Coffee Questions

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xactly
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Re: Coffee Questions

Postby xactly » Sun Aug 26, 2018 6:27 am

Rainbow wrote:Thanks xactly! I'll definitely look into Chris Masterjohn's resources. My mom and I both have COMT and MTHFR mutations.


Rainbow: If you are prone to anxiety, you might also want to take a look at the status of a gene called GAD1. The enzyme produces from the GAD1 blueprint, glutamate decarboxylase, catalyzes production of GABA from glutamate. If you have certain polymorphisms on GAD1, you can have high levels of glutamate, and excitatory neurotrasmitter, and low levels of GABA, an inhibitory neurotransmitter. The result can be anxiety, irritability, and waking up in the middle of the night and finding it difficult to go back to sleep.

Here are some of the SNPs: rs3749034, rs3791851, rs3791878 , rs3828275 , rs701492. If you have these variations, you should avoid MSG and other sources of increased glutamate.

Taurine, theanine (found in tea), glycine and NAC can help restore balance. You can also take GABA directly. If you or your mother have GAD1 polymorphisms, I'll be happy to share my protocol for restoring glutamate/GABA balance.

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Re: Coffee Questions

Postby Rainbow » Sat Sep 01, 2018 12:45 pm

xactly wrote:Rainbow: If you are prone to anxiety, you might also want to take a look at the status of a gene called GAD1. The enzyme produces from the GAD1 blueprint, glutamate decarboxylase, catalyzes production of GABA from glutamate. If you have certain polymorphisms on GAD1, you can have high levels of glutamate, and excitatory neurotrasmitter, and low levels of GABA, an inhibitory neurotransmitter. The result can be anxiety, irritability, and waking up in the middle of the night and finding it difficult to go back to sleep.

Here are some of the SNPs: rs3749034, rs3791851, rs3791878 , rs3828275 , rs701492. If you have these variations, you should avoid MSG and other sources of increased glutamate.

Taurine, theanine (found in tea), glycine and NAC can help restore balance. You can also take GABA directly. If you or your mother have GAD1 polymorphisms, I'll be happy to share my protocol for restoring glutamate/GABA balance.

Thanks. I checked my 23AndMe data, but unfortunately most of these SNPs aren't listed. I did find a TT for rs701492, though, which is a bad variation. Do you know of a DNA test that provides the other SNPs? Perhaps in future I might want to look into GAD1 more thoroughly.

Despite the lack of information, I'd definitely be interested to hear about your protocol, with the understanding that it might not be the correct one for me to follow.
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Re: Coffee Questions

Postby xactly » Sat Sep 01, 2018 2:05 pm

Rainbow wrote:I checked my 23AndMe data, but unfortunately most of these SNPs aren't listed. I did find a TT for rs701492, though, which is a bad variation. Do you know of a DNA test that provides the other SNPs? Perhaps in future I might want to look into GAD1 more thoroughly.

Despite the lack of information, I'd definitely be interested to hear about your protocol, with the understanding that it might not be the correct one for me to follow.

I don't know why 23andme doesn't show the other SNPs in your raw data. Unfortunately, I haven't looked into any other genetic tests for GAD1 status.

There are three basic forms of GABA you can take to restore glutamate/GABA balance: 1) synthetic GABA (gamma-aminobutyric acid), which is the same molecule you produce in the body; 2) PharmaGABA, which is the same molecule but produced through a fermentation process; and 3) phenylated GABA (4-amino-3-phenylbutyric acid HCl).

Research states that taking the first form of GABA shouldn't work to reduce anxiety because the molecule is too big to cross the blood/brain barrier. However, there are GABA receptors in the gut, and I'm not sure how they communicate with the brain, but synthetic GABA works for me and tens of thousands of other people who take it. I have it in several forms: Vitacost GABA (500 mg, used for sleep); and GABA Calm, 125 mg of GABA in a lozenge that also contains glycine, taurine, and N-acetyl L-tyrosine. This is great stuff for boosting GABA during the day, and it also helps me go back to sleep if I wake up at 2 a.m. with racing thoughts. (I keep a bottle in my nightstand.)

PharmaGABA should also be too large to cross the blood/brain barrier, but there are at least a couple of Japanese studies that claim it is better at that than synthetic GABA. I have 250 mg capsules from Thorne. I can't really says it works better than synthetic GABA, but I'm keeping a sleep log right now to see if I get more or better sleep with synthetic or PharmaGABA. There are so many variables that come into play with sleep that it may be hard to determine.

Phenylated GABA does cross the blood/brain barrier, and it's amazing stuff. However, it can be habit-forming, so I take it only when I feel super-stressed or I'm having a very difficult time with sleep. That means I probably take it only once or twice a month, if even that often. I have two versions of phenylated GABA: Kavinace (only used for sleep) and GABA Max (used during the day).

The other thing that really helps is glyine. Chris Masterjohn talks extensively about glycine in the Living with MTHFR podcast as well is in a separate panel discussion on glycine. I'm getting 3 g of glycine from one serving of Vital Proteins Marine Collagen, and I take another 3 g in powdered form mixed in water when I take my bedtime supplements.

Hope that helps!

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Re: Coffee Questions

Postby Verax » Sat Sep 08, 2018 9:26 am

I would suggest that if you are going to do a self-experiment with coffee, that you take the trouble to measure variables. The Dutch study referred to above (at http://care.diabetesjournals.org/content/27/12/2990 ) used 70g coffee to make 1L drip coffee with paper filters, and saw effect only at 2 weeks not 4.

This is more the American way than the Dutch way of drinking coffee, but I think it is a little strong. Other studies used the European style of making coffee (espresso, boiled, Moka, Turkish, Greek) not using paper filters, and there are some indications that the size of the ground coffee particles and the coffee variety and preparation method, as well as the dose by weight and volume, might have an association with remnant chemical ingredients ingested along with caffeine, such as diterpenes, and that this can have effects such as on cognition. For one review, see
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5420628/ Wierzejska, R. "Can coffee consumption lower the risk of Alzheimer’s disease and Parkinson’s disease? A literature review" Arch Med Sci. 2017 Apr 1; 13(3): 507–514.
Published online 2016 Nov 15. doi: 10.5114/aoms.2016.63599

I used to make (for the last dozen years) a liter of arabica coffee a day with 60-70g coffee in a French press at 200F for 10 min and drink the five cups in the morning. (Usually a coffee cup is 6oz not 8.) Then three months ago I changed, cutting the grounds back to 30g and using a "6-cup" paper filter drip maker in a shorter time. I am a fast metabolizer and suffer headaches with caffeine withdrawal but the dose reduction did not cause any headache or GI symptoms and I did not feel the beverage was too weak or robust. Also I noticed no change in vital signs or sleep or daytime alertness. I don't want to tell you what to drink, but only suggest that if you want to make an experiment you (better, somebody else) measure variables. N=1 experiments are hard enough when not able to be blinded. Or, just laugh at us intense people who brood over such details, and enjoy a different approach to your mundane life and change your habits for a new day.

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Re: Coffee Questions

Postby Rainbow » Tue Sep 11, 2018 2:47 am

xactly and Verax, thanks a bunch for all the information you provided. It's all so helpful!

Verax, if I do decide to experiment with coffee, what do you suggest I measure? You mentioned "vital signs" and "sleep or daytime alertness". Do you have subjective measures in mind, such as how I feel after [insert intervention], or rather something like blood markers?
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Re: Coffee Questions

Postby Verax » Tue Sep 11, 2018 6:30 am

Rainbow, to answer your question generally, I meant that in any experiment it seems to me a good idea to be careful about measuring variables, maybe setting goals and tracking progress. A "good" cup of coffee can be "good" in many different ways, such as taste or health effects or social or cultural acceptance. Your question as to which variables is quite appropriate. When I read a medical study about a drug or intervention I look beyond the abstract to try to understand the dose used, for example.

I can only report what I track, and I record many daily "vital signs" such as blood pressure, body temperature, weight, waist, heart rate variability, exercise, etc., but my main interest in coffee/caffeine at present stems from about five years ago (before knowing genomic data) when I was concerned about developing Parkinson's Disease, because of episodes of REM sleep behavior disorder. There have been many studies about possible preventive effect of coffee/caffeine on neurodegenerative diseases (see paper above) and I enthusiastically embraced them as something I could control. The variables I tracked were related to sleep, such as sleep onset latency, daytime sleepiness and alertness, sleep length, deep sleep, REM sleep, apnea/hypoxia index (I use CPAP), weight, blood pressure and heart rate, and mood. I found these variables gradually improved with 5-6 cups coffee, intermittent fasting, low carbohydrate diet, less saturated fat, calorie restriction, weight loss to waist < 0.5 height, and changes in circadian rhythm (3mg melatonin when awaken in middle of sleep, not at beginning of sleep--I am genetically advance circadian rhythm, short sleeper--no daytime naps, 5 cups of coffee in morning and not after noon--I am fast coffee metabolizer--and delaying sleep cycle with blue light in evening not morning). For sleep, the Epworth Sleepiness Scale is useful: http://epworthsleepinessscale.com/about-the-ess/

I also found I was having more GI symptoms such as urgency, diarrhea, and cramping when using 70 grams coffee a day and they went away when I reduced that to 30g, without affecting other variables such as sleep. I don't know the status of my microbiome otherwise.

Coffee variables have been studied by the Coffee Brewing Institute, for average consumers, and can be controlled to produce a perfect cup for your personal taste that also meets health needs. Several modern coffee makers such as the Behmor I use allow you to tailor the brewing temperature, time, grind, and variety, and you can learn the elements of taste such as acidity, flavors, robustness, etc., by experiments yourself, without having to rely on the Starbucks barista. As I said, I was able to experiment by measuring variables and seeing the results over a period of time, and I can make adjustments if necessary. Since my main goal is prevention, I really won't know myself until too late, of course, but meanwhile there are risk factors to control.

I was so anxious about my REM sleep behavior problems because of the risk of Lewy Body dementia or Parkinson's, and so maybe overdid the coffee drinking, but knowing I don't have genetic risk for those particular conditions now, and their disappearance with CPAP, fat loss, and other changes, has allowed me to feel more in control. But now I am anxious about late-onset Alzheimer's (e3/e4), and there are not so many biomarkers to be confident of control. (I have had a lot of tests from a clinical trial but await decision to accept).

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Re: Coffee Questions

Postby Rainbow » Fri Sep 14, 2018 3:12 pm

Verax wrote:Rainbow, to answer your question generally, I meant that in any experiment it seems to me a good idea to be careful about measuring variables, maybe setting goals and tracking progress. A "good" cup of coffee can be "good" in many different ways, such as taste or health effects or social or cultural acceptance. Your question as to which variables is quite appropriate. When I read a medical study about a drug or intervention I look beyond the abstract to try to understand the dose used, for example.

I can only report what I track, and I record many daily "vital signs" such as blood pressure, body temperature, weight, waist, heart rate variability, exercise, etc., but my main interest in coffee/caffeine at present stems from about five years ago (before knowing genomic data) when I was concerned about developing Parkinson's Disease, because of episodes of REM sleep behavior disorder. There have been many studies about possible preventive effect of coffee/caffeine on neurodegenerative diseases (see paper above) and I enthusiastically embraced them as something I could control. The variables I tracked were related to sleep, such as sleep onset latency, daytime sleepiness and alertness, sleep length, deep sleep, REM sleep, apnea/hypoxia index (I use CPAP), weight, blood pressure and heart rate, and mood. I found these variables gradually improved with 5-6 cups coffee, intermittent fasting, low carbohydrate diet, less saturated fat, calorie restriction, weight loss to waist < 0.5 height, and changes in circadian rhythm (3mg melatonin when awaken in middle of sleep, not at beginning of sleep--I am genetically advance circadian rhythm, short sleeper--no daytime naps, 5 cups of coffee in morning and not after noon--I am fast coffee metabolizer--and delaying sleep cycle with blue light in evening not morning). For sleep, the Epworth Sleepiness Scale is useful: http://epworthsleepinessscale.com/about-the-ess/

I also found I was having more GI symptoms such as urgency, diarrhea, and cramping when using 70 grams coffee a day and they went away when I reduced that to 30g, without affecting other variables such as sleep. I don't know the status of my microbiome otherwise.

Coffee variables have been studied by the Coffee Brewing Institute, for average consumers, and can be controlled to produce a perfect cup for your personal taste that also meets health needs. Several modern coffee makers such as the Behmor I use allow you to tailor the brewing temperature, time, grind, and variety, and you can learn the elements of taste such as acidity, flavors, robustness, etc., by experiments yourself, without having to rely on the Starbucks barista. As I said, I was able to experiment by measuring variables and seeing the results over a period of time, and I can make adjustments if necessary. Since my main goal is prevention, I really won't know myself until too late, of course, but meanwhile there are risk factors to control.

I was so anxious about my REM sleep behavior problems because of the risk of Lewy Body dementia or Parkinson's, and so maybe overdid the coffee drinking, but knowing I don't have genetic risk for those particular conditions now, and their disappearance with CPAP, fat loss, and other changes, has allowed me to feel more in control. But now I am anxious about late-onset Alzheimer's (e3/e4), and there are not so many biomarkers to be confident of control. (I have had a lot of tests from a clinical trial but await decision to accept).

Thanks for all the detail, Verax. This kind of tracking and testing seems like a really great thing for us E4 carriers to be doing. I admire that you recorded so much information. I'm curious: what did you use to measure your sleep-related variables (except for the Epworth Sleepiness Scale)?
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Re: Coffee Questions

Postby Verax » Sat Sep 15, 2018 6:18 pm

I had a couple of sleep studies before and after getting the CPAP machine. Nowadays most of the sleep studies for CPAP are done at home with fancier CPAP machines. But they don't track REM sleep, which was the variable so important to me, suffering from REM sleep behavior disorder. During the sleep studies they measured EEG and EMG but didn't pick up RBD for me in the lab. I bought a Zeo device which had a couple of EEG electrodes and algorithms to track sleep stages, and I found it was pretty accurate. But Zeo went out of business suddenly. For some time I used a cheap recording finger oximeter like in the sleep studies that tracked desaturation events, but the Chinese-made software and interface were obsolete and I couldn't upgrade it. I also bought a Basis Peak smart watch after I learned Intel founder Andy Grove bought Basis after he was diagnosed with Parkinson's. The Basis Peak was also very accurate in recording sleep stages with skin temperature and actigraphy. But Basis had to withdraw all the Peaks after a couple got hot enough and burned some customers, so that left me without a good way to track sleep. Until now -- now I use the Android app SleepCycle (it added a snore recorder a few weeks ago), and wear a Fitbit Alta HR. Plus a ResMed 10 CPAP gives me the total time I wear it plus the apnea/hypoxia index. I can print out the logs and take it regularly to my sleep doctor. I can also graph from a spreadsheet simple correlations such as between fat loss and AHI. I wish for better devices such as those that measure circadian temperature, but the SleepCycle and Fitbit Alta HR apps suffice for now.

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Re: Coffee Questions

Postby slacker » Sun Sep 16, 2018 4:50 am

Verax wrote: I wish for better devices such as those that measure circadian temperature, but the SleepCycle and Fitbit Alta HR apps suffice for now.


Dr Peter Attia uses an Oura ring, and there has been some chatter on our site about it (search for "oura"). This device may not be what you are looking for, but here is the website if you wish to investigate further.
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Re: Coffee Questions

Postby Verax » Sun Sep 16, 2018 9:42 am

thanks, Slacker, I will look into it. Rectal temperature is the gold standard, but messy. I would guess from your screen name you are too young to remember the craze (around 1970?) of biorythm watches and calculators (from Japan?). For fun, see https://keisan.casio.com/exec/system/1340246447


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