Biology in popular culture – neuroscience & movies

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?

 

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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 the Gyrus Journal; light pink stylized brain surrounded by Gyrus logo and topics
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 🙂

RTŠB 2019 – biospeleology field trip – PART 2

I hope you liked part 1 of my biospeleology field trip in Slovenia, because here is part 2! Here I write about other days & share the rest of my experiences.

Day 5

The day started with making some spreadsheets and entering coordinates for various water springs. After that, we visited the Rivčja jama again, but unfortunately we found no Proteus (or anything else for that matter) in our traps. However, we found a very narrow entrance to the other part of the cave, aaaaand I got stuck. Like properly can’t-move-in-any-direction stuck. Most of you who never visited a cave probably wonder what kind of feeling that was. I don’t have a straight answer for that, since it’s more a range of emotions being experienced all at once; I wouldn’t describe it neither as panic nor fear, although parts of that were present. It was more a desperation that I’m not strong enough to wiggle out, mixed with frustration and adrenaline rush. I didn’t feel claustrophobia, but that feeling might sometimes be present as well. In the end, I managed to drag myself up that hole, and enter another part of the cave. Tjaša went even further, to my amazement, but I stayed back with Ester & Eva and collected as many pieces of another fox skeleton I could. This was was almost hole, but I only took few limb bones, skull, jaw bones, and vertebrate. *expect a video about it soon
After this ordeal, we went back to swimming in beautiful Krka and went back to school for quasi picnic (a barbecue on the school meadow).

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Inside of the cave

Day 6

Day six was day off; Bruno, Paula, and me went to Ljubljana and visited huge mall complex. Why? Because they have Whoop!, a trampoline park. In our defense, we were not the only adults there. After an hour, we went on our merry way to Burger King, and then a bit of shopping around. The most important thing I bought were hiking shoes. Paula helped me choose a pair (she specializes in orientation running, so knows a great deal about it), and they are pretty neat. But why Emina, why didn’t you already have ones? Well… That’s a long story, but I never had to walk this much before, and didn’t have to constantly change from my boots to rubber ones. So yes, before buying this pair, made for walking around in the forest, I wore my black combat shoes, with metal caps. One boot weighs almost 1 kg, so you can imagine how easy I suddenly walked everywhere. Just a note, specialized shoes exist for a reason.

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Wasp spider, Argiope bruennichi, in the grass

Day 7

On this particular day, I was on duty. I already wrote what that means, and it was exactly like that – preparing breakfast and making lunch&dinner. Nothing interesting happened, after my group returned we talked a little bit where they went, some determination of specimens happened, and we also had another lecture, about climate strike.


Day 8

This day was special because we were joined by Teo. I think he was Ester’s mentor for her Master’s thesis, but I’m not sure. In any case, Teo is an achieved biospeleologist and obviously knows a lot. First cave we visited, Jama pod Gradom, was nice, but I honestly don’t remember much, apart from the fact that we were walking around for kilometer or two, before realizing we parked in front of it. The second one, Blatna jama v Šici, was, to me, quite a difficult one. We spent more than 2 hours inside, climbed up, and down, and up and down, we crawled, and had to use the before-installed rope in order to pass some sections (not with equipment, just good old hold-the-rope and walk really closely to the rock). Well, the fact these were old lead to the unfortunate fact that Bruno fell in the water, after part of the rope tore. I wish I caught it on the video, but, by then, my camera was already completely out. We did caught quite a lot of Proteus, and I honestly didn’t realize how big they can sometimes be. *I have to check, but if the footage is salvageable, you can expect some kind of video
In the evening, I did some more determination with Anja & Tjaša.

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Did you know spiders can also live in the caves?

Day 9

First cave (Vodna jama pod Zijalom) was flooded, so we were hanging out in the front, trying to catch some more Niphargus (them) or taking videos (me). Then, we went back to Velika jama pod Trebnjem, the first one we visited and where we laid traps for infamous Leptodirus. Unfortunately, we found nothing, every trap was empty. Of course, we went back, and then some of us went looking for bats with bat group. This catch-mark-release activity has taken place a bit further from the school, near the small pond. The pond which also connected to a cave system, but had no entrance big enough for us to go in. So, two wild-life cameras were put up, as the word from the village was that at night, Proteus came out to play, um feed? Swim? Enjoy the moonlight? I’m still not sure, but next day I was told that they were captured on video. All-together, 23 bats were caught, with 10 different species being noted, which is a lot. Like huge, because when we first started, the bat group was optimistic with the estimate of “maybe 10 bats, and maybe 3 species”. I didn’t handle any bat, because 1. I don’t know how and 2. I have a perfectly rational fear of rabies.

 


Day 10

No caves today! I switched, and spent the day with amphibian group. And since it was the last day, we mostly chilled. We did try to visit one pond, but it turned out it doesn’t exist. The second one was actually really close to the cave I visited previously (Pekel pri Kopanju), and there we found quite a lot of frogs (all stages) and salamanders. Honestly, they looked really cute too! Afterwards, we went to Krka for quite a long time (*and quite a nice footage!). For dinner we actually had a whole dinner&party, but I had to miss that one due to migraine.


Last day was un-adventurous, we packed, ate a lot at McDonalds, and finally arrived home. And I’m looking forward to going again.
I would like to say a big thank you to Ester, Tjaša, Anja, Eva, Teo, and Živa, as well as our organizers.

Biology & informatics &… olms?

Last Friday (8th of November) I was fortunate enough to hold a workshop (with Bruno) called “Little workshop of Bioinformatics” – the title is a bit wild, but we purposefully chose an “exotic” name in order to arouse curiosity.
This workshop, held in House of Velebit in Krasno, is actually a continuation of a two workshops we already held (one in a City Museum Samobor and another one at my old primary school) and which we designed to introduce school children of all ages to primary concepts of molecular biology & genetics. Of course, kids in 7th and 8th grade were already familiar with it.

We first designed the workshops, with the help of our mentor Dalibor Paar, associate professor at Department of Physics, Faculty of Science, and were nominated for Rector’s Awards in 2019.

Where is the informatics part, you ask? In the using of micro:bits, cute and small mini computers that are easily programmable in Python or JavaScript (we chose Python). Bruno wrote a very elegant code and I designed the rest of the workshop: ciphers to de-code, phenotypes, core of the workshop… In terms of design, my BFF Ivana generously lend her drawing skills and we were all set.

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How the workshop works?
First, I introduce students to basic concepts of the molecular biology: what is DNA, what is a protein, and that DNA codes for proteins. This part, depending on the ages (and attention) of children can last up to 15 minutes, then the fun begins. Every kid gets a cipher, which consists of four or five lines, each of those consists of nine differently coloured arrows that can point in one of four directions: up, down, left or right. micro:bits have motion sensors that pick up in which directions they are pointed and display one of the four letters: A, C, T or G. We also coded for a second program, in which kids enter those letters (DNA bases) and they show three letters that represent a very short amino-acid sequence (in this example, a protein). When they are finished with this part, we give them another paper, where they are supposed to find what is encoded by their protein (blue or green eyes, blonde or red hair…).
For the workshop in Krasno, we switched things up a bit, and our “proteins” encoded for different characteristics of two different olm subspecies: a pink one and a black one.
This might seem a bit complicated in theory, but in practice, children picked up everything really fast 🙂

Olms & micro:bits!
Olms & micro:bits!

So, how many of you have heard of olms, or proteus? And how many of you knew there is a black subspecies? 🙂
Olms (Proteus anguinus) are amphibians (like frogs), they are completely aquatic and live in dinaric caves. Noted sightings include Italy, Slovenia, Croatia, and Bosnia and Herzegovina. They have elongated bodies, external branchiae, and no eyes. The black subspecies (Proteus anguinus parkelj) is, well, black, and has eyes. The other notable difference is that pink olm lives in colder waters (up to 11° C). Another interesting fact is its name in Croatian: “čovječja ribica”, which roughly translates to “human fish”.

I think the name is appropriate, and you?

Neuro & speleo

As promised (to my two and a half readers and myself), I’m diligently writing another post, and this one combines my two greatest scientific loves – neuroscience and biospeleology!

Last weekend, I attended two very important conferences – 3rd Rijeka forum on neurodgenerative diseases – diagnosis and treatment in early stage of disease and 2nd Dinaric symposium on subterreanean Biology. There was one day overlap between the two, so I chose to spend my Friday in Rijeka, but more about that later on. Since this trip included a lot of walking and transport, for the simplicity I packed only the bare necessities, which included only one pair of booties (this comes in play later on).

The topic of neurodegenerative diseases is something I would really like to do all my future research in, and it’s also a subject of my master thesis (precisely, neurofibrillary tangles in rat brains). Also, there was no attending fee, which is pretty much amazing for the students. We (Bruno and me) arrived in Rijeka (from Zagreb) very early in the Thursday morning by bus and set to find the University campus where forum was taking place. This wasn’t my first time in Rijeka, so we didn’t have any problems with finding the venue. The forum consisted of plenary lectures held by renowned professors from all over the Europe (Sweden, Italy, Slovenia, England) and Croatia of course, and it was roughly divided into two parts, basic neuroscience and clinical research. As a biologist, I didn’t pay too much attention to clinical part, and instead was dutifully solving my programming homework. However, it was amazing to be there for both days, and just listening what was new in the world of neurodegenerative diseases. I didn’t find courage to ask questions (during the Q&A time, or even after), but I hope that one day I will. We didn’t “touristly” roam around Rijeka, but we stayed overnight in the most gorgeous apartment in the centre, I was seriously impressed!

On Friday, after lecture, I stayed in the venue for a little while (internet access!) and then we went to the train station. I love travelling by trains, and I try to do it as much as possible. Luckily, this train to Ljubljana (yes, Slovenia again!) also went through our next stop, Postojna. If that name rings a bell, that’s surely because of the Postojna Cave, one of the most famous caves open to tourists in the area. It is also special because there are many blind cave salamanders, which are part of the vivarium as well. Our plan was to visit this cave at Sunday, while Saturday was reserved for the Dinaric symposium. The symposium was held in Karst museum in Slovenia, and we caught the last plenary session and some posters. There was a short break (we went to the town centre to stock-pile some food) and then, the excursion!

Blonde haired woman sitting in a train (with a green background and glass reflection on the right).
It’s just me in a Croatian railroads train.

We were driven by car by our hosts, Teo and Ester (who we met during this summer – I will write about that in the next post!) to Rakov Škocjan. I would like to use this opportunity to say that Slovenia is really beautiful, full of intact nature and small roads. In Rakov Škocjan, we set for a quite a long walk to visit two natural bridges and caves near them. I had my shiny new camera with them, so I was taking as much photos and videos as possible, and honestly, I also used this as an excuse to stay behind, because I had a hard time keeping up with the rest of the group (I’m chronically out of shape). The trails itself is beautiful, a part of it also goes near the river Rak. Soon we came to the first natural bridge, which is completely made of stone. The only thing human hand built were protective barriers, so people don’t fall down. The story behind both bridges is that they used to be huge caves, but they collapsed, leaving only the bridges. Parts of the caves still remain, so most of the group went down to enjoy the cave and river that goes through it. I stayed behind, because I assumed it would take me too long to climb down and back up, and I didn’t want to hold back the whole group.

A stone natural bridge, infused with forest; green and grey colours are dominant.
Little Natural Bridge of Rakov Škocjan

After the first bridge, we went back to the meeting point, which was the hotel where we had lunch. Next, the second bridge, which is 5-minute-long car ride away, and about 20 minutes by foot from there. Usually, the passage under this large natural bridge is almost completely under water, but we were lucky, as it was completely dry. We carefully walked in the river canyon, up the entrance of the second cave. Since Bruno and I didn’t bring any headlamps, one of the organizers kindly borrowed us spare helmets with the lamp on. Which lamp, you may ask? Scurion, the best of the best! I was so excited to wear it that I made Bruno take countless pictures of me!


Then, we naturally went to explore the cave, which wasn’t as dry as the canyon. Sometimes, it was really hard to see how deep the water level is, and that’s how I ended up with a very wet right foot. Like, full on water in my boot, because the water level was just a bit too high then I anticipated. This didn’t stop me to try out my camera, and I was very satisfied with the photos, since they are a big step forward from the ones I took this summer (again, this will my next post!). The light from the Scurion was on occasion so strong, that some of the photos look almost burned, I couldn’t believe it.

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Biospeleologists in a cave

Some folks went through the whole cave, but I wanted to go back the same way, to take more pictures of the bridge and cave entrance, since I didn’t have enough time to do it the first time we went through. Honestly, at moments, I felt like everything is a bit too fast, especially for someone who wanted to take a quick break and just enjoy the nature or take a few snaps for the photo album. The whole time however, I was thinking only how wet my sock is, and couldn’t wait to go back to our apartment and change. However, the group had other plans and first we went to the small café close to the big lake, which I honestly didn’t see. We did say to Teo that we would like to go back and would skip dinner (programming!), so he organized a transport back for us, which we were quite grateful for.


The next day, the big day! Postojna cave, or at least we thought so. After waking up, we realized we should walk two kilometers up to the cave, with both of our backpacks and I also had a bag full of photography equipment. There were some taxi companies, but no one answered, and we also didn’t have almost any cash, since I’m used to paying with a bank card. This was actually a problem in Postojna – apart from big chain stores, everything was to be paid in cash, and all ATM-s were located in the city centre. All of this, combined with our train schedule and my sill wet boot, contributed to us giving up on Postojna cave, and heading for a train station… Where we realized that the ticket office is closed, and we can’t pay with bank card in the train. So, Bruno quickly headed back to the centre, and came back with some pastries as well. Our way back went smoothly – first train to Ljubljana, trying out new burgers at McDonalds, and then train to Zagreb. During that time, we decided to come back to Postojna during the winter, and explore that cave, as well as going back to Rakov Škocjan on our own, setting our own pace and excursion plan. However, apart from finishing my homework assignment, the most important thing, excluding pretty photos, is the fact that I finally finished reading Dracula, the book I struggled with for almost two years, for the reasons I still don’t understand.

A view from inside to outside of the cave; framed arch with the blackness of the cave forming an outside frame, and sky and forest being the picture in the centre.
The cave near the Big Natural Bridge; a view from the inside.

 

A short adventure in Pula

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.

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).


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!

 

 

NeuRi – Student Congress of Neuroscience

Hii everyone, and welcome back to my blog!

For this week’s post, I have decided to write about NeuRi – Student Congress of Neuroscience. I write about this particular meeting because I have been part of it since 2015. However, I believe any kind of involvement with this kind of events is extremely important to students, and I would like to encourage all my friends and colleagues who might read this piece to get involved!

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Day 1 of NeuRi 2019 – many happy reunions; Petar&me, we presented together in 2017!

NeuRi is a congress aimed at students who have interest in neuroscience; neurobiology, neuropharmacology, molecular neuroscience, neurology, neurosurgery, neuroinformatics, psychiatry, neurolinguistics… For nine years, it has been held in Rijeka, a city in the middle of Kvarner. It also includes an excursion to island Rab and visit to Psychiatric Hospital Rab. At NeuRi, students have an opportunity to present their work, form new friendships, and participate in the biggest gathering of young neuroscientists in the region. The congress lasts for three days; it consists of plenary lectures and workshops held by professors in their respective fields (from neurology to psychiatry and neurobiology), and oral and poster presentations by students. Student presentations include scientific investigations, case reports, and reviews. And there is a lot of free food 😊
Organisation of such event starts one year before, with writing projects for grants, brainstorming, inviting plenary lecturers, and of course, registration for passive and active participation, which is my job. I personally process and answer to all registrations and organize them in special tables, which are later used for logistics and accreditations. This might not seem like a demanding work, but at times, there are more than 80 registered participants in one day, and I have to process all of them. Which, again, might not be so demanding, if people could remember to input their contact details correctly 😉

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Day 2 of NeuRi 2019 – on a ferry to island Rab!

Apart from being part of Organising Committee, I was also an active presenter for the last four years, because I believe this is a unique opportunity to practice my presenting and gain input from my peers. First year, I submitted a review about different mechanisms of neurotoxins; in 2017, together with my colleague from Zagreb School of Medicine, we talked about levels of N-cadherin expression in human meningioma; last year I had a review presentation about possible role beta-Methylamino-L-alanine (BMAA) plays in neurodegenerative diseases, and this year, I, together with my lab partner from Department of Biology, presented about various bioinformatics tools used to manipulate proteins in silico. As an example, we investigated tau, showed how to find the gene in NCBI database, how to choose the right protein file from Protein Data Base, and how to run that same file through multiple simulations. In the end we compared healthy tau protein with mutated version and also got the audience award for the best presentation!

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Day 3 of NeuRi 2019 – we are presenting!

I’m interested about your experiences with student science manifestations? Do you like to go to a congress or a symposium? How did you prepare for your first active presentation? 😊 Let me know in the comments!

For more details, visit NeuRi official web-site

All photos by Helena Balaž