People With Lab Experience Or Chem/biochem Majors, Please Help Me Figure This Out

[explosionlord]

Hey all,

I'm currently in school for biochem, myself, and I'm trying to get clearance to do a certain research project. I got a greenlight for something, but I had to be specific; to the point, I figured I'd check about keto acids in potatoes, since it seems to be a topic that is oft spoken of ( @Westside PUFAs and @tyw , looking at you!)

I thought it might be prudent to do ion-exchange chromatography or gel electrophoresis (I know, the latter is usually done with full-on proteins), but I recall that Ray said he "couldn't get reagents for this," so I'm not really sure what that is referring to.

Also, I ran into a wall with the professor as he says "the ketogenic acid content of a potato has already been determined," and to my embarrassment directed me to nutritiondata.

So, what do you guys think? I'm assuming Ray was talking about lysine, leusine and other ketogenic acids; is this true, and if so, what is he talking about when he says they are "unknown" when I can look them up on nutritiondata? I really want to do this and probably still will if I can convince the prof maybe 1) the experiment will verify those numbers and 2) show some benefit for people (besides just CKD patients, maybe people with protein deficiencies who don't get potatoes because they're thought to be null in the protein dept.)

What do you guys think about the methods, also? I also thought of maybe trying deamination, or something as chronicled here: Estimation of α-keto acids in plant tissue: a critical study of various methods of extraction as applied to strawberry leaves, washed potato slices and peas | Biochemical Journal

@haidut ? Anyone else?

Also, sorry if this is posted in the wrong forum, didn't see any appropriate topic in "ask for help."

 

[Such_Saturation]

Wasn't he talking about fruit being unknown?

 

[raypeatclips]

This would be fascinating, especially if you could find out the keto acid content of fruits. Perhaps this would be a question best suited for Ray, to ask about the specifics.

 

[explosionlord]

Wasn't he talking about fruit being unknown?

Well, I listened to a few of his interviews on the specific topic of potatoes and ketoacids but I may have missed that, since I was skimming. Interesting topic, though; I may just switch to that.

 

[Westside PUFAs]

Are you going to do chromatography?

"And that's where RL Veech, an NIH - I think it was - researcher, proposed using ketone, keto acids, equivalent to the essential amino acids, which will absorb the ammonia, even when a person has no functioning kidney... ability to secrete ammonia. Just by feeding keto acids, if they are the equivalent of the essential amino acids, you create them in your body by absorbing the ammonia and then making your own protein, and that was where I got the idea that some foods would contain natural keto acid equivalents and we did chromatography on potato juice and found that they are rich in the keto acids which will function as amino acids, even though they contain no ammonia, because they can absorb ammonia from your blood."-RP

Try to do other foods too like fruits and other roots and maybe even greens.

Notice the word “hardly:”

“Nutritional research has hardly begun to investigate the optimal ratios of minerals, fats, amino acids, and other things in foods, and how they interact with the natural toxicants, anti-nutrients, and hormone disrupters in many organisms used for food.” - RP

“For fifty years, the mass media have been making the public think about the fats in their diet, filling the culture with clichés about bad saturated animal fats that raise cholesterol, or lately the trans-fats in margarine, and images of arteries clogged by bad fats. The public instruction about the fats we should eat resembles the owner's manual for a car, that tells you what kind of motor oil and fuel and coolant to use; they are telling us that they know how our body works, and that they know what it needs. But now, even after the human genome has supposedly been partly "decoded," the biological functions of the fats have hardly begun to be investigated.” - RP

“The amino acids in proteins have been defined as “essential” on the basis of their contribution to growth, ignoring their role in producing long life, good brain development, and good health. The amino acid and protein requirements during aging have hardly been studied, except in rats, whose short life-span makes such studies fairly easy. The few studies that have been done indicate that the requirements for tryptophan and cysteine become very low in adulthood.” - RP

 

[explosionlord]

Are you going to do chromatography?

"And that's where RL Veech, an NIH - I think it was - researcher, proposed using ketone, keto acids, equivalent to the essential amino acids, which will absorb the ammonia, even when a person has no functioning kidney... ability to secrete ammonia. Just by feeding keto acids, if they are the equivalent of the essential amino acids, you create them in your body by absorbing the ammonia and then making your own protein, and that was where I got the idea that some foods would contain natural keto acid equivalents and we did chromatography on potato juice and found that they are rich in the keto acids which will function as amino acids, even though they contain no ammonia, because they can absorb ammonia from your blood."-RP

Try to do other foods too like fruits and other roots and maybe even greens.

Notice the word “hardly:”

“Nutritional research has hardly begun to investigate the optimal ratios of minerals, fats, amino acids, and other things in foods, and how they interact with the natural toxicants, anti-nutrients, and hormone disrupters in many organisms used for food.” - RP

“For fifty years, the mass media have been making the public think about the fats in their diet, filling the culture with clichés about bad saturated animal fats that raise cholesterol, or lately the trans-fats in margarine, and images of arteries clogged by bad fats. The public instruction about the fats we should eat resembles the owner's manual for a car, that tells you what kind of motor oil and fuel and coolant to use; they are telling us that they know how our body works, and that they know what it needs. But now, even after the human genome has supposedly been partly "decoded," the biological functions of the fats have hardly begun to be investigated.” - RP

“The amino acids in proteins have been defined as “essential” on the basis of their contribution to growth, ignoring their role in producing long life, good brain development, and good health. The amino acid and protein requirements during aging have hardly been studied, except in rats, whose short life-span makes such studies fairly easy. The few studies that have been done indicate that the requirements for tryptophan and cysteine become very low in adulthood.” - RP

Thanks for that first quote, I think I will stick with chromatography. As far as what to test fruit-wise, I'm unsure. I know Peat talks fondly of citrus, melons, and cherries. I have e-mailed my professor about switching focus to fruits. I, of course, want to go as far as I can with this i.e. test all kinds of stuff, but being an undergraduate who happened to find a way to do my own research, I'm kind of low on the pecking order- so I'm not sure how much wiggle room I have. Therefore, I want to test a fruit that is both convenient to eat and Peat-approved, for the benefit of the most people.

I'm thinking about taking @raypeatclips's advice and e-mailing Ray about this whole ordeal, but I don't want to bother him when there are clearly decent quotes online that I haven't found. The question of the mystery reagents is bothering me, though.

 

[Such_Saturation]

Yes it was fruits not potatoes

Kasra: "Dr. Peat, In one of your articles, you mention that fruits contain "carbon
skeleton" equivalents of the essential amino acids. Does this mean that the actual protein content of a fruit could be substantially greater than what a nutrition database says?"

Peat: "Yes, the way a potato's effective protein content is much higher than the chemical protein content."

Kasra: "Could this mitigate the problem of protein deficiency on an all-fruit diet?"

Peat: "Yes, but since there isn't much known about their ketoacid content, it would be best to have a wide variety of fruits. A couple of times in the last ten years I've started a project to test some fruits, but because of the new laws since 2001, I haven't able to buy the necessary reagents. It would have to be done in some government approved institution."

 

[Westside PUFAs]

Yes it was fruits not potatoes

Both have them.

"we did chromatography on potato juice and found that they are rich in the keto acids"

 

[Such_Saturation]

Both have them.

"we did chromatography on potato juice and found that they are rich in the keto acids"

The unknown one that Ray Peat wanted to study was fruits.

 

[Westside PUFAs]

The unknown one that Ray Peat wanted to study was fruits.

The OP should do potatoes too and upload his results. We don't have Peat's potato KA results.

 

[Such_Saturation]

The OP should do potatoes too and upload his results. We don't have Peat's potato KA results.

I think there was an analysis posted on this forum... but is there even a full classification of keto acids...

 

[Westside PUFAs]

I think there was an analysis posted on this forum... but is there even a full classification of keto acids...

I didn't say "an" analysis. I said Peat's.

 

[Such_Saturation]

I didn't say "an" analysis. I said Peat's.

The OP asked about the tests Ray Peat couldn't get reagents for. Those were not potatoes, they were fruits. Additionally I think the OP's professor might have heard "ketogenic" instead of "keto-acid" because I'm pretty sure the latter wouldn't be on nutrition websites.

 

[Westside PUFAs]

The OP asked about the tests Ray Peat couldn't get reagents for. Those were not potatoes, they were fruits. Additionally I think the OP's professor might have heard "ketogenic" instead of "keto-acid" because I'm pretty sure the latter wouldn't be on nutrition websites.

Do you know the difference between the reagents for testing fruits vs. roots?

 

[Such_Saturation]

Do you know the difference between the reagents for testing fruits vs. roots?

I figure they're the same, why?

 

[explosionlord]

The OP asked about the tests Ray Peat couldn't get reagents for. Those were not potatoes, they were fruits. Additionally I think the OP's professor might have heard "ketogenic" instead of "keto-acid" because I'm pretty sure the latter wouldn't be on nutrition websites.

Yes, it's an important distinction. Unfortunately, most research in this sphere (e.g. that done on people with kidney problems) tends to use the blanket term "ketoacids" in reference to the ketogenic amino acids. So, trying to enunciate to my professor why I would like to investigate ketoacids is hard; I'm afraid he might ask me what link something like pyruvic acid has with protein synthesis, though I have mentioned the idea of bloodstream ammonia. He just e-mailed me after I inquired about fruit, and suggested maybe a ketogenic test on potatoes with differing nitrogen content, so this is kinda going in the wrong direction.

I went ahead and e-mailed Dr. Peat, hope he responds.

 

[Such_Saturation]

Yes, it's an important distinction. Unfortunately, most research in this sphere (e.g. that done on people with kidney problems) tends to use the blanket term "ketoacids" in reference to the ketogenic amino acids. So, trying to enunciate to my professor why I would like to investigate ketoacids is hard; I'm afraid he might ask me what link something like pyruvic acid has with protein synthesis, though I have mentioned the idea of bloodstream ammonia. He just e-mailed me after I inquired about fruit, and suggested maybe a ketogenic test on potatoes with differing nitrogen content, so this is kinda going in the wrong direction.

I went ahead and e-mailed Dr. Peat, hope he responds.

You could send your professor stuff like the wikipedia article on keto acid, and these Efficacy of the Essential Amino Acids and Keto-Analogues on the CKD progression rate in real practice in Russia - city nephrology registry data for outpatient clinic

 

[explosionlord]

Well, luckily I got a response from Dr. Peat and he linked me to this study: http://www.sciencedirect.com/science/article/pii/0003269768902947 which I of course immediately sent to my professor to delineate the difference. He also told me the "mystery reagent," which was DNPH. I wasn't so surprised to see he couldn't get that, because it's explosive; but he also said he couldn't get the straight ketoacids for comparison (which seems odd).

So, just waiting on prof's response.

 

[Such_Saturation]

Well, luckily I got a response from Dr. Peat and he linked me to this study: http://www.sciencedirect.com/science/article/pii/0003269768902947 which I of course immediately sent to my professor to delineate the difference. He also told me the "mystery reagent," which was DNPH. I wasn't so surprised to see he couldn't get that, because it's explosive; but he also said he couldn't get the straight ketoacids for comparison (which seems odd).

So, just waiting on prof's response.

Sounds like great thesis subject. Are you in PhD?

 

[explosionlord]

Sounds like great thesis subject. Are you in PhD?

Pfff, I wish; then I wouldn't have to play the begging game like I am. I'm an undergrad 4+1 masters student, doing something called an REU; it's basically paid-for undergraduate research and since I'm the only person in the molecular sciences utilizing it, I get to actually choose a project.

I think if I do a thesis, it will be on something similar to Gilbert Ling's work in cell physiology. Speaking of, I had asked raypeatclips in PM, but does anybody know how Ling is doing? His website has been offline for a while. I know it happens, time to time, but it's been months. I thought to ask Dr. Peat what he knows, but again I hate the idea of bothering him with stuff.

Update about my prof: He finally understood about the ketoacid vs ketogenic acid thing, and actually linked me to a study that I had open already on ways to do it, haha: Estimation of α-keto acids in plant tissue: a critical study of various methods of extraction as applied to strawberry leaves, washed potato slices and peas