Away From the Bench

The world outside of the lab

Archive for the category “Science”


I am a moderate Star Trek fan.  I have never dressed up like Uhura and gone to Comicon or anything, but I’ve seen all the Star Trek movies (most of them since Star Trek V in the theatre) and have watched many of the original TV reruns.  This is mainly because my dad was a huge fan, not able to go on dates on Fridays in the 60’s because he had to be home to watch the show (life was so hard before DVRs).  I never got into any of the TV spin-offs though.  So, when my husband watches The Next Generation (TNG), I refuse to watch it.  It’s not the original.  Cheesy sci-fi in the late-80’s and 90’s just isn’t the same, especially without Shatner.  However, it’s sometimes hard to avoid hearing or seeing some of it in our one bedroom loft.

You might have to squint really hard to see the nanites.

So when my friend Kari sent me an article about how nanoparticles can control blood sugar in diabetics for up to 10 days, I immediately thought of a TNG episode that accidentally seeped into my ear canals (and also guest-stars Dr. Bob Kelso from “Scrubs”).  It was an episode in which nanites, or microscopic robotic devices, could be put into humans and programmed to do medical tasks.  The actual episode storyline revolves around how the tiny computers “evolve” and start attacking the ship.  Eventually the nanites are given their own habitat to live in as autonomous creatures (reason #835 why I can’t watch this show).  But I digress.

Are “nanites” for medical use becoming a reality?

Yes and no.  Actual molecular nanorobots that can perform work inside cells are not a reality yet, but nanoparticles are.  Most nanoparticles used in the medical field utilize coatings that allow drugs or other useful molecules to be transported in the blood stream, targeted to a specific site within the body, or shielded from the immune system to avoid degradation.   Cancer drugs such as Abraxane and Doxil are two examples already in use.  Abraxane is a common cancer drug (paclitaxel) bound to a naturally-occuring blood protein (albumin).  The nanoparticle exploits the feeding system of the tumor, which takes in nutrients normally bound to albumin that are circulating in the bloodstream.  Tumors basically eat themselves to death when Abraxane is present, because they “eat” the albumin…and the drug that is bound to it.  Doxil is another cancer drug (doxorubicin) that is enveloped in a polyethylene glycol-coated liposome (similar to a cell membrane) and is used to treat Kaposi sarcoma, which causes skin tumors.  The coating targets the drug to the skin and the liposome reduces cardiotoxic effects (heart problems) of the drug.  There are many more nanoparticles currently in use, and if you want to read further, Wikipedia has a pretty good article on nanomedicine.

Using nanoparticles for long-lasting blood glucose regulation is a real breakthrough in the treatment of diabetes.  In a normal pancreas, the beta cells transport glucose from the bloodstream into the cell and metabolize it.  The energy and metabolites from glucose metabolism cause a series of events in the cell to release the hormone insulin into the bloodstream.  This mechanism allows the beta cell to sense the blood glucose levels and secrete the correct concentration of insulin in response.  People with type 1 diabetes have lost their beta cells (due to an autoimmune reaction) and can no longer produce insulin.  What makes this new nanoparticle exciting, is that it creates a closed-loop system that releases insulin by “sensing” circulating blood glucose levels, similar to a beta cell.  I have previously posted about an external “bionic” pancreas, which is an open-loop system that consists of an external continuous glucose sensor, an insulin pump, and a glucagon pump.  This type of system relies on electronic automation and accuracy.  Nanoparticles rely on chemistry for glucose sensing and insulin release.

WARNING: this paragraph contains chemistry, read at your own risk.  The nanoparticle that the Anderson lab created consists of insulin, glucose oxidase, and catalase inside an m-dextran matrix surrounded by a chitosan or alginate coating.  Insulin is usually released by the pancreas in response to increased blood glucose levels and the nanoparticle is able to “sense” blood glucose levels with glucose oxidase, an enzyme that converts glucose into gluconic acid.  Gluconic acid decreases the pH of the nanoparticle to degrade the m-dextran sphere and release the insulin.  The chemical reaction of glucose + oxygen + water catalyzed by glucose oxidase not only produces gluconic acid, but also hydrogen peroxide (which is toxic at high levels).  Therefore, catalase is the other enzyme in the particle that converts the hydrogen peroxide back into water and oxygen (to keep the glucose oxidase reaction continuing).  The spheres are coated with positively-charged chitosan or negatively-charged alginate to form an electrostatic network of nanoparticles, or nano-network.  Creating this three-dimensional, porous structure of tiny spheres increases the surface area-to-volume ratio to make the “sensor”, or the interaction between glucose in the blood and glucose oxidase in the nanoparticle, more efficient.

Nanoparticle montage

Upper panel: The nanoparticle. Lower left panel: The nano-network. Lower right panel: Insulin release response of the nano-network in a test tube with glucose concentration changes (100 or 400 mg/dL) every 2 hours.
From: Gu, et al. (2013) ACS Nano, 7(5): 4194-4201.

In case you skipped the previous paragraph, what makes this nanoparticle so great, is that it uses chemistry (which is usually infallible) to work.  The nanoparticle is engineered with many layers to encapsulate everything necessary for glucose concentration to be sensed, insulin to be released, and no cytotoxic (cell-killing) byproducts to be created.  And it works pretty well in mice.

Usually people with type 1 diabetes have to inject themselves multiple times a day with insulin.  They must also calculate how much insulin they should inject based on multiple factors: food intake, blood glucose measurements, and physical activity.  In this study, after injecting the 150 microliters of the nano-network into a diabetic mouse, it took 10 days for the nanoparticles to deplete.  Some mice maintained normal blood glucose levels for 15 days.  Two weeks after administration, the glycated albumin ratio (a measure of diabetic control over a few weeks) in mice treated with nanoparticles decreased from 10% to 6% (from a diabetic to a normal range).  If this type of system can be used in humans, it would increase the quality of life for diabetic patients considerably.

The problem with this nano-network system is that it is injected under the skin and sits in a visible lump until the nanoparticles break down and get cleared from the area.  Even though all the materials in the nanoparticle are biocompatible (not harmful to the body), there is local inflammation at the injection site while the lump of nanoparticles are physically there.  This system has yet to be tested in humans, who are much larger than the mice used in this study and may pose different problems.  The authors also don’t mention any experiments with a second injection after 10 days.  Insulin-dependent diabetic patients need to continue their insulin treatment for the rest of their life, so if the nanoparticles or certain components never get completely cleared from the bloodstream or begin building up after multiple injections (the authors do not mention blood pH measurements), then this treatment is not as feasible.

For now, nanoparticles are very promising in many different medical fields.  However, as electronic technology becomes smaller and smaller, nanorobots are not completely out of the question.  There is some really cool science going on in the John Rogers lab at the University of Illinois.  They have created dissolving electronics, stretchable lithium ion batteries, and malleable circuits that could be integrated into the body in the future.  Scientists just need to create electronics that are as reliable as biology and chemistry – and make sure they don’t evolve and take over the ship.


Marshmallow Fluff









Stinky Feet Beer

Cheese and beer go together like rama lama lama ka dinga de dinga dong.  Cheese is a great partner to beer and can provide a similar taste or a sharp contrast.  Historically, cheese and beer were both produced and eaten by monks and farmers.  Many pubs combine beer and cheese into dips or soups that are usually very delicious.  I am a beer lover, so when I popped open a bottle of Berliner Weisse aged on fresh blueberries from a local brewery, I was excited.  It poured out an interesting mauve color.  (This color description reminds me of another science story – but I’ll leave that for a future post).  Then, like a shovel to the head, it hit me.  It attacked my nose with tiny odor knives.  The smell.  Was.  Disgusting.  I expected a sour blueberry aroma, but instead I got cheese.  Stinky feet cheese.  My family used this term when the cheese my mom bought had a certain ‘odeur’ to it.  I clearly remember a few instances when I curled up my nose and reeled away from the table after taking a sniff of strong cheese.  I think this primal sensory memory was permanently burned into my brain.  I grew up thinking that this term was something my family had just come up with.  I had no idea it was a real thing.

Artist’s rendition of stinky feet cheese

There are several different organisms (bacteria and mold) that produce compounds to make cheese smell rank.  The bacteria that causes Limburger cheese to smell like a dirty foot party is Brevibacterium epidermidis.  Guess where this little guy was cultured from?  You guessed it – actual stinky feet (epidermis = skin).  This type of bacteria converts the amino acid methionine (found in foot sweat and dairy proteins) into gaseous methanethiol.  There are other places this methanethiol byproduct is lurking other than your cheese and your feet.  I learned this a few years ago from my friend Stef.  She made a comment about our pee smelling bad after we had asparagus at dinner.  I had no idea what she was talking about.  Turns out, the metabolism of asparagus produces a cocktail of volatile organic compounds that can cause your urine to have a sulfuric smell, and one of those compounds is methanethiol.  I apparently don’t have the single-nucleotide polymorphism (SNP, which is a DNA sequence variation) in my olfactory genes to detect it or am one of the few who may not produce ‘asparagus pee’ because my urine didn’t smell any different to me.  Another organism that is very sensitive to methanethiol is Anopheles gambiae, the principal type of mosquito that carries malaria.  Dr. Bart Knols and colleagues observed female mosquitoes were attracted to stinky feet – and created a mosquito trap baited with dirty socks (see Table 1).

Mosquito table2

CC copyright: Njiru BN, et al. (2006) Malaria Journal, 15:5-39.

Although I may not have mosquito-like senses when it comes to methanethiol, I’ve determined that I am pretty sensitive to isovaleric acid.  This fatty acid is produced on feet and in strong cheeses such as Durrus by the bacteria Staphylococcus epidermidis through metabolism of the amino acid leucine.  This bacteria can also grow out-of-control on your face and cause bad acne.  Whenever I smell isovaleric acid, you can bet that I’m calling the odor ‘stinky feet cheese’.  Similarly, another bacteria called Propionibacteria can be found on feet, in cheese (like Swiss), and on acne-laden skin.  This bacteria can produce isovaleric acid as well as propionic acid, which has a vinegar-like smell.  Who knew stinky feet and stinky cheese had so much (bacteria) in common?

So how did isovaleric acid get into my beer?  I’m pretty sure they didn’t brew it with dirty socks or pungent cheeses.  Hops contain three different types of alpha acids that create the bitter flavor in beer.  If the hops get old or are not stored correctly, one of those alpha acids, humulone, can oxidize and produce isovaleric acid.  You can even buy capsules of purified isovaleric acid to train yourself to identify this smell and taste in your beer.  Hops are usually boiled with the wort (the sugar-water produced from mashing the grain) to introduce the bitter flavor and the isovaleric acid byproducts will be drastically reduced.  However, Berliner Weisse wort may only be boiled for about a quarter of the time than as for other types of beer (or not even boiled at all).  This leaves the stinky, cheesy isovaleric acid in the beer.  The off-flavor is intensified by the low pH of the sour mash.  However, there are many Berliner Weisse beers that do not have this cheese flavor (and that are presumably boiled for a longer period).  The worst part was, the aftertaste of my beer had a strong cheese flavor…and it lingered.  Needless to say, I could only stomach two sips – and the second one was only to confirm its nastiness.  After chugging a glass of water, I found it quite unfortunate but necessary to dump the rest.

A few weeks after this beer was released and killed the noses and palates of its drinkers, the brewery admitted the mistake and recalled the beer.  Since then, they have brewed a new batch of the blueberry Berliner Weisse and also brewed a batch with raspberries.  I thoroughly enjoyed the raspberry beer and its tart, fruity flavor…and smell.  In fact, I might even pair the next bottle with a nice (mild) cheese.

Blue Lady

The second batch of blueberry Berliner Weiss

Hotspot to the Rescue

Last week, my friend Lauren asked me to talk to her 5th grade class about my job as a research scientist.  Her class was learning about the scientific method and that not everything may be as it first seems.  When they were asked to draw a scientist, they drew very Einstein-looking men with white, crazy hair.  When the class brainstormed questions to ask me, one of them was, “Do you wear glasses?”  She was able to massage that one into “Do you wear safety glasses?”, but you can see how these kids were thinking.  She wanted to break those stereotypes and show her class that anyone can be a scientist.

Her school is a solid hour away from my lab, so she thought a video chat would be the best idea.  She had never tried to video chat from her classroom before.  She tried Skype, which didn’t work.  She tried Google video chat, which didn’t work.  I tried to Google video chat from my computer on the hospital network, but I couldn’t get it to work on my side either.  It amazes me that in 2012, places where free video-conferencing should be used often (schools, hospitals) are denied access.  I understand that there’s only so much bandwidth available on certain networks (or only so much they want to pay for), but blindly denying access to certain sites makes it very hard to communicate.  There is also the security aspect of video-chatting in schools, but Lauren told me that her public school district restricts internet access much more than her Catholic school did 4 years ago.  (The Catholic school was under the impression that kids are going to go home, go on the internet, and find websites that aren’t appropriate.  Why not teach them how to use it properly at school?)  Nevertheless, teachers should be able to access internet sites they find helpful for their classes, regardless of student access.

I have an Android phone and knew I could connect my computer to video chat via hotspot over my cell network.  Unfortunately, she had an iPhone that couldn’t hotspot.  Apparently you have to pay for such service on iPhones (except maybe some plans on the new iPhone5).  Luckily, her husband’s jailbroken iPhone could hotspot.  So we video-conferenced between a school and a hospital using 2 hotspots and a borrowed phone.

This is what it felt like:

In the end, the connection was successful, if not a little jerky with an intermittent humming sound.  I think the kids enjoyed it (especially seeing the magnetic stirrer in action).

Magnetic stirrer

And it gave me a good feeling inside to think that I may have planted the seed for one of those kids to become a scientist someday.

Or maybe not.

Eat Your Nerd Grenades


Courtesy of



Juicing the Most out of Your Medication

Many of your medications may have warnings of TAKE WITH FOOD or DO NOT EAT 30 MINUTES BEFORE OR AFTER THIS MEDICATION because oral drugs may upset the stomach or not be absorbed as well depending on food intake.  Some foods, like the grapefruit, can act like a drug themselves.

Grapefruit juice contains a chemical called  bergamottin (and 6’,7’-dihydroxybergamottin, which were first found in bergamot oranges).  This chemical is a specific inhibitor of an enzyme in your liver and small intestine called cytochrome P450, family 3, subfamily A, polypeptide 4 (CYP3A4) that usually metabolizes macromolecules (lipids, proteins), but also drugs and toxins.  Depending on the drug, CYP enzymes can either increase or decrease the amount of active drug in your circulation (called bioavailability).  There are warnings not to drink grapefruit juice with some statin medications because that would increase the bioavailability of the statin and could cause side effects and organ damage.

Creative Commons Copyright John Steven Fernandez

Some researchers are actually using the power of the grapefruit to benefit patients.  They are investigating whether grapefruit juice could be used as a ‘drug booster’ –  the drug dosage could be lowered, but the resulting bioavailability would be the same.  Using less drug would translate to a lower cost to the consumer.  During Phase I trials in humans, researchers determined that an 8-oz. daily glass of grapefruit juice increased the bioavailability of 25 mg of sirolimus (a possible anti-cancer drug that is currently used as an immunosuppressant) to that of 90 mg of sirolimus alone.  That translates into taking 25% of the usual drug dose but seeing the same effects of the drug on cancer cells.

There are a couple of drawbacks to using grapefruit as a prescription.  The concentration of bergamottin can vary between grapefruit juice batches.  The authors of the Phase I study contacted the Florida Department of Citrus to obtain a frozen concentrate that was tested for bergamottin levels before they used it.  The other inconsistency is the variation between individuals.  Some people have higher levels of CYP3A4 enzyme in their small intestine (as much as 40-fold), and those people see the greatest effect from grapefruit juice.

Grapefruit could be a powerful medical tool because it is a natural, easily available, low-cost food that has a specific and well-known molecular mechanism.  Who said money doesn’t grow on trees?

Not Signed, but Sealed


Sad Corn



Apples to Apples



Some things still grow in Kansas

Clueless or Clued-in?

Note: Sorry to those who were interested in hearing about this topic a month ago.  I was sidetracked.  Life moves pretty fast – I didn’t want to miss it.

Birds do it.  No, not THAT.  Premastication.  The process of chewing food before giving it to your young.  Alicia Silverstone also does it.  There has been a lot of “gross” utterances after viewing this video.  Although Alicia Silverstone has done much more than Clueless (and Aerosmith videos!), she is best known for that classic 90’s movie.  Perhaps her inner Clueless Cher was coming out when she posted that video, because “anything you can do to draw attention to your mouth is good.”  She has been lampooned almost everywhere, especially by Jimmy Kimmel telling parents to premasticate for their own children.  I think he just likes torturing kids.  So I decided to look at this objectively and see if there are advantages to pre-chew food for children.

Premastication has been used to feed infants and wean them off breast milk in many cultures.  A 2009 article from Gretel Pelto and colleagues, “Premastication: the second arm of infant and young child feeding for health and survival?”, attempted to determine the prevalence of premastication.  The group mined Human Relations Area Files (HRAF) containing data on 370 different cultural groups around the world from the past 50 years.  They found 119 files from different cultures that contained text about infant feeding or weaning, and 38 of those mentioned premastication.  Of those 38 cultures, 31 practiced premastication solely to provide food to children (the others references spiritual or medicinal reasons).  That means, from this sample, at least 1/4 of cultures from hunter-gatherers to agricultural societies have practiced premastication.  To determine whether premastication may be under-reported in these ethnographic studies, they recruited Chinese students from the University of Beijing to interview their mothers or caregivers and ask about infant feeding practices.  From 104 interviews, 63% of caregivers had practiced premastication.  Based on these snapshots, the actual number of caregivers that use premastication to feed their children may be higher than reported.  A 2008 FDA study in the U.S. found only 14% of mothers pre-chewed their infant’s food, with an inverse correlation to education.  Premastication can vary greatly between regions and cultures within America, as 65% of African-American mothers and grandmothers from Omaha, Nebraska reported premastication practices.  These numbers my be surprisingly high for those that have not been exposed to this behavior, but clearly show that premastication is used to feed children in many modern societies.  The real controversy stems from whether this practice is actually beneficial to children.

Breast milk should be supplemented with other foods for children around 6 months old to provide proper nutrition. Several studies have determined that production of salivary enzymes change with age, tooth eruption, and diet.  There is an increase in amylase, or the enzyme that breaks down starches, as the child grows.  By 3 months of age, children have 66% salivary amylase activity as adults.  The importance of salivary amylase is somewhat controversial because the pancreas also secretes this enzyme into the small intestine during digestion.  By 9 months of age, children have adult levels of pancreatic amylase production.  In fact, many digestive enzymes that break down protein and fat are found past the mouth in the digestive tract.  Unless there is a known problem with a child’s salivary enzymes, there are no data I could find to support the need for adult salivary enzymes in children’s mouths.  In fact, as children are exposed to more foods, their bodies adapt to produce more enzymes on their own.

On the other hand, there is actually a lot of overlap between antimicrobial factors (which help the immune system), hormones, and growth factors between breast milk and saliva.  When a child is weaning off breast milk, premastication could provide some beneficial factors that the child is losing from reduced consumption of breast milk, but again, many of those factors children begin producing themselves.  Some believe premastication is a way to bond with your child, although you don’t have to perform mouth-to-mouth to transfer pre-chewed food.  A hug and a kiss might work to bond also.

The biggest problem with premastication arises from the transfer of pathogens.  This is especially problematic in less developed countries where more people unknowingly carry hepatitis, herpes, HIV, Epstein-Barr, and other viruses.  Peridontic diseases can also be transmitted from the mother to the child.  Even in developed countries where mothers know their viral status, premastication could transmit H. pylori, the bacteria that causes stomach ulcers.

Although some argue that premastication is beneficial and has just fallen ‘out of vogue’ much like breastfeeding did 50 years ago, the major benefits of premastication remain unproven.  There are no controlled trials on premastication because they would be unethical to perform.  Premastication was probably necessary before the average person could easily make or buy their own baby food.  The science behind premastication is just not there yet to promote the practice if other means to feed a child are available.  However, I don’t think anyone should be condemned if they choose to premasticate.  If a mother is free from transmissible diseases and feels like this might help a child wean off breast milk, then she could try it…but maybe don’t post a video of it on the internet.  For everyone else, just put the meat in the blender.

Shape-ups Ship Out








Beetle Juice: the next protein shake?





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