About bioinformatic, and fish eating starch

[A. Ekergård]

Writing as someone who couldn’t finish a very short online course in bioinformatic and as someone working with aquaculture. If I read the fish monkeyface prickleback (monkeyface prickleback) can break down starch, I should be able to open a database like https://www.ncbi.nlm.nih.gov/ and find other fishes with the same genes for breaking down starch? Right? 

Hope I’m not looking too lazy for asking if anyone could help me? Hopefully it’s not that complicated, but it’s also not as easy as just writing: “what fishes produce amylase?”

Kind regards

Anders

[Sean Sullivan]

I've thought a bunch about how much of a time-saver it would be for scientists to have the sort of natural language search of scientific knowledge that you are describing (there are a few LLM-type attempts at this underway but that's a different topic), but as far as I know it's not that simple.

Here's a couple things you can try (not exhaustive, this isn't really my expertise):

1. BRENDA database entry for amylase (https://www.brenda-enzymes.org/enzyme.php?ecno=3.2.1.1) has a section "Select one or more organisms in this record" - see if some fish scientific names are in the list.

2. UNIPROT database entry for amylase cross-referenced by its Enzyme Commission number (https://www.uniprot.org/uniprotkb?query=ec:3.2.1.1) shows a list of organisms that have versions of the enzyme. A quick scan of the list shows at least one fish (Japanese Rice fish) in the list --> keep scrolling.

3. Take the DNA sequence of the amylase gene that you know and do a nucleotide blast search (Blastn - https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=MegaBlast&PROGRAM=blastn&PAGE_TYPE=BlastSearch&BLAST_SPEC=). Paste the sequence in and search, it will pop up similar sequences it finds in different databases and will list the organisms the sequence came from.

These databases can be accessed programmatically via APIs if you know how to do that type of stuff. I hope you know lots of latin names...

Best,

Sean

[A. Ekergård]

I’m thankful for the help I got here. I tried to play with BLAST,  I didn’t change any algorithm parameters, and got both European Peach (Perca fluviatilis) and zander (Sander lucioperca) quite high on the “result list”. Both carnivores (both raised in aquaculture). Don’t know what to do with that fact. It’s close to hybris for me to start this threat , and one thing in life is that id you have a good idea, other people might have had the same idea before you. So for the record here’s an article that mentions the same thought I had. https://news.uci.edu/2020/02/19/veggie-loving-fish-could-be-the-new-white-meat/: “Heras, the paper’s first author. 'However, most aquaculture fish are carnivores and can’t handle plant lipids. Sequencing this genome has provided us a better understanding of what types of genes are necessary for breaking down plant material. If we scan additional fish genomes, we may find omnivorous fish with the right genes that could provide new candidates for sustainable aquaculture.'”

[Dan Kolis]

https://www.sciencedirect.com/science/article/abs/pii/S0959440X16300811

Make a sub directory for each inquiry and ignore similarities of human nomenclature like names amylase-XXX just plow through each top down.

Good luck, I suppose. 

gov/Blast.cgi?PAGE=MegaBlast&PROGRAM=blastn&PAGE_TYPE=BlastSearch&BLAST_SPEC=). Paste the sequence in and search, it will pop up similar sequences it finds in different databases and will list the organisms the sequence came from.

These databases can be accessed programmatically via APIs if you know how to do that type of stuff. I hope you know lots of latin names...

Best,

Sean

On Friday, March 17, 2023 at 8:19:15 AM UTC-4 A. Ekergård wrote:

Writing as someone who couldn’t finish a very short online course in bioinformatic and as someone working with aquaculture. If I read the fish monkeyface prickleback (monkeyface prickleback) can break down starch, I should be able to open a database like https://www.ncbi.nlm.nih.gov/ and find other fishes with the same genes for breaking down starch? Right? 

Hope I’m not looking too lazy for asking if anyone could help me? Hopefully it’s not that complicated, but it’s also not as easy as just writing: “what fishes produce amylase?”

Kind regards

Anders

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[Sean Sullivan]

It's a good thought, but my take would be that engineering single-cell organisms to utilize nutrients that they can't natively metabolize (what my PhD was focused on) is very different than engineering the same function into a complex multicellular organism.

It's more complicated that just changing the genome of the fish, you need the amylase expressed at the right level and in the right location - it's probably not gonna be very helpful in the brain.

I checked out the article - they very specifically talking about finding other non-carnivorous fish to use in aquaculture rather than trying to make carnivorous fish into vegetarians for essentially that reason.

If you want to make aquaculture more sustainable, I think you could try to identify the shortest/cheapest route from the starting carbon source (starch) to the food that a given fish normally eats. Not an ecologist so I could be wildly off here, but maybe you grow some microbes on the starch, them to some shrimp, then grind up the shrimp and feed that to the fish...

[A. Ekergård]

It’s possible that my question was wrong. That the interesting thing isn’t to find homologous genes to amylase from C. violaceus (tons, perhaps a majority, of all living organisms has amylase) but to find how many copies of the genes other fishes have? So how do one find fishes/organisms that have >2 copies of amylase or >2 copies of carboxyl ester lipase?

The thought of hacking gut bacteria to help predatory fish to eat a more herbivore diet is interesting. Also gives me an excuse to mention I have seen fry of Atlantic salmon (Salmo salar) die after being inoculated with ordinary intestinal bacteria. Making one think they could be sensitive to genetic engineered bacteria. But I’m sure that kind of dying of isn’t that common.

[Dan Kolis]

It's a sort of interesting conversation here.

If you want to make Species X munch on X' maybe there is a generic way to do that. Ex: seek genomic Germ line change so it can definitely benefit from eating it.

Then maybe a gain-of-function many generation corralled organisms to change the behaviours ?

This is basically, a huge, real science project.

Some lovers of spooky folklore would say: "Desire to eat it, is in the quiet ( not quite junk ) DNA and liberating it can't be too hard.

I think one way or the other, its a pretty big project generally. A more casual kick at the cat though might reveal some modality to move forward.

What eats what and gains from it, is essentially a nearly completely commercial question generally...

Regs

Daniel B. Kolis