Week 26.11 – 02.12

For this week’s exercise we performed an Electroencephalography, EEG for short, which means we recorded the electrical activity of the brain of a subject.

After some brief explanations we moved to the chamber to perform our little experiment. First it was necessary to measure the subject’s scalp, so we would find the size of the cap needed. After that, the thirty-two-electrode-cap was placed in the subject’s head and all the wires were connected. It was now time to apply the conductive gel, to lower the impedance between the scalp of the subject and the electrodes on the cap, that was similar to the one presented after.

Image available at https://pt.wikipedia.org/wiki/Eletroencefalografia

The subject was then exposed to two kinds of tests: visual and audio. This exercise took about 12 minutes, during which the subject was alone and focused inside a chamber.

There are plenty of methods to study brain function but this is still one of the most used, mostly because its cost is significantly lower than other techniques, even if its spatial sensitivity is relatively poor.

Week 12.11 – 18.11

This week started with the weekly quizz. This time it was the turn for the Wiring the Brain chapter in the book, where we could learn about how the brain comes to be what it is in its adult stage. From its synapses to its macroscopical structure, what lies behind the genesis of our most important organ ? That’s what we attempted to understand in this lecture.

We started by going through all the precursor cells and the paths and transformations they go through to achieve their final destination and structure. Soon enough, we concluded how the brain grows inside out, just like one of the questions on the quiz wondered on. It is said so precisely because the neutrons migrate from the inner part of the cortex to more superficial cortical layers, past already formed ones. We went through how each neuron grows until it reaches its target cell, aided by either chemoattractors or chemorepulsors.

Specifically in this topic it was very interesting to understand how scientists got their hands on this kind of information and perfected their theories throughout the years. Most studies were obviously made on animals, namely mice and frogs. This made me wonder a bit about animal experimenting. Of course most of neuroscience is based on it, and the authors of the book for this course do provide a good justification for its use in one of the initial chapters of the book. But how far can we go in the name of science ? Maybe for now that we know so little about the mysterious workings of our brain we are not comfortable experimenting with humans yet. But hopefully at some point we will be able to leave animal experimenting in the past and move to other methods of researching.

Synaptic rearrangement and elimination were extensively discussed along with the mechanisms behind ocular dominance shift or at least the theories surrounding it. It was widely interesting to finally learn that critical periods for human capacity plasticity really is a real studied and confirmed thing instead of simply a theory we tell ourselves to excuse our less capable selfs of learning new things as we grow older. Certainly a lot of research is still to be done in those fields.

The following day we went on our second excursion on this course. This one sparked our interest and curiosity much more than the first one we must say. This excursion was to the sooma medical company. None of us knew anything about it so we went with o expectations.

Our first impression was quite positive since the atmosphere of the company is super modern and has a little scent of innovation in the air. Was we sat down, one member of the company promptly introduced us to their main activities and devices. The product they offer is tDCS self-neurostimulator. They have been developing it and testing it for a few years now and have gotten groundbreaking results. The main advantage is that it is very easy to self administer, there is simply one button on it. It also has automated safety features to ensure the patient’s comfort.

So far they are only making it available for medical professionals instead of providing treatment themselves. It supports double-blind condition and can be configured for multiple study protocols.

Sooma is in fact the world leader in home-based neuromodulation at the moment. In the studies they carried out, the majority of patients experienced a marked improvement as a result of the Sooma Depression Therapy. The average improvement rate was 49%. This is quite impressive comparing to other existent solutions for depression. More specifically, 86% of the patients achieved partial response, the response rate was 59%, and the remission rate was 18%. This sounded very promising. Let’s see how this values evolve as it is increasingly used.

Depression is unfortunately an issue very much worth debating given its high prevalence in nowadays population, specially in younger age groups. If this turns out to be a reliable method, even to add to the already used ones including medication, it could make a difference in a lot of lives for the better and that should really always be researchers main aim at every point.

Week 05.11 – 11.11

This week we discussed about the Motor System – which are chapter 13 (Spinal Control of Movement) and 14 (Brain Control of Movement) of the book Neurocience: Exploring the Brain. Not without going back to chapter 10 (The Central Visual System) to explain something that had been left unsaid.

The motor system consists of all our muscles and the neurons that control them. The spinal cord contains specific motor “programs” for generating coordinated movements, being these programs accessed, executed and modified by descending commands from the brain. Motor control can be divided in two parts: the spinal cord’s command and control of coordinated muscle contractions and the brain’s command and control of the motor programs in the spinal cord.

The cells of skeletal muscle – which constitutes the bulk of the muscle mass of the body and function to move bones around joints, for example –, muscle fibers, are each innervated by a single axon. The ventral horn of the spinal cord contains lower motor neurons, that innervate these skeletal muscle fibers, and which are divided into two categories: alpha motor neurons and gamma motor neurons. The first ones trigger, directly, the generation of force by muscles. Muscle contraction results from the individual and combined action of motor units – which are an alpha motor neuron and all the muscle fibers it innervates.

If alpha motor neurons excite skeletal muscles, we need to understand what regulates motor neurons in order to understand the control of muscles. An interesting experiment to understand more about the innervation and the types of motor units (slow and fast) is one where you force slow motor units to innervate a fast muscle. What happens to the muscle? It will switch to assume slow properties; the types of proteins expressed by the muscle were altered by the new innervation.

The spinal cord contains an intricate network of circuits for the control of movement; it is far more than just a conduit for somatic sensory and motor information.

In this part of the lecture, we learned about movement and its spinal control from different points of view (biochemistry, genetics, biophysics, behaviour, etc.). And this knowledge, derived from every approach, made us achieve the most complete understanding of the topic, leaving us still with some questions that should be answered in the next part of the lecture.

How does the brain influence the activity of the spinal cord? First, it communicates with the spinal cord through axons that descend from the brain along two major groups of pathways: lateral pathways (2 tracts) – controlling voluntary movements of the distal musculature – and ventromedial pathways (4 tracts) – controlling postural muscles.

Several experiments were made on monkeys to prove the relation with the pathways and muscles, among other things. Next, this week we leave an interesting note on behavioural neurophysiology, taken from the book that we are following in this course.

Bear, Connors, Paradiso: Neuroscience: Exploring the Brain, 4th edition, Lippincott, Williams & Wilkins, 2015, 495.

Week 29.10 – 04.11

Lecture 29.10

The topic of this week lecture was the human auditory system and the vestibular system. The systems have different functions, one is to hear the sounds surrounding and the other is to be able to keep balance. Their respective functions are not the same but yet some similarities can be found in their mechanism.

First, we explored the structure of the human’s ear. It is composed of three parts: the outer ear, the middle ear and the inner ear. Each part has some unique features and characteristics. The pinna and the auditory canal form the outer ear, their task is to collect the sounds from the surrounding environment and lead them into the ear so that they can be analyzed. We learned later on that the structure of the pinna plays an important role in the evaluation of the location of a sound in the vertical plane. The shape allows the ear to receive two different sounds, a direct and a reflected one.

Then the middle ear, composed of the ossicles and the tympanic membrane, was studied. It is quiet impressive to think that these very little bones can totally change the way we hear and that they are a necessity in the human ear.  They have two major roles to play. The first is to amplify the sound force up to 20-fold amplification. The second is the attenuation reflex; it is a system that includes the contraction of muscles attached to the ossicles in case of a loud noise. This provides the human ear with a good protection against loud sounds that could damage the inner ear. The two roles combine to provide a great capability to the human’s ear.

Finally the inner ear, the cochlea, was inspected. It is a very important step in the auditory pathway. In the cochlea, the sounds signals are analyzed with the help of the hair cells. A quiet complex system of potassium pumps allows determining the movement of the basilar membrane, which characterize the sounds. The informations collected are then send to neurons to be translated.

The experiment described in the lecture shows that there is a relation between the nature of the sounds and the location they are processed in the brain. It is interesting because it shows that we already have an idea of the sounds before actually analyzing it. It allows the neurons to be more specific and therefore to ear better.

Week 15.10 – 21.10

Lecture 15.10

This week we discussed about the Visual System – which are chapter 9 (The Eye) and 10 (The Central Visual System) of the book Neurocience: Exploring the Brain.

This is a topic I particularly find very interesting. The complexity of this sphere, and everything that is behind, really fascinates me. We started by talking a bit about the anatomy of the human eye and how light affects it (the lens, specially). We briefly discussed some malfunctions of the eye, such as myopia or hyperopia.

Light must pass through many cell layers before it reaches photoreceptors at the back of the retina. These photoreceptors can be of two types: rods – that make vision possible in low light – and cones – enable us to see in the daylight. What photoreceptors do is transduce light energy into changes in membrane potential. We can perceive colours due to the contributions of short-, medium- and long-wavelength cones to the retinal signal. A curiosity on this topic: have you ever wondered if we all see colours the same way? The answer is no! Females are known to have more cones than males. That allows them to distinguish between similar colours better than men, who, in general, have more rods. Just as a conclusion to this curiosity, this happens because long time ago, men would go hunt, meaning they needed a better sense for shapes, whereas women would stay still gathering berries, for example, and needed to distinguish the colours to avoid poisonous food. Those who couldn’t do it would die, so the genes for more cones in women and more rods in men were passed onto the next generations.

About the central visual system, in this part of the lecture we explored how the information extracted by the retina is analysed by it. Our visual system provides us with a unified picture of the world around us, yet we have two eyes and therefore two visual images in our head that need to be merged. To see how the brain does that, we examine the stimuli that make different neurons in the visual cortex respond and how these response properties arise.

The left side of the retina is connected to the right side of the brain, as well as the right side of the retina is connected to the left side of the brain. This happens because the optic nerve fibers cross in the optic chiasm.

To finish the lecture we watched a movie about colour understanding and it was very informative.


Exercises Class 16.10

On this week’s exercise session, we answered some questions related to the topic. One of them was about optical illusions and how we can trick our eyes into seeing something that is different from the reality.


FOR FUN: visit https://eyewire.org/. It’s a 2012 game to map the brain that challenges players to map neurons in 3D. The goal is to identify and classify cell types as well as potentially expand the known broad classes of retinal cells.

Week 08.10-14.10

The class on monday started with a 5 minute quiz about the 15th chapter. Then we learned about the different diffuse modulatory systems : We started with the Acetylcholinergic pathway, and the implications that a malfunction on it mean. We then went over the Catecholaminergic, Norepinephrine and Dopaminergic pathways. Some malfunctions of these pathways were also discussed. How accurately can we really evaluate these malfunctions? How soon could we expect to see some more advanced interventions  in medicine on these pathways?

We then discussed the serotonin pathway and its mediation by the hypothalamus and the pituitary gland.

To get a full image, we went over each of the hormones secreted by the pituitary gland : Oxytocin, related to birth and therefore usually linked with love and compassion; Vasopressin, our thirst regulator; Cortisol, our main stress indicator; etc…

The following matter to be discussed was the Autonomic Nervous System. This was particularly interesting when the contrasts between the sympathetic and parasympathetic systems were drawn. (arousing VS calming).




The idea of how complex and interconnected these pathways actually are are highlighted numerous times. Each pathway influences all other making some imbalances very hard to track down.


To make some sort of introduction for the following day we started the subject of how we can see and study the brain through different imaging techniques.

The first one was the PET scan.

Then a super interesting study was mentioned and discussed for a bit. It was about Adult attachment styles in social bonding and how you can evaluate them through the level of attachment avoidance.

On that same day in the afternoon we had an excursion to a company called MEGIN. We arrived and were welcomed into a very nice environment where one of their employees walked us through everything that they do on that company.

MEGIN was originally named Neuromag, it was founded in 1989 and it has been a leader in whole-head magnetoencephalography ever since then. In the office we visited they no longer manufacture their products but instead develop new ones and take care of all the logistics and business for the ones already on the market.

To better make us understand why MEGIN is so innovative and essential to Neuroscience research he gaves a good insight on how the MEG and EEG work, how they can be filtered, improved, adapted to different kinds of patients, etc…

Then we got to see the MEGIN most break-through products, from the Superconducting SQUID sensors in liquid helium in a helmet-like structure that we got to hold in our own hands, to the  new TRIUX™ neo . We got an extensive scientific explanation for how all of them worked. Some questions were raised by students about adapting the different machines to children or babies but apparently there is no need to do so. This was quite interesting. Some signal processing with specific filters is apparently sufficient.

This was the first week we had an excursion so it was quite exciting. We are very much looking forward for the next ones J

Week 01.10 – 07.10

Lecture 01.10

The focus on this week lecture was the neurotransmitter, the chapter 6 – Neurotransmitter systems – of the book “Neuroscience: Exploring the Brain (2015)”.

The first transmitter studied further was the glutamate. It is the most common excitatory neurotransmitter in the brain and if it doesn’t work properly, it may causes some serious damages that can push to the death of the neuron.

On the other hand, another important neurotransmitter is GABA which is known to be the most common inhibitory neurotransmitter in the brain. Therefore it is mainly found in inhibitory synapse that when activated and located between the excitatory synapse and the soma, will dissipate the current signal and then no change of potential will be recorded in the soma.

The G-proteins were also an important factor looked into in the lecture. It is essential to understand how they work since they are really common proteins, especially in the brain. The G-proteins induce a cascade of called second messenger. It is a significant process since it can influence the signal a lot. The main second messengers cascades advantage is the signal amplification. In consequence, more than one protein can be activated from a single G-protein activation.

I think this week lecture was really interesting as we learned more about the complexity of the neurotransmitters. In addition, I was glad the teacher showed us some little videos about the different mechanism. I personally like it because it gives me a visual approach that helps me a lot to understand and remember the different processes.


Exercises Class 02.10

This week exercise session was a bit different from the others. We were in the computer room and actually did a real experiment; we were measuring the aural and visual speed of reaction. Even though the conditions might not have been the optimal for an experiment related on quickness of mind, I still think if was interesting. It gave me an good idea of how some easy tests can already give some good information about how the brain works.

Week 24.09 – 30.09

Lecture 24.09

Today’s lecture topic was the chapter 5 – Synaptic Transmission – of the book “Neuroscience: Exploring the Brain (2015)” and we followed the book closely, going through most of the figures in this chapter and having them explained by the professors.

Synaptic transmission is a complex topic since all the operations of the nervous system (action of psychoactive drugs, the cause of mental disorders, the neural bases of learning and memory, for example) can’t be understood without knowledge of it.

In this lecture the mechanisms and details of synapses were discussed. We started with the basics – for example, by defining gap junctions, the direct openings between two cells, or discussing their structure – proceeding then to more complex issues.

We discussed the different types of synapses (electrical or chemical). Both have their roles but chemical synapses – when chemical neurotransmitters transfer information from one neuron to another at the synapse – cover the majority of synapses in the brain, which is the reason why the lecture was focused on chemical synapses from this moment on.

Something interesting and to think about is the fact that we still don’t know a lot about all the molecules involved in synaptic transmission. Here is the Box 5.3 from the book where we can learn more about it:

Bear, Connors, Paradiso: Neuroscience: Exploring the Brain, 4th edition, Lippincott, Williams & Wilkins, 2015, 125.


Exercises Class 25.09

During this week’s exercise session, we had the opportunity to do a 3D model of a brain with playdough. It was an interesting way to learn the different parts of the brain, since we were listening the teacher’s explanations and learning while sculpting the different parts of the brain at the same time.

Week 17.09 – 23.09

Lecture 17.09

We started the class with a 5 minute quizz about the chapters 2 and 3 of the book: Mark F. Bear, Barry W. Connors, Michael A. Paradiso – Neuroscience: Exploring the Brain (2015).

After that, some big questions were raised. Those were the questions that propel neuroscience to move forward and neuroscientists to still strive to learn more about how our brain works. The motivation to pursue such achievement is no small one: brain disorders have been becoming increasingly prevalent in our society and in order to cure them we must endeavour through uncharted territories, learning more about how the brain works, from a molecullar to a cognitive level. Our central nervous system has an incredibly complex structure, featuring hundreds of different kinds of transmitters and over 86 million neurons. This can be partly explained and tracked by the evolution of our species. Some questions about human brain enhancement were raised which also arose some interesting ethical questions by students in preseemo. Should we aim to enhance our brain at all? We can probably do so through magnetic stimulation. Genetic enhancement/editing is also an ever expanding field, which might show us some surprising aids to our life sooner than later. It was also pointed out that eating well and resting is a key factor in keeping the brain’s function’s at bay. After this interesting debate, we moved on to the topics on Chapter 3 of the book: The Neuronal Membrane at Rest. We went over the three main contributors to the resting membrane potential:

  1. Cytosol and Extracellular Fluids – Water is the main fluid both inside and outside of the neuron. Because of its highly polarity, it acts as a very good solvent for electrically charged atoms or molecules (ions). The molecules of water surround each ion in so called spheres of hydration, and effectively insulate the ions from one another. Ions are the major charge carriers in the conduction of electricity in biological systems, including the neuron. Water molecules attach themselves to different ions in different ways, which leads into a different transportation and membrane permeability to those ions . Some ions of particular relevance for this studies are the cations Na+ (sodium), K+ (potassium) and cation Ca2+ (calcium), and the anion Cl- (chloride).
  2. The Phospholipid Membrane – The neuronal membrane is made up of a sheet of phospholipids. They feature a stable arrangement, named phospholipid bilayer, that organizes itself in such a way that the hydrophilic heads face the outer side of the membrane and the hydrophobic tails face each other. This structure separates the neuron’s cytosol from the extracellular fluid.
  3. Proteins that span the membrane – After reviewing the basic structure of a protein, from its primary to quaternary structure, the protein’s many functions in the phospholipid bilayer were mentioned. Firstly, they provide structure, forming a cytoskeleton that provides the neuron’s its shape. Then, some proteins (enzymes) are catalizers to certain neuronal chemical reactions. The also make up the receptors that are sensitive to neurotransmitters. And last but definitely not least, they form channels and gates across the membrane which are routes for ions to cross it .

This mechanisms play an essential role in maintaining the resting potential stable. This movement of ions, however, does not happen in a random manner, but rather follows physical (diffusion) and electrical laws.

We then moved on to how the neuron membrane is at its resting potential: what are the concentrations of ions on each side of the membrane, what mechanisms help them keep it that way. The ion Potassium is more concentrated on the outside whereas Sodium, Calcium and Chloride are more concentrated on the inside. The sodium-potassium pump is mainly responsible for maintaining this large potassium concentration gradient across the membrane. At rest, the neuronal membrane is highly permeable to potassium, because of membrane potassium channels and it is negatively charged precisely due to the movement of potassium ions across the membrane.

This electrical potential difference work as one of the battery, kept stable through the work of ion pumps. We then moved on to focus on the Action Potential. We discussed the mechanisms that are responsible for the action potential and how it propagates down the axonal membrane.

We went over the different phases of an action potential, in the following order : resting potential > rising phase > overshoot > falling phase > undershoot, and its trigger, called the threshold, and how we can measure them through different experimental methods (voltage clamp). We went over each step of the depolarization (through Na+ Influx) and repolarization (through K+ exflux) of the cell membrane and were introduced to the structure and function of a voltage-gated-sodium channel (analyzed through the patch clamp technique). This channels works its way through some phases called activation, inactivation and deinactivation in order to regulate the passage of Na+ through it. Next came the propagation of the action potential through the neuron’s axon, aided by the myelin sheath that allows for a saltatory conduction of the impulse. After came the different classifications of synapses, according to mechanism and structure (electrical – gap junctions – VS chemical synapses), according to connection (axodentritic VS axosomatic VS axoaxonic VS dendrodendritic) and the neuromuscular junction complex. Finally we went through a brief overview of all the process of neurotransmitters transmissions: from synthesis and storage to release, reception, recovery and degradation. This are all complex processes mediated by different cell components in the axon, voltage-gated ion channels in its terminal and different enzymes and ion channels across the membrane. It was also discussed very briefly how the synaptic integration happens when multiple action potentials reach different dendrites of the same neuron.

Exercises Class 18.09

In the first exercise class we went over the different exercises on our first assignment. These regarded the structure of a neuron, the function of the glial cells, the different phases of the action potential, the action potential propagation velocity and finally a derivation for the equation that allows us to calculate the Equilibrium potential for a certain ion.