Postgraduate paid internship: my time in Graz, Austria

August 24, 2022 EminaLeave a comment

What to do after graduating? I often asked myself that question during my last year, and some of you might ask yourself the same. Getting employed immediately would be ideal, of course, but I was aware that would be almost impossible. Mindlessly scrolling through my LinkedIn feed in breaks from writing my Master’s thesis, I found out about BioTechMed-Graz Lab Rotation Program after a friend shared about it and included a short summary of their own experience in Graz.

Immediately after reading the requirements, I realized I am in a bit of a time pickle: the deadline was six days away, including the weekend, and I also needed to find a mentor myself from a list they provided. I looked up every name connected to Molecular Biology, checked their websites and papers, and in the end made my top three choices, according to the rules of the application, which stated that you can not choose the field in which you did (or are doing) your thesis. I decided to send an email to the Professor whose work was most appealing to me and hope for a quick response. Somehow, I made the right choice, because the very next day, he replied with a positive confirmation, asking for an online meeting so we can go through the application together.

If you had followed me on my social media for a while, you know that I eventually got the scholarship and spent four months in Graz at the Institue for Molecular Bioscience, where I truly learned a lot. BioTechMed-Graz scholarship is appealing not only to students but also to labs because it secures monetary support for them as well. Although it is called a rotation, you actually spend all your time in one lab, but I really like that aspect, because it ensures you can learn how that one particular lab functions, and I feel like it doesn’t stress you out as much as an actual rotation might. Another thing that I really liked, is that, as a scholarship receiver, you still have some student rights, such as living in the student dorm, which greatly reduces anxiety about moving to another country, at least in my opinion.

In front of the Institute for Molecular Biosciences

I feel like I profited enormously from this internship, as I learned many new laboratory skills and methods, and learned how it is to work in an international team. I met new colleagues, and new friends, many of whom were very incredibly patient and helpful in my first two weeks when I was only working things out. I have to say, many things function differently than in the labs I was used to, and more often than not I had to stop and think where things were, going from chemicals to labs with equipment. My mentor was also incredibly approachable and understanding; honestly, you could not wish for a better boss.

When it comes to the non-academic part of life in Graz, I started just as another winter lockdown began. I was allowed to go to the lab and store, but that was it; cafes, restaurants, and museums, they were all closed. During spring I did finally visit some museums (you can get one year-long pass for something like 17 museums), a botanical garden (which is amazing), went hiking (Rettenbachklamm is so worth it), finally tried Dunkin Donuts (a little bit overpriced for my taste) and Nordsee fast food (I liked it and they also offer coupons on their Austrian website), and visited the Opera. I should also mention that Graz public transport includes trams and buses, and a monthly pass is 55€.

Altogether, I am so happy I had this wonderful opportunity of living and working abroad, meeting new people, and learning so many valuable skills; if you don’t have a job lined up, or just want that extra bit of experience, I would definitely suggest applying for this program!

I would also like to stress that you don’t have to already be a graduate to apply, you can be in the last semester of your program and still apply! I would only suggest starting the search for your mentors a bit earlier than I did 😉

If you have any questions about BioTechMed-Graz or would like to share your experiences with this one, or other paid post-graduate internships, please share them in the comments below! I always love to hear from you!

Movies | What They Had

February 22, 2022 EminaLeave a comment

What They Had is a 2018 movie focusing on the family whose matriarch suffers from Alzheimer’s disease. Although seemingly similar, this movie is very different from the more popular Still Alice, and, in my opinion, shows the difficulties of navigating everyday life better.
The movie, directed by Elizabeth Chomko, who drew inspiration directly from her personal life, stars brilliant Hilary Swank as a worried daughter Betty who comes back home in order to care for her mother Ruth, played by Blythe Danner. Michael Shannon, playing Swank’s brother Nicky, is masterful as ever, showing his impeccable acting skills, as he clashes with their father (Robert Forster) over the possibility that their mother should continue her life in an assisted living facility.

What I like about this movie, is that it isn’t solely focused on Alzheimer’s disease, but rather on family dynamics around it; it explores how members of the immediate family deal not only with their mother, wife, and grandmother as the illness progresses but also with each other.
Without revealing more of the plot, as I truly believe everyone should watch this movie, I have to praise it for tastefully and realistically conveying many symptoms of AD, such as when Ruth wanders away in the middle of the night, experiences speech difficulties or flirts with her adult son, not recognizing him.

The last scene I described isn’t brought on as a dramatic one, but rather a humorous one, albeit dark. As a matter of fact, the whole movie deals with the severity of the situation in a similar manner, but it will still bring tears to your eyes. This movie is honest, truthful, and above all, touching; I honestly can’t believe it’s not more known and as I’m writing this review, I’m quite anxious that my review isn’t presenting it in the best possible light, which it absolutely deserves. I hope my clumsy writing won’t discourage you from watching What They Had, a movie that beautifully reminded me why I chose neurodegeneration as my field of study.

If you watched What They Had, let me know if you liked the movie as much as I did.
I am also sharing the trailer here as well.

Short science posts | Eluding Ctenophora

February 14, 2021 EminaLeave a comment

Ctenophora, commonly known as comb jellies, are a rather perplexing phylum of beautiful pelagic creatures. Their evolutionary position has been debated for many years as is the origin of their nervous system (some scientists believe they are older than sponges and that sponges lost their nervous system, while others advocate the theory about the nervous system forming independently twice, once in cnidarians and once in ctenophores).
Ctenophora have two nerve nets: subepidermal and less organized subgastrodermal, which recent research identifies as a mesogleal nerve net. Nerve cells from this layer communicate with muscles by synapses and affect the locomotion of the body. The subepidermal net is denser around the mouth, the pharynx, and under the comb rows (comb rows are strips that run the length of the ctenophore body and contain cilia called “ctenes”). Ctenophore neurons can be iso- and multipolar.

They have sensory cells on the whole surface of the body and those correspond to vibrations and thermal and chemical stimuli: more receptors are located around the mouth and pharynx. Ctenophora also have an apical and aboral sensory organ. Such sensory organ consists of a statocyst, a sensor that contains a statolith that balances on four groups of long cilia connected to the comb rows. These organs help the orientation of the ctenophore body.
What’s extremely interesting is that ctenophores use different chemical signalling system than the ones described in the previous posts, mainly because these animals simply lack the neurotransmitters (and genes), such as serotonin, dopamine, noradrenaline, and acetylcholine; glutamate is the only neurotransmitter currently known to be present.

I gathered all this information from different resources, and some are sometimes contradictory or are generalizing conclusions about the whole phylum from the data of only one ctenophora species. This is the best overview I could manage, to show both the similarities and the differences of the ctenophora nervous system, when compared to the Cnidarian system. These lovely animals are not very well researched and I’m sure many wonderful breakthroughs about their anatomy, physiology, and their place in the evolutionary tree are to come.

Literature & more information:
^{Habdija et al: Protista-Protozoa, Metazoa-Invertebrata, Alfa, 2011, Zagreb}
^{Norekian & Moroz Neural system and receptor diversity in the ctenophore Beroe abyssicola J Comp Neurol. 2019;1–23.}
^{Ctenophores – quick guide}
^{Did the ctenophore nervous system evolve independently?}
^{Aliens in our midst}

Short science posts | Hydrozoa

September 2, 2020October 31, 2021 EminaLeave a comment

Hydrozoa are the last cnidarian class I’m going to write about. They can exist in two distinct shapes, as hydromedusa and hydropolyp (same as Scyphozoa and Cubozoa). Despite perhaps expecting hydrozoans to be the most advanced in both nervous and sensory systems, they don’t actually have any rophalium. Furthermore, some hydromedusae don’t even have nerve nets. However, they have two nerve rings (outer and inner) on the margins of their bells which are regarded as ganglia by some scientists.

These rings consist of neural pathways which process different sensory inputs (such as light and gravity). Aglantha digitale, a hydrozoan species, has been reported to have as much as 14 distinct neural pathways. A. digitale is also distinct from the other species in the class by having two swimming “modes” – slow (which is a characteristic for all hydrozoan) and escape mode. Transmission through giant ring neurons is responsible for both modes, but the escape mode requires a stronger contraction. The slow swim mode is activated by the input from the pacemaker, which triggers slow calcium spikes. Direct mechanical nerve ring stimulation by tentacles triggers fast sodium spikes. In short, giant ring neurons are capable of generating two different kinds of action potentials.

Gap junctions are also present in (and only in) Hydrozoa, and they transfer electrical signals through the musculature. Furthermore, I would like to emphasize that despite some hydromedusae not having a nerve net, some in fact do, and so do hydropolyps. In polyps, however, some groupings of the neurons could be found around their mouth.

Literature & more information:
^{Habdija et al: Protista-Protozoa, Metazoa-Invertebrata, Alfa, 2011, Zagreb
Do jellyfish have central nervous systems?
Jellyfish nervous systems}

Short science posts | Scyphozoa – more advanced nervous system

August 20, 2020October 31, 2021 EminaLeave a comment

Scyphozoa (true jellyfish) are much more interesting (in a neurobiological way) than previously described corals. One major difference is that Scyphozoa are pelagic animals, which means they are not fixed to the ground. They also have two diffuse nerve nets (subepidermal and subgastrodermal) that consist of bipolar and multipolar neurons – the impulse conduction has been measured at 0,15 m/s. Both nets coordinate the movements of an animal towards the food. Some scientists, however, differentiate one diffuse and one motor nerve net. The motor net is in charge of the activation of muscle contractions after receiving signals from the so-called pacemaker organs (which are in charge of the swimming rhythm). The diffuse net, in this case, is in charge of marginal tentacle contraction and it is also believed it communicates sensory information to jellyfish musculature. Neurons of the motor nerve net are connected by chemical synapses, while neurons of diffuse nerve net are connected by peptidergic synapses that were noted in Anthozoa as well.

Sycphozoa also have much more developed sensory organs than any of the animals previously mentioned. These sensory structures are called rhopalia and they are located on the edges of the jellyfish bell – there are usually four of them (or a number that’s a multiple of four). Rhopalia contain multiple sensory receptors – statocyst (balance receptor), ocelli (light sensitivity), a mechanoreceptor, a chemoreceptor, and aforementioned pacemaker neurons.

I would also like to note here that some authors (I’m referring here to the article “Do jellyfish have central nervous systems?” by R. A. Satterlie) believe this kind of nerve net explanation is rather simplified and that there exist some evidence suggesting that jellyfish have a centralized nervous system, mainly that rophalia are in fact rudimentary ganglia and could be regarded as integrative centers. However, any communications between rhopalia themselves exist only through the nerve nets.

Literature & more information:
^{Habdija et al: Protista-Protozoa, Metazoa-Invertebrata, Alfa, 2011, Zagreb}
^{Do jellyfish have central nervous systems?
Jellyfish nervous systems}

Studying | My favourite online courses

August 18, 2020October 31, 2021 EminaLeave a comment

I don’t know about you, but I just love doing online courses, especially when they deal in subjects I don’t get to explore in my college courses. Over the years, I tried many different platforms, such as YouTube, Google Digital Garage, Khan Academy, Udemy, and, my favourite, Coursera. As a matter of fact, I discovered Coursera back when they started in 2012; most of the courses I took were on topics of Neuroscience and Molecular Biology. At first, courses and certificates were completely free, but with time, they started offering paid vs. free, as well as many specializations and even some college degree courses. However, many of the courses are still available to watch and do quizzes, just without the certification.

Disclaimer: this post is not sponsored by Coursera.

Synapses, Neurons and Brains – available here

This course, offered by Hebrew University of Jerusalem, is actually the very first course I took, and at the time was one of the rare Neuroscience courses. I have only good memories about this one – it is a good introductory course into the field and the professor explained the curriculum very well. Also, the course mentions real projects that deal with neural networks and brain reconstructions, such as Blue Brain Project. I didn’t mention this previously, but every course also comes with subtitles (in English at least) and transcripts, so you can follow along easier.

The Addicted Brain – available here

The Addicted Brain (by Emory University) is another course appropriate for beginners in this topic – I was initially interested not only because of the topic of addiction, but also because various mechanisms of how drugs interact with the brain were presented. The course also covers the topic of drugs in society, although this part mainly concerns United States of America. Also, I don’t know if this is something that’s important to you, but I followed professor’s narration easily – his voice is calming and he speaks very understandably.

Medical Neuroscience – available here

Medical Neuroscience (by Duke University) is not only the most advanced course of the ones mentioned here, but the most advanced course I ever took. Actually, I started it once or twice before, but dropped out because it required a lot of time and dedication that, at times, I just didn’t have due to my University obligations. This course is really extensive and requires some before-knowledge, but is also very satisfactory when you finish it. The only problem I had with this one is that sometimes I felt that questions in quizzes were asking for details that to me seemed almost overlooked in the videos. However, I felt like this course was quite important for my studies, since I have a strong interest in Neuroscience, but lacked the medicinal perspective.

All quizzes are multiple choice answers, with usually one correct answer (sometimes more correct answers). I vaguely remember some questions where you had to connect some phrases (like 1-d, 2-c, etc) as well, but haven’t came across those recently. Also, the quizzes I did were never timed and you can take one quiz 3 times every eight hours (they keep your highest score).

Coursera also offers financial aid – you can fill out an application where you explain why is the course you’re applying for important to you and why you can’t afford it. So far, I’ve heard of many positive experiences where they gave grants.

There are also two Neuroscience related courses I am planning to take – Human Neuroanatomy (to revise a bit) and Computational Neuroscience, which deals with using Python in Neuroscience research. I would very happily review those for you, in a greater detail, if this is something you’d like to read about!

***

What is your opinion on online courses – do you think they’re useful or a waste of time? Did you perhaps take some of the ones I mentioned? If yes, I would love to hear from your!

Short science posts | Do sponges have a nervous system?

July 9, 2020October 31, 2021 EminaLeave a comment

Sponges (phylum Porifera) are sessile multicellular organisms that live predominantly in seas and oceans. They don’t have tissues or organs, and therefore, they don’t actually have a nervous system. However, they do have bipolar and multipolar cells that resemble nerve cells, which are found in the middle, “jelly-like”, layer.
Sequencing of some sponge species showed the presence of many genes associated with neural cells, such as genes that code enzymes for neurotransmitter synthesis and synaptic transmission. It is important to note that these genes have other functions in the organism. It has also been observed that some sponge larvae can respond to outer stimuli and show various “taxis” behaviour – phototaxis (response to light), geotaxis (response to gravity), rheotaxis (response to water current). Phototaxis has been closely studied in species Amphimedon queenslandica (class Demospongiae), a sponge native to Coral Sea.

*Aplysina aerophoba*, also of class Demospongiae, which can be found in Adriatic Sea.

Potassium channels have been observed in that same species, as well as glutamate, GABA, and NO systems, which have been investigated in Ephydatia muelleri, another species of class Demospongiae. Electrical signalling has been noted in glass sponges (class Hexactinellida). These sponges have bodies comprised of a syncitial tissue and their skeleton is made of silicon dioxide. The scientists were able to measure the action potential (5s long, with 29s refractory period) and deduce this signal relies on potassium and calcium ions.
Some scientists even suggest that sponges used to have a nervous system, but lost it during evolution – they introduced several hypothetical scenarios for this event, proposing that sponges lost their nervous system in order to focus on filtering.

Literature & more information:
^{Habdija et al: Protista-Protozoa, Metazoa-Invertebrata, Alfa, 2011, Zagreb
Evidence for Glutamate, GABA and NO in Coordinating Behaviour in the Sponge, Ephydatia Muelleri (Demospongiae, Spongillidae)}
^{The GABAergic-like System in the Marine Demosponge Chondrilla Nucula}
^{Where is my mind? How sponges and placozoans may have lost neural cell types
Elements of a ‘nervous system’ in sponges}

Short science posts | Nervous system evolution

July 2, 2020October 31, 2021 EminaLeave a comment

For the next couple of weeks, I would like to write a bit about the evolution of the nervous system, from early nerve cells to the human nervous system and brain evolution. Alongside nervous I will also focus, to a lesser extent, on sensory systems. These posts will be published on my Instagram account, but I decided to publish them on the blog as well.

Mostly, these posts will be about various animals and the nerve systems they have – nerve nets, nerve cords, complete systems. The main process behind this is called cephalization, and it starts with the groupings of nerve cells and ganglia at one end of the body. After some (long) time, this process led to us having a head with sensory organs and a brain inside it.

But when did all of it start? It is kind of hard to say, for even single-celled organisms, such as bacteria, have voltage-gated channels and genes that support the theory of possible synaptic transmission. These channels are potassium (the oldest), calcium, and, rarely, sodium channels as well. Action potentials have been detected in some algae and diatoms, although their function is mostly unclear. In Chlamydomonas (unicellular green algae) on the other hand, potentials were detected in flagellums, which clearly suggest they play the part in the movement of the algae. Action potentials were also recorded in the cilia of some protists, such as Parmecium.

Of course, the exact evolutionary processes are unknown, and there is a possibility that these organisms acquired the mentioned features later than scientists now assume. It is also possible that some more evolved organisms, such as sponges, subsequently lost some of the features discussed here (more about this in the next week’s post).

Literature & more information:
_{Habdija et al: Protista-Protozoa, Metazoa-Invertebrata, Alfa, 2011, Zagreb
Bacterial voltage-gated sodium channels (BacNaVs) from the soil, sea, and salt lakes enlighten molecular mechanisms of electrical signaling and pharmacology in the brain and heart
Early evolution of neurons
Deep evolutionary origins of neurobiology
From damage response to action potentials: early evolution of neural and contractile modules in stem eukaryotes}

Biology in popular culture – neuroscience & movies

January 10, 2020October 31, 2021 EminaLeave a comment

Hello everyone, and welcome to my new post! Yes, I’ve decided to try and write more often, and this time I will do a bit of self-promotion. As you may, or may not, know, I love watching movies – I think they are great past-time and I find them relaxing. Lately, I have had some troubles concentrating for more than an hour, but for now I would like to think that’s because I wasn’t choosing good movies to begin with. What does that have anything to do with neuroscience?

gyruslogo

Well, apart from writing this blog, I also write and edit for Gyrus Journal. Gyrus is student journal of neuroscience, where we write review articles about different topics: basic neuroscience, neurology, neurosurgery, and psychiatry. I have written some articles, and if you stumble across them, don’t judge me too hard – they are meant to teach us how to search databases, cite, and write in English, since our mother-tongue is Croatian. I feel very fortunate to be a part of this journal, since it helped me a lot in understanding of many scientific terms in English language, primary language of science; it also helped me to learn how to communicate with my authors, as well as how to dissect a topic I’m supposed to write/edit about. Of course, we also have reviewers, wonderful professors and scientists from University of Zagreb, who do the last editing before publication. (I would just like to say that we didn’t have reviewers from the very beginning, hence why some of the earlier articles perhaps lack in quality.) Lately, we have been struggling a bit with latest editions, but started to publish articles online – you can access them all on the link above. You can also follow us on Facebook page as well as Twitter!

A cover photo of Gyrus Journal

In Gyrus Journal, you will also find shorter articles and movie&book reviews, where title of this post finally comes in play! So far, I have written five movie reviews, with three still waiting to be published. For my first one, I picked the obvious choice: Memento (2000) by Christopher Nolan. Apart from being one of my favourite movies in general, I think it truthfully portrays anterograde amnesia.

In addition to portraying Leonard’s fragile mental state that makes us question not only his current objectives, but also whether his recollections of past are reliable, or simply figments of his imagination and almost fatalistic wishes, Memento is different in comparison with other films of similar genre, simply because it truthfully portrays the slow agony of losing the principal neurobiological process – a human memory.

You can access the full text here: Gyrus11-Memento

The second review I did was about movie that might not seem so obvious, but was quite intriguing: Side Effects (2013) starring Rooney Mara and Catherine Zeta-Jones. This movie also has a crime aspects but it deals with the psychiatric illness, for which we don’t know, until the very end, if it’s real or faked.

You can access the full text here: Gyrus12-Side-effects

Although dealing with semi-real thesis, the question still remains how the movie influenced real world cases. Did it help with recognizing the ones feigning the illness, or just put extra strain on the patients dealing with the illness that is already under deep historical stigma? Regardless of being the rather entertaining thriller, we are left wondering whether the movie deepened the negative view of the various psychiatric illnesses in the general public.

Three, still unpublished, reviews are:

100 Minutes of Glory (in Croatian) – a biopic about famous Croatian painter Slava Raškaj, who was born deaf, suffered from depression, and lived her last days in Psychiatric hospital “Vrapče”. In Croatian, title of the movie is also a wordplay on Croatian word “slava”, her name; it’s literal translation to English is “glory”
A Different Brain – famed documentary by Loius Theroux; it follows four patients who suffered through some sort of traumatic brain injury and consequences it brings
Still Alice – movie that earned Julianne Moore an Academy Award for Best Actress, Still Alice is a touching but often times difficult story about a woman with early onset Alzheimer’s Disease

What about you? Do you like watching movies – which ones are your favourite? If you watched any of these, please tell me what you think! I would love to discuss movies with you & I’m really interested what you watch in your free time 🙂

A short adventure in Pula

October 14, 2019October 31, 2021 EminaLeave a comment

Pula is a small town located in Istrian peninsula (Croatia), famous for it’s film festival, beautiful sea, and rich history. As such, it’s also a great choice for many symposiums, meetings, and congresses – I have visited it twice this year only!

My Pula adventure lasted for four days, during Croatian Neurological Academy, a medical congress dedicated to neurology (and neuroscience). The Academy was held in Histria hotel, on Verudela beach – this setting is wonderful, we were surrounded by sea for miles. Also, the food was superb; many choices for main dishes and desserts (sea food, vege options, pasta, various meats, pastries…).

Now, this blog is called Science Pit, because you know, science; however I also like to travel a lot, and I am a self-proclaimed history buff. So, this particular trip was a bit less neuroscience, and a bit more “look at that historic statue!” (Don’t worry, I went to a gorgeous science museum as well!)

When thinking about Pula, most of people immediately think about Pula Arena, an amphitheater distinct by being the only one that has all four towers still preserved. It was built between 27 BC and 68 AD. This was my first time visiting the Arena, and honestly, it’s impressive. Walking inside something so old, imagining what have taken place in this structure, which famous Romans were part of the fights… It’s a breath-taking experience, and words don’t do it justice.

Huge stone arches of Amphitheater in Pula; with sky seen through the arches. — Amphitheater in Pula; 2000 years old.

Another details of the Arena arches.

A stone lion statue, inside of the Arena.

After Arena, I visited Temple of Augustus, a temple dedicated to Augustus (formerly known as gaiusu Octavius), first Roman emperor. The Temple has been standing in its place for 2000 years (give or take a few years). When you are in front of it, the Temple seems as it was built couple of years, and not two millennia ago. The third historical landmark I saw was an arch – not Arch of the Sergii, but Porta Gemina (rough translation = Double door).

Temple of Augusts.

A stone statue.

After all this, I headed back to the direction of the hotel, with a twist – Aquarium Pula is just 15 minutes by foot from my hotel. At first, I was a bit taken aback by the ticket price (student ticket is 90HRK =12€), but my mom encouraged me to go with her anyway. And honestly, it was worth it. I was a visitor once before, as a part of my obligatory Field Trip during my Bachelor’s. Surprisingly, I was as fascinated this time, as I was the first time – the abundance of sea life in Croatia is staggering, and it always reminds me how little we know about our oceans. The aquarium also has reptile and butterflies sections, but those include species not found in Croatia (such as caiman). I would absolutely recommend visiting, and take your time while you’re inside – photography is allowed!
This photo is just a small glimpse of photos and videos I’ve taken – they deserve their own post, or even a video. P. s. Of course I’ve found a cave!