causes the cell’s ion channels to open. Again, they found that the sensor responded to the variations in calcium concentrations by brightening and dimming.

“We’ve shown that the approach works,” Johnson said. “Now we have to determine how sensitive it is. We have some indications that it is sensitive enough to detect the firing of individual neurons, but we have to run more tests to determine if it actually has this capability.”

Here’s a link to and a citation for the paper,

Coupling optogenetic stimulation with NanoLuc-based luminescence (BRET) Ca++ sensing by Jie Yang, Derrick Cumberbatch, Samuel Centanni, Shu-qun Shi, Danny Winder, Donna Webb, & Carl Hirschie Johnson. Nature Communications 7, Article number: 13268 (2016)  doi:10.1038/ncomms13268 Published online: 27 October 2016

This paper is open access.

A bionic hybrid neurochip from the University of Calgary (Canada)

The University of Calgary is publishing some very exciting work these days as can be seen in my Sept. 21, 2016 posting about quantum teleportation. Today, the university announced this via an Oct. 26, 2016 news item on Nanowerk (Note: A link has been removed),

Brain functions are controlled by millions of brain cells. However, in order to understand how the brain controls functions, such as simple reflexes or learning and memory, we must be able to record the activity of large networks and groups of neurons. Conventional methods have allowed scientists to record the activity of neurons for minutes, but a new technology, developed by University of Calgary researchers, known as a bionic hybrid neuro chip, is able to record activity in animal brain cells for weeks at a much higher resolution. The technological advancement was published in the journal Scientific Reports(“A novel bio-mimicking, planar nano-edge microelectrode enables enhanced long-term neural recording”).

There’s more from an Oct. 26, 2016 University of Calgary news release on EurekAlert, which originated the news item,

“These chips are 15 times more sensitive than conventional neuro chips,” says Naweed Syed, PhD, scientific director of the University of Calgary, Cumming School of Medicine’s Alberta Children’s Hospital Research Institute, member of the Hotchkiss Brain Institute and senior author on the study. “This allows brain cell signals to be amplified more easily and to see real time recordings of brain cell activity at a resolution that has never been achieved before.”

The development of this technology will allow researchers to investigate and understand in greater depth, in animal models, the origins of neurological diseases and conditions such as epilepsy, as well as other cognitive functions such as learning and memory.

“Recording this activity over a long period of time allows you to see changes that occur over time, in the activity itself,” says Pierre Wijdenes, a PhD student in the Biomedical Engineering Graduate Program and the study’s first author. “This helps to understand why certain neurons form connections with each other and why others won’t.”

The cross-faculty team created the chip to mimic the natural biological contact between brain cells, essentially tricking the brain cells into believing that they are connecting with other brain cells. As a result, the cells immediately connect with the chip, thereby allowing researchers to view and record the two-way communication that would go on between two normal functioning brain cells.

“We simulated what mother-nature does in nature and provided brain cells with an environment where they feel as if they are at home,” says Syed. “This has allowed us to increase the sensitivity of our readings and help neurons build a long-term relationship with our electronic chip.”

While the chip is currently used to analyze animal brain cells, this increased resolution and the ability to make long-term recordings is bringing the technology one step closer to being effective in the recording of human brain cell activity.

“Human brain cell signals are smaller and therefore require more sensitive electronic tools to be designed to pick up the signals,” says Colin Dalton, Adjunct Professor in the Department of Electrical and Computer Engineering at the Schulich School of Engineering and a co-author on this study. Dalton is also the Facility Manager of the University of Calgary’s Advanced Micro/nanosystems Integration Facility (AMIF), where the chips were designed and fabricated.

Researchers hope the technology will one day be used as a tool to bring personalized therapeutic options to patients facing neurological disease.

Here’s a link to and a citation for the paper,

A novel bio-mimicking, planar nano-edge microelectrode enables enhanced long-term neural recording by Pierre Wijdenes, Hasan Ali, Ryden Armstrong, Wali Zaidi, Colin Dalton & Naweed I. Syed. Scientific Reports 6, Article number: 34553 (2016) doi:10.1038/srep34553
Published online: 12 October 2016

This paper is  open access.

Listening to an individual brain cell using a carbon nanotube ‘harpoon’

Apparently, the prime motivation for listening to individual neurons or brain cells is to “better understand the computational complexity of the brain,” according to a June 20,  2013 news item on Azonano,

The new brain cell spear is a millimeter long, only a few nanometers wide and harnesses the superior electromechanical properties of carbon nanotubes to capture electrical signals from individual neurons.

“To our knowledge, this is the first time scientists have used carbon nanotubes to record signals from individual neurons, what we call intracellular recordings, in brain slices or intact brains of vertebrates,” said Bruce Donald, a professor of computer science and biochemistry at Duke University who helped developed the probe.

The June 19, 2013 Duke University news release by Ashley Yeager, which originated the news item, provides some insight into the current state of the art and how this new technique is an improvement,

Currently, they use two main types of electrodes, metal and glass, to record signals from brain cells. Metal electrodes record spikes from a population of brain cells and work well in live animals. Glass electrodes also measure spikes, as well as the computations individual cells perform, but are delicate and break easily.”The new carbon nanotubes combine the best features of both metal and glass electrodes. They record well both inside and outside brain cells, and they are quite flexible. Because they won’t shatter, scientists could use them to record signals from individual brain cells of live animals,” said Duke neurobiologist Michael Platt, who was not involved in the study.

This is not the first time researchers have tried to use carbon nanotubes for this purpose, from the news release,

In the past, other scientists have experimented with carbon nanotube probes. But the electrodes were thick, causing tissue damage, or they were short, limiting how far they could penetrate into brain tissue. They could not probe inside individual neurons.

To change this, Donald began working on a harpoon-like carbon-nanotube probe with Duke neurobiologist Richard Mooney five years ago. The two met during their first year at Yale in the 1976, kept in touch throughout graduate school and began meeting to talk about their research after they both came to Duke.

Mooney told Donald about his work recording brain signals from live zebra finches and mice. The work was challenging, he said, because the probes and machinery to do the studies were large and bulky on the small head of a mouse or bird.

With Donald’s expertise in nanotechnology and robotics and Mooney’s in neurobiology, the two thought they could work together to shrink the machinery and improve the probes with nano-materials.

To make the probe, graduate student Inho Yoon and Duke physicist Gleb Finkelstein used the tip of an electrochemically sharpened tungsten wire as the base and extended it with self-entangled multi-wall carbon nanotubes to create a millimeter-long rod. The scientists then sharpened the nanotubes into a tiny harpoon using a focused ion beam at North Carolina State University.

Yoon then took the nano-harpoon to Mooney’s lab and jabbed it into slices of mouse brain tissue and then into the brains of anesthetized mice. The results show that the probe transmits brain signals as well as, and sometimes better than, conventional glass electrodes and is less likely to break off in the tissue. The new probe also penetrates individual neurons, recording the signals of a single cell rather than the nearest population of them.

Based on the results, the team has applied for a patent on the nano-harpoon.  Platt said scientists might use the probes in a range of applications, from basic science to human brain-computer interfaces and brain prostheses.

Donald said the new probe makes advances in those directions, but the insulation layers, electrical recording abilities and geometry of the device still need improvement.

The research paper is available in the open access journal PLoS ONE,

Intracellular Neural Recording with Pure Carbon Nanotube Probes by Inho Yoon, Kosuke Hamaguchi, Ivan V. Borzenets, Gleb Finkelstein, Richard Mooney, and Bruce R. Donald. 2013. PLOS ONE. DOI: 10.1371/journal.pone.0065715

As for calling this a ‘harpoon’, these carbon nanotube probes really do resemble harpoons,

This image, taken with a scanning electron microscope, shows a new brain electrode that tapers to a point as thick as a single carbon nanotube. Credit: Inho Yoon and Bruce Donald, Duke.  [downloaded from http://today.duke.edu/2013/06/brainharpoon]

This image, taken with a scanning electron microscope, shows a new brain electrode that tapers to a point as thick as a single carbon nanotube. Credit: Inho Yoon and Bruce Donald, Duke. [downloaded from http://today.duke.edu/2013/06/brainharpoon]

You can compare it to this harpoon from The Specialists Prop House, Traditional harpoon page,

[downloaded from The Specialists Prop House, Traditional harpoon page, http://thespecialistsltd.com/traditional-harpoon]

[downloaded from The Specialists Prop House, Traditional harpoon page, http://thespecialistsltd.com/traditional-harpoon]

I have written about some of the neuroscience work coming out of Duke University in the past, e.g., my March 4, 2013 posting about Miguel Nicolelis’ work on brain-to-brain communication.