How to land a P.hD. interview

As many of you probably already know, I successfully graduated in November last year. After that, I have been working for four months in a laboratory in Graz on a scholarship (I will post all about that soon!) and I have also been religiously applying to various positions, both in academia and industry.

In March, when I started writing this post, I had two Ph.D. interviews for different projects, and both of these interviews were very different experiences, so I wanted to write about the whole process of applying, waiting, interviewing, waiting again.

Where and how I have been applying?

Honestly, all over Europe, including my homeland as well. Up until the moment of writing this, I have sent almost thirty applications (in Europe, you don’t have to pay an application fee), mostly to Universities in Northern Europe. Furthermore, there are different ways of applying, so some programs require that you find a mentor beforehand; I was thoroughly unsuccessful with those, as most of the potential mentors either didn’t have a placement or didn’t bother replying to my inquiries. I was not really deterred by this and continued searching for positions, mostly by searching the internet using a phrase such as “university of berlin neuroscience” and then trying to find open positions that I would find interesting. A couple of times a week I check various “open positions” pages that I previously bookmarked; I also set up searches for “Ph.D. neuroscience” on LinkedIn and ResearchGate, and I also signed up for a newsletter on the findaphd.com portal.

After finding a desirable program, I immediately check their requirements and deadline, of course. Most of them require a CV, motivational letter, transcripts of Master’s degree, and contact information for two of your reference letters writers. By now, I have most of that ready, as I only write a new motivational letter for each of those, and I tweak my CV a little bit. I have also attached reference letters that helped me land my BioTechMed-Graz scholarship.

After I got all my documents in order, I follow the application guidelines: some require you to merge all documents in one pdf (you can use adobe online merger) and send them directly to an email, and some have online forms on web pages that you are supposed to fill in.

What do my CV and motivational letter look like?

I found both templates on Canva and tweaked them to suit me better; that usually involves some changes in the general organization of the layout and changing the colours that I think represent me better. I also use the same colour scheme for both the CV and the letter, so they look uniform.

In the CV, I enter details about my current or latest employment status, education and thesis, and the most important presentations, publications, internships, and awards, as well as the most important activities I did (such as being editor-in-chief of In Vivo Journal or general secretary of Student Congress of Neuroscience – NeuRi). I also point out certain classes I took that I believe could be important for my application (Computational Biology, Neurophysiology), and I also mention that I am learning Python, doing online courses and I also mention my hobbies. Many people suggest leaving out the part about the hobbies, but I actually get asked about them, so I.

There are many ways in which you could make a CV, but I like to keep it neat and easy to the eyes, with larger fonts for main things and smaller fonts for details, so if someone would just glance at it, they would get a general impression of me.

Regarding my motivational letter, I like to keep them short, usually one page, two maximum. I always start by addressing the professor to whose program I am applying to, and then I introduce myself in the first paragraph, mentioning my name, when I graduated, what I am currently doing, and how I found the position in the first place.

In the second paragraph I talk a little bit about my interests and skills and compare them to the demands of the program: for example, if the program deals with rodent models, I write that I took a class handling them and that, despite not doing any substantial research on them, I am not afraid to handle them and would have no problem with carrying on the research. I also talk about my other qualities, which are more personality-based. I also openly admit not having experience with certain methods. This part can take two paragraphs, but both of those are focused on the same topic.

In the last paragraph, I thank them for their time and write that I am looking forward to hearing from them. I like to curtail each of my cover letters, from beginning to end, because I feel that is the best approach for me.

There is information that is repeated, but the cover letter does serve for you to elaborate on important things from the CV and is a really good opportunity to explain what you can offer and what you are willing to learn. The letter is also your opportunity to show how well are you using your English skills (if you are not a native speaker, that is).

How about the waiting part?

For me, waiting is not filled with anxiety, because I keep busy by finding and preparing applications for other programs. An acquittance who works in academia told me that I should consider myself lucky if I get an offer (an actual, satisfying offer) before I sent out fifty applications and that I should consider every interview as an opportunity to practice. I also made a spreadsheet where I keep track of my applications.

How to prepare for the interview?

After you finally received an email informing you that you have been selected for the interview, you will (mostly!) also get information about what you have to prepare. For the first interview, I had to prepare a ten-minute presentation about my Master’s thesis, and for the second, a ten-minute presentation about all of my current research I have been a part of so far.

I chose to do the presentations in Canva as well because when in full-screen mode, you can use that fancy cursor that is easy to follow.

In each presentation, I opened up with a slide of introducing myself, where I talked a little bit about my education and what I currently do. Then I explained my research, highlighting the most important parts, which include goals, methods, publications, results, and duration. I rehearsed both presentations beforehand, so I was confident I can present it in the allocated time.

How to do an actual interview?

I had both interviews online, over the Zoom platform, so I checked my audio, video, and sharing options before starting a meeting. For both, I was very nervous and anxious, but I suppose that’s just how stage fright works.

My first interview actually was several interviews that took almost a whole day, because I was not meeting just the supervisors, but all members of the lab, as the idea was to see if I were a good fit in the lab as a whole. I got asked a bunch of questions regarding my thesis; I could provide answers to some, but some were asking about part of the research that was just out of my scope, as my thesis is a part of a bigger Ph.D. project, as is common in Croatia. I also got asked personal questions about possible move and adaptation to the new environment.

In the end, I was told that they loved me personally, but couldn’t offer me a place due to fact that I didn’t have enough experience with the exact methods they needed, and they wanted to start the project as soon as possible, and I would need to learn all of it first. I thanked them for their feedback but was left a little bit confused as to why was I even asked to participate in the interview, as both my CV and the motivational letter indicated that I indeed don’t have the required skills.

The first part of my second interview was very similar, as I simply presented and then answered a couple of questions regarding my experience with certain methods. This project is focused more on Structural Biology, so I am honestly not sure where exactly I land here, as I never took any courses, and to be completely honest, I considered this program a long shot and only applied because it does deal in neurodegeneration.

However, what was interesting was the second part of the interview: a questionnaire. Basically, I was sent a word document where I had to answer a bunch of questions, and I mean a bunch. The first part consisted of reading four articles (all open access) and answering questions relating to them. The second part was what I would call a basic IQ and Math test (which number comes next, which symbol comes next), the only difference being that I also had to show my work. The third part was a social part, where I had to answer yes and no to questions such as “I prefer to work in a team”. I had two hours to fill it out and send it, and as of today, I still haven’t heard back from them, so I am assuming the answer is “no”, although I did expect to at least receive an email saying so.

Interview aftermath

I had completely different experiences with these two interviews, with the second one being more formal and the first one more easy-going. I am much grateful for both as I gained a lot of experience and met such accomplished scientists! Even before I started applying, I told to myself that I should not take anything personally and should just keep on applying until I find any kind of job, even if it’s only temporary. Moreover, I also wrote down the questions I was asked the most and I intend to add the answers directly in my future motivational letters (regarding my research experience and Master’s thesis), as it seems to be important for my future supervisor to know.

Conclusion

I think this is one of the longest posts I ever published, if not even the longest one. However, all of this was just a glance, and I could write a separate blog post for each of these paragraphs, and maybe even more about the interviews. Let me know if you liked my write-up and if you would like me to write a separate blog post about any of these! I was also asked by a follower if I talked about my health issues in the interview: I did, but I think that requires its own post, which I would like to publish if you are interested.


What are your top suggestions and advice for landing the Ph.D. interview, and the interview itself? Do you have more questions regarding the whole process? Let me know in the comments!

The most beautiful cave I ever visited

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 2021

Hello everyone, and, after a longer break, welcome back to my blog! As the title itself suggests, I was a part of another BIUS field trip, which was again located at the Žumberak Mountains. For the adventures from the previous year, click here and here.

Quick reminder:
BIUS is an association that gathers many Biology students from our department and focuses mainly on field trips, excursions, and expert lectures, all in order to complement and expand our Biology-related knowledge about certain topics. BIUS is also a publisher behind In Vivo Magazine, for which I served as editor-in-chief and I am now an adviser.

Initially, I planned to write this post as soon as I came back, back in May, but I felt rather overwhelmed by everything in my life, especially health wise. I decided to postpone all of my posts, both on this blog and social media, because I just didn’t have enough energy to dedicate myself to creating content in a way I thought I should.

If you read my previous posts about Žumberak, you already know that, despite wanting to spend my life working in a lab, I also like to explore nature. During the last field trip, I was part of the Crustacean group, and this year, I was part of a Butterfly group, although I don’t know that much about either of these topics. However, one of my main reasons to go to excursions is to learn and experience new things, connect with other people, and make great memories. And I must say, I had wonderful four days. I would also like to thank to two other members of our group, Filip and Ivan, for selflessly sharing their knowledge with me and having patience to answer all my questions!

Frist photo: Asplenium scolopendrium (hart’s-tongue fern) sprouts. Forests were full of these and, honestly, I was feeling like I was a character in a fantasy novel, surrounded by magical plants.
Second photo: A bee and a wild orchid. I must admit that I'm very proud of this photo 🙂
Third photo: Caddisflies! Every stream was full of the caddisfly larvae; you might think these are just some silly rocks, but those are actually insects of the order Trichoptera, who make these protective cases in their larval stage.

I arrived at Sunday, just a little bit before noon, and immediately joined my group; they were strolling down the road, mostly checking environment and inspecting passing butterflies. My main task was taking photos, especially if anyone caught a butterfly. The Butterfly group itself was only recently revived, after Filip showed amazing initiative and interest in butterflies, so we were all actually new to the group, trying our best to wave our little nets. Our main tasks were:

  • confirm the already recorded species of day butterflies
  • investigate and record species of night butterflies, which are not very well known in this area

I should immediately note that, despite being successful at both tasks, we noticed an alarmingly small number of butterflies and insects in general, especially for that time of the year. I am honestly not sure what is to blame; we had a weird winter that jumped right into high summer temperatures and our country is, sadly, generally not very preoccupied with the protection of nature, species, and habitats.
There were also fun moments, with Ivan very decidedly running after every butterfly in sight. Also, the Botany group brought us a little caterpillar for determination, which Filip then successfully nurtured to the butterfly stage, in order to determine the species.

Zoom in photo of FIlip's hand expertly holding a butterfly (scarce swallowtail).
Iphiclides podalirius (scarce swallowtail)

A bug (Meloe sp) is seen in the middle of a picture, standing on a fallen leaf, surrounded by green grass and sprouts.

After returning to the camp that same day, I investigated an area around it, with my friend Paula, who used to be a leader of a Beetles group (and is now leading Marine Biology). She was, naturally, much better than me in spotting hidden insects and even caught some water newts after we stumbled upon a puddle. It was such a fun and interesting day, and my only regret was forgetting my straw-hat at home, because the sun was really too strong for my taste.

(Photo: Meloe sp, probably violaceus)


My next day was, however, my favourite experience of the whole trip, because I joined the Biospeleology group and went caving! The last time I visited a cave before this was in 2019, and I must admit, I missed it so much; that specific smell of the cave air, wearing three layers of clothes, fixing my helmet all the time, and walking through impassable terrain. Wait, scratch that last one, I never miss walking on the extremely narrow mud path through the forest, holding onto branches we are passing on the way, barely catching my breath, trying to finally reach the cave entrance. Luckily, everyone in the group was completely understanding and wasn’t imposing any type of time restrictions. Three of us were students, but we also had an expert mentor, who was so kind, patiently answering our questions.

First photo: Mia & Martina looking for spiders
Second photo: Grasshopper sp.
Third photo: A flying insect, perhaps a mosquito, starting to get... Calcified? Mineralized? I'm honestly not sure what is the right word to use here.

The cave in question is called Zidane pećine (roughly translated as Masonry caves), and it’s a cave you can access without the ropes (helmets and speleo overalls are a must). The main task of the group was to collect various insects and bugs that might live in the cave, mainly spiders. Now, the focus was on the creatures that might permanently live in the cave, and not on the ones that only sometimes enter the cave in search for a hiding place. I was, unsurprisingly, mostly taking photos: of my colleagues, cave walls, and various animals inside, which include creepy grasshoppers (not their scientific name) and bats. The cave is also apparently an archaeological site, although I can’t find any verifiable information about that, apart from one mention in a blog post which states that archaeological find dates back to the 16th century and Ottoman attacks. What locals did tell us it that the cave used to be a hiding place during the wars.

Dimly lit photo of a part of the cave wall, it's partially hollowed out by the long-term effects of the dripping water.
A part of the wall inside the cave

Tuesday was a bit more challenging for me; our lovely group leader Filip decided we should check out a big meadow at a higher elevation, which doesn’t sound too bad, except the sun was plaguing me badly. However, we were hopeful we might find an interesting butterfly, but barely found any butterflies at all. As it turns out, it was simply too cold for them at that particular place. We spent the rest of the day mostly hanging around the camp, until evening, when it was time for the night hunt. And yes, it was as cool as it sounds. Around 10pm, a huge group of us gathered a bit further from the camp, in order to observe, and in some instances catch, bugs that are active during the night. To accomplish this, Mladen, mentor of the Beetles group, put up two pyramids, which are made of a metal construction with a simple fabric thrown over it, and a UV light in the middle of it. (Mladen also politely measured a safe distances for me, in order not to be harmed by the UV light, although I have to admit, I purposely got quite close couple of times, in order to take pictures). One of the pyramids was erected next to the road, and another couple of hundreds meters away, near the bank of a stream. It was really fun going back and forth, and taking pictures of all the insects and spiders we found on the road. This experience was also very educational for me, not only because this was my first night hunt, but also because I was surrounded by experts who gladly shared their vast knowledge about beetles, spiders, moths, caddisflies, and mosquitoes.

A night butterfly (moth) on a fabric of the pyramid; the front side is seen, showing moth's head, antennas, front legs, and a part of the body.
A beautiful night butterfly

My last day was Wednesday, and as a group, we honestly didn’t have much to do, due to changeable weather and very strong winds. We visited a bio-park nearby, where we saw llamas and walked next to donkeys and donkey-hybrids. It was overall a fun ordeal and we didn’t understand why are we the only visitors there. After a quick search on our phones, we realized that the park was a part of a small ecological scandal last year, so we left. The second part of the day was spent with the Crustacean group; together, we visited a beautiful creek, which was much bigger than I expected. Members of the Crustacean group were setting up traps, similar to the ones I was writing about last year, while the rest of us just walked around, amazed by the nature around us.

This is me (wearing an army jacket) kneeling, almost sitting on the riverbank and taking photos of newts and tadpoles in a muddy stream.
Here, I was trying to take photos of newts and tadpoles

As I was driving home that evening, I couldn’t help but smile reminiscing about the packed experience I just had, which included not only visits to the breathtaking places, but also learning more about the tiny world around me, taking numerous photos and videos, and meeting new people.


Here you can find social media of some of the members of the Butterfly group, as well as the link to official Instagram profile of the group. I am also sharing a social media link to Paula’s Instagram, who already shared impressive photos and videos on her profile.


Three people in embrace (two men, one woman) posing, on the road in front of the trees and thicket.
The Butterfly group

Biology in popular culture – movies&TV (part 2)

Hello everyone and welcome to another post in the series about biological topics in movies and TV series. You can find a link to the previous post right here. My intention with these is to clarify different claims made in various movies and TV shows I watched, and also to share perhaps some surprising facts mentioned in them. If you’d like for me to watch something specific, please let me know (I’m currently preparing another post focused on the German TV show “Biohackers”). So let’s start with some extremely popular offenders.

Friends – “Lobsters mate for life”
In a classical Friends episode, Phoebe claims that lobsters mate for life. They don’t. There are some animals that remain monogamous for life, such as wolves, swans, penguins, and barn owls, but lobsters are not one of them; in fact, male lobsters actually change mates frequently during the mating season.

Harry Potter and the Goblet of Fire
During the famous scene in which professor Moody tortures the amblypygi (of species Damon diadema; Amblypygi belong to class Arachnida) with the Cruciatus curse, poor creature starts to squeal in pain, but can amblypyg actually make that sort of sounds?
As it turns out, some species of spiders (which also belong to class Arachnida ) can tap on the surface or even vibrate (again, on certain surfaces) to make mating calls or communicate, but the type of screech depicted in the movie, under the spell or not, is physiologically impossible.

This beautiful Damon diadema belongs to my good friend Iva; for more photos like this one, you can follow her on Instagram

The Alienist – “Butterflies inflict pain during the coitus”
While I’m still on the topic of invertebrates, let’s divulge into this one. Now, pain is the subject of many definitions, but assuming it’s just an unpleasant physical stimulus, the question is raised whether insects can actually feel it? Until recently, researchers agreed that insects can feel nociception, which is the response to life-threatening stimuli, but most agreed that they don’t feel the pain like we do. A recent study, however, showed that fruit-flies could experience a chronic pain-like state, but the science still has a long way to go to conclusively show if insects can or cannot feel pain. Do butterflies feel pain when mating? Possible, but it seems that, until more evidence comes to light, it’s highly unlikely.

Rouge – “Lions are not afraid of fire”
This fun but quite forgettable B flick starring Megan Fox and a CGI lioness off-handedly mentioned that lions are, in fact, not afraid of fire. That didn’t sound right with me so I searched for it and it seems like it’s true. Apparently, not only they’re not afraid but like to check out what’s happening around the campfire. I would like to point out, however, that most of the web-sites are literally copying the same sentence about it, verbatim, and I didn’t find where it originated.

***

Did you notice similar misinformation or surprisingly correct information in popular movies and TV shows? Please let me know in the comments below, I love reading about movie mistakes!

Literature & more information:

11 Animals That Mate For Life

The Weird World of Lobster Sex

Spider’s Creepy Mating ‘Purr’ Recorded by Researchers

How spiders create the sounds of love

Pain in invertebrates

Do Invertebrates Feel Pain?

Insects feel persistent pain after injury, evidence suggests

Nerve injury drives a heightened state of vigilance and neuropathic sensitization in Drosophila

Is it pain if it does not hurt? On the unlikelihood of insect pain

How to Survive a Lion Attack

Short science posts | Eluding Ctenophora

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

Dry lab – why I suck at it, but don’t regret taking the classes

Hi everyone, and welcome to my first post of 2021! I hope you had a nice time over the holidays and that your year started well, both personally and professionally. For my first post of the year, I decided to write about my personal experience; how it helped me, and what I learned from it.

If you follow me on social media, then you probably know most of my path in education, but for the new readers, I’m going to write a short recap: I have a Bachelor of Science in Biology and I’m currently finishing Master of Science in Molecular Biology. In my country, a Master’s degree is needed for almost any kind of employment and is a condition for applying for a Ph.D. However, only some classes are obligatory once you reach the Master’s, and in the second year, you only need to hit a certain number of ECTS; you can choose any of the classes as you please. You can choose classes that are completely unrelated to each other or a complete “module” or a couple of classes that are dedicated to a certain topic; I chose Computational Biology.

I was always interested in coding, and coding in Biology sounded like such a good idea at the time. I already took another course, titled “Bioinformatics”, where I initially fell in love with this type of work. It was a very different class, as there wasn’t that much factual studying, but rather we had a problem that we had to solve using various online tools. This class was something new and challenging. Choosing that module seemed like a normal continuation of my interests; another very important reason was also that classes weren’t held every day and also weren’t compulsory. Now, I naturally tried to attend as much as possible, but with my illness and doctor’s appointments, not worrying about doctor’s notes and attendance quotas was a bonus.

My violin plots bring all the people to the yard

There are five classes in the Computational Biology module and I chose four of them: Algorithms and Programming, Computational Genomics, Machine Learning and Statistics, and Mathematical Foundations of Computational Biology. Structural Computational Biophysics, the fifth one, honestly didn’t sound as appealing. Most of those classes were held in blocks (only Algorithms for a couple of weeks, then Statistics, then Genomics), with Mathematics being the only one we had every week for the duration of the whole semester.
Very quickly, I realised this may not be it for me; my colleagues got a hang of things quicker than me, and I felt that I’m lacking quite a lot of the prior knowledge, things I should have learned in high school, but my high school course back then didn’t focus on that. There were also memory issues, probably due to rapid changes in the medication I was taking, which was taking a priority above everything else.

The whole module is not perfect (for example, I learned quite a lot of Statistics, but not much about Machine Learning), however, I think it’s quite rewarding, especially since it’s the only opportunity we have to even check out a dry lab. It requires a lot of dedication and a lot of free time; at least now I have a reasonable (beginner’s) understanding of how to use R. What I also had, was the knowledge that sometimes, your first choices may not be the best for you and that it’s quite normal not to be exhilarated about the classes you’re taking. See, if I chose anything else, I would be plagued by the “what if-s” and now, after passing all the classes, I can confidently say I’m happy with the decision I made, but Computational Biology is just not right for me.

I’ve learned a lot and my professors were very understanding, although I honestly believe they also figured out this field isn’t my strength, but they helped me navigate all the tasks anyway. I gained a deeper understanding and appreciation of this type of research and re-discovered my love for the wet lab. I don’t know how much this knowledge will help me in the actual research, but even if I won’t do profound coding, statistical analysis is always an incredibly important skill to have.
If you had a similar experience, don’t be too hard on yourself – sometimes, we have to try out different things, even academically, to realize what kind of research interests us. Of course, at times that can be rather difficult and not everyone has the same options and opportunities. Academia can bring about a lot of stress and pressure, even without us doing the same to ourselves.

Field | Crayfish alert at Žumberak Mountains

Hi everyone, and welcome back to my blog. I took a month+ long break, during which I focused on my health and final exams at my University. At the same time, BIUS – Biology Students Association was preparing for their annual field trip, that I really wanted to be a part of!
BIUS is an association that gathers many Biology students from our department and focuses mainly on field trips, excursions, and expert lectures, all in order to complement and expand our Biology-related knowledge about certain topics. BIUS is also a publisher behind In Vivo Magazine, for which I serve as editor-in-chief.


Firstly, however, I would like to write a bit about my love for scientific (and a little less scientific) field trips. My primary love is the lab, after all. However, I grew up in a tiny village, surrounded by a living world – woods, animals, endless fields of tall grass… I actually started to think about studying something science based, perhaps Biology even, way back in the primary school, after wanting to identify all the bugs and spiders I would find in my front yard.
During my first two years of Bachelor’s degree, the thought of going out to the field didn’t really cross my mind, but it all changed in the middle of my third year, when I realized that something was lacking in my life, and that something turned out to be raw nature.

Photo by Đina Nola

This year’s big field excursion lasted for eight days, but I was only able to attend for the last four. Usually, BIUS organizes this kind of excursions twice a year, in May and September, but due to the pandemic, it was completely moved to the end of September, when situation in Croatia improved. Every year, a new terrain is explored, usually switching between continental and marine area. For this year, the leadership chose the Žumberak Mountains which are located on a border with Slovenia, and are approximately one hour drive from Zagreb. Žumberak is a mountain range divided into two parts, the Samobor Hills and the Žumberak Hills, both comprising the protected nature park Žumberak – Samobor Hills. It is home to many plant, fungal, and animal species, some of which are endangered or sensitive.


At first, shortly after arriving I was planning to spend every day with a different group, but in the end, I spent all the days driving around with the Crustacean group. I wasn’t sure how much fun is that going to be, since I knew very little about freshwater crayfish, apart from researching crayfish plague for a little while as an undergrad during an elective lab course.
I was already familiar with two members, Lena and Ljudevit Luka, since we are the same generation and took multiple classes together, and I also knew Anita and Karla a little bit; the whole group was very determined to carry out their research but with the sprinkle of carefreeness. I didn’t feel excluded for one bit and they were extremely patient with me taking photographs and filming videos.

So, what did Crustacean group actually do? Anita kindly explained their goals:

  • monitoring of the species Austropotamobius torrentium, also known as stone crayfish (how many specimens, in which streams are they located, what gender…)
  • taking swabs of crayfish cuticles in order to check for crayfish plague pathogen; this is later investigated by using the PCR method
  • taking water samples using special filters in order to check for crayfish presence; this is later investigated by analyzing the eDNA (environmental DNA)

How does that actually look like out in the field?
The first thing we did every morning, was to check the map and the roads; sometimes, we drove for more than one hour to reach a destination. Then we walked up to a stream, which sometimes proved to be rather tricky, since some seemed to dry up overnight. The most important thing we did before and after walking in every stream, creek or puddle was to disinfect our rubber boots, in order not to accidentally transfer pathogens to different habitats.

The group was very active even before my arrival, so we checked some permanent streams where they already set up special crayfish traps, that were actually made of old plastic bottles, with some tasty hot dog sausages in them. (Don’t worry, those traps are reusable! They just have to be washed thoroughly.) After taking out crayfish, one by one, they are measured and gently rubbed with a toothbrush, in a special buffer, to collect possible crayfish plague pathogen. Every tube containing that buffer is then labeled and safely stored. Crayfish are carefully released back into the stream, at the same place where they were found.

However, sometimes we went to streams for the first time, which meant no traps. So how do you catch a crayfish then? With hands. Usually they were hiding under rocks, but what most people probably wouldn’t expect, is that they are freakishly fast. Still, even during night-time catching & release, every member of the group was highly skilled in catching them. They could also easily discern female from male specimens, and Ljudevit Luka readily explained how, and also sent additional images (the ones below). In short, the main difference is that male crayfish have gonopods, while females don’t. (Gonopods are modified legs that are substantial during mating.)

A female stone crayfish

In four days that I spent with this wonderful group, I learned a lot and had a really amazing time. I wanted this post to focus mostly on crayfish, but I’m planning to post another one, where I will write a little bit more about travelling, our camping site, and wonderful nature I was able to document. I also took many videos, which I’m currently editing in one coherent, presentable, work, which I initially planned to release at the same time as this article, but life got a little bit in the way.
I sincerely hope you liked this write-up, and will read my next one as well!


Here you can find social media of some of the members of the Crustacean group, as well as the KarioAstacidae website, a student project led by Ljudevit Luka and Lena, which focuses on Astacidae populations in Zagreb.

Short science posts | Hydrozoa

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.

bsh

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 | Cubozoa (most advanced cnidarian nerve system)

Cubozoa, or box jellyfish, are another cnidarian class. Their name stems from their distinct cube-like shape. Cubozoa are also distinct from other cnidarian because their venom can be fatal to humans. As with all cnidarians, box jellyfish have two nerve nets and, like Scyphozoa, rophalia. However, box jellyfish also have a distinct nerve ring, as well as more developed eyes that consist of a lens, cornea, pupil, and a layer of retinal cells. Altogether, Cubozoa have 24 eyes, which makes them the most advanced cnidarian class in the sensory aspect.

Rophalia are mutually connected via the mentioned nerve ring. This ring is believed to be an integration center for the swimming, visual, and tentacle systems; it is comprised of oversized neurons, as well as some smaller neurites.
The communication between the nerve net and jellyfish muscles is regulated by chemical synapses.

Most of the information relating to Cubozoa, I already mentioned in the previous post about Scyphozoa, so I only wanted to relay the main differences between the two. These two classes are so similar that, until recently, they were actually considered one class.

Literature & more information:
Habdija et al: Protista-Protozoa, Metazoa-Invertebrata, Alfa, 2011, Zagreb
The ring nerve of the box jellyfish Tripedalia cystophora
Do jellyfish have central nervous systems?
Jellyfish nervous systems


Biology in popular culture – movies&TV (part 1)

I already wrote couple of posts on this topic, and today I’m focusing on several examples from movies and TV shows I’ve recently watched. The movies I’m going to write about are Lara Croft: Tomb Raider – The Cradle of Life, The Good Liar, Charlie’s Angels (2019 version), and Paranoid TV show. So, if you are planning to watch those, just a warning that there will probably be spoilers below!

Let’s start with the obvious and amusing misportrayal: in Lara Croft: Tomb Raider – The Cradle of Life (2003 movie), Lara is riding sharks in the opening sequence. I think no one would believe this is actually possible, but shark petting videos recently became very popular. However, many researches are strongly discouraging this type of behaviour.


The Good Liar (2019 movie) is an interesting thriller with really good cast that I actually enjoyed. Without giving out too much of the plot, I’ll just mention one scene where Helen Mirren’s character gives the haircut to the character played by Ian McKellen. She uses cut hair for the DNA analysis, factually linking McKellen’s character for the past crimes.
Of course, we all know that without the root, there is no DNA to analyze, right? Not quite.
Most companies that do DNA analysis require hair with follicles in order to extract DNA for analysis; however, they mostly deal with paternities, so they need the nuclear DNA. Mitochondrial DNA, on the other hand, apparently can be extracted from the hair itself. For the movie’s purposes, I think nuclear DNA was needed, so this seems like a movie mistake. But, recently scientists did manage to successfully extract nuclear DNA from rootless hair, but that DNA is often fragmented and complicated to extract.
I would also just like to mention that I believe this movie explains trauma and coping surprisingly well for a Hollywoood movie.

In Charlie’s Angels (2019 movie), which I hoped would be more enjoyable than it was, a very interesting premise was introduced; in order to effortlessly communicate, members of the team get a certain tattoo (at least I think it’s a tattoo, but don’t 100% quote me on that) and they can hear thanks to it. So, my first thought was, wow, they really went sci-fi on this one, but it sounded too out there. And then I remembered bone conduction. Simply, bone conduction allows you to hear the transmission, without blocking the outside sounds. And yes, only you can hear it. There are headphones already in use for this type of thing, and they can be also used to help with some kinds of hearing impairments. These headphones are placed on the skull, and I haven’t seen it implemented in a tattoo yet, but it’s actually a neat idea.

Paranoid (2016 TV show) is, in my opinion, really bad, despite only tangential connection to Biology. This show feel anti-medication and anti-psychiatrists, portrays them in a very bad light, and chooses not to mention how much medications and psychotherapy are actually helping people. The premise is also built on one of the cliche “anti-big pharma” representations. I was honestly insulted, despite not working in any of these fields. There is a also a subplot concerning a female character who had provocative photos of her taken 15 years ago, and she is not longer in possession of said photos; she is blackmailed with the possibility of leaking those. Her love interest immediately accuses her of things I won’t write here, but you get the main idea. I mean, am I the only one who sees this as highly problematic
This TV show is doing some serious damage to the health care, it is insulting to physicians, it is insulting to patients, and I honestly can’t believe that no one during the whole production didn’t say anything.


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I hope you like these kind of posts, because I already have enough material for another one (there are a lot of Biology & science mistakes on the big screen). What is your favourite movie mistake related to Biology?