CUBE Chatshaala:- The Causerie will still be on!

Lydia · May 6, 2020, 11:26am

4th MAY, 2020

Webinar Summary

Possibilities or the sources of contamination in the home made media.
We discussed 3 main parts which could help us in solving out the problems!
1. The components or the ingredients used for making the homemade media
2. Cooking
3. Autoclave

1.When we look at the first part i.e. components or the ingredients used for making the homemade media…

While comparing with the Standard Corn Meal Media
Dextrose and sucrose are a source of sugars,
Maize powder a source of carbohydrates,
Yeast extract a source of proteins, vitamins and minerals and
Agar as a solidifying agent.

Now when we look to the ingredients in our Tomato Rava Homemade Media,
Table sugar is a source of sugar as in cornmeal media
Rava is a source of carbohydrates (73g in 100g rava)
Tomato puree is a source of proteins, vitamins and minerals
Rava here in this media acts as a solidifying or a binding agent as well.

So when we look at the components or the ingredients used…they are just perfect when compared with each other!
We were now clear with the first part!

2. Coming to the second part i.e. COOKING

We are not cooking just for the purpose of cooking for some time or so.
There is a purpose behind cooking.

What if we don’t cook?
was the question raised by @Arunan Sir.
We have in our mind that we require a solid consistency of the media.

Why do we need a solid consistency?
was the next question.
If we get a liquid medium then that won’t support the culturing of flies in a bottle
The flies would get stuck to the media and then they die!

What is this solid consistency, like how is it’s shape?
The media after pouring in the bottle should take the shape of the bottle or the container and should have an even surface!
If not an even surface, then the flies might get stuck somewhere and then they die!
All these factors should be kept in mind!

What is this cooking? Till what time do we cook? What should we achieve by cooking?
We need a homogenised mixture or a medium.
For this we need to cook properly.
What do we mean by cook properly?
We need to cook the ingredients in water till we are sure that all the components have dissolved in the water and are mixed completely.
Here the time take for cooking is not what is concerned rather, the homogenisation of the media is what we are looking for!
This is what is done with the standard cornmeal media too!

If there is excess of water, we can evaporate it by cooking while the ingredients are being mixed in the water.
Should not overcook as added by @ankitcube
Do not cook till the media gets thick or till it gets too thick in its consistency
Otherwise it would be difficult while pouring this media in the bottles.

If this much is taken care of, then we can to very much extent prevent the growth of bacteria or fungi or whatever unwanted growth was seen!

3. The third part i.e. AUTOCLAVE
We all have a pressure cooker at home.
As suggested by @Arunan Sir, we can pressure cook it for once and then our media is ready.

This much can be tried out and we can achieve what we want!

drishtantmkawale · May 6, 2020, 11:34am

Why is pressure cooking needed?
We are already cooking it right?

KiranyadavR · May 7, 2020, 1:43pm

Update on CUBE Room Webinar : Saturday,11 April 2020

Cubist from different Places/Cube Centers had joined the Cube Room Webinar, Saida Sayyed, Drishtant Maruti Kawale, Lydia Mathew, Isha Pawale, Mandar Chavan, Yash Shergare, Jai Kishan, Aashutosh Mule, Rafikh Shaikh, Zahra, and Priti Kanade are from CUBE HBCSE, TIFR Mumbai.

Joined bySavithri Singh Former Principle of AND College Delhi and Vaishanavi Mirdha.

KiranyadavR · May 7, 2020, 2:15pm

Update on Cube Room Webinar: 06.05.2020

Picture of Yesterday’s Cube Room Webinar( Date:06.05.2020) that was conducted on Google Meet Audio- Video Conferencing app and joined by Prof. MC Arunan, Drishtant Maruti kawale, Isha Pawle, Lydia Mathew, Saida Sayyed, Zahra and Kiran Yadav from Cube HBCSE Mumbai, Dr. Sarita Kumar and Komal Kotra from Cube AND College Delhi , Shalu Kumari from Cube Patna, Hina Mudgal from Cube Kanpur, Aswathy Suresh and Lakshmi P J from Cube SN Natika College

Above given is the link through which one can join the Cube Room Webinar, Everyday in the Evening from 5:30pm to 8:00pm.

Lydia · May 8, 2020, 1:19pm

Summary of Yesterday’s Online Discussion by @yash_sheregare
07/05/2020

Will Acetic acid be a mutagen to fruit flies ?
@aswathy a CUBist from CUBE SN Nattika who for some time is very well trying and learning about fruit flies, how to culture them, designing home made media

In one of her tomato rava medium, She added to her medium, ~ 10ml of Vinegar to a 100 ml medium containing bottle
(a lockdown substitute for propionic acid which is eliminate other fungal growth at low pH)
And now she had a burning question…
whether the acetic acid added to this medium for killing fungi, whether will it have any mutagenic effect on fruit flies?

We all tried to discuss her question and come to an easy suggestion
That Vinegar is evidently used by majority of people in various foods like pickles salads
If would have been a mutagen, it wouldn’t be a choice for us to use it for pickling or adding to salads
@Drishtant through some reference then found out that Acetic acid is not a Mutagen!

Now , we have a new opening and a question that sir asked as to whether propionic acid that is added in std corn meal agar medium, is it a mutagen?

Goof ups of no Expectation and Anticipation!
@YashSheregare, from CUBE Institute of Science, I try to explain everyone about the new tomato medium that is tested if it is a good medium for culturing fruit flies, larvae and pupae for 1 or 2 generations with no contamination.
2 medium bottles in which 10 and 6 fruit flies were added and comparing the observation made previously of a fantastic tomato slice that gave rise to next generation fruit flies, I should be expecting pupae in 4 days.

However I didn’t observe my bottles properly after 2 days for larvae and didn’t expect larvaes the next day when gravid females after laying eggs on the same day!

There is a very high possibility that gravid fruit flies will lay eggs in the medium the same day they will be transferred which got ignored…

Highlights of Gooof up - The goof up that I did was not observing and anticipation of what is to be OBSERVED and EXPECTED everyday!!
The idea of Feeling for the organism should be practised by me and others who working on model organisms!

Discussions on How should we include Goof ups and the importance of Highlighting goof ups in our fruit fly ebook

Lydia · May 8, 2020, 2:04pm

Here we are trying to design a protocol that would exactly be like the standard corn mean media that we make in the lab for our standard CsBz flies i.e. Drosophila melanogaster flies.

It would be better if I explain the method of preparation of the standard corn meal media (250ml).

Dextrose - 12.5gms
Sucrose - 6.25gms
Maize powder - 20.75gms
Yeast extract - 3.75gms
Agar - 4gm
Mix all these components in water.
Add water to make up the volume of the mixture to 250ml
Mix all the components in the water well.
Then cook the media mixture on a medium flame.
Cook till all the components in the media are homogenised completely and that there are no lumps in the media.

Next comes autoclaving
We autoclave using a pressure cooker.
The reason for autoclaving is to kill the spores and microorganisms present and to sterilize everything.
We sterilize the glass bottles and the media by autoclaving in a pressure cooker.
Trying maximum to minimize the possibilities of getting any fungal or bacterial growth we autoclave

Once the media is autoclaved,
We add acids in the 250ml media
Orthophosphoric acid - 0.17ml
Propionic acid - 1ml

This is what we want to do exactly in our homemade media.
So that we can standardize our homemade media as well.

This is a site as a reference for the standard cornmeal media that we make…

drishtantmkawale · May 8, 2020, 4:41pm

Can we summarize the work each of us has been doing since the lockdown started?

I think there has been a lot of work done in the past two months.
We have done many improvisations in the Homemade Fruitfly medium, changed our traps, discussed on different media, etc, discussed the identification of flies and much more.

Every day I get to see a lot of photos and videos!
But, the point I would like to emphasise on is that do we learn or infer something from those photos, small write-ups!!!?
Writing a summary about the discussion and our work would help us in gathering points for the E-Book as well as our own knowledge and furthermore, it would make it clear that how much do we understand what we do?
Are there any conceptual gaps?
There must be many gaps which we can fill by understanding it collaboratively leaving no stone unturned!

And also, while starting something new or continuing the previous work, we should put the following things (which I have learned and have been learning in CUBE) in the discussion
Starting with the Plan of Work which will include the things which we are planning to do in the coming days or on the same day, Design of the Experiment/Set-up which will tell us that how is our experiment going to work exactly!, then will come to our Hypothesis which should say what do we anticipate/expect from this experiment and regardless of the result we should propose a hypothesis which we would be disproving or proving by our experiment along with cited references and cross-references from authentic authors, journals, websites, labs and universities will be helpful! and then the Procedure of the experiment.

Writing or posting this in the groups or discussing all this before performing the actual experiment is essential because someone would suggest any changes or we think that this should be done and this should not be done i.e. improvisations will be suggested which would take us a step ahead in doing it.

The most important thing would be posting regular updates with a breaking news! as @Arunan Says, if there won’t be any catchy headline, no one will be interested in reading which means that our breaking news is the bait!
These updates should include each and every detail which was observed by us because Science is very weird (for me), one day we would observe one thing, then the next day something other which tells us that something unexplored is waiting for us!

And reporting the Goof-ups which happened during the course time is essential as it would have a direct impact on our results if some mistakes will go unnoticed!

URGENT!

drishtantmkawale · May 9, 2020, 8:21pm

8th May 2020 Summary of the CUBE Room Webinar!

So, Nikhil Sharma from Acharya Narendra Dev College (AND College) had joined along with @GN, @KiranyadavR, Aswathy Suresh from Nattika, Oyindril Dutta from Asansol, Abhishek from Kolenchery, @Arunan from Mumbai and myself.

So, the discussion started with Kiran asking Nikhil about his further plans on the Drosophila Model System on which he was working. He said that he is going to set traps for trapping the flies with his further plan to study the life cycle, life span and classify the fruitflies on the basis of their characteristics!

I know all these are a lot of things at once so we started step by step by asking the design of his experiment.
We came to know that he was just planning to keep one trap but CUBE doesn’t believe in keeping all the eggs in the same basket!

So, we made him understand the importance of having replicas.

Nikhil said that he will be taking plastic bottles and in that, he will be adding banana as the trap in one bottle and banana peel in the other bottle which will act as a medium too. But I asked, why two different traps?

To which he answered that he wanted to try out, how will it work?
So, we suggested that he should try both and see along with replicates and put regular updates. But GN added, there would arise a problem with the banana peel bottle. He asked what?
So, Sir said that we should find out the answer by ourselves!
How?

We should try keeping a banana peel in an empty bottle and then close it and observe what happens over a period of time.
And GN asked, what are our expectations!
The most important thing!
To which I replied, as the bottle will be closed, there are no chances of air passing inside, so the banana peel will get dried up, it will darken, it would shrink.

Then GN asked only these many things?
I said, yes.

Then asked about something which we have been learning in our textbooks - Spontaneous Generation!
What is it?
Spontaneous Generation means something arises from nothing!
Here, the something can be fungal or any other type of invasion on the banana peel!
We can say, that earlier nothing was visible on the peel but later, there is a chance that as we are not using a sterile (free from contamination) bottle or a sterile banana peel, we can observe growth in the form of fungus and the chances of it getting inside the bottle are more from the banana peel as compared to the bottle as the banana peels are having cells from which the fungus is deriving its nutrition!

So we saw, we got a context here which was directly related to our curriculum.

Then, carrying on with our discussion, Nikhil said he wants to study the life cycle of the fruitfly for which he will need at least some flies to start with.
But the question arises, is Nikhil actually culturing fruitflies!!?
How do we confirm that the animal which we have inside the bottle is actually the ones which we are looking for!!?

Here is where Taxonomical Classification pitches in!
Classification on the basis of its characteristics!
Kingdom, Phylum, Class, Order, Family, Genus and Species, this is the hierarchy of classification.

Crow and Fruitflies fall in the same kingdom!
What makes them different?
Their size?
Yes, but Noo.
@Arunan joked, does the difference in the height of Sir himself and Amitabh Bachchan make them fall in different species!!?

No right!!

So, what is that which makes them different?
Fruitflies and freshwater-crustacean Moina fall under the same phyla because of the presence of a segmented-body, compound eyes, jointed appendages and chitinous exoskeleton!

What makes them different?
The presence and absence of wings!

This diverges them into a totally different Order, which is Diptera for Drosophila and Branchiopoda for Moina.

Dipterans (Di- two and ptera- wings) are characterised by the presence of a pair of wings.
And Branchiopods (Branchio-something related to bronchioles of the lungs/gills and poda-feet) are characterised on the basis of the presence of gills on some of their appendages!

I have been working on Moina Model System from the past 8 months but this is when I recalled the meaning of Branchiopoda!
And this is how to further both the organisms differ in their classification!

We see that at a point, two distinctly different organisms are related!
This is too, a beauty of Science in itself where to some, taxonomy seems booooooring and to CUBists, it solves questions!!
If we develop an interest in what we work, we will be able to pass in on to others very beautifully!

And in the end, we discussed the relation between Cardamine and Drosophila!
Yes!
Botany and Zoology, the offsprings of the same parent Biology, but often considered un-related, but we CUBists have an opportunity to prove that they are related!

Further, we should discuss this and also we should bring back our Nobel-Prize winning works (as much as 6 Nobel Prizes for the wandering beauty - Drosophila!) and see whether we are able to understand these works and relate them!

Please contribute and start posting regular updates as well as a summary!
@Lydia @yash_sheregare @saida786110 and others!

saida786110 · May 11, 2020, 4:52pm

[5/11, 10:05 PM] Saida: in today’s discussion we talked about floral dip method in cardamine plant
floral dip method is basically diping the flower:hibiscus: in plasmid and detergent.
plasma containing gene of interest
and we are using detergent so that it can make pore in the cell membrane of the plant so that the plasmid can get incorporated in it.
[5/11, 10:05 PM] Saida: and the gene of interest that we talked about was antibiotic-resistant Gene that is kanamycin resistant gene
so why antibiotic resistance gene?
does antibiotic affect plants
certainly not antibiotic is used to kill bacterias and not eukaryotes😅
now the question is how would an antibiotic will effect a plant if yes then how🙄
[5/11, 10:05 PM] Saida: so as an example we took penicillin which affects the cell wall of the bacteria
and even plants have cell wall so can antibiotic effect plant cell wall
the cell wall of the plant is made up of cellulose basically glucose β(1→4)-glycosidic bonds.
and cell cell wall of the bacteria is made up of peptidoglycan. peptide is a compound consisting of two or more amino acids and glycans are compounds consisting of a large number of monosaccharides linked glycosidically.
so if penicillium affects the glycosidic bond of bacteria then and it can also affect plant cell wall. but Penicillin prevents peptidoglycan from cross-linking and cross linking is through peptide so penicillin will not be able to effect plant cell.
[5/11, 10:05 PM] Saida: now coming back to kanamycin. kanamycin prevents Protein synthesis and there is protein synthesis in plants so maybe it can stop
Protein synthesis in plants as well .
but kanamycin bind to the 30s subunit of bacterial ribosome. and in eukaryotes there is no 30s subunit of ribosome there is 40s and 60s so it should not affect plants but plants also have mitochondria and cytoplasm that are of bacterial origin which have 30s and 50s subunits of ribosome. so technically kanamycin can affect eukaryotes as well
[5/11, 10:05 PM] Saida: so supposingly if I take animal cells there is no cell wall as well only cell membrane and I take some detergent to interrupt the cell membrane of the cell and add some plasmid will there be a gene transfer taking place??
[5/11, 10:05 PM] Saida: we have figured out how would kanamycin will affect the plant cell and if there is gene transfer of kanamycin resistant Gene then cardamine can be grown even in kanamycin.
but how would we by detergent disrupting the cell membrane of plant incorporate our gene of interest?!

drishtantmkawale · May 19, 2020, 10:14am

18 May 2020, CUBE Room Webinar Summary

We started with @Rechel_tirkey ⁩ from CUBE Ranchi updating about her Moina cultures in her home lab.

Then, Gaurav Aggarwal⁩ studying at the Central University of Punjab joined us. We came to know that he has been working on Soil Worms or Nematodes.

We asked him about the things done by him before the lockdown.
So, as every nematode CUBist starts with, Gaurav also started collecting soil samples from the campus in a petri plate

Then, he prepared 2% Agar media and then poured it into another petri plate.

Why was 2% Agar used?

He also mentioned that 70% Ethanol was used by him as an attractant for the nematodes.
Why 70% Ethanol?
For me, it is used to make aseptic conditions and here it is being used as an attractant!
And Gaurav also said that Escherichia coli, a bacterium will be used by him to feed the nematodes.
I am sure that in their natural habitat, i.e. soil, not only E. coli, but many other bacteria would also be there on which the nematodes would feed.

So, Why specifically E. coli?
I suggested if bacteria are only needed, then the simplest source of bacteria would be milk which has nutrients in the form of carbohydrates, proteins, vitamins, minerals and fats as well as bacteria!
Instead of giving a Rajshaahi E. coli, milk bacteria can be used.

Can we start isolating the nematodes in our home labs?
What would be the procedure or design?

Originally asked by @Arunan
@Anshu_kadam_2813 ⁩ @bivasnag⁩ @⁨Kunal Kadam⁩ @⁨Omkar Badnale⁩ @Shivamkumar_Sriwas - How will you guys start isolating the soil worms with the minimal required things available at our homes!!?

All this would be further explained by Gaurav.
This was done as his immediate objective was to isolate the nematode and identify it.

But @Lydia and many others questioned, how do we identify the nematode or the worm which we have got.
Gaurav⁩ said about DNA sequencing!
It is not a thing which we can do at home! Is it?

@PChitralekha added that sequencing can be done for identifying the animal or plant at the species level. She gave the example of Chlorella algae which at the species level, would need DNA Sequencing.

Arunan Sir⁩, @Lydia, Mayur Gaikwad Sir⁩, Aashutosh Mule Sir⁩, @yash_sheregare ⁩said that can’t we proceed in identifying the nematode taxonomically?
Caenorhaditis elegans is the soil nematode which has Nobel-Prize on its name!
So, we can start identifying the nematode and take the characteristics of C. elegans as the Control or Standard, to match with, along with pictures and references.

First of all, how do we know that the animal which we have is an animal?
If we start with addressing such basic questions, we will we able to get a context which we can relate to the school/college curriculum!

Taxonomy is anyways thought of as a boring thing to teach as well as to learn.
So why not make it interesting by discussing with the help of a whole library in our hand; our mobile phone.
Along with gathering some pictures and examples at each taxonomic hierarchy.

Answering questions like how can a soil nematode be differentiated from an Earthworm!? would give us a good start.
If we show a microscopic image of a nematode, a child would say, "Arey, this is a small Earthworm!"

If I show a layman, my Moina culture bottle, he would say, “Aye, ye toh keeda hai”! (Oii, this is an insect!)!
For them, it may be a "keeda* or an insect, but for us, we know that it is not. So, how do we convince people about our organism!!?

We can start by relating it to some other organisms which anyone could be familiar with!
If we see, Nematodes, Earthworms, Frutiflies, Moinas… at some point in their classification, they are grouped together say in Kingdom: Animalia, then as we go further, we come to know that there are some characteristics, which make them different from each other due to which some end up in the soil, some fly in the air, and some swim in the water!

The only wait is for getting a good context to start with, rest, the CUBists will handle!

We also discussed the taxonomical classification of the Standard Drosophila melanogaster CsBz fly and Moina macrocopa, both of which are Model-organisms in CUBE.

Later, in the end, @saswathy679 from CUBE SN College Nattika, Kerala shared her Fruitfly Homelab Medium story and updated us about the cultures and current happenings at her place.

yash_sheregare · May 22, 2020, 3:52pm

Online Discussions
17/05/2020 CUBE Room Webinar

We had discussions today on varied different
Topics starting from
Our special lockdown stimulated Home Made Medium for fruit flies - Tomato Rava SugarVineger Medium (TRS-V Medium)
To Moina Culturing, Circadian Rhythm studies in fruit flies, topics like Genetic drift in brief and many more!

Most highlighted Take home from Today’s Discussion

As @mayur sir added while discussing Moina Culture for Sweta CUBE Ranchi

Don’t put all your in one basket

In our CUBE , the context goes for every model system
Be it, Moina cultures (keeping of replicates)
Fruit fly cultures
Hydra cultures
Cardamine studies
And so on!
We need to have replicates for each time we try to do anything
Be it

culturing or maintaining Moina cultures, or making a new setup for Subculturing!
Maintaining fruit fly cultures and even testing home made medium for Culturing fruit flies!
Culturing Hydra, Having replicates!

@⁨Ashwathy CUBE Nattika⁩ , a Nattika CUBist has very well tried and made a working home made TRS V medium which worked well to give rise to larvae (in three days) pupae (in another w days) and next generation fly (after another 3 days, which means next generation fruit flies in 8 days! ) in her single medium bottle! ( This result we see evidently also in our Std Corn Meal agar medium)

Now, to confirm and say, it’s a medium that functions well
Or lets say,
To make this our standard Medium, we all together need to Design and make medium with Replicates and control

Which means?
When we make and test the medium and say the medium is working well for getting us larvae, pupae and next generation flies, it shouldn’t be giving us the result in just one medium bottle but atleast 3 replicates and even better for more bottles tried and tested by all other CUBE centers working on fruit fly and culturing them during Lockdown Collaboratively!

For that we all together must discuss it in length with details
The design of medium
The protocol of medium
Modifications in the medium if any
Number of replicates to be made
Number of fruit flies added in each bottle (keeping in mind and also adding and counting number of gravid females in each bottle)
Types of Control setup needed?

Please add in your inputs!

drishtantmkawale · May 23, 2020, 12:42pm

22 May 2020 CUBE Room Webinar

Yesterday’s discussion started with CUBist Abhijeet Singh, a Class XII student from Mumbai, sharing his experience in CUBE; he told us about the model organisms he worked on, the basic understanding of it. Abhijeet has worked on the Ventral Nerve Cord Regeneration in Earthoworms, on the Fruitflies as well and has also studied on Mosquitoes.
About Mosquitoes he told us about keeping Ovitraps. Abhijeet and @Hinaiqbal_Mudgal from Kanpur were discussing about their own experiences with mosquitoes, their current status and further plan.

Then, we came to the Drosophila-Fruitflies where @saswathy679 from Thrissur has been working a lot on the Fruitflies, be it trapping, medium preparation, preparing single line cultures. So, Abhijeet was new to this so we heard the summary of @saswathy679’s work so far and her further plan.

Then from South, we went to East-India in Asansol, West Bengal where @OYINDRIL is also working on fruitflies. As of now, the Circadian Rhythm Studies are being done by him.
We would like to know about your work @OYINDRIL DUTTA…!

@OYINDRIL is also planning to prepare media to maintain his fruitflies. So @saswathy679 is also working on fruitflies. As of now, the Circadian Rhythm Studies are being done by @OYINDRIL DUTTA…
We would like to know about your work @OYINDRIL DUTTA…!

He is also planning to prepare media to maintain his fruitflies. So Aswathy, who is now confident of sharing the Procedure (secret recipe🤭) of her media, we should look forward to get updates.
So her we saw that CUBE is acting as a connecting link between Thrissur, Kerala and Asansol, West Bengal where collaboration is taking place at every step and problems are being solved!

As @Arunan said, there is lack of anticipation/expectation from our work!
We should expect something in order to get something. If we aren’t expecting only, then what are we going to look for?
And also when proposing a hypothesis, design of an experiment, we should not do it vaguely but proceed with confidence so that the fellow viewers would be eager to know what is happening.
The way of presenting our work with proper headline/breaking news, plan, expectations matters the most!

Not to forget, Evidence based Research is what we should focus on, otherwise it would be like doing a ritual of which no one cares of!
Evidences, archives in the form of Research Papers (from recognized labs, universities, journals, authors/scientists along with cross references), Photos and Videos with a proper hypothesis/strong statement are the things which we should look for, further which would convince our audience!

For example, if we are preparing the Fruitfly medium at home, then we should start mentioning the quantity of media, the requirements of it, the texture, the procedure, cooking time…
If we say that 100mL medium was prepared just like that, then some fellow CUBist trying to reproduce the same medium won’t be able to do it.

Why?
Because we lacked in details!
This is why Arunan Sir always emphasises on giving the details because The DEVIL and the DEVINE is in the Detail!

But, if we go by saying that 100mL medium was measured using a cup or any other utensil, then it would be somewhat relatable otherwise people won’t do it saying that "we don’t have the sophisticated equipments for measuring and all… so we won’t proceed!"
@mayur added that simply relating the amount which we want by imagining/visualising the ~measurements which we use in our labs, will do the trick! (not necessary that the amount should be accurate everytime!)

Looking forward to get updates from everyone!

A short-summary after the Webinar will make sure that the discussion starts in the group!

Lydia · May 27, 2020, 9:27pm

26th May & 27th May 2020
CUBE Room Webinar (A short summary)

While discussing in the webinar for the past 2 days,
@saswathy679 and many others were believing or claiming that temperature might be a factor that gave a delayed life cycle.

So, the story goes like this…
@saswathy679 as a very good or a very thriving culture which started from 6th May.
Within 8 days, i.e. on the 8th day (14/05/2020), new generation flies ecloded from the pupae.
After 4 days i.e. on 18th of May, another set of media was made and the newly emerged as well as the parent flies from the 6th May bottle were transferred into the newly prepared 18th May media bottle.

In this 18th May TRSV media bottle, Aswathy could not locate any larvae for almost 7 days i.e. from 19th May to 25th May…but on 26th May, small and big larvae could be seen by @saswathy679 as a very good or a very thriving culture which started from 6th May.
Within 8 days, i.e. on the 8th day (14/05/2020), new generation flies ecloded from the pupae.
After 4 days i.e. on 18th of May, another set of media was made and the newly emerged as well as the parent flies from the 6th May bottle were transferred into the newly prepared 18th May media bottle.

In this 18th May TRSV media bottle, Aswathy could not locate any larvae for almost 7 days i.e. from 19th May to 25th May…but on 26th May, small and big larvae could be seen by @saswathy679 i.e. on the 8th day!

During the webinar,
Aswathy claimed that temperature might be the factor responsible for this delay.
When asked what was the temperature, it was told that it’s 27°C.

For me, and @yash_sheregare ,
We had 2 reasons for ruling out the factor of temperature!
27°C is normal (lab temperature) where we used to culture our fruit flies, the standard as well as the native single lines. And within 8 days we used to get the next generation flies.
Aswathy herself got a thriving culture in the same place at the same location using the same media (without making any changes) few days back…not even a month old story…
And I looked for the temperature of those days.

There isn’t much drastic difference in the temperature that would affect the life cycle of fruit flies giving a delayed cycle.

If you ask me what was the temperature during those days.
I’m giving a reference along with the data of the temperature on all those days from 6th May to 16th May (the bottle which had a thriving culture) and from 17th May to 25th May (the newly made same type of media which was claimed to show a delayed life cycle of almost 7 days!!)

Reference: https://www.accuweather.com/en/in/thrissur/188812/may-weather/188812

May
6th - 34°/24° C
7th - 34°/22° C
8th - 32°/26° C
9th - 33°/25° C
10th - 33°/25° C
11th - 33°/25° C
12th - 33°/26° C
13th - 33°/26° C
14th - 34°/25° C
15th - 33°/26° C
16th - 32°/25° C

17th - 33°/26° C
18th - 29°/25° C
19th - 31°/25° C
20th - 33°/24° C
21st - 31°/28° C
22nd - 32°/25° C
23rd - 33°/29° C
24th - 33°/27° C
25th - 33°/25° C

@saswathy679 prepared media on 17th May too…
But, I emphasized more on 18th media as that was a replica of the media made on 6th May.
On 18th May, the 6th May media was replicated and flies from the 6th May bottle were transferred into these 18th May media bottles.
So we have the temperature range from 17th May to 24th May as well.

Do we really see a temperature difference or drastic deviation in these day??
I dont see any!!
Is it really a temperature bhagwan at fault or is it some other factors???

Today,
when we were again discussing about the same thing,
still we were stuck in the temperature thing!
Surprisingly, diapause & humidity factors also came up…okay…agreed…

So…What is Diapause?
A period of suspended development in an insect, other invertebrate, or mammal embryo, especially during unfavourable environmental conditions.
Unfavourable conditions!!!???
What unfavourable conditions did Aswathy or her flies faced??
Humidity was an answer…okay

So…What is Humidity?
Its the quantitative amount of water vapour present in atmosphere.
How can this affect the flies which are cultured inside a bottle which is kept closed all the time and is opened only when we have to transfer flies…??

[size=4]Now, I would like to tell what could be the reasons along with the explanations for the so claimed delayed life cycle of Aswathy’s flies.[/size]

According to @saswathy679’s observations,
She saw larvae on 26th May (both small and big)
And then, today i.e. on 27th May, she got pupae!!
Can a larva turn into a pupa within a day?
Its impossible according to my experience and observaions with the standard and the native fly cultures.
It takes minimum 2-3 days for a larva to turn into a pupa.

What can we infer from this?
Observation is lacking because strong expectation is missing
LOGICAL EXPECTATION…that has a great role in science, especially in DESIGN

I’ll explain it more…
If Aswathy saw a larva on 26th May and it turned to a pupa on 27th May…
That means there were larvae in the media 3 days before.

So…
On 23rd May, the flies had laid eggs,
On 24th May, the first stage of larva (1mm size)
25th May, second stage larva (2mm size)
26th May, third stage larva (3mm size)
On 27th May, i.e. today, we got to see pupae!!

So what happened??
Expectations were missing
Keen observation with interest was missing
Its ok, she might have missed out…this happens with many of us…but directly taking temperature as the sole reason is not right…
Human errors are to be first analysed.

Its not that temperature cannot affect.
But we need to have the proper data giving evidences that there was a drastic change in the temperature.
As well as we need to be sure that there wasnt any missing out of observations or expectations that happened from our own side.

There could be one more reason,
A normal female fly can be mistaken for a gravid fly.
May be that those female flies weren’t gravid or fertile

This is my comment on the summary of the webinar that we had.
Waiting for comments from everyone.

drishtantmkawale · May 29, 2020, 10:35am

Summary- CUBE Room Webinar
Thursday, May 28th 2020

Moina-A brief discussion

The discussion started with the freshwater-crustacean Moina. I updated everyone about the Moina cultures at my home lab.
Then, I shared the breaking news of observing yellowish-green colour on the base and walls of the bottles.
I suspect that it is Algae which is taking over in the Yeast bottles. I added that once I see more greenish growth, I will add ~10 Moinas in both the bottles.
@KiranyadavR and Abhijeet Singh asked that how will the Moinas survive in those bottles? If we look at their natural environment which is ponds and lakes, the Moinas feed on Algae, Bacteria and Fungi (Yeast and others) present in the fresh-water bodies there.*

It will be interesting to know about their feeding mechanism on Algae and Fungi.

Abhijeet Singh asked about my Research Question and how am I working on that.
Research Question: How do the Moinas undergo colour change (colourless to coloured and vice versa) in less-oxygen condition or hypoxia and is it due to Histone modifications?

I said that it is very simple to induce hypoxia and observe the colour change of the Moinas. Everyone (if they have Moinas at their place) can do it in their home labs and the first possible colour change would be noticed by them in 72 hours!

And once the Moinas become coloured ones, we can turn them back into colourless Moina.
How!!?
By again keeping them back in Normal oxygen condition or Normoxia.
Here too, after a day i.e. ~24 hours or less than that, the 3rd day Pale Yellow or coloured Moinas will turn into colourless Moinas.

So we see that such simple experiments which can be done at home are the base of understanding the complex mechanisms like Histone acetylation/deacetylation, Remodeling and others.

Yesterday, a major goof-up happened by me that I burdened everyone present in the Webinar by explaining these complex mechanisms (without the help of any diagrams as such) instead of starting with the basics and explaining it simply!

My Apologies to everyone

I learnt that evidence based research is essential in explaining a complex system.
I have data, so I am able to explain.

Later, many others questions were asked.
Let us discuss them here. CUBists please repost the questions here.

Then, there came an issue of misunderstanding Milk as a Mutagen!!
@Vaibhavib99 and later @Shalu added that many people assume that the colour change of the Moinas from colourless to coloured ones and vice versa is due to mutations and reverse mutations respectively!

How is that even possible?
Does that mean many of us are consuming a mutagen?
No way!

Mutations take place when there is a change in base-pair sequence of the DNA.
They take time to get expressed.

And as I mentioned earlier, only the configuration of DNA and Histone is changed and rest all remains the same.
THE DNA SEQUENCE DOES NOT CHANGE!

So milk in any form, is not a mutagen which will cause mutations in Moinas!!
This is where we go wrong in understanding the TEXTBOOKISH things!

Instead of ending it here, we took it somewhere else.

Fruitflies-the flies on demand

We discussed about the current status of the fruitfly cultures maintained by @saswathy679 at her home lab in Thrissur, Kerala and @Hinaiqbal_Mudgal too, at her home lab in Kanpur, Uttar Pradesh.

As they are having many bottles with as many flies in them, all of us suggested that they should start with the identification of the dead frutiflies in their bottles.
Even if they do not belong to a single line culture of flies, any random fly can be used just as a warm-up for identification.

Starting with the family identification and moving further on.
Yash, Aswathy , @Lydia and others please add to this and let us start with the identification procedure and its design!

Shedding some light on the slow-mo guys: Snails
As we were wrapping up, we came upon the Snails which are maintained by @Anjani from CUBE Elphinstone, Mumbai, in his home lab.
His collaborators Manasi Prasad, Nishmita Amin, Nikita Dhuri updated that one of his snails died.
How do we know that a Snail has died? It may be that the snail must be inactive or sleepy!

They said that a stench was coming from that snail.
Was that a result of any bacterial, fungal infection?

Zahra Risalawala said that she had read a paper (please share that!) where it was saying that the excess of salt can harm the Snails.
Is it?
What will happen if we take a mouthful of salt?
What happens when our fellow Earthworm is exposed to high salinity.
I have seen that the earthworm tries to move away from it.
It may shrink too.

Why?
Does dehydration take place?

Nishmita Amin said that it is osmosis taking place.
What is osmosis? Do we really understand it?

We can simply start saying that because there is high salt concentration outside and low/normal salt concentration inside the body cells of the Earthworm, the salt will try to diffuse inside and in the process, it will dehydrate the Earthworm as more salt would be present inside which is harmful.

Why is it harmful?
Is it not a CONTEXT TO CURRICULUM question?

Let us solve it!

Arunan · May 29, 2020, 11:11am

Which curricular questions are being addressed here? @drishtantmkawale Please like at them with an one line description.

Kunal_Kadam · June 2, 2020, 2:38pm

Nematodes are generally found in soil , garbages, etc. So following the procedure of placing the soil sample on the periphery of 2% Agar surface and then adding the feed at the centre and thus isolating the nematodes is possible. But during the Lockdown some requirements such as :-

Dissecting Microscope.
Agar .
Petri Plates ,etc. Are not present at home. So the isolation and identification of the nematodes might be a problem. Even the foldscope would just show an organism like a nematode but it can’t be proved as the Characteristic features won’t be visible through it.
I guess isolation or even culturing nematodes during a lockdown would be difficult at Home labs without the instruments or material mentioned above.
I am still searching for alternatives that can be used to observe the nematodes and a culture/surface media that can be made at home instead of using agar . Will come up with some idea ! Others can also look for some ideas that can ensure the idea of culturing and identifying the Nematodes at our home labs. This would come up with a great result and create new alternatives for the species to work upon from Home Labs.
@Anshu_kadam_2813 @Arunan @bivasnag @Bunny @Shivamkumar_Sriwas @Ritam007 @Garima_kalakoti @jaikishan @drishtantmkawale

drishtantmkawale · June 2, 2020, 3:05pm

I would like to contradict you @Kunal_Kadam.
You must be familiar with the current happenings in the CUBE Fruitfly Model Organism group.
We are doing fantastic work there. A home-made fruitfly medium has been devised (incomparison with the Standard Cornmeal Medium) to culture fruitflies at home and it is working incredibly well!

Why not we think of doing the same here?
I bet no one in the world must be doing things at home which CUBists do!!

Not even isolate, but can’t we just look for nematodes or even soil worms.
Dissecting Microscope is too sophisticated! Our phone camera shall do the trick.

Well, we can find alternatives for Agar! As the lockdown is easing now, we can make a search for agar alternatives and then start with it!
Agar, if we see is used as a solidifying agent or gelling agent (the lab one’s are too expensive!).

As mentioned earlier, the Fruitfly guys have found out Rava/Semolina/Suji as an alternative for agar.

Petri plates can be replaced by transparent lids or plates maybe.

Pinning Prof. Obaid Siddiqi’s Quote

"Sophistication should be in mind, not in lab"

Kunal_Kadam · June 2, 2020, 5:12pm

@drishtantmkawale
Here you are comparing two Different Model Organisms !! They are different in Size , Characteristic and even feed and substrate . Keeping in mind the size of the single Adult Nematode is 1mm approx. The mobile phone cannot zoom in to that level as it does help in case of the drosophila as it is visible through the naked eyes too… Now talking about the isolation of the nematodes - the nematodes are found in soil , it is very tidious to islolate them from the soil.
The media on which we would place the soil should not get affected by the soil itself. And the media should not get affected by the bacterial feed too . If we compare the transferring of the nematodes from one media to another would be more tidious work to do… As in drosophila the bottle transfer is done by the drosophila otself by flying to the other Bottle.
Soo it’ll be little difficult to find an alternative but not impossible !!! If everyone put forth their views or thoughts on this !!! It’ll be easy , not that difficult to find alternative for all and start with nematode isolation at home!!!

@Anshu_kadam_2813 @Bunny @bivasnag @Arunan @jaikishan@ @Ritam007 @Garima_kalakoti

Lydia · June 8, 2020, 9:05am

Combined summary of all the CUBists who gave a summary of 3rd June webinar…for all those who missed out the summary.

[03/06, 10:54 pm] Prathamesh:
Summary — CUBE Webinar , Wednesday 3rd of June, 2020
Today’s discussion was based on viruses. The discussion was started as I have raised the question that how the first person got infected with the dengue virus; i.e. if we search for the cycle of the dengue virus, it starts from an human who is infected by the dengue virus and when the aedes aegypti i.e. the species of mosquito which is capable to carry dengue virus bites that infected person , these mosquitoes carry these virus in their salivary glands and then it spreads to the other person. So like this the discussion started and then Ashutosh connected this dengue virus with currently spreading coronavirus and we further discussed on this topic , that how the first person of this covid would got infected with this virus . So Rahul gave me some informative clues about viral transmission and structure of virus. Saida and others also joined and discussed on the raised question . As virus contains a protein coat and inside it there is DNA or RNA present . So we thought that covid is because of bats and this virus has been mutated in the bats and at last it was cleared that the first person of covid eould be infected by the mutated virus in the bats as in china people sells and consumes the bat .
So we reached at that point of coronavirus and further this coronavirus is transmitted through human to human , but the question of dengue remained unsolved may be because I was not able to connect the links given by Arunan sir and Rahul or may be some another reason .
But then too, I will think and search on it, that how the first person got infected with this dengue virus.
We all should search about it and discuss on this question and put forward our thoughts.
Thank you:blush:

[03/06, 11:48 pm] @khushdeep :
In today’s webinar, there was a discussion on the Corona Virus.
We were discussing that how did the virus got transferred from bats to humans?

My question here is,
Did they eat the bat raw or they cooked it?
If they would’ve cooked the bat, then the virus would’ve got killed there itself.

How did it transmit then?
@ Arunan Sir⁩ @drishtantmkawale @⁨Prathamesh Elph CUBE, Lydia, @KiranyadavR and others member…

[04/06, 12:34 am] Prathamesh:
Mutation is not a sudden change, it takes years to get mutate and so now it would be mutated at that level where it can replicate in humans and spread the disease
And another reason for it can be the dormant state of a virus i.e. to undergo dormancy until the specific conditions or suitable environment is available

[04/06, 10:13 am] @Hinaiqbal_Mudgal :
Last evening s ROOM WEBINAR discussion DT 3.06.20.
RAHUL PUT UP STRONG ASSERTIVE QUESTIONS…
How viruses who live in animals ,like bats, cats, or dogs, have started INFECTING HUMANS OR AFFECTING HUMANS
WHAT COULD HAVE CAUSED THIS INFECTING/ AFFECTING CHANGE ?
IS IT MUTATION?
CUBIST SAIDA MENTIONED RANDOM MUTATION,
HOW DID THIS VIRUS FIRST BECOME ACTIVE IN HUMANS.
TERMS LIKE DORMANCY, LYSOGENIC, RANDOM MUTATION WERE DISCUSSED…
IT WAS A STEAMING FLOW OF ANALYSTS, BIOLOGIST. WHO SHARED THEIR VIEW IN THE SUBJECT.
***INDEED SARS. COVID - 19, MERS, BIRD FLU, SWINE FLU ARE THEY VARIANTS??? MUTANTS??
WHAT HAS CAUSED THIS SPECIATION @ hina cube kanpur

[04/06, 11:03 am] @saida786110 :
Summary of yesterday’s discussion
@Prathamesh Suryavanshi questioned how does dengue spread in first human
and to answer that question @Aashu Sir tried to relate it with covid-19 how did that virus started affecting human? @Rahul kushwaha added this virus was in bats or some other mammals
Is it that one day decides to affect humans?
several cubist answer it to be mutation. mutation must have occurred in covid-19 virus such that the outer protein is transformed which helped the virus to get inside human cells
so in the case of covid-19 the virus was supposing in bats and it got muted and when came in contact with humans it started to affect humans. so earlier when humans were in contact with bats the protein of this virus was not mutated as such that it could affect humans. but then the question arose where did the mutation took place? probably in bats as the virus was living inside the bats cells but what happens in the case of dengue virus. because there mosquito is just a carrier. so is it that the virus would have remain dormant until human life? certainly not @Prathamesh Suryavanshi added that even monkeys were affected by dengue virus so that could be a possibility that this virus got mutated in monkeys and and with the help of mosquitoes got transmitted to humans and started affecting humans.
@ Arunan Sir⁩ connecting it to drosophila work done by cubist Lydia and @yash_sheregare. Lydia and Yash sheregare with several other cubist want to compare CsBz drosophila melanogaster cultured in labs for more than 60 years to drosophila melanogaster found in native.
Lydia added that they are looking at the olfaction of the flies and expecting different kinds of olfaction in CsBz flies. meaning flies with good olfaction moderate olfaction not so good olfaction where as in the nature they will find flies with good olfaction because of natural selection
@Hinaiqbal_Mudgal added that in CsBz flies which are cultured in lab for more than 60 years if mutation must have occurred in it, won’t be naturally selected because the environment in the bottle is such that the food is already present at all times so the flies with good olfaction will also survive and flies with weak olfaction will also survive

[04/06, 1:42 pm] @magpie :
Take away points w.r.t Context to Curriculum
Yesterday’s Causerie where Cubist Rahul Kushawa from Delhi steered the causerie with Suryavanshi ,Saida and other cubists on how did the first human get infected with dengue or Covid.

We are exposed to microbes all the time from animals birds around us just as humans they shed their virus through bites,droppings,feathers,animals sneezing, physical handling etc.
We develop an infection when the virus/bacteria multiplies in our body.
We develop a disease when the viral/bacterial multiplication is not controlled effectively by our immune system.
To gain entry into our cells the pathogen has to cross the cell membrane. There are receptors on the membrane made of glycoproteins binding to which can help it to enter.
The Covid 19 virus has a mutation in its spike protein which helps it fit snugly to the ACE 2 receptor protein, which helps it enter our cells easily.
How do we know there has been a mutation by comparing genetic sequences with other viruses of Coronavirus family.

Causerie is moderated by Dr Arunan

Lydia · June 8, 2020, 9:28am

Hello everyone
4th June Webinar Summary

We had a deep discussion on the model system FRUITFLY.

A hypothesis was made at the very beginning which said that the standard CsBz flies (which are lab bred for the past 80 years) would have a deprived olfaction as compared to the flies present in the wild environment

Another hypothesis or statement was that the CsBz flies which are inside the bottle will have all sorts of sensitivity of olfaction i.e. low, moderate and high sensitivity of olfaction.
@Rahul CUBE TIFR thought of trapping those CUBists with this hypothesis into a bait (question) that he thought of.

The trap bait question was that “In a single line culture of flies belonging to a one single mother inside a bottle, what would be the outcome”
Will there be different sensitivities of olfaction?

@Hina Ma’am CUBE Kanpur wanted to help those who were in the trap by asking a question… “Do all the siblings belonging to a parent look alike”
So this question helped…
Some of our CUBists then gave an answer saying that there would be all kinds of olfaction (low, moderate & high).
The reason for such an answer was that the female gravid fly must have mated with a male…so variations are expected.

@Aashutosh Sir wanted to put forth one question in 2 different cases or in 2 different conditions.
2 out of 100 flies have good olfaction…what would be the condition or the percentage of flies having good olfaction after 100 generations? Will there be a difference?

1st case: Inside the bottle???
“After 100 generations, there won’t be much of a difference in the number of flies having good olfaction… because all are surviving in the bottle (as food is readily available) the ones with low olfaction, moderate olfaction…” was the answer of the people in the trap.

2nd case: In the wild environment???
After 100 generations, the ones having good olfaction will survive as they will be able to smell and reach the food while the ones with low olfaction won’t be able to reach the food and hence starve and die…the ones with low olfaction won’t die immediately but will die gradually.

We had @Suman sir with us.
He was not much familiar with all of this…and hence he asked questions which cleared some basic doubts that a common man would have…
What are single line cultures?
How to identify a gravid fly for making a single line culture?

The main important question by sir which is our objective of our research question
How can we say that the wild environment flies would have a better sensitivity olfaction than the flies that are being bred in a bottle for 80 years?!!
On what basis??
Here we had to explain the design of the experiment that we do to prove such a hypothesis.

Olfactory assay was explained by @yash_sheregare .
(Yash will give a summary of the design of the olfactometer that we had discussed yesterday.)

What are we actually finding out by doing this whole experiment thing?
(@Arunan Sir helped in building up the whole thing so that everyone could understand.)

We are finding out, that which is the lowest concentration of the banana essence chemical [(IAA: Iso amyl acetate) (used in the experimental olfactometer)] where maximum number of the CsBz larvae are not able to smell or get attracted to the attractant that is kept.

There are 2 scenes here that are being compared which connects to our hypothesis.

Scene 1:
The lowest concentration of the banana essence (10^-6 conc.) chemical which attracts CsBz larvae towards it and then after which (10^-7 conc.) maximum number of the larvae is not able to smell the attractant.

Scene 2:
The lowest concentration of the banana essence (10^-7) chemical where maximum number of the CsBz larvae is not able to smell the attractant but the wild environment larvae are able to smell much more lower concentration (10^-7, 10^-8 conc.)

The difference in the 2 scenes here is compared and hence such a hypothesis that,
Standard CsBz flies (which are lab bred for the past 80 years) would have a deprived olfaction as compared to the flies present in the wild environment.

I hope I’m making things clear. If not please ask. Because of our discussions and the doubts raised during the webinar help us in getting some of our concepts clear.