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....

Regards,
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.

"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.

Traveling...

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?

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.).

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, K_i, 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:

• Database of Interacting Proteins (DIP)
• Protein-Nucleic Acid Interactions (ProNit)
• K_iBank
• PDBBind Database
  

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.