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!

The most beautiful cave I ever visited

December 11, 2021 EminaLeave a comment

In the first week of July this year, I applied for a “Little school of speleology” which included a week of evening classes and an excursion on a Saturday. I did finish my speleology school in 2018, but I wanted to brush up on my knowledge, meet new people, and, naturally, visit a cave. Since at the time Croatia was under certain COVID restrictions, all classes were held online; the excursion was allowed under the condition of following all the guidelines and restrictions (which we, naturally, did).

At first, I thought the classes might be a little bit boring; these kind of topics sometimes have a tendency to drag out or be repetitive. However, I was very satisfied with with the range of covered topics which included speleology & caving basics, geology and geomorphology, orientation, biospeleology, bioarcheology, and first aid. The presenters were engaging and to the point, and I enjoyed listening to them. I was happy that I already knew quite a lot, but also that I learned quite a lot as well!

After that week of classes was done, Saturday followed, which was reserved for the previously mentioned one-day excursion. I prepared my back-pack the night before, filling it with small snacks, extra clothes, and my waterproof camera, which I was trying out for the first time. I usually take photos with my DSLR, but I wanted to be more focused on the experience itself, than worrying if too much moisture is getting in my NIKON. Our destination was Modrič cave, near Maslenica bridge, 30 kilometres away from Zadar. This cave is a part of Nature Park Velebit and is also open to tourists under the guided tours (previous caving experience not necessary!).

First, however, we needed to reach it. Our trip started in Zagreb, during quite a hot morning. I sat alone in the half-empty bus, mostly listening to music and starring out the window. From the time to time, I would talk with people around me; some also have had previous caving experience, some were to visit a cave for the first time.
I like watching out the window, especially when I’m travelling by bus or train. It feels homely, rewarding. The first part of our path is quite familiar to me, as I travel through these parts often. The highway goes directly through the forest, coniferous trees as far as you can see, covering the mountains, with sparse settlements, sometimes only houses, on the clearance. What I love the most is that often, you’re seeing it all from the above, as the bus is carrying you on the overpass.

On this particular trip, I was, however, most impressed by what came after this. Still in the bus, I barely noticed when environment around us started to change. Mountains increased, by they started to go bare, exposing its layers and layers. Rays of sun were reflecting of the karst, those grey, barren rocks that I so strongly disliked as a child, and learned to love during past couple of years. I wondered, how many beautiful vipers are hiding in its crevices, how many lizards are catching the midday sun near scarce bushes, on these stones that seem so empty, but are actually brimming with life? I was in awe, almost like I’ve been seeing this place for the first time ever and wondered how many other people out on the road that day were appreciating the sights around them. As we were driving through the Sveti Rok Tunnel, the second longest tunnel in Croatia (5.6 kilometres), I couldn’t believe that we actually dared to drill through the mountain.

After reaching our initial destination, we still needed to take a short hike to the cave itself. Short, but exhausting, at least for me, because the sun was at its highest. When we finally entered the cave, it was literally a breath of fresh air, except it was that distinctive, earthy smell which never fails to put a big smile on my face. The whole visit lasted for approximately two hours, during which, under the expert guidance, we learned a lot about it. Some parts of the cave were off-limit, because scientist are using those particular spaces to study paleo climate, general cave conditions, geological processes… To be completely honest, I didn’t remember too much of it, because I was so taken aback by the beauty of it.

Stalactites, stalagmites, columns, draperies, straws, pearls, flowstones… Wherever I looked, the light from our lamps illuminated another wonder, right next to me or high above me. I tried to take some photos, but believe me, when I say, none of those do justice to what I actually saw. In all sincerity, this was the most beautiful cave I’ve ever visited; just standing there, experiencing something so ancient, made me feel so fulfilled and so relaxed at the same time. I felt like I was witnessing something profound, like standing in the museum in front of a priceless painting. Words, truthfully, can’t really describe that feeling, although I hope my photos can at least offer you a glimpse into it.

The events that happened after we exited the cave were interesting as well (small-talk at lunch, participating in the speleology workshops at the beach), but in my mind, they were still overshadowed by the experience in the cave. Not even on the drive back home, I couldn’t stop thinking about it. A part of that magic eventually passed, and it wasn’t reignited to the fullest even as I was writing this, but if I’m sure of one thing, it’s that I will be returning to that cave again, one day.

Field | Žumberak Mountains 2020

December 8, 2020October 31, 2021 Emina1 Comment

In a previous post about my time at the Žumberak Mountains I mainly focused on my time with the Crustacean group, but today I’d like to write a bit more about my general experience out there in the field. As I already mentioned, I was unable to attend for the whole week, and instead opted for four days only, but all of those four days were completely filled with exploring and socializing (which was, at the time, allowed in our country and county).

Žumberak Mountains, and its Nature Park, is only one hour drive away from Zagreb, however, due to the proximity to the Slovenian border, GPS can steer you in couple of wrong directions, so after collecting some extra things for the campsite, I called Petra, one of the camp leaders, to give me right directions. Everything went rather smoothly, until I almost hit a llama that was chilling in the middle of the road, just behind a steep curve. After my initial confusion cleared up, and the llama left the road, I cautiously continued to drive, wondering what all these llamas were doing in the middle of Europe anyway. As it turns out, there is a bio-park in close proximity, and I guess they escaped their enclosure.
Couple of kilometres down, the road suddenly turned into a macadam, as I basically entered the woods, followed by the sound of a strong stream that was following the road. Well, the road followed the stream, more or less. That evening wasn’t very eventful – I was mostly talking to colleagues and taking pictures; it was rather cold, so we lit up a big fire in the pit, the only one I experienced during my time in the camp.

Buphthalmum salicifolium – ox-eye
Araneus diadematus – cross spider

As for sleeping arrangements, we had a huge meadow where most of tents were already erected. However, despite bringing my own tent with me (and later borrowing it to my friend Iva), I actually decided to sleep in the car. For one, I was already too tired, and it was way too dark for me to set it up, and I also hypothesized that, since everyone was in a very good mood, people could be loud at night, returning to their sleeping places. Since my strict medication schedule requires interrupted sleep, I rolled down my passenger seat, changed into warmer clothes, and slipped into my sleeping bag. I remember falling asleep slowly, feeling as if I was in a horror movie, as branches were slowly snapping and the big drops of rain were hitting the car.

My next day was a big crayfish adventure, as was the day after it. Honestly, remembering it after all this time, both days somehow melted into one big experience of driving around, asking for directions, walking too much for my taste, and laughing in the car, courtesy of the Crustacean group, who are ones of the funniest people I’ve met.
What I would like to write in a greater detail than I did in my previous post, is the “night-hunt”, or night-time crayfish catching & release session. We started the walk when there was still light out, but it got dark even before we reached the stream; during this year, due to heavy COVID-19 restrictions I couldn’t go anywhere, and it seems that I also forgot how dark it can actually get in the woods. Literal pitch black.
That, however, didn’t stop the group from catching crayfish (they also visually inspected them for the signs of the crayfish plague). We all had lamps, of course, but like I already pointed out, crayfish are surprisingly fast – catching them with your bare hands definitely requires skill!

My last day at Žumberak was magical as well. It was actually a day off, so most of groups decided to just go see-sighting, including the Crustacean group. We drove for an hour or maybe an hour and a half to reach a road with many stunning waterfalls. We set our own pace, and set to investigate and take as many pictures as possible. I wasn’t able to enjoy it as much as I wanted because I had a really persistent abdominal pain (at one point, I couldn’t even walk properly anymore, and had to wait in the car), but despite that, I still managed to take some photos and videos. I hope you’ll enjoy them as much as I did!

With the year we have, with pandemic still raging, this expedition is the only one I was able to be a part of, but I surely hope 2021 will bring new expeditions, new adventures, and new opportunities 🙂

*Asplenium scolopendrium* – hart’s-tongue fern

RTŠB 2019 – biospeleology field trip – PART 2

December 11, 2019December 11, 2019 EminaLeave a comment

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).

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.

wasp-spider — 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.

It me

If you look closely, you can se Colembola sp.

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.

spuder — 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.

Niphargus sp under the microscope

Tick in the tube

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.

Salamanders everywhere!

A blue beauty

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.

RTŠB 2019 – biospeleology field trip – PART 1

December 8, 2019December 8, 2019 Emina1 Comment

Finally, I write about this astonishing field trip which has taken part from 17th to 27th July this year in Ivančna Gorica, a small town south of Ljubljana, Slovenia. Me and Bruno were part of biospeleology group, and my friend Paula, who was the only other participant from Croatia, was a part of reptile group. Paula has a nice Instagram page about biology as well.
This camp, organized by student’s biology group from Ljubljana is very popular with students from the ex-YU countries, and this year there were also colleagues from France. Also, being a biology student is not a must, we had humanities student as well.

How does the camp work?

First, you have to apply; you can choose between three groups (my choices: biospeleology, reptiles, botany) and with the application you pay the 93€ fee that includes breakfast and dinner every day and driving around during the camp. When there, we sleep in our sleeping bag in the gym of the nearby school. Breakfast is every day 7-8.30am, and dinner was usually 4pm+. There was also one rest day (during which us three went to Ljubljana) and one day when couple of us were on duty – we were cleaning and cooking for that day.
One group usually consisted of 5 members, and every day we went out to field, trying to find caves or catch some cave dwelling insect.

We travelled, you guessed it, by train. I have already mentioned 9€ one-way-ticket from Zagreb to Ljubljana, and then we went to Ivančna Gorica, that ticket was around 3€. The way back was almost the same, with the difference we went by bus to Ljubljana, since there were no trains at that part of the day.

How was my experience?

Honestly, I would really like to go again next year, but honestly I don’t know how I made it. I was not in a shape I should have been, I had migraines, I got stuck, I had very suspicious bruises and I strongly disliked walking around under sun.

How many caves I visited?

Number of caves: 9
Total number of cave visits: 11
Number of water springs visited: 4
I also spent one evening with bat group & one day with amphibians group.

ich — Me, before first cave visit, unaware what was waiting for me

A short summary of my days in Slovenia

Day 1

We met other members of the group: Ester, group leader, Tjaša and Eva. Anja was also part of our group, but she joined us couple of days later. Apart from going to the field, every evening we were supposed to try and determine our specimens we collected in caves, label them, and fill out special documents about our visit (who, when, why, where, what was collected and how).
We also prepared live traps for small insects. The traps we made consisted of putting tuna fish with gorgonzola in small tubes and closing them off with cotton pads. The insect we were trying to catch was Leptodirus hochenwartii, member of Coleoptera, the only beetle that lives in the caves. This species is endemic to Slovenian, Croatian, and Italian caves. For other creatures we had prepared small tubes filled with 70% ethanol which we held in the pockets of our overalls, together with pincers.

live-trap — One live trap, buried in the ground – it also needs to be covered with a big rock.

Day 2

Frist cave we visited was Velka jama nad Trebnjem. The way up to the cave was steep and exhausting; it was very hot & moist in the forest. However, I took my camera with me, and took many pictures. I was surprised how many invertebrates live there, since Croatian caves I visited were almost completely empty. However, these animals are not usually found in the caves, here they are living kind of opportunistically, since the cave was also filled with garbage. We set up the traps for Leptodirus, and went back. We had a small lunch next to our car, and then went to the cave number two, called Rojska jama 2. We had GPS coordinates, but Ester was sure they are wrong (they were), so we asked a local villager for help. He kindly led us to the cave entrance, where we suited up, and in we went. The cave was quite interesting, we spent an hour or so inside. After we returned, mr. villager welcomed us back with home-baked strudels and soda. It was honestly, very nice. We also visited two water springs, and went back to the school. After dinner, Ester taught us how to fill out the papers I mentioned, and we tried to the best of our ability, determine all the specimens. The most important we had to discern were small freshwater crabs called Niphargus and Gammarus. The main difference is that Gammarus have eyes, and we really wanted to collect the other one.

skakavac — Caves were usually full of these grasshoppers, and they were scary huge!

Day 3

During day three, we visited one cave, Pekel pri Kopanju. We did find some cool animals, like Colembolas, but our trip was short, since main channel was full of tree branches and garbage. We tried visited the cave number two, but soon realized that we would need a 40m rope to climb down, so we gave up on that. We also visited two water springs, and headed back earlier, since one of the mentors had a lecture about global warming. After that, back to determination. We found some Niphargus (yay!), Gammarus (fine), and rat-tailed maggots. What are those, you wonder? Those are the larvae of certain species of hoverflies. What are hoverflies, you wonder? Those are flies that pretend to be wasps.

Day 4

This day was tough for me, we walked 5-6km on the trails and through the woods, but we also visited three caves! First two (Dolnja vodena jama & Antokov skedenj) were close one to another and extremely spacious inside. I roamed around with my action cam (results were so-so, not enough light) and Bruno and me found a bunch of Niphargus in one puddle. I also saw some fox bones, and Ester was kind enough to fetch them for me! The third cave (Rivčja jama) was the one we visited three times all together and was really interesting. The walk towards it is around 1km on the forest trail, next to beautiful river Krka. The entrance to the cave is enormous – I would use the phrase “you need to be blind not to see it”, but that’s incorrect – even from the trail you can feel temperature drop and the specific smell of cave air.And this cave had bats. Bunch of bats (Myotis myotis), and they were loud, much louder than people would expect. We climbed up, on mountains of their poop, in order to take pictures, and the temperature soared at least 10 degrees there. Afterwards, we went through a narrow passage (here I took neat footage) and tried to catch some Proteus anguinus, the olm (I wrote about them here!). These traps were different, since they live in the water. We also tried to lure them with pet cookies (can’t remember if it was cat or dog food, sorry!).
After all this, we went swimming in Krka, water was around 15 degrees, but it was so nice and relaxing. The river is truly beautiful, and I would like for everyone to experience this kind of nature at least once in their life.

ich — The only not-blurry photo of me in the cave

End of part 1

I hope you liked this not-so-short overview of my time in this summer camp, part two will be up soon. Please tell me what you liked the most and about what would you like me to write more! I would like to thank all of you who read this, thank you for time and attention!

Another Vienna adventure!

December 4, 2019December 3, 2019 EminaLeave a comment

Hi everyone, if you follow me on Twitter and/or Instagram, you have probably already seen my pictures from Vienna this last weekend. However, I would like to share a bit more, and write about it too!

At Saturday at 3.30 in the morning, my sister & me boarded the bus in Varaždin, and started our one-day adventure. Our destination? Vienna, capital of Austria! With the trip we booked through Galileo Travel came scenic sightseeing of the city, and a visit to Schönnbrun castle, but we skipped that and with U4 headed directly to city centre, Schwedenplatz more correctly. After short breakfast in McDonald’s (I know, I know), we headed to Natural History Museum. On the way there, we took some typical tourist pictures, in front of Stephan’s Cathedral, at Hofburg… And then we finally reached NHM.

Me in front of Stephen’s Cathedral

Me next to big cave mineral 😉

I’ve visited the museum two times before, but my enthusiasm was still through the roof. Firstly, the museum is huge. Permanent exhibition spans two floors and numerous specimens. Roughly divided, first floor is mineralogy and second floor is dedicated to zoology. I took some pictures, which I will share with you, but I didn’t take my camera; everything is taken with my Huawei mobile phone.

Student’s entrance fee is only 7€ (~8$), and taking photographs is allowed. The whole museum is, honestly, overwhelming. I have never before seen so many specimens at once place. My sister, who visited it for the first time, often commented that a building itself could be a museum, due to it’s rich, ornate walls. First floor is, like I already mentioned, full of minerals. I don’t have much interest for them, but I made me think about how old our planet is, and what makes it. Also, one of the rooms is completely dedicated to jewellery, both modern and historic.

The floor dedicated to zoology was full of models and real specimens of animals around us, as well as evolutionary artifacts. As is common, first rooms were dedicated to invertebrates, building it’s way up to vertebrate groups. I was particulary amazed by the size of dinosaur bones – no matter how many times I see it on the TV, or visit this museum, I stand in awe in front of them.

Unfortunately, due to morning sun, I wasn’t able to capture nice photographs of invertebrate collections, but trust me when I say those are so beautiful. Everything is o neat and organized that, since then, I’ve been toying with idea of collecting my own specimens. There are also rooms dedicated to fish, amphibians, reptiles, birds… Those are usually held in special containers or stuffed. There are also many skeletons on display on the walls. With dinosaurs, there were also animatronic models, which both excited and frightened children in the museum.

There is also a separate room dedicated to evolution of human. I already posted that interesting picture where an app transformed me into an early human, but in this part of the museum, you can see many different skulls belonging to Homo sapiens, Homo neanderthalensis, Homo habilis… I consider this part of the exhibition very important, especially in today’s time, when so much misinformation is present on the Internet.
Another important historic specimen is Venus of Willendorf figurine, which is dated to 30 000 years BC.

What would you like to see, if you could go to Natural History Museum in Vienna? Would you like me to write about something in more details?
Please let me know in the comments 🙂

Biology & informatics &… olms?

November 15, 2019November 15, 2019 Emina2 Comments

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.

fbt

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 🙂

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

October 25, 2019October 25, 2019 EminaLeave a comment

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 – 3^rd Rijeka forum on neurodgenerative diseases – diagnosis and treatment in early stage of disease and 2^nd 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!

Me, wearing a really awesome helmet!

Bruno in the cave

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.

A cave detail

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.

Big Natural Bridge of Rakov Škocjan

A view from under the Big Bridge

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

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!