Wiring the brain

This week began with a lecture on wiring of the brain. We learned about the genesis of neurons. Briefly put, it begins with the cell proliferation: neural stem cells give rise to neurones and glia. This is followed by cell migration, where pyramidal cells and astrocytes migrate vertically from the ventricular zone by moving along thin radial glial fibers, where as inhibitory interneurons and oligodendrocytes migrate laterally. The brain structure could be said to evolve “inside out”, since the cells to first migrate move to the subplate layer, and the cells that next divide migrate to the cortical plate. Following migration cells differentiated begin to serve their programmed function. All this happens in a very controlled way — intuitively it can be assumed that small changes in the initial steps can result in quite drastic developmental errors. Nevertheless, what these errors look like were unfamiliar to me; it was quite interesting to see the structural deficiencies in monkey striate cortex when LGN input is degenerated early on in fetal development.

This week included an excursion to BABA centre at the Helsinki Children’s Hospital. This was one the most interesting excursion so far, as we got to hear a lot about different occupations held by non-physicians at the hospital. It was also interesting to see similar equipment (for example, EEG) in a hospital setting and hear about job opportunities we as engineers could apply for to work in a hospital. Not having heard much about what a medical physicist does, it was interesting to hear all the details directly from one. We also had the privilege to listen to a presentation given on one of the employee’s master’s thesis. Listening to all this we came to realise that even though the topics were never related to solely brain structure and operation, having prior knowledge on those topics surely helps in the job on a daily basis.

Excursions here and there

This week we had a double dose of excursions taking place in Otaniemi and then in Helsinki. Instead of our Monday morning lecture, we visited Aalto NeuroImaging (ANI) research infrastructure in Otakaari 5. The class was divided into three groups which rotated around the different facilities in the building. Firstly, we saw the MRI system which included and MRI scanner and RF-coils. There, one thing surprised me when we were shown the health and safety checklist that all have to fill before going in the MRI scanner: a tattoo meant that someone might not be allowed in scanner. Since I did not know much about tattoos, I was later explained that some tattoo inks contain metals, which could cause serious damage to the skin when exposed to the magnetic field of the MRI scanner.

Secondly, our group moved to the Aalto Behavioral Laboratory (ABL). This was a facility that had the space and equipment for carrying out studies focusing on behavioral research. Different responses like eye movement, EEG and more can be recorded there. As a demonstration, we saw how eye movement on a computer screen could be visualised and tracked using special devices (Eye Tracking systems) placed on the head and the eyes. I myself got to try some cool specs which recorded my eye movement and pointed out where my eyes were focusing. The lab had two rooms that allowed controlling certain conditions (for e.g. displaying something on a computer screen or introducing sound stimulus) and recording responses from outside these rooms.

The third facility we visited was Aalto TMS (for Transcranial Magnetic Stimulation). There they have neuronavigated transcranial magnetic stimulation systems combined with electroencephalogram (EEG) mapping. This setup allows not only neuroimaging but also mapping stimulus responses simultaneously. The benefit of having this in the same building as the MRI scanner is that a person’s brain can first be scanned and then the equipment used for magnetic stimulation and mapping responses can be co-registered using the brain scans.

The second excursion of the week was in Sooma Oy in Helsinki. It is a medical device company specialising in non-invasive brain stimulation devices used for treating neurological and psychiatric disorders. They do this using transcranial direct-current stimulation (tDCS). They have developed a tool/instrument which allows for transcranial magnetic fields to be simulated at specific parts of the brain, bringing a balance/restoring the level of neurotransmitters in affected areas in the brain. The interesting thing was to discover the history of this treatment type, which dates back to thousands of years. The ancient Egyptians and Romans used electric fish like Torpedo to treat neurological and psychiatric disorders. Epilepsy, headaches and depression were treated by placing a live fish on top of the affected area, curing the disorder or alleviating it. From another perspective it was also interesting to find out that this is the only device that a psychiatrist was able to use and experience themselves before suggesting it to patient.


Torpedo (Electric ray)


Image result for torpedo fish

Sooma Oy medical device



Motor Systems

The topic of this week was the human motor system: the spinal and the brain control of movement. I was a little surprised to learn that taken the brain aside, the spinal cord contains quite complex neural feedback and control systems. If we think about an alpha motor neuron, it only receives input from three different places: sensory information from muscle spindles, input from upper motor neurons from the brain and input from spinal interneurons. The input from spinal interneurons is the largest of these three, and there is quite a lot going on there that I had not come to think of earlier. The crossed extensor reflex, for example: if you suddenly lift up your right leg because you stepped on a lego block, the activation of extensor muscles and inhibition of the flexors on the left side compensates for the withdrawal of antigravity extensor muscles on the right side. This keeps you from falling down. This is something I have always taken for granted, and never stopped to think about what kind of control system lies behind it. Thus, the interneurons in the spinal cord play a very important role in our daily life.

One topic I found truly fascinating from a cell biologist point of view was the different types of muscle cells and neurons that innervate them. The are different types of muscle fibers: slow and two types of fast, fatigue-resistant and fast-fatigable. Each type has an innervating neuron that is the same type, because slow fibers require different signal frequencies from the neuron than fast fibers. It seems that the muscle fibre and the neuron are always a matching pair, so to say. But now we get to the truly interesting part: it is possible for the muscle fiber to change phenotype to match the changed phenotype of the innervating alpha motor neuron. This has been tested in a study where a fast muscle fiber was stripped of it’s original neuron and innervated with a slow alpha motor neuron. The muscle fiber adapted and changed it’s properties to be like a slow muscle fiber, and not just the contraction type but there was also observable changes in the underlying biochemistry of the cell. These studies are something I am going to have to look into more properly, because I am interested to get a more detailed view on the changes of the gene expression in these cells. After all, this is something that might be behind our learning and memory.

Expyriments, Ears and Elekta

Diving straight back to where we left off. The reaction times to aural and visual stimulus were tested using the Expyriment python program. From the figure shown last time, it was evident that the reaction times decreased in both cases as the repetition number increased. Also in general reaction times for aural stimuli tend to be quicker than for visual stimulus (although my own results seemed different). Now we can get to the why. The two stimuli are perceived and processed differently in our brains, resulting in different reaction times. Firstly the more we practice something, the more neural connections are formed in the brain and the time to process and react is decreased as a result of training. On the other hand, the information about seeing visual stimulus (the green box) travels longer in the visual pathway in comparison to the information of the auditory stimulus (the beep sound), which travels through the auditory pathway. According to research carried out by Kemp, the auditory stimulus takes only 8–10 ms to reach the brain, but on the other hand, a visual stimulus takes 20-40 ms.

This week’s lecture was about the human auditory system. It was interesting to visualize and affirm the point made earlier about how fast it takes for stimulus to reach the brain from the ears. The auditory cortex is removed only by two synapses from the cochlear hair cells whereas the visual cortex is all the way at the other end of the head from the eyes. Another interesting aspect was learning how the visual and auditory system are connected (audiovisual integration). Our vision can affect very much of what we hear. This was illustrated in the lecture with a YouTube video, where a person in two cases made the same sound but moved the mouth in different ways in each case. It caused many in the lecture hall to hear two different sounds, simply because the eyes were dominating what sound was expected to be heard.

Finally, we had our first excursion to Elekta! There we were introduced to the company, their history and what they do. The presentations went into quite a lot of detail on how their devices work and the current problems they are trying to solve. The coolest part was connecting how much of the theory presented to us related to other courses some from our group are taking (for example Principles of Biomedical Imaging or Signal Processing in BME). It was also in a sense a form of motivation as to why what we are learning in this course is so valuable, as it is constantly applied in other fields.

Week 5

The fifth week’s lecture handled topics like acetylcholine pathways and how this is involved in perceptual learning; the norepinephrine and serotonin system; stress response as a result of the mechanisms of the autonomic nervous system and more. What was interesting to see was how each neurotransmitter’s pathways reach different parts of the brain, and how the excess or absence of one neurotransmitter can have unforeseen effects on the functioning of another.

The first task of the given exercise, which was handed out last week, was about finding a drug or disease that affects the central nervous system. It was intriguing to explore and find out for example how an excess of a chemical call tryptophol can completely disrupt the circadian cycle and as a result daily functioning. Through a disease called Sleeping Sickness (or African trypanosomiasis), parasites producing tryptophol enter the hemolymphatic system. Eventually the chemical crosses the blood-brain barrier. Tryptophol can be a functional analog to serotonin or melatonin which are involved in sleep regulation and as a result causes symptoms simulating the effects of excess melatonin or serotonin.

The second exercise was an experiment measuring reaction times to aural and visual stimuli made with a python program. Having studied computer science, I naturally went to check the code. The timing as randomized to make it so that you cannot guess when the stimulus will come. The results of the experiment revealed differences in the reaction times in the beginning and end of the study. Also overall reaction times varied between the two stimuli. The figure below displays these differences. More detailed explanation on how these results came about will be discussed in the next blog post.



Sadly the excursion that was planned for this week got postponed due to scheduling issues, so this week consisted of a lecture as well as an exercise session that was supposed to introduce the python-based problem.

After having studied the basic structure of neurons and the principles behind synapses the past couple of weeks, it was interesting to finally go a bit deeper into the topic and learn about neurotransmitters. The basic functions of them were introduced already in the previous lectures so this week dealt mostly on the classes they are divided into, the most common neurotransmitters and their functions. One of the most interesting topic was the recent studies on the function the opioidergic system plays on behavioral reinforcement and social behaviour overall. We take so many things as given; for example, it does not surprise us that alcohol might make us more social, and many times people use it as a way to become more social and feel more confident. Having thought it was primarily due to becoming more relaxed, it was fascinating to find out that it might be related to alcohol releasing beta endorphin, which again strengthens social behaviour by modulating the opioidergic processing in the brain.

Diving into the material

“Since it is the third week of this course, it is about time to take a look at the studying material! At the first lecture we were given the names of the three books used in this course, plus the lecture notes from Risto. I have to admit that having three books plus notes seemed a bit excessive and complicated at first. But it seems to be working out just fine: every week the reading required for the next lecture is clearly stated, and I don’t feel confused about the amount of the material at all. Especially this week I have relied only on the reading material, since I could not make it to the lecture or the exercise session, and I have grown very fond of the Bear, Connors and Paradiso’s book. It is a wonderful example of a great course book: everything is explained very clearly and with lot of pictures, examples and even metaphors to help the reader understand what is going on. These things make the book very easy to follow.

Chapters 3, 4 and 5 from the book (some of these things also covered in the lecture this week), talking about neuronal membrane at rest, action potential and synaptic transmission, gave a really solid and even detailed ground on which to start building on understanding the operational aspects of the human brain. This ground is made even better in the next lecture, when we will start talking about neurotransmitters. Then we are starting to really get into the stuff that I am mainly interested about as a chemist! This week has been and the next weeks will be very important in the sense that it is crucial to understand the way neural cells communicate in detail to be able to affect it somehow.

One thing I also particularly like about this course is that we are encouraged to use more imaginative ways for our learning as well. This week the materials section was extended with tips for helpful apps and flashcards. The 3D brain structure app is very useful especially for me! I sometimes feel that it is difficult to try to comprehend the complex structures of brain with the help of the the “normal” brain structure pictures, since they can only display a limited segment at a time.”

– The Chemist of the Team


Neuronal Functions and Play-Doh Brains

The content of this week’s lecture focused mostly on neurons, action potentials and how they propagate. A lot of the material was somewhat familiar through previous courses, such as biophysics, but a recap is never a bad idea.  It would, however, be interesting to hear more about different neurons, and if different types of neurons serve only certain functions; i.e. if some neuroimaging techniques measure mostly the activity of pyramidal neurons, do pyramidal neurons account for most of the cortical activity? Is measuring them an accurate representation of what is happening in the brain?
In addition to having a lecture in the beginning of the week, this week’s exercise session offered us a practical way to to study the structure of the human brain. At the beginning of the session we were given tubs of play-doh and told to construct a model of the human brain. We were guided to construct each section of the brain at a time, while going  through the main functions of the section we were modelling. This hands-on session was a fun way to explore the different brain structures and their sizes relative to each other, as well as getting to know one another. Moreover, it was fun to see what structures other students payed more attention to and how different the outcomes were.

Below are results of the first workshop session.3D-BrainModel

Introduction Round

Greetings to all readers!

This blog post serves as a learning diary for students taking the course Structure and Operation of the Human Brain. During the first lecture we went through an introduction to the subject and practical matters on completing the course. Also, students introduced themselves to each other in the lecture, telling their background and motivation to choosing the course.

Halfway through the week we formed a group for writing these blog posts. The group is formed of three students as follows:

Anastasia Lowe is a Biomedical Engineering student with an interest in neuroscience. She has taken a few courses on Cognitive neuroscience before and is interested in the structural aspect that this course deals with. For her bachelor’s degree she studied Bioinformation Technology.

Iiris Hakaste is a Chemistry and Biotechnology student. She is mostly interested in chemical reactions in the brain. She is very interested in how drugs affect brain activity, and what kind of molecules are able to do that at all. She wishes to work with pharmaceutical research one day, so she feels that it is important for her to understand the brain’s structure and functions to be able to design effective medicine.

Alison Tshala is also a Biomedical Engineering student. She studied Computer Science for her bachelor’s with Bioinformation Technology as her minor. Choosing Bio-IT as her minor pivoted her towards the Life Sciences track. With her CS background she still hopes to be able to adapt to the major and specifically to this course. Due to her programming background, she is interested to learn how to apply Matlab for the course’s exercises and more specifically on its applications to the operation of the human brain.

Each week that there is contact teaching, will be followed by a blog post so watch this space for our thoughts, questions and observations on what we learn!