Friday, June 29, 2012

Blog Challenge 2

Blog Challenge #2

1- Why is the basis set B3LYP the most optimal for our simulations?
2- Why are theoretical pKa's necessary if the experimental pKa's have already been found?
3- Why are quinones the only molecules we are testing?
4- Why do we only use certain data from our simulations in calculations?
5- Why must we use the lowest energy form of each molecule in our simulations?
6- What applications will our research have in the world of computational chemistry?
7- What makes the Gaussian program the best for our simulations?
8- What exactly are our simulations simulating?
9- Once the theortetical pKa's are found what will they be used for?
10- Besides pKa's, what are the other things we can pull from our data?

Tuesday, June 26, 2012

Blog Challenge #2

1. What type of cosmetic benefits will there be if we are able to mutate the NapA?
2. How are we going to get rid of the insertion loops from the NapA inside C. jejuni?
3. Why are we focused on the reaction of the molybdenum enzymes if we mainly care about the NapA?
4. Are we able to use a zwitterionic detergent as a way to stabilize the NapA?
5. Why do we mainly care about the Histidine Amino Acid above all the other ones?
6. How does the Bradford machine work?
7. Why is it necessary for us to use pure Ethanol when we are straining the bacteria on the Agar plates when we are just gonna mix it with water anyways?
8. What does the R. spaeroides have to do with our project?
9. Will I get the chance to use the Mass Spectrometer or see an example of a sample that comes out successful?
10. What is the next step after we are able to mutate the NapA inside the C. jejuni?

Blog Challenge #2

First, I want to congratulate blog challenge #1 victor: Chelsea Weidaw.

Secondly, I want to thank all the Project SEED students for making a contentious effort to complete the first task despite the challenges that come with learning new material.

Finally, I am now going to post your second blog challenge:

Your task is to come up with 10 questions (List) that you have about your project for the summer. The questions should be specifically related to your project. The questions should not be general. The goal is to promote expansion of your knowledge about the topic and show where future studies may lead. Not to mention, this way you can ask questions you are afraid to ask to your mentor or anyone else. Remember, there are no stupid questions. The person with the most thoughtful, insightful questions will be declared the winner.


* The Prize will be disclosed before the deadline.

Friday, June 22, 2012

Blog Challenge #1

  Our focus for this year is on reactions of molybdenum enzymes and proteins in organisms. The protein we are most interested in is paraplasmic nitrate reductase A in C. jejuni, which is one of the most common causes of human gastroenteritis in the world.  One of the things that we do is grow bacteria.We grow bacteria by making plates.  We had to first make up the Agar and mix it.The reason we use Agar is because the bacteria loves it. Then we had to put it in the Autoclave for a half an hour. When it was done we took it out and waited till it cooled down enough to handle, then we began to pour the plates. When I was pouring the plates for the first time I had to work as close to the Bunsen Burner as I could so there was a less of a chance for unknown substances to contaminate and ruin them. I also had to move very fast so the Agar didn't coagulate. I was excited when I was done, because Andrew told me that I made 17 plates. After that we streaked the plates with old bacteria, which will allow us to organize how it should grow, and put them in the Incubator at 37 degrees Celsius. We put them in at 37 degrees Celsius because that is the temperature that they are most active in. The next day we took them out of the Incubator and started to seal them with para film. We seal them to cut off all of the oxygen. After sealing them we put them in the fridge at 4 degrees Celsius.   

Blog challenge 1

The goal of my project this summer is to create and test labs involving electron microscopy. Electron microscopy is the science and technology of using an electron beam to form magnified images of a specimen. There are many different types of electron microscopes but the one I will be working with is the SEM(scanning electron microscope). In the process of creating an image, the first stage is the production of a beam of electrons. The SEM uses the electron beams to scan the surface of a specimen, whereas a standard microscope would use several lenses and light to produce an image. The only downside to this is that the images are produced in black and white. Compared to a light microscope, the SEM is capable of showing details more in depth than the light microscope would ever be able to. Without the SEM, there were things I would not have been able to notice about my samples otherwise. During my time spent here so far, I have completed 2 different labs involving the SEM. One of the labs I have done was the Synthesis and SEM Analysis of Tamarugite. The objective of this lab was to create a sample of Aluminum Hydroxide and examine the collected sample under the SEM. Today I was able to take the samples of the Aluminum Hydroxide I had previously made and observe it using the SEM. In the next few weeks my job will be to think of a lab, much like the ones I have completed this passed week, and make sure that they appeal to high school students and also the teachers. I will be testing numerous labs until I come up with the best experiment possible.

Blog Challenge 1

My project this year is to create ligands. Later, the four ligands will be used as a base to create a complex, which is a ligand with a metal bound to the center of the molecule. The four ligands will be made from the precursors of Tris-(2-aminoethyl) amine in each and benzaldehyde in one, 4-chloro benzaldehyde in another, 4-methyl benzaldehyde in a third, and 4 (triflouromethyl) benzaldehyde in a fourth. These percursours will be made into ligands and each will bound to copper I and copper II. NMRs and IVs will be taken of each complex and they will be determined what the complex will be called and what it can be used for.

Blog Challenge #1

This summer I will be continuing on my research from last summer in the forensic lab. The title of my research is Forensic Analysis of Hairs: Identifying Styling Product Residues on Hairs by GC-MS.
Last summer different types of hairsprays were tested in various solvents before residues were actually pulled from hair samples for best possible results. The solvents that the hairsprays were tested in were acetone, hexane, isopropanol and methanol. The methods used for testing were each of the hairsprays were mixed with 2mL of each of the solvents listed above. These samples were then placed into the sonicator 25 minutes. After sonication, samples were each syringe-filtered through 0.2 µm nylon membrane filters into GC-MS vials. The solutions in the vials were then set at different injection temperatures into the GC-MS at 200°C and 250°C. The solvent that showed the best results was isopropanol and the injected temperature that will be used is 250°C.
This summer I will be testing actual hairs to see if the method above with be able to extract hairsprays from a single hair. Four different hairsprays will be tested one by one in students hair. For testing a strand of hair, it will be cut into pieces into a test tube so all possible hairspray residues will be extracted. The pieces are then mixed with 2mL of isopropanol. The test tube is then sealed with parafilm and then sonicated for 20 minutes to an hour. These will be sonicated for two different times to see if the hairsprays will be extracted from the hair more. After being sonicated the samples will be transferred into a different test tube through a pipette without the hairs then syringe-filtered through 0.2 µm nylon membrane filters into another test tube. The solution in the test tube will then be dried out with nitrogen and then 100µm of isopropanol will be put back in the test tube. The solution will finally be transferred into GC-MS vials and be ran in the GC-MS.

Blog Challenge 1

This year I will be working on a continuation of my project from last year, which was predicting pKa of molecules found within the protein Cytochrome bc1. This project is important for the simple fact that Cytochrome is found within every animal on the planet. When the protein malfunctions it can lead to a devastating physical disorder like cardiomyapathy, which is a usually fatal muscle rotting disease.
The reason I am trying to find the pKa (acid dissociation constant) for this particular molecule is the promise it holds for future research. Because Cytochrome has different conformations in mammals than it does in bacteria, finding how to make it dissociate can provide a new anti-biotic. The pKa is the point at which hydrogen atoms start to leave the molecule. The absence of one of those hydrogens would set off a devastating chain reaction, for Cytochrome is essential in the storing of energry for organisms. If something is not able to store energy, then it is not able to live. This fact of the world provides us with all the motivation we need for the project to continue.

Thursday, June 21, 2012

BLOG Challenge #1

In your first challenge, you have quite a daunting task. You must write, in as much scientific detail as possible, about your project for this summer. You should include the objective of the research, what you will be asked to do, and how you will do it.

You should write clearly, concisely, and scientifically.

The person with the most well written and detailed piece will win a *FREE lunch at any location in Pittsburgh courtesy of Mr. Larry. (dessert included)

CONTEST ENDS FRIDAY, JUNE 22 at close of business. WINNER chosen Monday

* You may choose the date and time for your free lunch

Wednesday, June 20, 2012

Project SEED 2012

Well here I am back again! I am very excited to get started back on my project. The past few days have been a breeze for me because I already knew what I was doing. It was interesting to see how the new SEED students would react over the first couple of days. When I got back to my lab on the second day I seen no familiar faces of the graduates and undergraduates from last year but new undergrads that were very welcoming and excited to work with me this summer in the lab. I hope that I accomplish a lot on my project this year and hopefully get some great finishing results. Even though I have given up my 2nd summer in a row I love the advantages that this program gives me. So with that being said let the summer begin!! :)
This being my first year of Project SEED I was a little bit nervous on my first day. Although, I was extremely excited to meet my professor and mentors that will be helping me throughout my time spent here at Duquesne. On my first day, all of the SEED students went through safety training. It helped inform me about a lot of the signs posted around the chemistry department that I wouldn't have recognized otherwise. The lab group that I'll be working with all summer has some of the nicest people in it. My main mentor, Kim, has the same bubbly attitude as I do so it is great talking with her. Especially because she explains everything in an easy an understanding way if I don't understand something right away. My second mentor, Joe, organized a folder for me with suggestions, meeting times, and overall just things that would help me out, which was extremely nice of him. Today, I was trained to use the SEM, which is a scanning electron microscopy. What the machine does is, it uses an electron beam to form magnified images of a specimen. At first I was a little uneasy about using the machine because I didn't want to damage anything but it actually ended up being pretty simple to use. I am very excited to see what I'll be doing in the next few weeks here! :)

Tuesday, June 19, 2012

Project SEED blog

So far Project SEED has been fun and very interesting. The first day was very challenging for me because I didn't really understand what I was doing, but after my mentors explained everything to me I sort of got the hang of it. That day I received a "Crash course" in Molecular Biology from Sammy and Andrew so I could have a better understanding of everything that we are doing. Today Andrew and I created a Tris buffer, Sucrose buffer, and a Sodium Chloride buffer. It was pretty easy doing these things, because all we really had to do was measure and mix each substance. We also had our very first group meeting which was very interesting and frightening. I also got to meet Dr.Basu who, if I may say, is a very kind and intelligent man. The only challenge I have, as of right now, is reading and understanding all of the packets I received.    
This Project SEED thing is starting off well. I already learned a lot of things that I would've never even came close to learning if I was at my regular school-and It's only the second day! So far if I were to grade this program, it would be a B+, but only because I lost most of my summer vacation for it, which isn't necessarily a bad thing since this early in vacation I would most likely be bored out of my mind! I bet that if I work hard enough, though, I will be able to teach my classmates back home, most of which love chemistry, so I'm looking forward to that, too.
  Its that Project SEED time of year again. The time when highschool students like myself say goodbye to their just beginning summers and hello to the enormous workload that is this program. I may sound like I'm complaining, and maybe it is because I am. Only a little. And it is only a little because I am well aware of the benefits that SEED provides me with.
 While this is only the second day of the program, I already feel myself getting swept up in the swing of things; the dedication to the research, the endless tune of fingers tapping against keyboards, heated discussions about subjects so confusing thatthe general public would assume it was in a different language. That is SEED in all of its glory, and I couldn't be happier to be back.
 Without SEED my summer would be pretty standard for a teenage boy; wake up, video games, nap, video games, and repeat. I'm not saying I wouldn't enjoy that, because I'd be lying if I said I wouldn't. But I can honestly say I'm happy that I'm breaking the stereotype and am looking forward to this summer.
Sonny Smarra

First week-Project SEED

Being that this is my first year participating in Project SEED, I am both extremely excited and incredibly anxious. I feel very priveleged to have the opportunity to join the Project SEED family.  I am very familiar with the Project SEED program because of its close affiliation with Sto-Rox High School and my colleague Josh Lucas. When Josh asked me to possibly take over, I quickly responded with an enthusiastic yes, completely disregarding potential issues with working in the summer and finding a babysitter for my now 13-month old son. Thankfully, arrangements were made and I was now able to put my focus on the Project SEED summer of 2012.

My first week without the students was completely overwhelming. I was given countless articles to read and reread and reread and ask questions about and reread and read again. I am just a Biology guy, so some of the chemistry in these articles required me to conjure up my chem knowledge from about 10 years ago. Luckily, with the help of some outstanding grad students, I am slowly but surely ascertaining the knowledge I am going to need to present said reasearch in a couple months. TO BE CONTINUED...

Project SEED 2012

Alas, we bid a farewell (sort of) to Mr. Josh Lucas, high school liaison to Project SEED, chemistry teacher, entrepreneur, and friend as he moves on to pursue other business ventures. On a positive note, we are happy to introduce Mr. Nolan Larry, colleague of Josh Lucas, who will now be taking over as the high school teacher/leader for Project SEED. Guided by the veteran Josh Lucas, Mr. Larry hopes to contribute another positive role model to the program.

We are also excited to bring back second year students Sonny Smarra, Chelsea Weidaw, and Dwayne Coleman and welcome in newcomers Haniyyah Wheeler, Emily Janicki, Charles Thornton, and Aaron Trischler.

With the combination of promising newcomers and 2nd year returnees, Project SEED 2012 is looking to continue to surge forward making an impact in the chemical world.