AP Biology class blog for discussing current research in Biology

Tag: neuroscience

Could A Simple Plant Principle Help Us Better Manipulate The Brain?

The researchers and scientists at Weill Cornell Medicine are working on a family of light-sensing molecules with great haste. This research can advance the very complicated field of optogenetics. There are light-sensitive proteins that play a very important role in the field of biology as a whole. This has to do with topics ranging from its use in photosynthesis to even our own vision. In photosynthesis these proteins are how plants are able to absorb the photons given off from the sunlight and react by using it as an energy source. Most of the information on these types of proteins are from the specific protein bacteriorhodopsin, which is seen in these photosynthetic reactions. However we can only study this protein to a certain point given the technology we have which has lead researchers to a road block. This new study which is being called; line-scanning high-speed atomic force microscopy, will help pass this block. 

Rat primary cortical neuron culture, deconvolved z-stack overlay (30614937102)


The problem that was occurring when studying this field was that the tracking of activity of individual molecules was too slow to see the protein actually change, for example how bacteriorhodopsin reacts to light. The new approach involves sacrificing the image detail of the altering molecules for a much faster frame rate. It is as if one was taking blurrier pictures of a horse in order to capture its entire journey. According to Dr. Perez Perrino they are tracking the protein every 1.6 milliseconds in order to speed of bacteriorhodopsin in its natural, wild-style habitat. As a result of light it will switch between open and closed states. With this new method of imaging they have concluded that the transition to the open state and the its duration always happen at the same speed. However the molecule remains in the closed state for a longer period of time as the light increases.

Optogenetics begins to play a role because researchers in this field insert genes for light-sensing molecules in neurons or other cells, causing them to alter the cell’s activity. This work could potentially help us control the brain in ways we could never imagine. This could lead to eventually treating neurological diseases in the near future.

Dead Pig Brains Were Brought Back to Life…Kind Of

A recent article published by Christof Koch raises the question of if death is really as final as it seems.

Koch highlights a study undergone by a sizable team of physicians and scientists at Yale School of Medicine, led by Nenad Sestan. This group used hundreds of slaughtered pigs from the Department of Agriculture to carry out a rather extraordinary experiment. 

The experiment began with the removal of the pig brains from the pigs’ skulls. The veins and carotid arteries were then connected to a perfusion device that created the effect of a heart beating. This perfusion device circulated a synthetic concoction, or a type of artificial blood, containing drugs and oxygen with a specific molecular constitution that would protect the cells from damage. Sestan’s team studied these pig brains’ capability to survive four hours after the pigs had been electrically stunned, bled out, and decapitated. His team also compared these pig brains with others that were not connected to a perfusion device. 

A closer look on a pig brain (not from the actual experiment)

The tissue integrity of the pig brains that were connected to the perfusion device was preserved and there was also a decrease of the swelling that causes cells to die. In addition, synapses, neurons, and output wires (axons) looked normal. The glial cells, which support neurons, had some function, and the brain consumed glucose and oxygen. This means that there was some metabolic functioning. The researchers seemed very satisfied with their findings and titled their paper “Restoration of Brain Circulation and Cellular Functions Hours Post-mortem.”

However, brain waves, like those from EEG recordings, were not found in the pigs’ brains that were connected to the perfusion device. There were electrodes put on the surface of the brains but no great global electrical activity was recorded. This, although, was intended. In theory, bringing a pig that had just gone through such trauma back to life could’ve led to a number of horrible side effects. Some include massive epileptic seizures, delirium, deep-seated pain, distress, and psychosis. It was because of this fact that Sestan’s team ensured the artificial blood contained drugs that suppress neuronal function. 

According to Koch, this experiment causes a new question to surface: “What would happen if the team were to remove the neural-activity blockers from the solution suffusing the brain?”. In reality, it is probable that nothing would happen. Even though some neurons responded to the stimulation doesn’t mean that millions would be able to. However, it can’t be completely disregarded that maybe with some external support the seemingly dead brains can be brought back to life.

Keeping this in mind, one may wonder if this can be applied to human brains. The pig brain is the most popular laboratory animal as it has a fairly large brain that has a folded cortex similar to that of a human brain. Because of this, in theory, the human brain could undergo the same experiment. Even so, the question of if this would really be ethical or not is a factor that should definitely be taken into consideration.

If possible, do we have the right to bring dead brains back to life?

How Did Our Baby Learn That Word?!?!

Jason Sudeikis’ character is hosting a nice dinner party with his wife played by Jennifer Aniston, and all seems to be going great. Then, all of a sudden, their 12- month-old baby blurts out a curse word! “How could our baby learn such a thing?” In a flashback 8 months earlier, we see the less-experienced parenting pair blurt out some pretty R-rated things in a fit of frustration on the road with their baby in the backseat. And so the punch line sinks in.

In modern day parenting comedies, scenes like this fabricated one are a dime a dozen. But these humorous takes on life always get at least one thing right: babies are sponges. Let’s take a look at why on a cellular level.

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Prior to birth, most neurons migrate to the frontal lobe of the brain where, during postnatal development, they link together and forge connections, allowing a baby to learn proper responses to stimuli. The “circuits” formed by the neural connections are incredibly flexible during the early months of development (roughly the first 6 months) and can quickly be formed or severed, resulting in a remarkable neonatal human ability to rapidly pick up new knowledge about our surroundings. But how are they so malleable?!

Researchers at the University of California, San Francisco may have the answer! In a study coauthored by neuropathologist Eric Huang, they found neurons forming a chain moving towards the frontal lobe from the sub ventricular zone, a layer inside the brain where nerve cells are formed, in infants up to 7 months old!

This research seems to point to the idea that these new brain cells form connections with the pre-existing neurons in the frontal lobe later in the infant’s development, resulting in more cognitive flexibility for a longer period of time.

To quote the original article by Laurel Hamers, what the new neurons are doing is analogous to “replenishing the frontal lobe’s supply of building blocks midway through construction”.

Huang’s team observed postmortem infant brain tissue under an electron microscope and discovered a group of neurons synthesizing migration proteins, but the real major discovery came with the observation of rare tissue acquired moments after death. The team injected viruses tagged with glowing proteins into the neurons (thus making the nerve cells glow) in the sample and tracked their movement. While infants up to 7 months old were observed with migrating neurons, the researchers recorded the number of migrating cells at its highest at 1.5 months old and saw it diminish thereafter. The migrating neurons usually become inhibitory interneurons which, to quote the original article, are “like stoplights for other neurons, keeping signaling in check”.

So there you have it! To make sure your baby doesn’t learn that bad word, just suck up all the migrating neurons from its brain!

All jokes aside, this research presents an amazing window into the brain development of the most intelligent species on earth! It’s fascinating how it breaks down psychological mysteries using cellular evidence. And it raises new questions about these mobile neurons: When are they created and how long does it take them to move to the frontal lobe?

How do you think this new research will influence our understanding of the creation of social biases? Do you think this will lead to breakthroughs in research on the foundation of Autism spectrum disorders?  Do you have any funny baby stories? Let me know in the comments.

Google Maps… But for your BRAIN?

We have mapped our roads such that we can explore our communities through interactive map softwares, such as Google Maps and Google Earth.  Google Map cars are a common sight every few years as Google endeavors to maintain a hyper-accurate account of the roadways in many countries worldwide.  We are relatively familiar with the world around us, however, we are significantly less familiar with our brains.  The brain is a vastly complex organ of your body, and is the center of the nervous system.  Globally, neuroscientists are studying the brain to similarly map the brain. Presently, we are limited in our understanding of the extent of and interaction within the neural networks.  Nevertheless, we do have a massive understanding of the brain’s macrostructure and its mechanisms of function.  Through the development of advanced imaging softwares in the recent decades, research on the more intricate systems of the brain has intensified. fMRI scans have allowed greater insight on the brain’s “connectome.” This “connectome” comprises the many links to the hundreds of regions in the brain and the billions of neurons. Through computer modeling, we have been able to augment our understanding of the brain and create these amazing (and beautiful) models of brains:

The Human Connectome


The Human Connectome:

The Human Connectome Project began in 2009 and has been organized into two consortiums by the National Institute of Health: The Washington University in St. Louis – University Minnesota consortium and the Harvard University/Massachusetts General Hospital – UCLA consortium. The goal is to compile massive amounts of data on the healthy adult brain and map it down to the neuron– just like Google has mapped (nearly) every road in the US. Additionally, the project seeks to  facilitate research into brain disorders such as dyslexia, autism, Alzheimer’s disease, and schizophrenia through developing more advanced neuroimaging platforms and creating a wealth of information to study the effects of these neurological disorders and diseases, insofar as how they function and change the interaction of the brain–similar to how you would take use the navigation functions in your GPS.


Similar to the Human Connectome Project endeavor to map the brain, a “citizen-science” platform for brain mapping, Eyewire, seeks to map the brain by providing the fMRI scans of the brain and allowing users to build the 3 dimensional structure of a section of a single neuron.  This program is a fun online game that actually contributes to science, in that users can map sections of the brain, and be checked by the computer.  This allows for error mitigation, where the computer model may be erroneous, and corrected by the many users mapping the neuron at a time. The link can be found here, as well as below.

The Human Connectome Project and the Eyewire mapping game are both revolutionary research projects studying the amazingly intricate brain neuronal structure and networks, with very promising results in the near future.


Original Article:

Eyewire Project Game:

While studying the brain there arises the need to activate or inhibit certain cells. The most common process for doing this in the past was optogenetics. Optogenetics is the use of light to activate or inhibit cells. While optogenetics is very precise, it has some drawbacks and limitations. Light is scattered in the brain and to reach deep in the brain scientists usually insert a fiber optic cable which is highly invasive. This practice is still used today, but there has been a new development: sonogenetics. Researchers at the Salk lab have been working on this new technique. Sonogenetics use sound waves, low-frequency ultrasound waves to be more specific, to activate the neurons. This new method allows scientists to reach neurons deep in the subject’s brain without having to perform a surgery to implement a fiber optic cable. It also has the potential to have no effect on the surrounding neurons. In the Salk laboratory, the scientist used worms to study the use of sonogenetics. Worms would normally be impossible to work with as performing surgery to implement a fiber optic cable is nearly impossible, but with the use of sonogenetics the scientist were able to activate certain neurons. The sound waves were aided by microbubbles outside the worm that oscillated in size in conjunction with the wave. The scientist then discovered TRP-4, an ion channel which can be affected by the sound waves. They found that the sounds waves along with the microbubbles can open these channels and activate the cell. Though this process they activated cells that would normally not have been activated by ultrasound. Although it all sounds very promising, sonogenetics has only been used on Caenorhabditis elegans neurons.



A picture of Caenorhabditis elegans

The next step in the research would be to get the sonogenetics to work in a mammal’s brain. This could potentially lead to therapies that are non-invasive for humans. However, how comfortable would you feel with doctors using sound waves to control neurons in your brain? Sonogenetics sounds very promising and contains a lot of upside, however, the research is not far enough along yet to completely tell.


Original Article:


For More Information:


How to stick with your New Years Resolutions


bicycling  In Tracy Cutchlow’s article “How to Trick Yourself into Exercising” she talks about the difficulty of sticking to your new years resolutions.  Year after year peoplecreate resolutionsthat involve things such as consistent exercise, but they struggle to actually act on their resolution.  So Tracy spoke with a psychologist about possible techniques that would enable her to “trick herself into exercising.”  The psychologist’s technique involved a relatively simple three step procedure.  The first step is to create a “ridiculously realistic goal.”  For example, rather than say you are going to exercise everyday, start off with three days a week.  The next step involves accountability.  This could mean writing notes in your phone or putting a calendar up on the fridge to remind you about your resolution and to help you keep track of your progress.  The final, and most important step, is to create a “painful consequence.”  For Tracy this meant that if she ever failed to maintain her three days a week resolution, she would have to give $500 dollars to an organization that she “hates” (Comcast).  The purpose of the painful consequence is to essentially make breaking your resolution so unappealing that it eventually becomes a rule.  In his book How Children Succeed: Grit, Curiosity, and the Hidden Power of Character, author Paul Tough describes thegeneral science behind how creating rules for yourself is an effective method for maintaining discipline. He writes, “When you’re making rules for yourself, you’re enlisting the prefrontal cortex as your partner against the more reflexive parts of your brain. … Rules are a metacognitive substitute for willpower. By making yourself a rule (“I never eat fried dumplings”), you can sidestep the painful internal conflict between your desire for fried foods and your willful determination to resist them.”  So Tracy Cutchlow’s article provides a means through which we can create rules for ourselves and in turn, successfully adhere to our resolutions.

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Dying Brain cells signal new brain cells to grow in songbird



Original article:

In a recent paper written by leading author Tracy Larson and co-authors Nivretta Thatra and Brian Lee, they discovered a brain pathway that replaces brain cells lost naturally. This study could further the progress of using replacement cells for the neurons lost during aging, Alzheimer’s Disease, and other natural causes.

These scientists used songbirds, specifically Gambel’s white-crowned sparrows, as a model and observed that the area of their brain that controls song increases during breeding season, and decreases during other times in the year. After breeding season the cells in the area of the bird’s brain that controls songs undergoes programmed cell death. What is noteworthy about these dying cells is that they are also releasing a signal that reaches certain stem cells in the brain that will eventually redevelop the singing part of the brain by the time the next breeding season arrives. This process of developing new neurons from stem cells called neurogenesis normally occurs in the form of “regenerative” neurogenesis post brain trauma in mammals; however, it also occurs in the hippocampus in small amounts.

These songbirds could provide insight on how the human brain can perform natural neurogenesis and help replace neurons lost because of aging and neurodegenerative diseases. These finding may pave the way to alternative treatment for repairing human brains using neurogenesis and replacement cells.

Antidepressants Change Brain Connectivity After One Dose



Lloyd Morgan- “Despair”

The prescribing of anti-depressants is a controversial topic in that most scientists are unaware how these medications work. Previously, SSRIs (serotonin reuptake inhibitors) were thought to have taken effect after a few weeks. Recent studies show, rather, that these medications take effect in a matter of hours.

SSRIs are very widely prescribed and frequently studied as antidepressants. They work by fundamentally changing brain connectivity and the way in which the brain undergoes simple processes. New studies are showing that this rewiring of the brain occurs after only one dose of this medication, producing dramatic changes.

The Institute for Human Cognitive and Brain Sciences conducted this study by conducting extensive brain scans, allowing participants to let their minds wander so that the lab technicians could accurately measure the oxygenation of the blood flow in the brain as well as the number of connections between voxels in the brain.

This lab yielded interesting results. Scientists discovered that one single dose of SSRI reduced the level of intrinsic connectivity in most parts of the brain, but increased connectivity within the cerebellum and the thalamus.

This study opens up a lot of opportunities for deeper investigation into antidepressants. It can help researchers to understand why some people do not respond well to this form of treatment, and how to better individualize treatments for depression patients. Depression is a serious and life-altering illness that effects every sector of a person’s life. With added research and understanding of treatment methods, there can be hope for the many that struggle with this mental illness everyday.

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The Movie of Autism

Stacking repetitively is a behavior often associated with Autism

According to a recent study, “children with autism spectrum disorders (ASD) have trouble integrating simultaneous information from their eyes and their ears,” which has been compared to by Stephen Camarata, Ph.D., professor of Hearing and Speech Sciences at Vanderbilt as similar to, “watching a foreign movie that was badly dubbed.” This study was recently published by Mark Wallace, Ph.D., director of the Vanderbilt Brain Institute and co-authored by Camarata. Their work is incredibly important in the field of diseases such as Autism. Unlike many other

researchers, Wallace and his team have focused on sensory function. Their experiment involved putting groups of children, both with normal function and with high functioning Autism and putting them through a variety of audiovisual stimuli that included, “simple flashes and beeps, more complex environmental stimuli like a hammer hitting a nail, and speech stimuli.” After these tests were done, the researchers asked the subjects to identify which auditory and which visual stimuli occurred at the same time. These test showed that children with Autism have, an :enlargement in something known as the temporal binding window (TBW),” which means they have trouble associating sights and sounds with specific times.

A second aspect of the study also showed that children have trouble associating visual and auditory stimuli from speech, which may have something to do with their constant covering of their ears. Although the data here is not conclusive, it has lead the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition to add sensory processing as a key problem for those who suffer from Autism. The whole study has opened up a new field of inquiry on Autism studies and has the possibility of leading to new advances with other psychiatric diseases such as schizophrenia.

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