Category: Seth M.

Week 8: Troubleshooting and Misfires

This week has been really busy in the lab, but that’s nothing out of the ordinary. What is out of the ordinary is some of the results we have been getting for the new substance I am working on, the Glc-C3-N-C10, as well as the mRL. So, this week has been repetition after repetition of trials in an attempt to find the cause of the problem. To elaborate, the surface tensions that we are expecting for both substances are supposed to max out around 70, close to that of water, but we are unable to get past 65 or 66. So this last week or so has been us trying to figure out where the contamination could possibly be. We have tried multiple possible sources, all ending with the same results. For example, we use a buffer solution in order to dissolve the mRL and measure the CMC value, and one possible source of contamination could be from the substances used to create this buffer. So, in theory, re-crystallizing and purifying those substances would get rid of any contamination coming from the buffer, but it turns out that the problem was not the buffer solution. We have also tried using two different samples of the mRL to see if it was the source of the contamination, but that was not the problem either. Another source could have been the type of buffer we were using, so we changed out the NaOH we were using and replaced it with Na2HPO4, and, if you haven’t caught on yet, no success. This has proven to be quite a difficult problem, and it has prevented us from moving on with my research, which is not good since I have to begin presentations soon.

Speaking of which, even though I am going to go through presenting my work so far and the senior project term is almost up, I have been given the opportunity to continue my research here at the lab and am very eager to continue here. I have really enjoyed the atmosphere, the people, and the work environment, and I am very grateful for BASIS and my BASIS adviser for showing me this lab. Thank you to everyone, and I will likely have one or two more blog posts before the project is over.


Week 7: New coworkers, New substance, New experiences

This week has been filled to the brim with new events happening in the lab. We have gotten our two new workers, and they are research technicians that will most likely be staying here longer than I do. However, since they are new to this lab, they have gotten a similar tour of the lab as I did and they have begun to learn how to work the instruments here. The first day they were working on the HPLC instrument as I had done in my beginning week. I was not able to accompany them for that training because I was working on a new surfactant with a fancy name, Glc-C3-N-C10. Poetic, isn’t it? Anyways, I have ran only one experiment so far on this substance, and the resulting graph and maximum surface tension that I obtained were good, but the CMC value I had gotten had deviated from past experiments, but my sample had been purified significantly more than those before me, so only more experiments will tell. One of the technicians has shadowed me as I run a couple more tests on the mRL.

I have also learned more this week as well. I am learning a new purification process known as re-crystallization, which is partially shown below.

To elaborate, we take the SDS in a solution of approximately 95% ethanol and 5% water and force the SDS to dissolve by applying heat. We then let it adjust to room temperature to prevent any impurity from crystallizing and then put it in and ice bath to form the crystals of the SDS. Then we vacuum pump the crystals and then lypholize it overnight. I also recently found out where we keep most of our bottles of chemicals, like methanol and acetonitrile, for example. That was more for my convenience and not a necessity. I also painstakingly found out that if you create a 600mL solution of acid, its going to take a generous amount of base to get to pH7. I know this is basic chemistry, but going through the process of having to do so while trying to prevent an overshoot can be quite tedious. I am very excited to start diving deep into my work with Glc-C3-N-C10, and I will keep you guys updated on how it goes!

Week 6: Preparation for change

This past week has been very busy: I have completed my laser training course, I have prepared and ran 10 or so samples on the tensiometer and have been able to process that data to obtain the CMC values as well as working my way towards finding the absorbance value for our sample, and we have placed some older samples on the lyophilizer in order to purify the samples so that I can began some of my own tests on them. I have also begun work on a process known as Dynamic Light Scattering (DLS), which is meant to determine the size of the aggregates that form in our sample. I am fairly new to this process and am still learning about what the results mean, so by next week I will most likely be able to expand on why we are doing this.

All of this has come in very quickly, but for good reason. At our group meeting last week, the head of our research group announced that we are getting two new workers as mentioned in my previous post. However, there is still quite a bit of stuff I need to learn before I am prepared for these new arrivals, because all of the data we are processing is taking more time to understand than I hoped for. I understand why we are doing these calculations, it is just the method in which we are obtaining these values is tedious and has a lot of potential for error. For example, yesterday I had to catch up with my data processing due to the laser training on Monday, so I was given three new tests that had to be processed, as well as learn how to calculate the absorbance value and the molecular area of the molecule. That whole “excursion” took a good couple of hours to do, but luckily for me, we were waiting for our sample to stabilize before we began our DLS tests. My apologies for the lack of pictures this post, but rest assured I will have more next week as I begin my own tests on a different surfactant known as Sodium dodecyl sulfate (SDS). Thank you for reading!

Week 5: Working towards Independence

Lately I have been working towards being able to work on my own without the supervisor keeping an eye on me due to the possible addition of two new workers in our lab. It is possible that one of the new workers is going to be occupying the same office as I, which entails my supervisor the task of teaching him what goes on around here, as he did for me. The new workers are technicians, so I am not positive that they will be doing the same work as me, but in any case, my supervisor has made it his (and my own) goal to become more independent in the lab. This means that I can work on creating the samples that I am testing as well as cleaning and maintenance of the instruments that I use. Currently, that basically only includes the tensiometer and the materials. But independence here does not only mean being able to set up and executing the experiments, but also analyzing and understanding the results.

I have been learning how to process the data slowly throughout the whole time I have been here, but this past week or so, I have collected the data from the software and analyzed it myself and then compared it to what my supervisor has gotten. I have a feeling that I am understanding more and more what to expect from these results, as well as the trends that are apparent as we transition from different pH values. This change has proven to be quite the task, as we are not exactly getting similar results as we had with a previous pH value. It is possible that there is slight contamination in our sample, but we are awaiting one last test run. One of the difficulties we had was creating the buffer for the sample, as shown below.Buffer solution

Using these, we have had to make two separate samples of our molecule, one in which our pH is adjusted after adding the buffer, and one where the sample is not adjusted. These have gotten us mixed results and is a bit frustrating, but that doesn’t stop our progress. Thank you for reading!

Week Four: A lot more instruments to learn, so little time.

My apologies for the late post, last week was crazy busy. Here at the lab, I have begun to grow accustom to the equipment I will be working with and have even been able to do work on my own! My supervisor has told me that I am making great progress in the goal to have me be able to work on my own without having him over my shoulder making sure I do things right. But that is still a work in progress, and I am very excited to be able to work on my own and contribute as much as I can to their research. Now, on to what I have  accomplished so far. First, a note: surface chemistry is very sensitive to contamination, and cleaning and drying all of our instruments and vials is pertinent to our data. A lot of what I have been working on is how to operate and clean these instruments after use, like the one pictured below, which is called a tensiometer.

. Tensiometer

This instrument has been one of my most instruments, so I know my way around this expensive and fragile device that is used to measure the surface tension of our sample.Frozen mRL using liquid nitrogen

Here, we have flash frozen our sample because we had detected acetic acid in our glycolipid, which we had detected through a process known as NMR, and using this big machine that requires special training to operate.NMR Magnet

There will be more this week, as we are in the process of analyzing our data and comparing our trials. Thank you for reading!!

It’s never a quiet moment in the lab

Whether it be me meeting someone around the lab in case I have questions, or the whirring of the instruments that we are using, the lab is never dull or quiet. It has been a week since I have worked at the lab, and I have to say that I am really enjoying it! I have met most of the members of our research team, and they are all very nice people. First, I had to go through training, but it was more like online safety training. It was a simple task, and I was finished the first day. I was given the tour of the lab and shown some of the equipment that I will be working with. That was the extent of my first day. My second day was more interesting, as we got to prepare a solution that we would dissolve one of our glycolipids in. We did this in order to put it into the tensiometer, which I learned how to operate and clean. Learning how to do all of that was very delicate and fragile, and it’s going to take some time to master.

The third day was a shorter day, we had to take our results from the tensiometer and analyze them. I was taught how to use the software that came with the instrument, which wasn’t too hard. The last thing we had to do was get my lab notebook, and I was shown the where I could purchase supplies for the lab. Today was a long day, as we had to prepare another solution for the instrument known as a rotovap, a device that uses evaporation and a condenser to remove unwanted substances from our mixtures. In our case, we had to remove acetic acid from our solution, and we also had to ethyl acetate as well. So I was tasked with that, which took quite some time. We also received a new part for an instrument that performs HPLC, so we prepared a new batch of methanol for cleaning it, and we also purged the detector unit. Lastly, we ran into some trouble with the internal heater in the detector, so we spent the last bit of time replace nitrogen tanks for the purging and cleaning process.hplc-system

ABOVE: HPLC System with new batch of MeOH and a new column attached.


Rotovap with a sample lowered into a hot water bath.

Week 2: More reading, more waiting

I am still waiting on my 18th birthday to come around as well as the paperwork necessary to work in a lab on campus, so I have more research that I have conducted, but this research is more important in my opinion because it came directly from the lab that I will be working in. Before I met the head of the lab and my daily supervisor, I was sent a copy of their latest paper on the type of molecules I will be working with. I read it once before I went into the interview, but I decided to read it again and take note on some of the things I could possibly be doing.

Their paper was talking about two types of molecules that they tested to see if they were more efficient than previously used glycolipids. The most simplified names of these two molecules are alkyl cellobiosides and alkyl melibiosides. What was tested and determined was the Critical Micelle Concentration (CMC) and the structure and internal environment of the micelles because they affect many of the functions of surfactants in possible applications, such as drug and gene delivery and biological mimetics. I learned about some of the processes that I possibly could be utilizing for this new molecule, but what I want to focus on here is the results they found. When 2 methylene groups are added to the alkyl chain, the CMC decreases by an order of a magnitude. What is more important is that the cellobiosides have similar CMC values to its predecessors. This meant that the melibiose exhibits a reduction of hydrophilicity and is less soluble. They also affirmed a relationship between the length of the carbon chain and the CMC value, which is an indirect relationship. The longer the chain, the more spherical the micelles are, which are more useful in surfactant applications. That’s the extent that I will share on my blog, but I have more notes on this paper for my own tests when I begin work.

Independent Research: Learning more about Glycolipids

I have been doing independent research this past week due to the strict guidelines of the University of Arizona of not allowing minors to work in the lab setting on campus. While I was in the interview with the lab director and my daily supervisor, they began talking about how the molecule I will be working on could be linked to cancer treatment, so I decided I would look more into how glycolipids are involved in cancer patients. I found that glycolipids play a key role in the development of tumor cells. The molecule I will be working with is not a part of the development of tumor cells, rather another form of glycolipid known as a ganglioside, has a more prevalent role. According to a scientific paper I read, there have been studies that linked gangliosides, which are glycolipids attached to sialic acids, to the immunosuppression quality of tumor-bearing animals and humans.  Gangliosides have also been linked to regulation of cell adhesiveness and the loss of some gangliosides could explain the anchorage-dependent characteristic of tumor cells. There are a lot more roles that glycolipids play in the development of tumors as well.

A process known as aberrant glycosylation, which is the divergent reaction that attaches a polysaccharide to a protein, lipid, or other organic molecule, has been observed in tumor-associated cells, and this process has been linked to glycolipids. It has been discovered that these glycolipids are under the control of transforming genes that are triggered by oncogene activation. It has been hypothesized that glycolipids regulate cell growth, which has been examined with a decrease or deletion of glycolipids in fibroblasts (cell that makes collagen and other fibers) that are associated with oncogenic transformations, which resulted in a loss of growth control, another trait of tumor cells. Enzyme activity could also be the source to aberrant glycosylation; for example, the assembly and organization of the enzyme multiglycosyltransferase could be altered. If this were the case, then further studies of the mechanism of activation or inactivation of transcription would be required. Lastly, glycolipids have also been linked to the membrane fluidity in tumor cells, but this is only a hypothesis with little evidence to support it. Doing this research on the biological process of tumor formation has made me hopeful that my lab is granted the ability to test the new molecule for cancer treatment because the difficulty to cure cancer has been an enormous issue in society, and I have learned that my work as a chemical engineer or as just a chemist in general could be applied to biological aspects that I was unaware of.

Determining the characteristics and sustainability of Carbon-Linked Glycolipids as Surfactants

I have found an internship at the University of Arizona under the Pemberton Lab of Research, where I would be working with surfactants that are made from glycolipids. My job would be to test whether a new series of glycolipids are more chemically stable in an acidic environment than a previous series of surfactants. I am also supposed to find the surfactant properties of this new series of glycolipids. Hopefully, I would be able to produce a presentation or lab report for the end of the senior project, but that all depends on the copyright stance of the lab. If I can present my findings of my research, I would produce some sort of presentation describing the process in which I tested the new glycolipids as well as some of the properties that we determine. These properties will be tested using several processes including surface tensiometry, UV-Vis spectroscopy as well as other processes.