Monday, December 31, 2007

10 commandments for keeping a lab notebook

Another list, just in time for the new year! My boss recently reminded us what it takes to keep a proper lab notebook, and I wanted to share it with you.

Here is the list:
1) Reference for the reaction (from the literature or from one of your or another lab member's lab notebook, for instance Amanda's Notebook VI, page 228)

2) Structure of reactants and expected products

3) Table with mgs/mmols/equivalents/densities/origins of reagents. That last one is really important. If you used a mysterious, old reagent that has been sitting on the shelf for 20+ years and got great results, when you buy a brand new bottle and don't get similar results, you have a reason. The impurities in reagent that is 99% from Sigma might not be exactly the same as a 95% reagent from a different supplier. Also, write down where you found the reagent. I don't know about your lab, but mine has about 10 different fridges/freezers, and sometimes it is difficult to remember exactly where you put something.

4) Reaction procedure--we all already do this, right?

5) How did you monitor the reaction? Draw your TLC or attach your HPLC trace.

6) Workup procedure--sometimes I get a little lazy here.

7) Purification procedure. Include the size of column, amount of silica used, etc.

8) Results. mgs of product obtained, % yield, and physical state of material -- bright orange powdery solid, 239 mg, 98% yield

9) Characterization of products. Include reference to your NMR (if you keep electronic copies, write down the filename!) and explain. For instance, 13C NMR (Amanda_VI_228b_pure), for spot at 0.6 Rf (1:1 EtOAc:Hexanes) consistent with expected product X.

10) Don't forget to write down the date!

And as a general rule, try to write down things within 24 hours of completing them. You tend to forget things if you wait too long.

Anyone have anything to add to this list? While I generally know what to put in my chemistry lab notebook, I must say that I don't necessarily include all of these things every single time. Maybe that will be one of my resolutions for 2008. On a similar note, I also tend to do quite a bit of biology. Do any biologists out there have any suggestions for what to include in a biology lab notebook?

Saturday, December 15, 2007

10 Simple Rules for Graduate Students

One of the professors here recently sent around an article with advice for graduate students. As I'm already in my 5th year here, many of the 10 simple rules aren't so relevant for me any more, but I wanted to pass them along anyways.

A short summary--

1. Let passion drive you.
You had better be excited about the project to which you are going to dedicate the next 5+ years of your life. If you don't like reading and thinking about it now, it probably won't grow on you. And those crazy experiments that come to you in the middle of the night? Go into lab the next day and try them out, because you never know what might work.

2. Select the right mentor, project and laboratory.
Mentor: It's this simple: pick a mentor that you can get along with in a professional atmosphere. Young or old, male or female, it doesn't really matter as long as you respect him/her and can understand his/her expectations of you.
Project: It is very painful to fail again and again for months at a time. Sure, it builds character, but that doesn't make it any easier. Make sure to talk with group members and find out the inside scoop as to what projects seem to have a lot of potential at the moment.
Lab: Work with people you like or at least those you can stand to be around for 10+ hours a day, 6+ days a week. If you can't talk with your lab members at least in a work related fashion, you really are going to be struggling when it comes time to ask for help.

3. Be an independent thinker.
It is okay to disagree with your PI on a scientific hypothesis, as it will only make both of you stronger. Just make sure you have all the data to back yourself up.

4. Balance is a necessary part of life.
Go to the gym, plan movie nights on the weekends, make group dinners. Some of the best friends that I have made during graduate school are the ones that I met biking 30 miles one or two times each week. Although the field of chemistry is relatively large, the people you meet and work with now will be your peers/reviewers/interviewers in the future. It is good to have friends in the field.

5. Think ahead to your career.
Take advantage of everything your school has to offer. Take extra classes if you want. Try to have as many different experiences as possible so that you know what you would like to do when it comes time to look for a job.

6. Remain focused on your hypothesis, but don't let it take over your life.
Set up experiments to prove your hypothesis, but set up just as many to disprove it. Don't forget the big picture. Sometimes proving that a theory is wrong is just as important as showing that it is right.

7. Fix problems now.
If you are struggling with some aspect of research or graduate school, talk to someone before it gets to be a big issue.

8. Publish! Attend meetings!
Other scientists may reveal tidbits of information at small meetings that they might not otherwise discuss in the literature. Often times these little things are the key to your success.

9. Be confident (but not arrogant), be thick skinned.
At some point your committee, group or class will question you until you feel like crying. More than likely this will happen multiple times. This is normal and hopefully will help you build confidence. Over prepare for everything.

10. Pick your thesis committee wisely. Stay in contact with them throughout your time in graduate school.
These will be the people writing your recommendation letters. Make sure they know when you make significant progress. Email them your most recent papers and set up meetings with each committee member at least once each year.

Thursday, December 13, 2007

3-D Sugar Printer

Well, the people at Evil Mad Scientist Lab-
oratories have come up with something pretty sweet--a 3-D sugar printer. I have always thought that three dimensional printers are very cool and I even remember the first time that I even learned that they exist--on my tour of the Beckman Institute at University of Illinois.

The basic concept of the 3-D sugar printer follows standard solid freeform fabrication techniques. Simple two dimensional layers are stacked on top of each other to form a more complex 3-D form. So how do the Evil Mad Scientists do this with sugar? First, a layer of low melting "granular printing media" (sugar) is placed on a flat surface. By applying a technique called selective hot air sintering and melting, a burst of hot air is applied to the sugar in preselected locations. As the sugar melts, it fuses together with other sugar grains and eventually a two dimensional image appears. Next, the flat surface is lowered slightly and a second layer of sugar is sprinkled on top. Again hot air from a heat gun is applied to the surface in preselected locations. This time the new two dimensional image that is formed is also attached to any overlapping fused spots in the underneath layer. Repeating this process over and over again eventually yields a three dimensional object made completely out of sugar!

The inventors claim that their production process is very similar to selective laser sintering (SLS), but at a fraction of the cost. SLS is commonly utilized in manufacturing and uses a very expensive high power CO2 laser (thousands of dollars), whereas the Evil Mad Scientists' technology only needs hot air from a $10 heating element.

If you are really interested, you can visit the CandyFab project, which has all the information you need to build one of these machines at home for yourself. Now I'm hungry--anyone up for some caramelized almonds?

Tuesday, November 27, 2007


On one of the bulletin boards outside of our labs someone recently posted a brochure about the Atomium, and it really caught my attention. This interesting-looking building was erected for the International Exhibition of Brussels in 1958 (the World Fair in Brussels). Based on the structure of solid iron (which by the way is body centered cubic) magnified 165 billion times, the Atomium was designed to "embody the audacity of an epoch that seeks to confront the destiny of man with scientific discovery." Though I don't believe the individual spheres of the building are 165 billion times bigger than a real life iron atom (an iron atom is approximately 2.5 Angstroms in diameter x 165,000,000,000 = 135 feet, and the actual building spheres are only about half that size), the distances between the atoms are supposedly magnified to that size.

Visitors are only allowed in 5 of the 9 spheres--the base (Henri Storck sphere), where you will find an exhibit dedicated to the 1950's, the top restaurant sphere, the central (Waterkeyn) snack bar sphere, the sphere named after the Belgian artist Marcel Broodthaers, and the children's only sphere. At 115 feet long, the escalators found inside the tubes of the Atomium are some of the the longest in Europe.

Why make a body centered cubic building modeled after the structure of iron?? It was a tribute to the steel companies that helped to sponsor the construction by providing raw materials.

After seeing these pictures, I really want to visit. Thanks to Mirth (and her family) for the lovely photographs.

Stairs connecting the spheres:

A view to the outside

Artwork inside of the Atomium

Wednesday, November 21, 2007


Tuesday, November 20, 2007

Cockroach behavior

There is quite a cockroach infestation in our chemistry building here (although come to think of it, I haven't seen any bugs in at least 6 months, hmmm...), so I was naturally curious when I came across this paper in Science. For a second think back to all of those science fiction movies you watched as a kid (and you probably have seen at least a few if you are a scientist), especially the movies involving robots--in particular robots that were integrated into human society and took on some seemingly human emotions (R2D2 and 3CPO from Star Wars are my all time favorite robots)...Now think about the social integration of robots on a slightly smaller scale (with insects), and that is exactly what José Halloy and coworkers have accomplished.

American cockroaches typically recognize chemical cues from their neighboring cockroach friends, and utilize these signals to act as a group and make self-organized choices. Self organization complements the preexisting environmental signals and coexists with status levels between the insects such as leader/worker relationships. Halloy and coworkers claim to have socially integrated cockroach-sized robots into a cockroach collective. How was this achieved? You guessed correctly--through chemistry! Basically by extracting and characterizing the hydrocarbons found in the cockroaches' exoskeleton, researchers identified compounds that were key in inter-cockroach recognition. By coating the robots in these extracts (which included compounds such as 6,9-heptacosadiene and 3-methylpentacosane), cockroaches accepted these robots and, even more amazingly, allowed the robots to influence decisions made by the cockroach community.

My only question is who got to perform the extraction of the cockroach exoskeleton into dichloromethane? That just sounds pretty icky to me.

Tuesday, November 13, 2007

Ham Flavor?

When I think about all of the artificial flavorings that go into foods, it always makes me feel a little disgusted. Sometimes even the so-called "natural" ingredients creep me out, so I really hate to think what might go in this soda to make it taste like ham. But I do give them credit for a cool (yet slightly disgusting) idea.

For your enjoyment, I've compiled a short list of the some of the more common flavoring molecules below.

Wednesday, November 7, 2007

Flu Vaccine and Thiomersal...

Today I got a flu shot. In my past life, I used to consider people who got such unnecessary vaccinations as "weak," but now I just figure, why not? Who wants to deal with a bad case of the flu, miss work, and possibly end up in the hospital (as I did this summer with a severe case of the stomach flu)? Of course the vaccine doesn't catch all strains of the flu, but hopefully it will at least give me some protection, which is certainly worth suffering through one day with a sore arm.

As I was signing my life away while waiting for the shot (no, I won't sue the school if I have an adverse reaction to the ingredients of the vaccine), the information packet warned that this shot contains thiomersal and that people with known allergies to this preservative should not be getting the shot. We have all heard about the controversy assocaited with vaccines; one side believes that some vaccines might cause autism and other disorders associated with brain development, while the other side does not believe this to be the case. Thiomersal is at the center of this debate.

Looking at its structure, it is easy to see why this compound might be considered suspicious. While it is a powerful preservative because of its antifungal and antiseptic properties, it also is an ORGANOMERCURY compound. Basically one of the reagents that I wouldn't like to work with in lab. You only have to read the story of Prof. Karen Wetterhahn (which was posted for some time in our group's hallway as one of those 'be more careful in lab' warnings) to know why I might refuse to work with alkyl mercury compounds. Basically the harmless sounding name thiomersal actually refers to a compound that probably breaks down to ethyl mercury inside of your body. At the same time, it is a necessary part of the vaccine and works to prevent possible adverse side effects like as bacterial infection that might occur in vaccines lacking preservatives. And is ethyl mercury just as bad as methyl mercury? Apparently not [1], but that doesn't stop parents from worrying about their children.

Personally, I wouldn't be too worried about thiomersal containing vaccines. In general, very few vaccines contain thiomersal any more, and those that do have extremely low levels present. Looking at this table, some vaccines contain 0.01% thiomersal. In studies, levels of thiomersal producing inorganic mercury levels ranging from 201 micrograms/Liter to 50 milligrams/L were shown to be toxic in cell culture, (and, for those interested, these levels induced activation of caspase-3). Levels of thiomersal used under normal vaccination conditions are much much lower. In the worst case scenario, after a complete series of vaccinations a very very small child would receive less than 50 micrograms of inorganic mercury per kg of body weight. Additionally, ethyl mercury (half life of about 18 days in the bloodstream) does not bioaccumulate like methyl mercury (half life of 50 days).

So go ahead and vaccinate your children. And why not get a nice flu shot for yourself while you are at it?

[1] How do I know ethyl mercury isn't near as toxic as methyl mercruy? Of course there have been some scientific studies completed on this very subject, but I also have some firsthand experience. Thiomersal was once sold as Merthiolate. I am not that old yet, but I still can remember back to when my dad would put this bright pink solution on any little cuts or scrapes that I would have. It always stung for a second, but nothing ever got infected. Strange to think that it was actually an ethyl mercury containing product. In 1998 the FDA banned the use of thiomersal in over the counter products, which explains why I haven't been able to find this wonder drug from my childhood in any stores.

Wednesday, October 31, 2007

Which one of these is not like the others?

I finally got a picture from the East Coast PARP Conference that I attended way back at the beginning of October. Other than the obvious difference of being the only female non-faculty presenter (speakers are in the front row), I am pretty sure that I was the only chemist there!

Monday, October 29, 2007

Tattoo Chemistry

After I recently read a book about about words on skin, I jokingly told my husband that I wanted to get a tattoo. Now we both know that the likeliness of that is about 0.1% (firstly, needles are one of my least favorite things, and even working with them in lab sometimes gives me chills, and second I can't stand seeing blood, particularly my own), but I must have worried him somewhat, because the he gave me the September issue of "Nachrichten aus der Chemie" (kind of a German version of C&EN News, but not quite) that contains an article on tattoos. Other people have written about it--Carbon Based Curiosities comes to mind--but I hadn't really ever seen the actual structures of tattoo pigments, so it was actually quite an interesting read.

In the past, inorganic pigments such as titanium dioxide (white), cadmium sulfide (yellow) and iron oxide (black) were used as pigments. These compounds are relatively insoluble and thus produce long lasting color. Today organic compounds make up the bulk of colored tattoo pigments, while totally black tattoos are still made out of carbon black which unfortunately contains toxic impurities associated with its production. I've drawn out some of the structures of common organic tattoo pigments for you to see; most of the structures contain polycyclic azoles, which I guess isn't very surprising.

Not to scare anyone away from getting an awesome tattoo of their favorite natural product, but the bulk of the article is dedicated to the dangers associated with tattooing. Amazingly, some pigments that aren't allowed in cosmetics due to toxicity are still used in tattoos (at least in Germany, and I wouldn't be surprised if the same is true for the United States). Also, there are many dangers associated with the breakdown products of the pigments that are utilized, especially in the case of red pigments. One can imagine that these decomposition products could be oxidized in the body to produce an even larger number of unknown chemicals that could potentially be hazardous to you health. But don't let any of that stop you from getting that tattoo of the periodic table on your arm like you've always wanted--tattoos can't be any worse for your heath than washing your hands in benzene (which from what I hear was a relatively common practice for chemists 50 years ago).

Thursday, October 25, 2007

Cool toaster...

Not exactly related to chemistry, but I just read about this toaster on and I think it is really cool. Sasha Tseng, a Japanese designer, came up with the concept of the toast messenger to make your meals a little more interactive. Basically you write a little note on the screen and then it can be toasted into your bread (or whatever you prefer to eat) OR a little printer (with jelly as an ink of course) can squirt out a color message. Neat. Now you can draw molecules on your toast!

Wednesday, October 24, 2007

Ego boost

Well, I've finished 2/3 of my North American speaking tour (as my boss likes to call it), and it is actually nice to spend some time in lab after all of that traveling. I do enjoy visiting new places quite a bit though, almost as much as I enjoy giving seminars. No, I am not being facetious--under the right conditions I actually enjoy public speaking. As long as I have had a chance to prepare and am interested in the subject (in this case, my research), it is kind of fun to watch an audience respond and react to what I am saying. Anyways, my PI got an interesting email after I had returned from one of of my speaking events. The general gist of the is shown below, with my comments shown in italics:

"Mr. H...(my boss who is most certainly deserving of a Prof. or at least a Dr. in front of his name),

I did not found the email address of A (referring to me)... who gave remarkably interesting talk regarding enzyme Y (go me!!!)....Can you please forward this email to Dr. N (once again, referring to me)? We are very excited about the possibility of a collaboration....

X (eager grad student who got some details a little mixed up)

Luckily my PI has a good sense of humor, and we joked about the whole thing.....It is kind of fun when someone thinks that you are deserving of a "Dr." title when you don't actually have one yet.

But don't worry, I'm not letting it go to my head.

Wednesday, October 10, 2007

"Girl Chemist"

Walking down the hall earlier today, I noticed that one of my labmates had posted an interesting article near her door. Taken out of a Science Illustrated (no, not Sports Illustrated) issue from 1949, the article entitled "Girl Chemist" made me stop in my tracks and take a look. Of course if the photos don't make you laugh (no goggles, gloves, labcoats, eating lunch right off the bench, etc.) the text certainly will. "Chemistry, once strictly a man’s profession, has become increasingly hospitable to women" Hmmm, from the title "Girl Chemist" I wouldn't have thought that. If the point of the article was to show that women can do chemistry too, wouldn't "Female Chemist" or "Woman Chemist" have been more appropriate?

And it goes on..."At 22. Jackie Bates has made chemistry her career. Although it is a lonely, tense, exacting, sometimes frustrating profession, she enjoys it. She finds her work satisfying, her day full, her advancement altogether satisfactory. After 18 months on the job she regards herself as a veteran: 'The sulphur dioxide smell doesn’t bother me any more.'"

Taking a look at the chemistry section of Modern Mechanix, there are certainly a few other articles worth looking at. Some of them that I found particularly interesting--the very instructional "How to set up your chemistry laboratory, "Fun with explosive gases,"Thrilling stunts with a glass eating chemical,"Mercury the liquid metal," and last but not least "Chemcraft for victory". Enjoy.

Monday, October 8, 2007


Do you ever have weeks (or months) where nothing seems to get done? Unfortunately, as much as I am trying, it feels like for the last few weeks my research has been on pause and nothing seems to move forward. Not a good thing for a student starting their 5th year. At the beginning of my grad school career I loved "slow" weeks, when I had the time to read/write/think. Now it makes me nervous not to have an experiment running, and I miss the fluttery feeling I get in my stomach when I am waiting for the results of an important NMR or biological assay to appear on the computer screen. Lately I've been chained to my desk, working on various presentations (3 different ones in all), writing, and reading. (Don't get me wrong, I also enjoy the quality time spent at my desk, but I do want to graduate in about a year, so I like to stay busy).

This past weekend I was at the East Coast PARP Conference in Quebec City. Not only attending, but holding a 40 minute seminar on my research. As sick as it sounds, I actually enjoy public speaking, but in this case it was particularly nerve-wracking. Imagine--I was the only non-professor presenting (except for the guy from NIH, but he doesn't count since he has a Ph.D. already) to an audience of experts on my particular subject. Also, I was the only female presenter. After my talk was finished (luckily I was the second speaker of the day), I was able to enjoy the meeting, learn about some awesome research, and meet all the "famous" people in my field. It's a good thing that I remembered a pen and paper despite my nervousness; I took over 20 pages of notes. While I was at the conference on Saturday, my husband got out and explored the old part of the city, so that he could serve as my tour guide on Sunday. Early October is the perfect time to visit Quebec--the leaves are at their peak and the weather is still relatively warm.

On Thursday I'm off to Michigan to visit my alma mater and once again give a little presentation, only this time my main audience is undergraduates--a huge difference from the conference this last weekend. The last of my seminars will be in the middle of November, and I keep telling myself if I can last until then everything will be smooth sailing.

I hadn't been to an airport in a few months, and was pretty surprised at some of the new security measures. Basically I had to enter a walk-through "portal," stop inside for about 20 seconds while puffs of air shot at me from all directions. It is pretty funny to watch people going through these machines for the first time--almost everyone that I watched go through jumped when the first puff hit them, and then gave a little shiver as they walked through the exit. After a little internet searching, I confirmed my suspicion that this little machine is just a glorified mass spectrometer. According to the Smiths website, the Ionscan Sentinel II (the machine at both airports that I went through this weekend) can detect almost any explosive (RDX, PETN, and TNT to name a few) as well as narcotics (Cocaine, Heroin, THC, and Ecstasy). For the few seconds that I was standing under the puffing air, I was thankful that I hadn't done any real chemistry in lab the last week. What would have happened if the "Sentinel" would have found traces of a NO2-bearing compound on my shoes, hair or clothes?

Do chemists need special notes when we go through airports now?

Friday, September 14, 2007

Small molecules that modulate quorum sensing

On Thursday Helen Blackwell from the University of Wisconsin Madison braved the cornfields and soybeans that pave the way south to the U of I and gave an awesome seminar. Unfortunately I didn't get to go out to lunch with her, but several other members of my group did. From what I hear, she is quiet, witty, observant, and very interested in hearing what students have to say. Although I was a little disappointed that she didn't mention much about her group's work on small molecule macroarrays, she did discuss their recent article on quorum sensing in Vibrio fischeri, which is a fascinating story for anybody interested in chemical biology. She even satisfied those hard-core organic chemists with some microwave assisted reactions. If I remember correctly, they have been able to reduce the reaction time from 24-48 hours to under 30 minutes for the final cyanogen bromide mediated cyclization step in the synthesis of N-phenylacetanoyl-L-homoserine lactones. Pretty amazing what microwaves can do.

Bacteria are able to control their population growth through a process called quorum sensing. By releasing certain molecules into their media, bacteria can signal to each other and thus are able to alter their mode of growth; essentially this communication allows them to function as muticellular communities rather than single celled organisms. Gram negative bacteria are known to use N-acylated-L-homoserine lactones (AHLs) for communication. Previous studies have shown that phenylacetanoyl-L-homoserine lactones (PHLs) can act as antagonists of quorum sensing, so Blackwell and coworkers created a small library of PHLs and tested their activity in the bioluminescent bacteria Vibrio fischeri. While this library contained less than 30 compounds, it included some of the best antagonists AND agonists of gram-negative bacteria that are known to date. Very small structural changes elicited huge differences in activity.

In my opinion, one of the most interesting points of the talk was Blackwell's discussion of the Hawaiian bobtail squid. Apparently its light organ (which is used for hunting and prevents the squid's shadow from alerting potential predators/prey to its position) is inoculated with V. fischeri shortly after birth. Quite an interesting symbiotic relationship--the squid provide the bacteria with a home and food source in exchange for light. Blackwell shared some preliminary data with us indicating that the superagonist discovered in the small PHL library is well tolerated and active in vivo. The juvenile squid utilized for these experiments are tiny enough to fit into the wells of a 96-well plate, and in my opinion they are very cute (as illustrated by the picture above, V. fischeri image from Geske, G.D. ; O’Neill, J.C.; Blackwell, H.E. (2007) ACS Chemical Biology 2(5), 315-320.).

Saturday, September 8, 2007

Binding DB

As brought to my attention by my PI--the Gilson lab at the University of Maryland Biotechnology Institute has been working to develop a database of known protein-ligand binding affinities, also known as the BindingDB. While the BindingDB currently contains only about 15,000 small molecule ligands and 30,000 affinities to proteins measured through isothermal titration calorimetry (ITC) and enzyme inhibition methods, the database is rapidly increasing in size, at a rate of about 10,000 new data points per year.

You can search for your favorite protein or ligand, but there are also several other search features such as molecular weight, Ki, and substructure. Users are encouraged to deposit data from their own published binding experiments, so hopefully this database will continue to grow in the future. Once enough information has been collected, I can imagine that the BindingDB will become a powerful tool in drug discovery--Not only can you download computer models of compounds and affinity measurements, but there is also an interesting virtual screening section of the website that I'd like to explore when I have some spare time.

Of course, this isn't the only database that characterizes molecular interactions. Some of the others include:

Monday, September 3, 2007

Ocean breeze...

While I've always thought the smell of the ocean was quite a pleasant one, I'm apparently mistaken. According to Andrew Johnston and coworkers, dimethyl sulfide (DMS) is the major form of sulfur released from aquatic environments and contributes highly to the distinctive smell of the ocean. Honestly, I've smelled a bottle of DMS before and the thought of comparing its smell with that of a gentle sea breeze never crossed my mind. Production of DMS in the oceans stems from dimethylsulfoniopropionate (DMSP), which is a metabolite produced by seaweed phytoplankton, seaweed macroalge, and salt marsh grasses. During times of stress (like those times you come back from the beach looking worse than a lobster, when the UV-index is extremely high) plankton release DMSP, which is subsequently catabolized into DMS. One of cool fact--oxidation products of DMS are known to seed clouds--so do these creatures purposefully secrete DMSP to generate clouds and thus protect themselves from the sun's harmful rays? Something tells me that this is not the case, but it is interesting to consider nonetheless. DMS production protects cells from ROS and has been shown to prevent some kinds of viral infections in algae, and these are the more likely reasons for DMS synthesis. A potential downside of DMS production for these creatures?? They get eaten. Both crustaceans and birds are known to be attracted to its smell as it serves as a chemical indicator for food[1],[2],[3].

Note: Be sure to check out the "CLAW hypothesis" if you've never heard of it before...

Idea Generator

Not related to chemistry, but worth the visit.

Monday, August 20, 2007

Moving on up...

I have officially moved up in the world of graduate students. As of 4:00 this afternoon, I have an "undergrad" at my disposal!

Friday, August 17, 2007


Friday evening after work I popped a Lean Cuisine into my trusty Kenmore microwave, turned the time to 3 minutes, and went to check my email. After I heard a loud popping sound, I went back into the kitchen only to discover that my microwave had caught on fire. Tons of disgusting-smelling smoke filled the air, and I could barely see my kitchen. Luckily, I'm a chemist, so I was prepared to pull the trigger on the fire extinguisher. Amazingly, the chemistry microwave we have in lab has never created any problems, but my own food microwave decides to blow up in my face! My new cat and I ended up spending the night at the Ramada Inn to avoid inhaling the nasty smoke.

So I am wondering--do all of your chemistry departments offer safety training before you start working in the laboratory? We had to take a laughable online safety exam--but also had a small practical course in which we were required to put out a small fire using an extinguisher. Although I found it annoying at the time, I'm very grateful for that hot summer afternoon that we spent putting out fires. I had never used a fire extinguisher before in my life.

Monday, August 13, 2007

Won't you try some of this lovely lemonade?

Where have I been? Well, among other things, I was getting shot up with iopromide and drinking a lovely lemon-flavored mixture of 2% barium sulfate. (If I hadn't sick already, that concoction would certainly have done the job). While barium is a toxic metal (atomic number 56, which makes it perfect for CT scans because it readily absorbs X-rays), barium sulfate has a very low aqueous solubility and is quickly flushed out of the body, thus preventing any extremely bad side effects. (On a sidenote, barium carbonate, which is soluble in stomach acid, is toxic and used as a rat poison). When I mentioned to the CT technician that I am a chemist, he was super nice and even showed me the drug data sheet on iopromide (which even had a structure!), so I could get a glimpse of the lovely iodinated compound that would soon be running through my body. As far as I can tell, iopromide was developed in the early 1980s and is one of the safest nonionic contrast agents out there. Nonetheless, it is necessary to sign an "informed consent" form before the drug can be administered. With an iodine content of almost 50%, iopromide is able to enhance the visibility of organs and blood vessels during radiographic procedures. Once it is injected, it feels like you are on fire and you get a yucky taste in your mouth, similar to the one you had in 1st grade when you licked the flagpole :o)

Sunday, July 29, 2007

Mosquitos and cat(nip)...

Earlier this month I was quite confused. Although we are in the prime of summer--hot and humid Illinois weather--I hadn't gotten a single mosquito bite. Unfortunately I had that thought a little too soon. Last weekend when I awoke on Saturday morning I was covered in tiny red welts, evidence that my screen windows just aren't doing their job and that the little vampires had attacked me in the night. So what chemicals can help to keep away these pesky insects?

DEET, or meta-N,N-diethyl toluamide, is one of the most common mosquito repellents that I have seen used in the United States. While I haven't read any complete studies describing exactly how DEET works, it is believed that this molecule somehow binds to female mosquito sensory receptors (on a sidenote, generally it is only the female mosquitos that practice hematophagy, as they require extra protein in order to reproduce) and prevents them from recognizing some of the chemicals excreted by the human body, especially lactic acid and carbon dioxide. Inhibition of these receptors leaves the mosquito circling in confusion and allows us to enjoy itch-free summer evenings by the lake. DEET does have some unpleasant side effects; it can damage many synthetic fibers (though leaves cotton and many natural fibers untouched) and has long been known to have negative-side effects in aquatic life. Additionally, studies published in the Journal of Toxicology and Environmental Health and Experimental Neurology by Mohamed Abou-Donia and coworkers have shown that prolonged use of DEET in rats can cause neurodegeneration, particularly in the cerebral cortex, the cerebellum, and the hippocampus [1], [2].

In Europe Icaridin / Picaridin is a common insect repellent, and some studies have shown that its activity is similar to that of DEET, but without any of the toxic side effects. Of course we all have heard of "natural" alternatives to these compounds, including citronella, beautyberry, geranium, lemon and eucalyptus oils, but did you know that catnip* (nepetalactone) has also been promoted as a "chemical free" means of eliminating mosquito bites [3], [4]? Interesting how the word chemical is generally considered taboo when promoting a new product; nepetalactone sure looks like an organic chemical to me!

If you are interested, the University of Florida has complied a list of several commonly available insect repellents with their effectiveness here.

*At the risk of sounding like carbon based curiosities, I just had to include some kind of reference to cats in this post. Last week I adopted a wonderful tabby! Isn't he cute?

Friday, July 20, 2007

Wednesday, July 18, 2007


Well, I seem to be having some sort of internet connection problems at home, thus the lack of posts of late. It is very frustrating to pay for something and then not have it work, don't you agree?

Yesterday I was once again allowed to "play" with the confocal microscope; actually this was the second of my training sessions (for a total of 4 hours), so now I'm kind of an expert (not really) and allowed to use it on my own. Certainly I'm not close to being a know-it-all with the confocal scope, but it is nice to be able to make the judgment between just a pretty image and an accurate representation of what is on the microscope slide. I was quite surprised to learn that sometimes the two things don't go hand in hand. Today the first sample that I worked with came from Zeiss, and thus all of the names on the microscope slides were in German. While my instructor had never heard of a Maiglöckchen, if you have ever been to Germany in the spring, then you certainly have seen lily of the valley flowers. Though I have to admit that I don't know much about plant biology, the images are of the rhizome, which is the underground stem of the plant. The dyes used were a rhodamine derivative and fluorescein isothiocyanate (FITC) .

Monday, July 9, 2007

Fullerenes and the allergic response

Last year I was quite intrigued when I learned that cosmetics containing fullerenes are actually already on the market, so when I noticed this paper, I decided to look it over. Everyone has heard of "bucky balls," an allotropic form of carbon named after the architect famous for building geodesic dome structures. Incorporation of C60 into skin creams has been the subject of much debate; while known to be quite stable, only a handful of biological studies exist and some of them hint at the possible toxicity of fullerenes.

Interestingly, this recent study from Ryan and coworkers in the Journal of Immunology indicates that polyhydroxy C60 and N-ethylpolyamine C60 (water soluble "bucky balls") are capable of inhibiting the allergic response of human mast cells and peripheral blood basophils. Even though the electrons of C60 are not fully delocalized throughout the entire molecule, fullerenes have long been known to be radical sponges, and it is believed that this contributes to their negative regulation of the allergic response. Mice injected with up to 250ng of fullerene showed no adverse affects, and the authors demonstrate that the concentration needed to inhibit anaphylaxis in mice is 400,000-fold lower than the dose that has been shown to be toxic in vivo. As C60 is believed to reduce cellular ROS levels, it has been proposed that its antioxidant effects might be useful in the treatment of neuordegenerative diseases such as Parkinson's, Alzheimer's and Lou Gehrig's disease.

Me?? I'm just waiting for B80.

Thursday, June 28, 2007

Poetic Chemistry

Today at the Sceptical Chymist, Catherine wrote an interesting post on poetry in the scientific literature. One of the comments contained a link to this 1971 JOC paper, which is written in quite a unique style. I suggest that you take a look.

Also, as Catherine suggested, I tried to write some chemistry/biology related haikus, and here are my attempts.

For the chemists:

Stirring at reflux
Overnight. Leaky tubing
Flooded his office

(As a side note, that didn't ever happen to me, but a post-doc in my lab managed to flood the office below his lab with some tubing that wasn't properly secured. That office luckily belonged to one of the nicest faculty members here).

For the biologists:
Oh dear western blot
where is my protein hiding?
not on the membrane

Tuesday, June 26, 2007


Today was my first time trying out confocal microscopy, and I enjoyed it quite a bit. Seeing stained cells through the microscope was pretty amazing. Unfortunately the camera doesn't capture the images quite as well as the human eye, but I wanted to share one of the pictures that I captured today.

Monday, June 25, 2007

Visualization of Single Electrons

Yes, you can believe your eyes. The above image has captured the movement of a single electron through liquid helium, with a velocity of 6 cm/s. Researchers at Brown University have captured these traveling electrons on film in a recent Journal of Low Temperature Physics article. (You can also watch a movie on the Maris group website).

How does this work? Well, the Pauli Exclusion Principle tells us that a free electron injected into liquid helium would experience some repulsion from the atom's own bound electrons. Thus, the electrons are encapsulated by so-called "electron bubbles." Electron bubbles can't be seen under normal pressure because of their tiny size (on the order of 10-23 cm2, but utilizing soundwaves to explode and expand the electron bubbles, Guo and Maris were able to actually see the movement of electrons through a 6.8cm long helium cell that was kept at an extremely low temperature (1.3o K which is approximately -457o F or -272o C). Although most of the observed bubbles traveled in a straight line, some of them followed a snakelike path, most likely following a superfluid vortex.

One question still remains--Where are these electrons coming from? As the authors point out, the liquid helium cell does not contain a source of electrons. One theory is cosmic rays might cause ionization of helium atoms, producing UV photons. As these photons hit the cell wall, it is possible that electrons could be ejected into the helium due to the photoelectric effect. A simpler explanation might be that some other kind of charged particles (such as muons) simply ionize helium atoms, producing positive and negative particles. While most of these charged particles would recombine, some might escape, allowing researchers to track their movement.

Tuesday, June 19, 2007

Comic Clumsiness

My husband pointed out the Periodic Table of Comic Books this morning, and while I haven't had a chance to check out all of them, so far my favorite one is this Wonder Woman strip. I just love the end, where Wonder Woman says, "The hydroxo gas is transforming you into an electron and me into a proton."

Also, I thought I'd share some of my clumsiness with you. Today in Cardio Camp! I somehow managed to tear my deltoid ligament and am now restricted to hobbling around on crutches for the next few weeks. Right now I'm not sure how this will affect my labwork, but maybe I found those comic books just in time...

Monday, June 18, 2007

Top 200 Drugs...

As my boss pointed out earlier this month, the Njardarson group (Cornell) currently has a listing of the 2006 top 200 generic and brand name drugs with structures. You can download the pdf files for your own pleasure or have them blown up to poster size as my group did. (The posters currently reside in our group breakroom, so that even at lunchtime, we never totally leave the realm of medicinal chemistry). It's amazing how many of the drugs that I recognized by name--and of course now it is handy to know their structure. Who knew that the estradiol analog found in many birth control pills contains an alkyne (ethinyl estradiol) that (according to wikipedia) was apparently key in creating a compound resistant to degradation by the liver? Or that the brand name drug Klor-Con (#153 on the list), which made $160,000,000 last year is actually only KCl?

Absorption of Polyphenols from Black Tea,,,

Yay! According to a study in J. Agric. Food Chem., I can once again start drinking my black tea with milk.

Wednesday, June 13, 2007

Getting Closer to Open Access?

While reading C&EN today, an advertisement promoting the ACS AuthorChoice free access option caught my eye. Maybe I am just a little behind the times, but I didn't actually know that something like this existed (and looking at the release date, it has been around almost a year). Basically, in exchange for a fixed fee (ranging from $1,000 to $3,000, paid by the author(s) or their funding agencies), the ACS allows unrestricted internet access to an author's article published in an ACS journal. This is different than the ACS Articles on Request policy which I had previously heard about; through this FREE policy, the ACS gives authors a URL that they can email out to colleagues. In this way authors can distribute up to 50 free copies of their published work, and after 12 months access to articles is unrestricted through this unique URL. Of course, Wiley journals have a similar policy (with a similar price, but limited to only the biomedical journals) called Wiley Funded Access Service.

Looking at the list of published ACS AuthorChoice Articles, I was slightly surprised to see that only 24 papers have been published in this way. Apparently the fee, while not too hefty in my opinion, prevents most authors from choosing this option. Hopefully with time, we will see more open access articles available through programs like ACS AuthorChoice and Wiley Funded Access Service. Although I like the idea of peer-reviewed open access and hope that it becomes the wave of the future, something in me says that it will be a long journey...

On a related note, these posts at In the Pipeline and Chemistry Central
discuss the important role that open access journal articles play for those in the field with no literature subscription (such as the retired on unemployed).

Sunday, June 10, 2007

Chemistry in my life...

While reading one of my favorite non-chemistry magazines the other day, I came across the advertisement pictured above for the Lexus RX hybrid. In the closeup picture, you can see why I've decided to include it here. Whenever I see chemical information or structures in real world situations, it makes me excited that non-chemists are getting a little exposure to what I work with every day. Usually the chemistry isn't great (and sometimes it doesn't even make sense), but at least our industry is getting some recognition. Although I tried to find some connection between the structures pictured and hybrid cars, I couldn't find one. Any ideas?

Saturday, June 9, 2007

Pictures from Sao Miguel

My husband took most of the pictures while we were on our vacation in the Azores. While I took only about 200 pictures, he snapped approximately 1,000. He is the more advanced photographer, but it is hard to make any picture of such a beautiful landscape look bad, so most of the pictures that I took turned out pretty nicely too. Sorting through the pictures to pick out the "best" ones is difficult, but you can see a small selection below. I've left out some of the more stunning ones (taken by my better half of course), so that he will have a chance to post them himself.
Lagoa do Fogo Lagoon of Fire

cliffs down to the Atlantic

São Miguel


baby volcano

one of the many small "ports"

I also have to add that our accommodations were absolutely wonderful: Casa Vitoriana in Ponta Delgada, Quinta das Queimadas in Nordeste, and Quinta Altamira in Caloura (near Água de Pau).

Thursday, June 7, 2007


Looking through the literature, you see some papers with twenty-plus authors and others with only two or three. Maybe it is just a difference between papers coming out of industry versus those produced by academia. Sometimes I have to wonder if all twenty authors really contributed much at all to a six page paper, or maybe it is just a system of "you pat my back and I'll pat yours" (or "I'll include you on this publication if you include my name on your next one"). On the other hand, how many key people were left out of the typical two author paper? Does the undergrad who helped synthesize a key compound (through a method you carefully worked out for weeks beforehand) get left out of the author list? How about a visiting scientist that contributed ideas and demonstrated new techniques to a group? Is she kept on a publication because of the contribution of original ideas and thoughts, or do you leave her off because she didn't physically complete any of the actual experiments?

Is it enough to contribute time/manual labor? Is it enough to contribute only ideas? Or is it necessary for one to contribute both to be worthy of authorship? I've heard people say that it's only really necessary to look at the first and last author of an article, and if that's the case the debate over authorship doesn't really matter.

I'm for citing ALL of those involved in a project, no matter how small a part they played (meaning inclusion as authors, in the acknowledgments or in the references section under "personal communication"). What are your opinions?

Back from vacation

I'm officially back from vacation! Expect some pictures from the Azores soon. Until then, I'll catch up on some reading ;o)

Tuesday, May 22, 2007

Where in the world?

Well, I'm off on vacation for the next two weeks! As my better half lives in Germany, we don't get to see each other as often as we would like--we saw each other last at Christmas. This time we are going to meet "halfway." Technically, it is closer for him, but I'll take a 5 hour flight (from the east coast of the US) over a 10 hour flight any time. If there is internet access available, I will be posting updates from time to time. Otherwise expect to see pictures when I get back :o)

Sunday, May 20, 2007

DNA detection

Picture taken from Hammond, D.M., Manetto, A., Gierlich, J., Azov, V.A., Gramlich, P.M.E., Burley, G.A., Maul, M., Carell, T. Angew. Chem. Int. Ed. 2007, 46, 4184. 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

In my mind, the future of cancer therapy is in the hands of personalized medicine; as the genetic makeup of each patient is different, it only makes sense to utilize customized therapies depending on the mutation affecting the individual. (Just look at the story of Iressa, and how well it works for Asian nonsmoking women with mutations in the EGFR tyrosine kinase domain). While the idea is a great one, personalized therapy is not a reality yet. Currently treatment options are too limited and often unspecific; methods to detect various disease markers are lacking. Personalized medicine depends upon the detection of minute amounts of DNA as well as isolation of particular genes from biological samples of interest, and the Carell group has developed a method to help with this.

Typically PCR is used for standard DNA amplification, although newer, more sophisticated techniques have allowed for detection of DNA down to the zeptomolar 10-21 level. (I'd never even heard of that one, my super-geeky husband had to fill me in). Unfortunately, such methods require the use of expensive/complex technology, so Carell and coworkers have developed a simple method of DNA detection based on standard black and white photography techniques. First, a pinacyanol dye was modified to contain an azide functionality, and several alkyne-containing oligodeoxyribonucleotides (ODNs) were synthesized. After a copper catalyzed Huisgen cycloaddition, various concentrations of modified ODNs were spotted down on commercial photopaper, irradiated, and developed according to known methods (standard photographic darkroom setup). This simple procedure allows for the detection of ~300 attomoles (10-18) of DNA!

Wednesday, May 16, 2007

Blogging Scientists...

Earlier today the paper fairy left the most recent Cell on my desk, open to the page "Scientists Enter the Blogosphere." Actually it was left on my chair, as my desk is currently a mess of papers (it's called writing a review), and I might not have seen it otherwise. There are a few people in my lab (including my boss) to whom I have casually mentioned my blog, but I'm pretty unsure if they have ever looked for it on the web. So it made me feel pretty good that my boss remembered I am a blogger.
Some fast facts from the article: Of 50 million blogs that exist, 4% of them deal with technology issues on a regular basis (20,000 of them are labeled as "science" blogs, although the term science is used loosely), 8% of internet users in the US write a blog, and only about 1000 of the science blogs out there are actually considered "authoritative."
I've been reading one of the featured blogs, In the Pipeline, for quite some time, and was thrilled when I was recently added to his blogroll. Some of the other blogs mentioned in the article that I found particularly interesting: Aetiology, The Daily Transcript, Sandwalk, and Useful Chemistry.
On a slightly related note, this recent post by Excimer (and all of the commenters there, especially Chembark) really got me thinking--Do blogs already serve as an unofficial review/comment system for scientific articles?

Sunday, May 13, 2007

Going Decaf...

Several months ago, Justin P. Gallivan gave quite an entertaining seminar for the chemical biology department. While I'm officially a member of the organic division, I really enjoy the biological side of things, so I try to attend these seminars as often as possible (or sometimes I attend them when my boss sends out an email "please attend," which really means "required seminar"). If I remember correctly, Prof. Gallivan did a little "bacteria dance," and if a speaker goes that far to get our attention, he has my respect :o) His lab actually has done some extremely interesting work, and I've been waiting for a publication to come out ever since that seminar.
Last week, the article "Guiding Bacteria with Small Molecules and RNA" finally appeared in JACS. E. coli have 5 chemoreceptor proteins and thus can maneuver their way through complex chemical environments. While they naturally perform chemotaxis toward 30+ compounds, it would be useful in terms of bio-nanotechnology to reprogram these bacteria to respond to new and unique chemical signals. The pathway responsible for converting chemical ligand binding into a change in direction of the bacteria consists of 6 chemotaxis proteins, with the protein known as CheZ ultimately responsible for bacterial motility. With this in mind, Shana Topp from the Gallivan group created a theophylline-sensitive synthetic riboswitch to control translation of CheZ; without theophylline, the conformation of mRNA prevents translation of CheZ, forcing the bacteria to tumble in place. Once theophylline is added to the mixture, the mRNA adapts a different conformation in which the ribosome binding site is open, which allows for expression of CheZ and forward movement of the bacterial cells. Caffeine, which has a structure similar to that of theophylline, did not elicit a response from bacteria, indicating that the observed changes in bacterial motiliy are dependent on the riboswitch. As Topp and Gallivan jokingly state, "E. coli pick decaf!"