Claudia Greco 🇮🇹 @corvina@qoto.org

Here I am again with my #SystemsBiology notes.
In this lecture the professor has taught us the basis of Network analysis, but what I find particularly interesting is that these concepts are applicable to so many fields!

But how are networks useful when we are talking about genomes? Well, for example researchers built networks to try to understand why the deletion of some genes that are in common to both yeasts and mice (like Map2k1) don't impact the yeasts' fitness, but if deleted in mice they cause embryonic lethality.

Researchers discovered that this might be due to the fact that during evolution these genes became more and more connected: if we consider each gene as a node of a network, the betweennes centrality of genes that are not essential in yeasts but are essential in mice increased a lot, suggesting that those genes in complex organisms became crucial in some biological pathways or protein complexes. For example, in mice Map2k1 is a member of the Ksr1 scaffold protein complex, while in yeasts it is not part of any protein complex.

From this discovery, they derived the centrality-lethality rule: in complex organisms, if a gene is highly connected it is probably also essential.

Source:
Kim, J., Kim, I., Han, S. et al. Network rewiring is an important mechanism of gene essentiality change. Sci Rep 2, 900 (2012). https://doi.org/10.1038/srep00900

"89 years have passed since Thomas Parnell (...) wanted to demonstrate to the students the liquid nature of pitch. When it is cold, this material is so hard it could be hammered; nonetheless it is still a liquid. Now, to show that a material is liquid, there is nothing better to pour it into a funnel to see it drip. In fact, the pitch really does that: however, a little slower than the liquids we are used to. Today those students (who in the meantime we presume graduated, besides those as dense as the pitch) have seen just 8 drops falling, with the patient yet incessant rate of a drop every six-twelve years.
Mainstone took charge of the experiment on his 2nd day of work, in 1961, and today still waits to see his first drop fall: the poor man was never present when it happened.
Unfortunately, even if a drop takes a few lustra to form, it only takes 1/10 of a second to fall - 3 billions times less than what it takes to become a drop. The probability of catching the moment in which the drop falls are quite low, especially if you think that people have other things to do - sleeping, taking a shower, combing their hair and go out to dinner with their friends, presumably laughing if some of them complains of how boring their job is.
Thinking he was clever, in the '90s Mainstone installed a webcam in front of the funnel, to record all day and night and finally assist to the moment a drop falls, if not live, at least on streaming.
But destiny had been twice as cruel with this man.
First, causing a malfunction to the camera exactly that night in 2000 in which the drop number 8 met its fate and fell from the exit of the funnel. Then, allowing a camera, at last, to record the moment a drop succumbed to the law of gravity, and eventually fell.
But not in Brisbane.
Instead, exactly on the other side of the globe: in Oxford, where in 1944 an analogous experiment to the Australian one was set up.
The 70-years-old Mainstone, however, does not surrender; he has already found among his colleagues of Queensland someone who, after his death, will keep following the experiment."

- Marco Malvaldi, "L'infinito tra parentesi"

Translation by me, because apparently this book has not been translated in English so I apologize for any eventual mistake. It's 1:23AM, I'm tired but I truly wanted to share this piece from a book I'm loving. I can't wait to finish it so I can write a decent review. It's truly a pity that we don't seem to have an English version of this book.

#sciencecommunication #scicom #marcomalvaldi #malvaldi #book #bookclub #chemistry #physics #reading

It's 9:40PM and I'm too tired to continue reviewing my #SystemsBiology notes. But I'm quite excited because finally the "...and #NetworkAnalysis" part of the course has started!

By the way, during my breaks I often went on Mastodon to see what the community was up to and I have read tons of introductions. It's funny to me that you (experienced, qualified and accomplished) managed to write a synthetic and straight to the point introduction, while I (messy student with no experience at all and really nothing to say) wrote an entire assay like it was even interesting 😂 I don't have the gift of synthesis, but I'll try I promise!

I wonder if there are other students here...

#notes #digitalnotes #university #università #stem #stemstudent #student #mastersdegree

Today I fixed my notes of two #SystemsBiology theoretical classes.

This one was about the circadian rhythms and I learnt about an interesting experiment which suggested that the superchiasmatic nucleus (SCN) of the hypothalamus might be involved, since transplanting the fetal SCN in arrhytmic mice seemed to restore it. Not only that, but the periodicity of the rhythm depends on the donor!

Source
DOI:https://doi.org/10.1016/S0960-9822(03)00222-7