S3E12 Cube chatShaala: Exploring new ways of Learning

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Timing:5.30 pm to 9.30 pm
Webinar will be recorded and recording link will be post in the same thread after the webinar.

Looking forward to your participation.

CUBE ChatShaala: 20th Nov 2020

A discussion that started initially with the smell sensor (proposed by @palaneprashant ), caught pace when we started with the question; what is smell?
How do we come to know that there is something around us even without looking at it, say a perfume?
What happens when we suspend a crystal of potassium permanganate (KMnO4) in a bowl of water?
Is there a concentration gradient of the smell/chemical?
How is this gradient getting created?
A simple process though appears to be complex in different contexts. We misinterpreted diffusion with entropy.

Talking about smell, how can we leave our model organisms; Snails and Fruitflies?
How do snails perceive smell and come to know that their food is in this/that direction?

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Meanwhile discussing this, there were new CUBists who had joined for the first time so, an introduction of our model organisms was needed.
A naive question; what are model organisms and why are they called so?
A model for what?
If we want to study neurobiology or epigenetics, we can’t really do experiments on humans directly! Is it not?
Though smaller than us, these animals share the same level of complexity as humans; this is what makes them a MODEL (organism😅)
Snails share a direct relation with the 2000 (year) Nobel Prize-winning model organism Aplysia (Sea slugs) that was studied by Eric Kandel (he is still alive!) et. al. The discovery was on learning, memory and signal transduction in the nervous system.
Moina (a model organism to study epigenetics) is indirectly related with the 2019 Nobel Prize-winning study on hypoxia and its effect on the cells.

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We had CUBists from DKW College in Nellore, Andhra Pradesh. Cubists from cube zebrafish model system have been maintaining Zebrafish (a freshwater fish-yet another model in CUBE). While discussing their maintenance, we got to know that Artemia (brine shrimp-marine crustacean) is used (in laboratories) as a live feed for the zebrafish.
It is used to feed Hydra (freshwater cnidarian) as well. But in CUBE, Moina (a freshwater crustacean) is given as a live feed to the cnidarian.
And also Moina is preferred over Artemia because;
i) protein content in Moina is higher than artemia
ii) artemia isn’t readily available, it is available in the form of cysts that needs to be hatched and then treated in saltwater (as they are marine).
We culture Moina in our HomeLabs at ease! Why is sophistication needed!?

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Why are zebrafishes called zebrafishes?
Is it due to the stripes (that resemble stripes of a Zebra) on their body?

The most intriguing question was, why are zebrafishes seen in different colours?
We see them in their characteristic (above) colour, they are seen to be orange, pink as well!
Why that?
Are they of different sub-species?
Have they been genetically modified and then introduced in the water bodies?
It should surely have economical importance!
There are chromatophores (pigment-containing and light-reflecting cells, or groups of cells, found in a wide range of animals including amphibians, fish, reptiles, crustaceans and cephalopods; https://en.wikipedia.org/wiki/Chromatophore) that have pigments such as melanin (dark/black), xanthin (yellow) and erythrin (red) that are responsible for pigmentation. One and two of these pigments are found in humans and plants respectively.

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Generally, when we talk about the long term objectives/questions of the Rotifer (a freshwater organism) and Nematodes (soil worms), we come across the green-fluorescent protein (GFP).
It is a protein responsible for luminescence.
In the above picture, we can see four different-coloured zebrafishes (I don’t know whether it is in real or just a representational graphic).
Anyways, let us say if we want to introduce the GFP in zebrafishes, how do we go about doing it?
I think we will have to introduce it in the embryo stage, right?
What exactly needs to be done on a molecular basis?

As GFP is a protein, it must have the gene(s) that code(s) for it. How do we isolate this/these particular gene(s) from a long stretch of DNA!?
Before asking the scientists who have done this, we thought of building a proposition with whatever knowledge we had.

Referring to the picture here, we can see there are rectangular drawings at the bottom that represent a train.
Upon being asked, “what is the difference between DNA and a gene?” we thought of answering it in this way.
If we assume DNA as a whole train, then the bogies/coaches of the train would resemble the genes.
DNA is a polymer of nucleotides that is made up of sugar (deoxyribose)+nitrogen bases+phosphate.
And genes are short segments of DNA that are code for proteins (not all DNA codes for proteins).

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In our college/institute laboratories, majority of us must’ve done DNA extraction and its further screening by extracting DNA from bacteria, etc and then running it on the AGE (agarose gel electrophoresis) equipment.
Can DNA be extracted at home?
Why? Why not!?
DNA is present in fruits/vegetables that we eat! We never bothered to look for it though😉.
How is the laboratory method of DNA extraction different from the HomeLab method?
I think the main requirements would be
i) a fruit/vegetable ii) alcohol (rum/whiskey? no! in COVID times, sanitiser with 70% alcohol is enough!) iii) detergent/soap iv) warm water v) salt.

In this slide from the whiteboard (almost a self-explanatory slide), we arrived at the conclusion that DNA can be extracted from things available at home, with ease! This was followed by a discussion on the importance of each requirement; mortar pestle (for grinding/making a paste), soap/detergent (to disrupt the cell membrane; as soap does to the COVID19), alcohol, etc.

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CUBE Chatshaala on 20th November 2020
45 CUBists from 33 centres joined the webinar.

Nellore: Anoopa. O, D. Indira, SaiChethana, Tejasree, Ujwalaraj, Vakulananda

Narsing HS, Silchar: Hasina Begam
Sonari: Susanta Tanti

Sitamarhi: Anamika Singh

Dyal Singh College: P. Chitralekha

Kanke, Ranchi: GC Baskey
Kokar, Ranchi: Manjuel Jojo
Morabadi, Ranchi: Rechel Tirkey

Bangalore: Deepika Iyyangar

Kozhikode: Arunima
Malappuram: Devika Dasan
Ernakulam: Aishwarya Elizabeth, Bhavya, Devika Devanath, Pooja Baiju, Yami George
Palakkad: Nisy Prasad, Shrudhiga
Kolenchery: Sagar Alias
Thanniam: Sidhy

Indore: Farhan Ashraf, Firoj Patel

South Bombay: Arunan MC
Ghatkopar: Aashutosh Mule
Thane: Anshu Kadam, Prashant Palane
Nerul: DK
Powai: Lydia Mathew
Mulund, Mumbai: Omkar Badnale
Dahanu Road, Palghar: Sachin Pradhan
Panvel: Shraddha Sonavane
Prabhadevi: Yash Sheregare

Moradabad: Kiran Yadav

GHS, Kolkata: Aranyak Sarma, Koulab Mukherjee
Kolkata: Batul Pipewala

Shaikh Ashefa