The technique operates on the idea lipids in the bilayer of a cell’s plasma membrane block visible light. This is why the brain is normally not transparent. Removing these lipids but still keeping the other parts of the cell and its environment intact would render the brain “see-through” and allow for much easier imaging of large pieces of brain tissue, if not the whole brain at once. This idea is carried out by taking the brain and infusing it with acrylamide, which binds proteins, nucleic acids and other molecules, then heating the tissue to form a mesh that holds the tissue together. The brain is then treated with SDS detergent to remove the light-blocking lipids resulting in a stable brain-hydrogel hybrid. From here the transparent tissue can be fluorescently labeled for certain cells and analyzed. Through the whole process there is less than 10% protein loss in the brain tissue compared to around 41% for other current methods. This is an amazing improvement!

Example of brain image produced by CLARITY from neurons in an intact mouse hippocampus. (http://med.stanford.edu/ism/2013/downloads/CLARITY/CLARITY_stained.jpg)

Until now it has been common practice to use histology to analyze brain tissue in a study. This method involves slicing a section of brain up into extremely small pieces and dying certain slices for various cells and molecules of interest. If a researcher wants any idea of the bigger picture he/she must reconstruct the brain from these small slices. With the CLARITY technique slicing the brain up is no longer necessary. Never before has it been so easy to view full brains, or sections of brain, down to the cellular and molecular level. It is now easy to follow the trajectory of a single neuron through the whole brain.

The development of this brain imaging method comes at a time when much money is being put into uncovering the complete biological workings of the human brain. President Obama has announced his BRAIN initiative and the US National Institute of Health is working on its Human Connectome Project. CLARITY has big potential use for these initiatives and as the technique is refined it seems that it will have a large role in uncovering more about the elusive question of how our brains really work.

For more information on CLARITY view this video on Nature’s website:

http://www.nature.com/news/see-through-brains-clarify-connections-1.12768

- J. Daniel Bireley

Sources:

Structural and molecular interrogation of intact biological systems – Nature

See Through Brains Clarify Connections – Nature

At Brookhaven, researchers combined light-activated proteins that stimulate specific brain cells, a technique known as optogenetics, with positron emission tomography (PET) to observe the effects of stimulation throughout the entire brain. Their paper in the Journal of Neuroscience describes this method, which will allow researchers to map exactly which neurological pathways are activated or deactivated downstream by stimulation in specific brain areas. Hopefully, following these pathways will enable researchers to correlate the brain activity with observed behaviors or certain symptoms of disease.

Three markers on the head of a mouse enable the AwakeSPECT system to obtain functional images of the brain of a conscious mouse as it moves around. (Credit: Image courtesy of DOE/Thomas Jefferson National Accelerator Facility)

Scientists at Oak Ridge used dynamic imaging in mice to examine changes in brain chemistry caused by disease or application of a drug. They hope this research tool will be used to develop better disease diagnostics as well as better treatments. The newest aspect of this study, however, is that unlike most nuclear imaging studies where laboratory mice are drugged or kept in place so that their brains can be studied, the new technique allows for moving subjects. The researchers from Jefferson Lab, Oak Ridge, Johns Hopkins and Maryland used their new system to obtain functional images of the brains of conscious mice that were free to move. The system, called AwakeSPECT (Awake Single-Photon Emission Computed Tomography),  was then used to examine the effects of anesthesia on the action of a dopamine transporter in the mouse brain for the first time. These types of dopamine transporter imaging compounds are used for Alzheimer’s, dementia and Parkinson’s disease studies. The technique entails injection of a radionuclide, which gathers in targeted areas of the brain. The radionuclide emits gamma rays that are detected in separate scans from many different angles, all of which are combined by an algorithm to produce a three-dimensional image.

Martin Pomper led a group of researchers at Johns Hopkins Medical School to conduct the first mouse imaging studies with the new system. Their study showed that AwakeSPECT can be used to obtain detailed, functional images of the brain in a conscious mouse that was able to move freely around in an enclosed space. “We’ve shown the technology works. Now, you just have to make it a tool that more people will readily use” says Jefferson Lab’s Drew Weisenberger, who led the multi-institutional collaboration that created the novel technique.

One area of active research that would benefit from such imaging techniques is the question of how animals orient themselves in space. Existing experiments have all looked at how animals move around in two-dimensional settings and they have made the important discovery of place cells, neurons located in the hippocampus responsive to spatial orientation. Populations of place cells working together can produce full representations of an animal’s environment, the only problem being that in the real world animals have to navigate in three dimensions unlike the laboratory experiments. That’s why Dr. Nachum Ulanovsky of the Weizmann’s Institute’s Neurobiology Department chose to study the Egyptian fruit bat to look at how three-dimensional space is perceived in mammalian brains for the first time. His research used a miniaturized neural-telemetry system developed especially for this task, which enabled the measurement of single brain cells during flight. The activity of the  hippocampal neurons in the bats’ brains showed that the representation of three-dimensional space is just like in two dimensions: each place cell is responsible for identifying a particular spatial area in space and sends an electrical signal when the bat is located in that area. The population of place cells provides full coverage of the particular area, say a cave, left, right, forward, back, up and down.

These results give new insights into navigation, spatial memory and spatial perception, all basic functions of the mammalian brain. The study’s success is due to the development of the technology that allowed looking into the brain of a flying animal. Single cell measurement is only the first step, looking at neural circuits can reveal much more about how these place cell representations are then used in conjunction with other brain areas resulting in the behavior we see. Development of new brain imaging techniques continues to provide a more complete understanding of basic human and animal behaviors, and hopefully one day will lead to a full understanding of the human brain.

-Leo Shapiro

Sources:

Lights, Chemistry, Action: New Method for Mapping Brain Activity – ScienceDaily

System Provides Clear Brain Scans of Awake, Unrestrained Mice – ScienceDaily

Neural Activity in Bats Measured In-Flight – ScienceDaily

Inside of you there are 10¹³ human cells and 10¹⁴ bacteria cells.

In other words, for every one cell of you there are ten that are not you…Wait, what? The first question this recent discovery may fuel is a stumbled WHAT? But lets digress for a moment and ask, why?

The initial visceral curiosity here arises from one major assumption that the Western psyche makes about the world, that I am an individual and am derived in my current form from the process of competitive selection. The reality however, is that none of us are individuals and we are all derived not just from natural selection, but from collaborative efforts between tens of thousands of species of organisms acting in symphony to produce the emergent concert that is: us. That may be a bit heavy. Let me explain.

Again, there are ten times the number of bacterial cells throughout the human body and they are mostly centralized to the digestive tract. This internal ecosystem of microbial flora is referred to as one’s “microbiome”. Each person’s microbiome is different, in a similar way that we are all different. The distribution of species in the digestive tract reflects one’s life experiences, adventures and location of upbringing. For example, the typical gut flora of a person raised in the United States has more bacteria specialized in processing fat and protein. This is in part why people immigrating to the United States often have problems with gaining weight in the first few years, because their microbial counterparts are ill-equipped at handling the amount of fat in American foods.

Another astonishing example of this “microbial footprinting” is in the microbiomes of people who have lived their entire lives in Japan where seaweed is a dietary staple. Throughout the world the microbe Bacteroides plebeius has been observed in the gut of various people. Curiously however, the B. plebeius microbe in some Japanese people has incorporated a gene passed to it, via horizontal gene transfer, from Zobellia galactanivorans, a marine bacterium. The gene in the Japanese form of B. plebeius expresses enzymes specializing in the degradation of certain polysaccharides found in seaweed. Implications for the exhausted “Nature vs. Nurture” debate abound, these findings are Earth-shattering in more ways than the hands can hold. Oh, by the way, this doesn’t stop at digestion.

Bacteria Are Everywhere in the Human Body

The real sexy aspect of this new vein of research is the implications for the behavioral sciences. In 2011, a series of papers came out linking a lack of adequate gut microbial populations to an anxiety disorder. Researchers raised a brood of mice in a germ-free environment, i.e. from birth they had little to no exposure to the typical microbial populations they may encounter, and the results were a bit unsettling. The researchers noted significant defects in the development of the Amygdala which subsequently showed in behavioral studies that the sterile mice had major issues with anxiety and depression. In another similar study, it was shown that feeding normal mice probiotic bacteria significantly reduces depression-like behavior.

Right now, this is the biggest emerging area of research worldwide. Finally, the notion that we are not individuals, but emergent structures of ecosystems is taking hold. The result of such novel understanding is entirely uninformed and preemptive attempts at targeting this new world to cure and change. Currently, probiotic medicines are starting to crop up, each of which will soon be shown to have more “side effects” than efficacy in the expected. When we make a discovery, we immediately assume we understand how to manipulate the system, unaware of how the vastly complex structures we are changing. We are always confidently overzealous. These recent discoveries are awesome, they really are, but I want to stress that we cannot let our zeal overtake us. This time around, we must admit a lack of understanding and re-realize the feeling of awe. Again, upwards of 40,000 different species of bacteria, right inside of you, are talking to one another; buffering carcinogens and reward hormones, digesting cellulose, fermenting, interacting in ways we really will never know although they may be helping “us”!

“We” would not be alive if it were not for our microbial brethren. Let me pose this question: Is taking the step to understand this internal ecosystem the next step in consciousness. Until now, we have had a very elementary understanding of who we are and why we are who we are. Is this the next step?

- Jesse Bryant

Animals in a microbial world, a new imperative for the life sciences – McFall-Ngai et al. 2012 PNAS

Mood and gut feelings – Forsythe et al. 2009 Elsevier

An ecological and evolutionary perspective on human-microbe mutualism and disease – Dethlefsen et al. 2007 Nature

At his State of the Union address nearly two months ago, President Obama announced plans for the Brain Activity Map (BAM) project (see The Nerve blog Part 1 and Part 2), a billion-dollar ten-year research initiative to gain a better understanding of the brain and to provide deeper insights into diseases like Alzheimer Disease, Parkinson Disease, and Autism Spectrum Disorder.

On Tuesday, April 2^nd, the President announced that he plans to include the BAM project – now termed the BRAIN (Brain Research through Advancing Innovative Neurotechnologies) Initiative – in his 2014 budget proposal. The director of the NIH, Dr. Francis Collins, notes that one of the major goals of the project is to simultaneously sample from many neurons in real-time. Although existing technology can measure the activities of single neurons and of brain regions, it cannot measure those of circuits. Because existing technology has not yet advanced to a level that allows such complex analysis, the BRAIN initiative will be initially funded $100 million for the year of 2014 to develop and advance neuroscience technologies. Yearly negotiations will take place to determine future funding.

Over the next several months, 14 leading neuroscientists from Stanford, CIT, Harvard, Brown, Princeton, and Brandeis will serve on the advisory board (also called the “dream team” or the “brain trust”) to refine the project’s immediate and long-term goals. They will need to decide which research areas are of high priority, which projects require more funding, and which technologies need to be developed and employed. Additionally, President Obama has required a study to explore the ethical, societal, and legal problems associated with the project’s advances in neuroscience.

Dr. Francis Collins and President Obama on Tuesday, April 4th at the White House

Although $100 million may not be sufficient to transform neuroscience, it may “help get this project off the ground,” as President Obama says, and forge a new path for advancing neuroscience. In fact, Francis Collins notes that the Human Genome project was only funded $28 million for its first year. Further, private organizations including the Allen Institute for Brain Science, the Salk Institute for Biological Studies, the Howard Hughes Medical Institute, and the Kavli Foundation have already committed $158 million.

Just as genetics research had been underway before the Human Genome Project, neuroscience research has been going on long before the announcement of the BAM project or the BRAIN initiative. Hopefully, this investment in neuroscience research will do for neuroscience the same that the Human Genome Project did for genetics: provide a plan considering the state of current research, speed up the process of improving the state of knowledge, bring more money into the economy than funded, recruit additional experts to foster an interdisciplinary effort, and capture the interest of the general public. The BRAIN Initiative should provide a goal-oriented long-term focus and allow the coordination and collaboration of neuroscientists in advancing biology, health, medicine, and society.

“Of course, none of this will be easy. If it was, we would already know everything there was about how the brain works, and presumably my life would be simpler here. It could explain all kinds of things that go on in Washington.” – President Obama

-Margaret McGuinness

Sources:

Eve Marder joins Obama neuroscience ‘brain trust’ – BrandeisNOW

Obama outlines private-public project to study the brain – Los Angeles Times

Neuroscience: Making connections – Nature

Obama to Unveil Initiative to Map the Human Brain – New York Times

BRAIN Initiative – NIH

A Brief History of the Human Genome Project – NIH NHGRI

Researchers Question Obama’s Motives for Brain Initiative – NPR: Morning Edition

President Obama Calls For A ‘BRAIN Initiative’ – NPR: Talk of the Nation

BRAIN Initiative Challenges Researchers to Unlock Mysteries of Human Mind – The White House Blog

Fact Sheet: BRAIN Initiative – The White House: Statements and Releases

“Man had always assumed that he was more intelligent than dolphins because he had achieved so much — the wheel, New York, wars and so on — whilst all the dolphins had ever done was muck about in the water having a good time. But conversely, the dolphins had always believed that they were far more intelligent than man — for precisely the same reasons….In fact there was only one species on the planet more intelligent than dolphins, and they spent a lot of their time in behavioural research laboratories running round inside wheels and conducting frighteningly elegant and subtle experiments on man. The fact that once again man completely misinterpreted this relationship was entirely according to these creatures’ plans.” – Douglas Adams, The Hitchhiker’s Guide to the Galaxy

As tempting as it may be to believe the science fiction version of the intelligence rankings, real-life science has spoken and suggests (much to my displeasure) that humans may actually be the highest on the intelligence scale.

Glia are non-neuronal cells found in the brain mainly described as performing “housekeeping” functions, for example, providing structural support to neurons, and providing them with nutrients. Astrocytes are a specific type of glia, and as one might hypothesize, they are bigger in humans than in mice. Was this just a consequence of humans having more complex brains, or do these astrocytes have different functions in humans beyond the basic housekeeping functions? To test this, scientists grafted human astrocyte progenitor cells into developing mouse brains to create chimeric mice.

Human astrocyte (green) and mouse astrocyte (red)

The human astrocytes that matured successfully matured as human cells; characteristics such as their size were unaffected by being in a mouse environment. But they did not remain completely foreign – they successfully formed electrical connections with the mouse cells. Their differing cellular properties were thus propagated into the mouse neural networks. Of particular interest is the hippocampus, the brain region important for learning and memory. Chimeric hippocampal slices had a higher level of baseline excitatory activity, and long-term potentiation (LTP), or synapse strengthening, was much greater. At the molecular level, this can be explained because the human cells express higher levels of a protein that promotes an increased number of glutamate receptors at the synapse.

There were also clear differences in the behavior of chimeric mice. Experiments were performed to test learning and memory abilities to corroborate the cellular results observed in the hippocampus. A classic fear conditioning experiment involves pairing a tone with a foot shock; mice learn to associate the two and exhibit freezing behavior after hearing a tone. Chimeras learned the association after only one tone/shock pairing. The learning persisted for several days, during which time control animals did not learn the initial association. The experiment was repeated as context fear conditioning, meaning that the mice were placed in different chambers that had varying floors and odors. Chimeric mice were able to differentiate between chambers significantly better than their control counterparts. In other learning and memory tasks, these mice learned their way through mazes faster and were better at familiar object recognition in novel contexts.

The results of this study show that glial cells have much more function beyond their basic housekeeping properties. A single cell graft manipulation was enough to significantly improve mouse performance on learning and memory tasks. Complexity of these cells has evolved with the brain, and this provides important new insight on how exactly this complexity has come to be. Future experiments could involve grafting chimpanzee or macaque glia, any differences observed could be key in outlining how our processing abilities evolved from our monkey fathers (I additionally support research with dolphin glia grafts, keeping on the theme of the three most intelligent species). Unfortunately, without the higher processing abilities made possible by human cells, mice likely cannot achieve the tasks and level of status they exhibit in the science fiction. It seems as though man has indeed correctly interpreted his relationship with the mouse.

So long, and thanks for all the fish.

-Reena Clements

References:

Human Brain Cells Boost Mouse Memory – ScienceNOW

Forebrain Engraftment by Human Glial Progenitor Cells Enhances Synaptic Plasticity and Learning in Adult Mice – Cell Stem Cell

In the past 150 years it has been noted that the onset of depression is occurring at higher rates and at younger ages that ever before. This data could be the result of factors including an increase in patients coming forward to be diagnosed, improved diagnoses, or simply better record keeping. Whatever the reason, it is estimated that 15 to 20% of the population is experiencing symptoms of major depression at any given time, with a greater occurrence in women than in men. Many are affected by this disorder and a cure has yet to be found. But before we continue, a distinction must be made between major depression and “reactive depression” in which a person may feel depressive symptoms because of a single event like the loss of a loved one or a failure of some kind. Major depression is a prolonged state in which an individual may display a number of symptoms including depressed mood, loss of interest in most activity, change in body weight or appetite, changes in sleep patterns, psychomotor agitation or retardation, fatigue, difficulty concentrating, feelings of worthlessness or guilt, and suicidal thoughts. Depending on the severity of the depression a patient may display many, or only a few of these possible symptoms.

Research has yet to find a definitive neurological cause for depression and other affective disorders. Studies of fraternal and identical twins have attempted to determine the role of nature versus nurture on the matter and animal models of depression as well as human studies have been used to develop drugs and other treatments for depression. Through this work different hypotheses have developed about the neurochemical basis of depression. Some are convinced a monoamine imbalance is responsible while others say it is an issue with serotonin dysfunction. These hypotheses have led to the development of different treatment methods and the utilization of a few classes of drugs. Drug classes include monoamine oxidase inhibitors, tricyclics, and selective serotonin reuptake inhibitors (SSRIs) which all have slightly different mechanisms of action in the brain when treating depression. What is most interesting is that after all this research and development none of these drugs stand out as the best treatment for depression. They all tend to improve depressive symptoms anywhere from a week to a month after drug therapy begins, and they all carry different, sometimes nasty, side effects. The main reason for the current love affair with SSRIs in the medical world is that they carry the most favorable set of undesirable side effects, not that they treat depression best.

Enter ketamine. This compound has a street reputation as a club drug and is derived from phenylcyclidine (PCP), another drug known for its powerful and potentially dangerous psychological and addictive affects. Both drugs were originally developed as alternative analgesics (pain relievers) to drugs like barbiturates that had a higher risk of respiratory depression and subsequent death. PCP and ketamine did produce analgesia, just not in the way they were originally thought to do so. Patients report feelings of detachment from their own body and reality when under the influence of these drugs. They can’t feel pain because their minds are off in another reality, essentially too distracted to feel anything. At high doses PCP and ketamine have been shown to induce schizophrenic symptoms in humans, or worsen previously existing schizophrenia, and research on schizophrenia uses ketamine to bring about a schizophrenic state in animal test subjects. So how on earth can a drug like this have any useful therapeutic application?

http://drug-effects.us/what-is-ketamine

http://www.guardian.co.uk/society/2010/apr/02/drugs-ketamine-bladder-problems-incontinence

Researchers at Yale University and the National Institute of Mental Health have recently found that administering a low dose of ketamine to a patient affected by major depression has been able to lift the patient’s mood and subdue the depression for about a week at a time. It is an astounding find given the known effects of ketamine on the mind. One study reported that 70% of patients treated with ketamine experienced an improvement in mood. One of the best parts about the treatment is that it takes effect immediately, unlike the other antidepressants on the market, which can take up to a month to work. It has also proven effective even to patients who have been resistant to other treatments. Ketamine is already an FDA-approved analgesic, usually used in veterinary settings, so further studies of this compound are now being developed in humans.

The mechanism of action for this drug is not yet clear but it is known that ketamine and PCP are nonselective NMDA receptor antagonists. They affect the glutamate pathways within the brain and also seem to have the remarkable affect of strengthening and restoring synaptic connections. In the human model of depression where it is thought that symptoms are caused by atrophy of neurons in various brain areas, it makes sense that ketamine is an affective treatment because it encourages neuron regrowth and connection. This may be done through the production of brain derived neurotrophic factor (BDNF) or other molecules that influence neuron health and maintenance. More work must be done to determine how this unlikely drug accomplishes its therapeutic affects. There are still dangers associated with taking ketamine, especially if it only works for a week at a time to treat depression and repeated use has already been shown to produce schizophrenic symptoms in some. It is an amazing and surprising find and hopefully it leads to more improved treatments of affective disorders like depression.

- J. Daniel Bireley

Sources:

Ketamine Relieves Depression By Restoring Brain Connections – NPR

Signaling pathways underlying the pathophysiology and treatment of depression: novel mechanisms for rapid-acting agents - Trends in Neurosciences

Meyer, Jerrold S., and Linda F. Quenzer. Psychopharmacology: Drugs, the Brain, and Behavior. Sunderland: Sinauer Associates, 2005. Print.

- Natalie Banacos

Scientists from Duke University and Brazil claim wires connecting one rodent to another can allow communication spanning continents via the internet. Professor Miguel Nicolelis of Duke University in Durham, North Carolina, led a team of researchers who demonstrated that it is possible to transmit instructions from one animal to another by brain-to-brain communication, a process akin to telepathy.

Brain-to-brain communication could be the start of  organic-based computing based on networks of interconnected brains. Pairs of laboratory rats were able to communicate with each other using microscopic electrodes implanted into their brains. This occurred as part of an experiment where the two rats had to work together in order to receive a reward (see video at source).

The researchers had this to say: “as far as we can tell, these findings demonstrate for the first time that a direct channel for behavioral information exchange can be established between two animal’s brains without the use of the animal’s regular forms of communication.” One rat in each pair, assigned to be the encoder, detected the signals of where to find a food reward and had to communicate these instructions to a second decoder rat. Once the second rat followed the first rat’s instructions, both rats would receive a reward. These communications were able to be sent over the internet, with rats at one lab in Brazil communicating with rats at the other lab in North Carolina.

Professor Nicolelis inserted micro-electrode implants into the rats’ brains to record the neuron activity associated with decision-making. Putting these signals through a computer encoder transmitted them to the second rat via wires connected to another set of micro-electrode implants. The second rat learned how to decode the signals quickly for its own use.  Each rat was trained to find water in its cage based on the type of signals they were given. However, only the encoder rat was actually exposed to the signals, which it had to pass on  correctly to the decoder rat. The decoder rats managed to find the reward in about 70% of trials.

What is most interesting, however, was the scientists found that when two rats were paired up they quickly established a rapport based on  some sort of sensory feedback. If the second rat failed at its task, the first rat would modify what it was transmitting to help the second rat. Both rats worked together since they were sufficiently motivated by the reward.

Future work could encode entire thoughts, hopefully connecting more brains to each other, boosted by the effect of sensory feedback rapport.  Professor Christopher James of the University of Warwick, who conducts similar research, said that the technique is still very crude since it relies only on monitoring one part of the rat’s brain for its nerve activity. “Leap into the future by, say, 50 years: if you could stimulate many multiple sites, and if we knew what patterns to use and when, then we may well be able to conjure up complex ‘thoughts’,”  Professor James said. “Abstract thoughts are harder to read and represent; but not impossible technologically.  We can already do that … we just need to understand the brain better.” Professor Nicolelis hopes brain-to-brain communication will expand the capabilities of  intelligence one day, saying “we cannot even predict what kinds of emergent properties would appear when animals begin interacting as part of a brain-net. In theory, you could imagine that a combination of brains could provide solutions that individual brains cannot achieve by themselves.”

Mind-reading rodents: Scientists show ‘telepathic’ rats can communicate using brain-to-brain connections – The Independent