Week 12

This week we visited Aalto Behavioural Lab (ABL) to collect EEG data for exercise 6 report. We had a volunteer wear the EEG cap and we learned how to inject gel into the holes of the EEG cap. We took turns injecting enough gel to each hole til it glows green. First, we rotate the syringe in an opening to get rid of the air then inject some gel. Then we check whether the light on the opening shines green to indicate the gel applied is enough. This is repeated for every opening.

Once the cap is properly prepared on the subject, we close the doors and move into the observation room. One of us was responsible for starting the experiment. The experiment used the same python script from exercise 4, but this time we get more fine grained results with the use of the EEG cap.

Another of us was responsible for starting and stopping the EEG data collection. In addition to that, anomalies and disturbances needed to be recorded. The data seemed quite clean so nothing was really recorded. The experiment took about 10-15 minutes. It was interesting to see how eye blinks look in the EEG data and how it affects the data for other areas. It was also interesting to see the EEG data for closed eyes. This helped me to be able to recognise these patterns when they appeared in the data.

After the end of the experiment, we learned how to clean the EEG cap and then we were dismissed. We will get the data from Monday and Tuesday soon and then be able to construct our report for exercise 6.

Week 11

This week we had our third excursion and we visited the Aalto NeuroImaging Infrastructure (ANI) in Otaniemi. Our group was divided into three smaller groups in which we were demostrated different topics. Some of the demonstrations and presentations were of old topics. For example we had a brief recap on transcranial magnetic stimulation in 10 minutes. We had previously gotten a quite extensive presentation on this topic at Nexstim but a little recap never killed anyone and it was nice to know that TMS is possible here in Otaniemi also. The second pitstop dealt with MRI.

For us the most interestin gvisit was to the Aalto Behavioural Laboratory. There we were presented modern eye-tracking methods and we even got to try them. It’s quite extraordinary that we can actually track someones focus of eye-sight. This also felt weird as we got to try it. Suddenly you’re very aware of where you are looking. Furthermore, we got a little demonstartion on lie detection. One of the group was instructed to write a number on a paper between 1-5 and then to lie of the written number when asked. The audience got to see the eletrcis responses of the liars body as she tried to get away with a lie. She wasn’t successful.

As a whole this week was pretty quiet in terms od this course, which is a blessing really. It seems like every other deadline on other courses strikes in the end of November.

– Pekko & Maria


Lecture 9: Mental Illness

This week’s quiz was about attention while the lecture was on mental illness. Mood disorders seem to the most expensive in costs for society, Europe spends billions due to mental health issues of the general population. 5% of taxes go to psychological disorders. Mood disorders apparently have the highest cost because of indirect costs like sick leave, early retirement etc.

The mental health of children shapes them when they are adults. It has been suggested by earlier researchers that humans are just a sum of their experiences throughout their life and the choices they make are only a consequence of the events that have occurred in their life. This theory was debunked when a researcher proved that humans have conscious thinking and make decisions based on other factors rather than the sum of their life events.

We learnt that amygdala of the brain drives a stress response. It activates the hypothalamus which releases corticotropin-releasing hormone (CRH). This hormone acts on the pituitary gland which releases ACTH into the blood which causes the adrenal gland to release cortisol into the blood which helps to restore the energy lost in the stress response (increased heart rate, heightened senses, etc.). The hippocampus has glucocorticoid receptors sensitive to cortisol and this inhibits the stress response. When the stressful event is over, cortisol levels fall and the body returns to normal.

A moderate amount of cortisol is good for the body, however, a prolonged stress response accumulates large amounts of cortisol in the blood which causes the hippocampus cells to die. This is why patients with Post-Traumatic Stress Disorder (PTSD) have a lower volume of hippocampus cells. Hence, the patient is stuck in a vicious cycle of increased cortisol build up which kills more hippocampus cells which increases the level of cortisol.

There are two possible treatment plans. Psychotherapy involves talking to a professional counsellor about thoughts, feelings and reflections. Taking medications are an alternative treatment which include pills such as Benzodiazepines which bind to a site on GABAa receptors making it more responsive to GABA neurotransmitter causing the brain to slow down. Another medication is SSRIs that inhibit the re-uptake of serotonin.

One question on mind is how can hippocampus cells be regenerated? What diet or methods could help that? Is it reversible? Are people exposed to extreme trauma doomed to live a life with excess cortisol?


Week 9

This week started normally with a quiz and a lecture and on Tuesday we visited the Cognitive Brain Research Unit in the University of Helsinki. The chapter for the quiz was  about the wiring of the brain. The topics were a bit more difficult than before in our opinion but the lecture after the quiz clarified some things. We for example studied the production process of neurons, which includes cell proliferation, migration and differentiation. On the cell profileration, precursor cells are neural stem cells. Immature neurons are called neuroblasts and they were pictured slithering upwards to the cortical plate through the subplate in the migration phase. At first this mechanism seemed quite strange. The whole neurogenesis process includes neural precursor cells production in the lateral ventricle area, migrating neuroblasts and finally newly generated neurons in the cortical plate. The neuroblasts always go on and form a new cortical plate, which then becomes a new layer. The differation order is neurons first, actrocytes second and oligodendrocytes last.

After the migration the neurons begin forming an axon and the axon travels from the gray matter to the deeper structures in the white matter. Guidance proteins either attract of repel the axon, which guides to axon into a correct direction. There was a good demonstrative video from youtube of this topic, which helped understanding this. There was also interesting information of the connection between neurotrophins and apoptosis. The survival of  neuron depends on neurotrophins provided by target neurons and without the neurotrophins, apoptosis (systematic disassembly of a neuron) begins. Neurotrophins switch off the apoptosis.

The excursion was very interesting but seemed a bit rushed at times. First we visited the no interference room where the test subjects watch silent movies while their brain reactions are tested. After that we had a little presentation of the areas experimented in this unit. We found out that sounds development is affected by native language learnt as a child, particularly the difference between Finnish and Estonian language development. The difference was apparently due to the differing ö and õ sounds, which was interesting to know. We also saw how neural sound discrimination can be improved in dyslexic children using audio training game and a comparison of how MMN differs for different types of musicians. There also seemed to be a correlation between positive brain development and learning music, which was interesting. Furthermore, only listening to music is believed to improve verbal memory, mood and attention.

  • Pekko & Maria

Week 8: Minibrains, Auditory System & First Excursion!

Quizzes & Lectures

This week’s quiz was based on only one chapter which had some pre-acquired information which included; the basic functioning of a conducting structure, how the location of hair cells is related to the frequency and function of the round window, and the effects of damage to conducting structures and nerve and hair cells.

In addition, there was a lot of new and more specific information as well. We knew that the round window in the cochlea is important since it regulates the pressure inside the cochlea. However, we learned this week that it is substantially more important since without it the fluid would not be able to move in the cochlea and therefore, there would be no stimulation. Furthermore, we learned that in the mechanism of sound localisation, the time delay and intensity changes because of our heads altering the intensity sensed are the factors that enable us to know where the sound is coming from.

This week’s lecture began with an interesting talk about artificial mini-brains and the philosophical approach to the topic.This may be a discussion to have in the future when it is possible to add sensory and motor abilities to Artificial Intelligence.

The topic of this week’s lecture was about auditory systems. We leaned about the auditory tract which involves the auditory receptors, the brain stem neurons, the MGN and the auditory cortex.

First Excursion: Nexstim!

We had our excursion to Nexstim company this week. Nexstim produces Transcranial Magnetic Stimulation (TMS) which is a device used to map cortical language and motor areas, for instance a pre-surgical procedure (navigated TMS).

Deep TMS is used to treat depression when all other methods and medications do not seem to work. In reality, deep TMS has various other applications since it is far stringer than regular or navigated TMS and can be used to excite or inhibit different tracts in the cortex.

The presenters at Nexstim showed us a live demo of navigated TMS. We are extremely interested and Pekko might apply for Nexstim in the future since he is very interested in TMS and Nexstim seems to have a great advantage in the Finnish market as well as some parts of Europe.

We think that if all the excursions are as interesting and well as this then we are very pleased with this course’s custom!

Week 6

This week had a similar structure as the previous ones except that there was no exercise session for Tuesday. On Monday we begun with a quiz like before and this time there was only one chapter for studying. Sometimes the preparation for quizzes has been quite tough because the work must be done on weekends with numerous pages to be read. This time the workload was okay and we think we managed to study the chapters quite well. Also we think this might have been the first time none of the questions in the quiz were from review questions from the end of the book chapter although the questions there required quite long answers.

Chapter 15 dealt with chemical control of the brain and behavior. On the lecture we took a look at different neurotransmitter related pathways. It is useful to categorize different brain areas by the neurotransmitter used. For example we concentrated in the differences of acetylcholinergic and dopamine pathways. Also we returned to similar topics with the exercise two as we studied, which neurotransmitters are active in specific brain structures. In our opinion this recap came in a good spot as we’ve forgotten many of the studied brain areas and structures. For example we learned that Substantia nigra, striatum and nucleus accumbens are related to dopamine pathways. Also we learned that the first stages of Alzheimer’s occur because of the death of acetylcholine producing cells in the acetylcholinergic pathways a bit similarly as Parkinson’s disease is due to loss of dopamine producing cells in the Substantia nigra structure. Much of the topics we studied for the quiz were new information but there was something familiar too like the relation between pituitary and hypothalamus.

On the lecture we abruptly examined the differences between catecholaminergic substances. We already knew that dopamine, noradrenaline and adrenaline have similar origins but it came as a little surprise that their chemical structures are that similar. We are looking forward to the excursions, which might well be the most useful take from this course after all as we should probably begin planning for the future after university.

  • Pekko & Maria

Week 5: Chemical control of the brain

Been over a month since we started this course and we can say we have learned quite a lot about the functioning of the brain already. While last week we read chapter 6 which covered the functions of neurotransmitters in depth, this week’s lecture was based on that. We saw a few simple videos demonstrating the action of different types of post-synaptic receptors. They were very easy to understand and solidified knowledge that we already learned earlier in the course. We saw how ligand gated channels work by opening gates upon a neurotransmitter binding to its receptors.

We also saw how secondary messengers work with the help of a g-protein and the production of cAMP from ATP.

Rewatching the video on the cause of depression with sound was very interesting and new. We learned that depression is caused by the lack of enough neurotransmitter Serotonin and Noradrenaline and so anti-depressant drugs block the re-uptake channel of the post-synaptic neuron increasing the concentration of these neurotransmitters in the synaptic cleft.

This week’s reading is based on chapter 15 which we have started to read already. The chapter informed about the role of the hypothalamus and how vast its functions are in the human body. While we already had an idea about what functions the hypothalamus is responsible for and its location in the brain, this chapter goes in depth into the actual implementation.

The chapter mentions that the hypothalamus controls the pituitary gland which controls a lot of human behaviour and functionalities, making it the “master gland” of the human body.

The chapter briefly talks about the effects of stress on the brain which was interesting to read. Apparently prolonged stress can cause premature ageing of the brain. This is a good motivation to take time throughout the day to destress and take time to relax.

– M & P

So we got our exercise 1 results this week! A bit disappointed with the results since the questions were not so specific but the answers were required to be specific. Was a little confused with what was required so did not get full marks for the exercise although this could be the easiest exercise for this class. Well, this tells me about how I should modify my submission for the next exercise to include more detail and go more in-depth to score higher points.

Have not started the exercises after the second since the deadlines are quite far away, although with a quick peek they seem quite interesting and interactive (the reaction time one)

– M


Week 4

This week we had to read quite a lot of pages in preparation for the quiz (from chapter 8 to 10). It was pretty time consuming but gained a lot of knowledge about the role of neurones in detection of taste and light. Again, the ten word or less principle seemed quite awful in our opinion and hope that points will not be deducted for exceeding the limit.

Since the quizzes are held on Monday mornings, the preparation work is usually done on Sundays which is a nuisance. However, the quiz preparation have found to be quite useful in learning and keeping track of the course topics.

There is a lot of excitement for the excursions this week. Hoping it is as interesting as expected. Since the deadlines for the new exercises are quite far in the future and there is a lot of pending work from other courses with upcoming deadlines, decision has been made to not attempt the new exercises yet.

Week 3 – Lecture 3 and trillions of brain structures

This week begun similarly with the previous one: we had a quiz. The quiz was about chapters four and five from the book and the topics included the action potential as a whole and synaptic transmissions. This time we had only five minutes to finish the quiz and some of the questions had a word limit of ten words which didn’t feel practical at all. This might have resulted in a worse performance than in the first quiz.

There were a lot of old and familiar information but also new. Basic properties of action potential; dividing it into phases of depolarization, repolarization and hyperpolarization and the fact that action potential transforms into a chemical form between neurons in the synaptic clefts was old information but a recap was useful because we had forgotten many details of this chain of events. Furthermore, the difference between agonists and antagonists was a useful recap and this topic as a whole is something to look forward to as the function of many modern day medicines are based on the manipulation of synaptic transmission.

The differences between resting membrane potentials in different cell types was new information for us although afterwards it seems quite obvious. We also found it interesting that the difference in the size of the diameter has such a big effect on the conduction velocity of an action potential. Myelin sheath obviously has a great influence but it was difficult to understand how the thickness of myelin makes a difference. We also learned about different types of synaptic transmission and whether the transmission is excitatory or inhibitory. An interesting example of inhibition was that hangovers are caused by body trying to excite the over inhibition of neurons after drinking alcohol. Learning about shunting inhibition and how to kill an action potential was new as well and quite interesting.  Finally, the production mechanism of different neurotransmitter was new for us. It was fascinating to see that some of the neurotransmitter are actually created in the soma and how this chain of events leads to a complete product.

On Tuesday we had a brain composition session which supported our learning of different brain areas. This week had an exercise where we had to identify trillions of brain areas and structures. We think that the main input from this weeks exercises was that flash cards are going to be useful in our learning process of brain anatomy.

  • Pekko and Maria

Week 2 – Lecture 2 + Chapters 3-4

Week 2 lecture began with the first quiz based on chapters 2 & 3. The exam was quite short and easy. We did get 2 extra points for being present so that was a nice surprise.

After the quiz in the class, we spent some time going over the questions asked in presemo during the previous lecture. It was nice to see the presemo questions being properly addressed with concise and focused answers. One of the students asked about the book about free will and it was good to receive the answer to that question since some of us were curious about it as well.

Following that, we learnt about action potentials and its role in neuroscience. The subjects were quite familiar from lessons in high school biology so it was a nice refresher for those of us who have not used this knowledge in the past few years. We learnt about reflex actions, the resting membrane potentials and the structure of the cell membrane including the membrane proteins.

Moreover, we went into more detail about the process of a neurone impulse which was new knowledge for some of us. We saw that the threshold for action potential and how the magnitude of the spike remains the same but only the rate at which it is fired differs. This provoked a thought about how all humans feel the same amount of pain but the rate of it and the time period of how long the pain last differs based on the source. Also it is interesting to know that mental pain feels exactly the same as physical pain and it could even be more “painful” since mental pain could last longer and be triggered more often than physical pain.

Moving on this week’s exercise session, we felt the workload was manageable and the derivation of the Nernst equation was intriguing. While the exercise included information that we already learnt in high school, such as the structure of a neurone, classification of glial cells, description of action potentials and the function of myelination, it also included new knowledge such as the calculation of equilibrium potentials for ion with the Nernst equation, the velocities of action potentials and the delays in synaptic clefts.

So far, a key challenge for some of us with a Finnish background has been language, since, all the terms and phenomena were taught to us in Finnish language, hence it adds a bit of work to translate it all to English. It happens often that the content seems unfamiliar but upon translating, we realise it was familiar information after all.

On the other hand, for those of us without a Neuroscience background, for example with a Computer Science background, there is a bit of extra work revising through old topics that were taught in high school and not used at all in the past 5 years. Even so, it is very exciting and interesting to be able to apply this knowledge again.

– Maria & Pekko