Synthetic Biology by JackTsuchiyama

Synthetic Biology

It’s almost time to go back to school, so here’s a topic I’ve been needing to write a paper on for a while…

Synthetic Biology is an extension of genetic science and it has the potential to reduce research and development time as well as increase the speed to market of a drug. For those not in anything pharmaceutical related, this can take around 10 years with the clinical trials and as mentioned by acetylide previously, 99% of these compounds don’t pass the final stage. Therefore, it has been increasingly desirable to reduce this time period.

Synthetic biology uses microbes to create biofuels, cells as memory devices, and drugs. It’s typically broken down into two categories:

1. Entire Genome Engineering (produce & manipulate whole-genome sized DNA and function in new cells)
2. Small Devices & Systems Engineering

The 1st step has been approached specifically by Craig Venter and his team, (in)famous for their assistance in the Human Genome Project. His team claims to have made the first synthetic bacterium (Synthia), but really they created an artificial bacterium. This new bacteria had no traces of the original genome in its final form.
The majority of researchers focus on the 2nd step, however. This involves treating biology similar to mechanical or computer engineering. The biological pieces are defined as “parts” and are organized into “devices” to get the final “system.” As such, synthetic biology uses four main principles:

Abstraction (think of a DNA sequence as a part)
Modularity (parts, devices, & systems can be connected and combined in any way)
Standardization (standardize aspects of design to improve function)
Design & Modeling (models needs to built and tested to improve design)

There has been advancements in synthetic biology already. The BioBricks foundation collects standardized pieces of DNA which can be used interchangeably to create and modify living cells. These pieces are designed to work in all cell types. Academic groups often compete against each other in synthetic biology through iGEM teams and have a registry of primers and DNA fragments.

Synthetic Biology was used to create Artemisinin, a drug that is crucial to treatment of malaria. This drug takes 14 months to produce via plants and has large spikes in production and variable pricing. An engineered E. coli or yeast can produce the drug in 14 days.

There is plenty of controversy and benefits surrounding Synthetic Biology. The government has currently taken a stance of little regulation with careful watching. With too many restrictions, it’s likely that true benefits may not emerge; however, as the technology increases, the chance of it falling into dubious hands increases. And the question arises: who really owns biotechnology? Should it be open-sourced? Or does this increase the risks?

Resources & Sources
KQED. “Decoding Synthetic Biology – KQED Quest” (22 Jul 2009). [Youtube video]. Available.
“What is Synthetic Biology?” Available
M. Specter. “A Life of its Own” (28 Sep 2009). Available
W. Saletan. “Faking Organisms” (1 Feb 2011). Available
G. A. Petsko. “Hand-made biology” (30 Jun 2010). Available
N. Gibbs. “The Risks and Rewards of Synthetic Biology” (28 Jun 2010). Available
B. Erickson, R. Singh, P. Winters. “Synthetic Biology: Regulating Industry Uses of New Biotechnologies” (2 Sep 2011). Available

Hangovers by JackTsuchiyama


For those of use who’ve never had one (including me), the typical symptoms of a hangover are bleary eyes, nausea, and a headache.

The cause is how your body breaks down alcohol! The alcohol is aborsbed into your blood stream through your intestines and is then processed by your liver. Once in your liver, it’s processed to acetylaldehyde and then to acetic acid. The acetylaldehyde build-up is what causes the hangover symptoms. The breakdown is dependent on the presence of enzymes and other chemicals which are dependent on genetic factors. Therefore, everyone is different!

There’s no quick fix either. However, since alcohol is a diuretic, make sure to drink lots of water before and during! This won’t actually help the hangover, however. For the headache, OTC anti-inflammatory meds may ease the pain but won’t get rid of it. Also! Avoid tylenol; acetaminophen is processed via the liver and will only put more stress on the organ!

There is a possibility that darker liquors contain chemicals that when broken down, make you feel worse. Otherwise, all alcohol is broken down equivalently; there is no “hangover-safe” alcohol.

Be safe and be careful! I look forward to another year with you all.

Mohney, Gillian. “Learn the Science of Hangovers Before Your New Year’s Eve Bash” (31 Dec 2015). Available

Darvaza Crater by JackTsuchiyama

Since we were talking about the ocean earlier, I got to thinking about bacteria in extreme conditions!

Darvaza Crater – “Door to Hell”

Darvaza gas crater was created in the 1950s when a Soviet gas drilling rig fell into an underground cavern The crater was set on fire shortly afterwards and has been burning ever since
Figure 1–The Darvaza Carter in Turkmenistan.

The Darvaza Crater, commonly referred to as the “Door to Hell”, has been burning at 1000°C since it was set on fire over four decades ago. It is approximately 225 feet wide and 99 feet deep. When the local government considered filling the methane-filled pit in, a Canadian explorer, George Kourounis, decided that he wanted to investigate the flaming crater. His experience can be seen on the National Geographic series “Die Trying.”

George practiced, prepared, and assembled a team for a year and a half beforehand. They practiced with a rope-rigging system over a river gorge with all his supplies for the excursion: heat-reflective suit, self-contained breathing apparatus, and the climbing harness. The harness was custom-made of Kevlar because a regular climbing harness would melt under the extreme heat.
He even hired a stunt coordinator to light him on fire so that he would be prepared for the flames. That’s some dedication!

Darvaza gas crater was created in the 1950s when a Soviet gas drilling rig fell into an underground cavern The crater was set on fire shortly afterwards and has been burning ever since
Figure 2— George inside the crater.

Once inside the crater, he needed to be aware of checking his air, clearing the ropes, gathering samples, and preparing the video amongst other things. As such, he says he didn’t feel afraid. He described the scenery as a “coliseum of fire.” There was no smoke and the sound was loud like a jet engine.

They found some bacteria in the soil samples that were not present outside the crater. Their presence was sparse, but they were able to survive in such an extreme environment. This may indicate that planets we’ve previously considered to be uninhabitable may contain life.

Charlton, Corey. “See you in Hell: Explorer becomes the first person to descend Turkmenistan’s 1000C pit of fire which has not stopped burning since 1971” (6 May 2015). Available
Nunez, Christina. “Q&A: The First-Ever Expedition to Turkmenistan’s ‘Door to Hell’” (17 Jul 2014). Available

Flesh-Eating Bacterium by beyondandabove

@JackTsuchiyam: Think it might have been this: It would mostly shape the early human microbiome. I’m not talking about the gut microbiome, by the way. But the skin flora. When delivering a baby via C-section, it will be in an environment that’s as sterile as possible. Natural childbirth will cover the baby in some of the mum’s microbiota. So that would make sense. (:

Atm I am looking for anything that is remotely related and would give me some experience. I don’t need to be in the lab, tbh, and I lost interest in pursuing a PhD because I want to turn my back to academia. Good luck getting into grad school!
Anyway, a little something on necrotising fasciitis:

Necrotising fasciitis This is what the so-called “flesh-eating” bacteria are generally known for. It is a rare, but life-threatening disease that mostly affects the extremities (hands, feet), perineum and truncal areas. However, any part of the body can be affected.

Most commonly patients present with signs of inflammation, pain and swelling at the site of infection. These are non-specific symptoms, and therefore can lead to a misdiagnosis. In later stages, the skin might become more tense and change its colour to a darkish blue. Then it will progress to necrosis and become haemorrhagic, meaning that the skin at the site of infection will be dead and practically torn open (better not look up pictures if you’re squeamish. They showed us a couple of pictures in our lectures, of course right before lunch).

Thankfully it’s rare and in the UK about 500 cases are reported every year.

When looking at the microbiological nature, most studies show that more than one species of bacteria seem to be involved in necrotising fasciitis. Most cultures result in a mixture of aerobic and anaerobic organisms, this can also depend on the site of infection. For example, the perineum might have a higher proportion of anaerobic bacteria (you could see why). Single pathogen infections can also occur (roughly 15% of the cases).

The most common causative organism is the streptococcus, more specifically M types 1 and 3 (which produce exotoxin A and streptolyisin O). Another variety is toxic shock strains (Group A streptococci, aka GAS, so something like Strep pyogenes). They can result in organ dysfunction along with fasciitis.

– Streptolysin O causes an immune response and is one of the bases of this organism’s beta-haemolytic property (complete lysis of red blood cells).

– Exotoxin A is a superantigen, responsible for the rash in scarlet fever and many of the symptoms related to toxic shock syndrome.

– M proteins of M types 1 and 3 prevent phagocytosis, so white blood cells can’t swoop in and get rid of the bacteria through this process.

There are actually quite a lot of bacteria and organisms in general identified in necrotising soft tissue infections, including GAS, Group B streptococci,Staphylococcus aureus, Bacillus species (think of gangrene), Escherichia coli, and more. The matter can be even more complicated if antibiotic-resistant bacteria are involved.

I read this:

Hasham, Saiidy et al. “Necrotising Fasciitis.” BMJ : British Medical Journal 330.7495 (2005): 830–833. Print.

Sadly, since I’m not a student anymore, my sources are limited thanks to a lot of articles being behind a paywall. Yay.

Incretins by JackTsuchiyama

If anyone has diabetes or is worried about their blood sugar and loves to eat rice, it sounds like you should eat meat first to keep your blood sugar stable. In the article they specifically mention fish and beef.

I looked into what incretin is, as the article specifically mentioned the chemical. Turns out that incretins are gut hormones “that are secreted from enteroendocrine cells into the blood within minutes after eating.” These hormones are what regulate the amount of insulin released.

There are 2 types of incretins: Glucose-dependent insulinotropic peptide (GIP) and Glucagon-like peptide-1 (GLP-1). These have a common action in the pancreas but differentiate their function once outside the pancreas. They are enzymatically degraded rapidly by dipeptidyl peptidase 4 (DPP4).

Typically, Type 2 diabetes targets GLP-1 receptors since GIP is incompetent for beta-cell function as it no longer modulates glucose-dependent insulin secretion. Basically, GIP is made useless in the physiological conditions of Type 2 diabetes, though I’m not too sure why.

So it sounds like, from the article, eating meat prior to rice increases the incretin production so that there’ll be insulin to degrade the rice when you eat it.

Kim, Wook; Egan, Josephine. “The Role of Incretins in Glucose Homeostasis and Diabetes Treatment” (12 Dec 2008). Available

Caffeine Overdose by JackTsuchiyama

I’m going to do a real one later today, but here’s a post on caffeine overdose that I found interesting…

Apparently caffeine intoxication has been a problem globally (especially the united states), but Japan has never had a confirmed case of it before. Moral of the story I guess is to avoid too much coffee and don’t ever drink coffee with alcohol!

I’m considering trying to research the effects of caffeine at some point… I feel like it’s one of those very tricky substances. Can’t remember if it has a lethal dose or not…

Ahhh of course when I search for it, all I can find is a lot of argument over whether or not there’s too much caffeine in our beverages. Perhaps the lethal dose of caffeine is known but harder to find because it’s not something companies want as public information. Or maybe it’s just too dependent on the individual so it’s hard to get a number. Maybe rats and the like metabolize coffee differently so we can’t use them as models? Lots of questions.

Even if not today, I’ll probably cover caffeine sometime in the future. Especially since I react so weirdly to it.

Bed Bugs by JackTsuchiyama

First of all, MERRY CHRISTMAS and HAPPY HOLIDAYS to everyone who celebrates!!

Since it’s Christmas, I want to start with a topic that’s not too difficult for me to handle, but might be a bit disturbing for those who are more squeamish.
This topic is a pretty personal one for me at the moment, as I’m struggling with a bed bug infestation in my apartment. There tends to run the high tensions of “who brought them in,” “who’s going to pay for the treatment,” and “when can I get my life back on track?”
While bed bugs are not known to transmit infectious diseases to humans or their pets, they are a nuisance. To most, it may just be the uncomfortable stigma, but for those who are sensitive to insect bugs (ie. Me), they can be a nightmare of itchy rashes. The stigma, however, may be the most difficult to deal with because of the constant wonder people have when they interact with you. Even if they don’t say it, everyone seems to be wondering “are there any on you right now?” And no matter how many times it’s explained to be independent of living conditions, people are probably going to assume you’re a dirty, unsanitary person.

The CDC has the broad lifecycle of the bed bug covered pretty well. They tend to feed from humans, but other mammals and birds will suffice if humans are absent. Bed bugs take about 5-10 minutes for a full meal and adults can live for 6-12 months. (Aside: bed bugs also secrete a chemical in their saliva which numbs the skin during feeding, making it highly unlikely that you’d ever notice them during feeding. They can also survive for long periods of time without feeding). Females lay about 5 eggs daily through their adult lives in a sheltered location (likely due to the mating ritual… you can read that one yourself as I’m not sure how nsfw/disturbing it is). The eggs will hatch in about 4-12 days. (Aside: As a result, bed bugs do NOT form colonies. This is another reason why bed bug infestations are so difficult to treat).

Dissertation (2009)
It’s been found that bed bugs exhibit a natural circadian rhythm, which allows them to be more active during the night regardless of the light stimuli received throughout the day. Additionally it’s been found that short-term starved adults move more frequently than long-term starved adults. (Aside: This decrease in locomotor activity likely allows the bed bugs to survive for extended periods of time and may result in the probability that treatment misses a certain population of bed bugs.) The effects of insecticides was also evaluated. The typical insecticide on the market are pyrethroids; as a result, the resistance to pyrethroid insecticides is widespread. Deltamethrin (pyrethroid pesticide) and chlorfenapyr (pyrrole based pro-insecticide) were used on 20 bed bug populations to determine effectiveness. Deltamethrin was occasionally effective in the presence of an inhibitor (P450 inhibitor piperonyl butoxide) but resulted in beg bug avoidance of treated areas. Chlorfenapyr does not result in bed bug avoidance, is effective against the pyrethroid resistant strains, and has long residual activity. However, it doesn’t result in quick knockdown, so bed bugs will be able to freely move before death.

Bed bugs are spreading throughout a large majority of cities in the United States. On the 18 of December in Minneapolis, MN, a 62 year old man was reported to have murdered his 89 year old mother as a result of the bed bug infestation in her apartment. He claimed that she would be evicted and he would have to help her move as the main stressor behind his actions.

What this means to you
While it seems a little extreme to murder someone over a bug, it must be remembered that bed bugs are an infestation. Due to their biology, they are hard to eliminate and multiply quickly. They are unlikely to transmit diseases in their current state but are heavily associated with negative stigma and can be traumatizing for both the person with the infestation and their friends or family. It’s important that if you suspect you may have bed bugs or know someone who might, that you look into proper techniques for bed bug treatment. This post was merely to discuss the biology, not the proper techniques to take if you or someone you know is infested. If anyone would like to know the information I’ve gathered in regards to that, please let me know and I’d be glad to share! If anyone has any experiences to add, those are more than welcome as well.

CDC. “Parasites – Bed Bugs – Biology” (17 Mar 2015). CDC. Accessible:
Romero, Alvaro. “Biology and Management of the Bed Bug, Cimex lectularius L. (Heteroptera: Cimicidae)” (2009). University of Kentucky Doctoral Dissertations. Paper 762. Accessible:
Kes, Tyler. “Man murders mother with statue of himself over bed bugs,” (22 Dec 2015). WOWKTV 13 News. Accessible: