Still going...

It has been a while since my last post...lots of stuff going on! I really liked Blake's last blog title, "It seems the more we find out, the less we actually know." This is so true! As we dig deeper into the chemistry of DCQ, i am afraid to say that i don't think any of the previous literature on this topic is 100% free of errors. After each experiment B2 says, when are we getting that mass spec! A mass spec will certainly enable us to fully interpret the chemistry. As we move into the latter bit of the summer, B2 are working more independently.

The NSF-MRI grant is coming along. I will have it completed by the end of this week (July 31st). As Blake points out, the more i write the less i seem to know...thank goodness for page limits. I am quite hopeful on getting funding...i started this proposal ~ 2 yrs ago...submitted it once...it was rejected (or as NSF likes to say, declined)...got great comments...and now have hopefully i have now address my error. I am sure there will be something wrong, but not too wrong :)

We have one more trip to Iowa to collect ESR data probably on Aug 7th or 11th?

Theodore William Richards...quote...

As we tear into the walls of HT, dig behind cabinets not moved for years, we find treasures left behind. Sitting in the hallway this morning i found a small framed picture (possibly from Gebauer's office) of Theodore William Richards. In the frame was the beautiful quote that follows:

"First and foremost, I should emphasize the overwhelming importance of perfect sincerity and truth; one must purge oneself of the very human tendency to look only at the favorable aspects of his work, and be ever on the lookout for self-deception (which may be quite unintentional). Next, one should never be content with a conventional experimental method or scientific point of view; one should be open-minded as to the possibility that the procedure or hypothesis may be incomplete. Each step should be questioned, and each possibility of improvement realized. And then, patience, patience! Only by unremitting, persistent labor can a lasting outcome be reached." T.W.R. (1868-1928).

Back to lab...

It has been a week since i have been in lab. I took a vacation to VA to visit family and friends. I am anxious to see the work that B2 have done while i was gone. Ben sent me some data while i was gone, but i did not get a chance to think hard about it. I am also excited to see the work done on HT while gone...??? It is going to be a busy rest of the week...i am giving a beer talk in Davenport at the German Heritage Center on Sat and we start construction on the "rain garden" at the Monmouth Community Garden" on Sun at 2 pm.

Visit to Madison area...

On Friday, July 3rd, we took a lab break and traveled to Madison Wis to visit Om at the University of Wisconsin, Madison, Biochemistry Department, NMR Facility. In the pictures are Ben, Blake, and Om next to the Varian 900 MHz NMR spectrometer...or is that the moon lander? Om shared with us his project related to biofuels and then we enjoyed lunch together at the Student Union on the lake...nice place!

After U of Wis, Madison, we visited Gorst Valley Hop farm outside of Madison. Here we learned about the chemistry, biology, and business of hop growing. James gave us a tour of his experimental hop plant and then the larger 1 acer hop field (sorry no pictures...i was asking too many questions). We may collaborate with James on some chemical analysis.

Overall it was a LONG day (6 am-9 pm), but well worth the trip!

B2 at work...

Blake hard at work running the HPLC.












Ben hard at work at the UV-Vis.

Stefan visits...

On Friday, June 19th we had a visit from my collaborator, Stefan Franzen from North Carolina State University, Dept of Chem. While our discussion was interrupted by the potential of a tornado, we were able to spend a few hours discussing TCP/DCQ and DHP/HRP. The visit did prompt a publication idea, but we are not really lacking data, only the time to organize and write it up! Blake is in line to put together a nice little paper...

The weather has been terribly hot in Monmouth...as well as the majority of the Midwest. We have managed to keep cool in HT with our new window unit in our lab, but we had to postpone some ether experiments until we could cool down the lab a bit more. We also had to move an analytical balance into our lab since TFP get quite sticky when massing...at ~80 deg C.

back from U of Iowa

I should have shared our plans to go to U of Iowa before we left, but in the flurry of activities to prepare, i failed to do so...so here is an update...

B3 needed to collect some ESR (electron spin resonance) data to finish up the "story" on trihalophenoxyl radicals. We left Monmouth at 7 am...stopping at the worlds finest truck stop, "Iowa 80" for a coffee and morning snack. We arrived at the Medical Center in Iowa City at about 9:15 am...chatted with our host Garry Buettner...and got to work. The morning was productive. We confirmed that our immobilized enzymes can be packaged in 100 ul pipets and loaded into the ESR...and an IE-ESR experiment can be carried out. This is important since the usual sample holders ("flatcells") for ESR are $400 each...they are fragile...and do get broken. The 100 ul pipets are about $20 for 100 and are disposable. This will be very important advancement to allow for screening for enzyme stability. Having said that, the 100 ul pipets gave a signal that was ~5x less than the more expensive flatcells...so this is not a replacement, but rather a complement.

After a bit more "capillary" ESR work, we ended our day early (3:30 pm) so we could go visit Bio-Research Products in Coralville, IA. This is a small biochemical company that provides some very nice, high quality products. Brian Mundell gave us a tour of their facility. We discussed potential opportunities for Monmouth College and Bio-Research Products to establish a mutually beneficial relationship..connecting science with small business.

After a great visit to Bio-Research Products we checked into our hotel and headed out for a Mongolian grill dinner...we eat (and drank - water) TOO MUCH!

We returned to the ESR facility at 9 am Thursday to start our ESR data collection. It was a busy morning...not totally productive... lots of good science discussions with the medical student (Jason) the PhD student (Joast), researcher (Brett) and of course our host (Garry). Our efforts paid off and at about 3 pm, we were able to to collect the "money spectrum"...a clear assignment can be made to the TCP radical...chlorine hyperfine observed in the ESR spectrum!!!!

On Thursday we had lunch with Matt Faron. Matt is a PhD student at U of Iowa in genetics; a graduate of Monmouth College; a chemistry major. He seems to be enjoying his research.

After one last ESR data collection adventure, we packed up and left town at about 7 pm...happy with the collected data. We stopped at the Iowa 80 for dinner, got back to lab to drop off supplies at ~9:45pm and called it a night! B2 did a great job assisting in the data collection...they are very patient!

change in direction...

As is often the case, B3 has shifted our attention to a "different" problem while we await the arrival of our supplies from Sigma, BioRad, and Wilmad. We are working on finishing the data collection for the TCP (trichlorophenol) radical paper. I have been working on this paper for over 5 years and have finally honed it down to a nice story. Ben is working on collecting some UV-Vis data, Blake is working on HPLC data, and B3 will collect the final set of ESR data next week at U of Iowa. While we are at U of Iowa, we are also going to take a side trip to visit Bio-Research Products Inc., a small company that specializes in bio-products. We are setting up an informal collaboration to explore the stability of one of their peroxidase products using the IE-ESR technique.

two weeks in...

The first week of our research experience was filled with some challenging activities; our second week extended the research experience by focusing on specific "projects." Blake shared a quote...something along the lines of, "...you know when you are doing research, when you don't know what you are doing;" he has obviously caught on! Even Ben has gotten to the point where he will sheepishly smile and say, "i have no idea what you are talking about." We are moving in the right direction!!!

While at the CUR Dialogs meeting in April (2009), we heard a talk from the Dean of Arts and Sciences at William and Mary and he pointed out the book by Ron Gross, The Independent Scholar's Handbook. In this book he states,

"Established researchers rarely portray the faltering steps by which they came to pinpoint their purposes, chose their subject, sharpen their skills. By the time the work of the scholar or scientist comes to our attention, it is usually well packaged as a finished monograph, a carefully-crafted article, a well-honed paper, a polished book, a museum worthy collection or display, a documentary on film or videotape, or as some other finished work. This final project seems to have sprung full-grown from the author’s head. So we get a misleading picture of how intellectual and creative projects get started."

I love this statement...it essentially tells us, that as researchers, it is okay to be confused...and more importantly...if you are NOT confused, you may not actually be doing research!!! Rest assured B2...your projects are a result of a "well packaged" grant that resulted from many hours of confusion.

Another excerpt from Gross' book states,

"Rarely do researchers or writers “let their hair down,” revealing that they started where each of us must start — with mere infatuation for a subject."

This statement may be less relevant in the context of working on other's projects...like in this case of B2 working with me on the grant objectives, but it is critical to understand that when one engages in a project as a result of "mere infatuation" then you have launched your research career...it is my hope that your infatuation is of interest to others as well...it is hard to get funding otherwise.

Curiosity goes hand and hand with infatuation. I was reading this morning a book by Tom Shachtman, titled, "Absolute Zero and the Conquest of Cold"...there is a NOVA program based on this book called, Chasing the Ultimate Freezing Point: Absolute Zero"...and on page 11, it is discussing that in the early 1600s that there was a "lack of curiosity that ran throughout society at that time"...they go on to say that, "Today we believe that curiosity is central to science and perhaps to all human progress; curiosity is the engine that drives the intellect to seek the causes of things." Samuel Johnson is then quoted (1751);

"Curiosity is one of the permanent and certain characteristics of a vigorous mind."

A great start...

It was a busy first week. I am excited to say that i have 100% confidence in B2 (Ben and Blake) in terms of: 1) proper pipet usage, 2) buffer prep, 3) making enzyme solutions and corresponding calculations, 4) using the nanodrop to determine concentrations, AND 5) immobilizing HRP. We also spent some time using the amperometric H2O2 sensor and amazingly it worked perfect (sorry Josh G and Matt F)! B2 also survived the following: 1) 3 hour mega-lecture on peroxidases, oxidative phosphoryation, apoptosis, hemes, O2, superoxide, peroxide, cyt c, microperoxidases...to name a few, 2) an interactive (WinSim) ESR discussion, and 3) a 1.5 hr webinar discussing the NSF-MRI and NSF-ARI programs.

This week is also off to a great start. General projects goals have been outlined and we should be ordering enzymes and lipids by the end of the week. B2 will also be leading an informal discussion of their project on Friday at noon.

First day in lab...

Great first day in lab! After getting all of the paper work done, we started our day christening the new lab chairs! As i told them, they will spend lot of time at there desks documenting their work so they should be as comfortable as possible. We talked about keeping a lab notebooks, the new printer/scanner/copier/fax, and a few other topics before heading to the balance room to validate the pipets they will be using all summer...1 bad out of 8 is not too troublesome...we even have an extra p5000, so not a problem at this time. After a fine lunch at the local Chinese restaurant, we discussed buffers. These guys actually remembers the technical aspects of buffers...thanks Audra. We proceeded to the lab to make some buffers...along the way talking about RO and nanopure water. All in all a great day...i hope they agree!

CREATE...

Create...this is what we were told by one of our commencement speakers Amy Shapiro, a fine arts teacher at Bolingbrook High School. "Create something" she said; this feels like a good motto for our summer research efforts. Now Dr. Shapiro is an artist, so "creating" works of art is what artist do, but as a scientist we create knowledge! Go forth and create...

My first entry..

I am honored to be working on campus this summer with Ben Battenburg and Blake Lyon with support from a Cottrell College Science Award (received from Research Corporation for the Advancement of Science) and Monmouth College. The award is for a two year period, which started in Jan 2009.

The title of the Grant is "ESR Investigation of the Peroxidase Activity of Modified Cytochrome c" the abstract reads:

Free radicals serve many functions critical to normal human physiology; in addition, they foster many disease-related conditions. As we unravel the molecular-level details of cellular function, the mitochondria clearly play a significant role. This proposal is particularly interested in the role of cytochrome c (cyt c) in mitochondrial processes. With respect to oxidative phosphorylation, the role of cyt c is well understood. In an apparently unrelated chain of events, cyt c also plays a significant role in mitochondrial signaling leading to apoptosis. There are indications that cytochrome c has a “gain of function” related to the oxidation of lipids. Cytochrome c is a heme protein that has the potential to carryout peroxidase reactions resulting in free radicals. We propose to observe directly, using ESR, the free radical products resulting from the cyt c oxidation of lipids. This proposed research will take advantage of a recently developed electron spin resonance (ESR) method for directly detecting free radicals from enzyme reactions. This method uses immobilized enzymes to routinely achieve in situ ESR detection of transient radicals with lifetimes on the order of milliseconds. The method is extremely frugal in terms of the quantity of enzyme and substrate needed to perform an ESR experiment.

As of this date, the award has supported the purchase of the WebMO Pro, web-interface to Gaussian 03. Currently the free version of WebMO and Gaussian 03 is running on a MAC Pro and will soon be installed on Chris Fasano's (physics) parallel computer.

Ben, Blake, and Brad (hence referred to as B3) will begin our full time research efforts on May 26th, 2009. Stay tuned...